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Conserved domains on  [gi|564333452|ref|XP_006231334|]
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PREDICTED: APOBEC1 complementation factor isoform X1 [Rattus norvegicus]

Protein Classification

hnRNP-R-Q family protein (domain architecture ID 11492981)

hnRNP-R-Q family protein

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
hnRNP-R-Q TIGR01648
heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the ...
2-594 0e+00

heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q, and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.


:

Pssm-ID: 273732 [Multi-domain]  Cd Length: 578  Bit Score: 901.29  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452    2 ESNHKSG----DGLSGTQKEAALRALVQRTGYSLVQENGQRKYGGPPPGWDTTPPERGCEIFIGKLPRDLFEDELIPLCE 77
Cdd:TIGR01648   1 RSREKQGskvqEGTKGTPDEAALKALLERTGYTLVQENGQRKYGGPPPGWSGVQPGRGCEVFVGKIPRDLYEDELVPLFE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452   78 KIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRLLGVCASVDNCRLFVGGIPKTKKREEILSEMK 157
Cdd:TIGR01648  81 KAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISVDNCRLFVGGIPKNKKREEILEEFS 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  158 KVTEGVVDVIVYPSAADKTKNRGFAFVEYESHRAAAMARRRLLPGRIQLWGHPIAVDWAEPEVEVDEDTMSSVKILYVRN 237
Cdd:TIGR01648 161 KVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRN 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  238 LMLSTSEEMIEKEFNSIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSYVRYTRGTG 317
Cdd:TIGR01648 241 LMTTTTEEIIEKSFSEFKPGKVERVKKIRDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTG 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  318 GRNTMLQEYTYPLSHVYDPTTTYLGAPVFYTPQAYAaiPSLHFPATKGHLSNRALIRTPSvreiymnvpvGAAGVRGLGG 397
Cdd:TIGR01648 321 GRGKERQAARQSLGQVYDPASRSLAYEDYYYHPPYA--PSLHFPRMPGPIRGRGRGGAPS----------RAAGGRGYPP 388
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  398 RGYLAYTGLGRGYQVKGDKRQDKLYDLLPGMELTPMNTISLKPQGVKLAPQILEEICQKNNWGQPvyqlhsAIGQDQRQL 477
Cdd:TIGR01648 389 YGYEAYYGDYYGYHDYRGKYEDKYYGYDPGMELTPMNPVRGKPGGRGGRPAIPPPRGRKNGAPPP------AIGQDGRQL 462
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  478 FLYKVTIPALASQNPAIHPFTPPKLSAYVDEAKRYAAEHTLQTLGIPTEGGDAGTTAPTATSATvFPGYAVPSATAPVST 557
Cdd:TIGR01648 463 FLYKITIPAGYSQRPAPHPLGPPRGSAFVRGARGGPAQYQQRGRGSRTSRGNGRGGTAGGKRKA-FDGYAQPDATARQTN 541
                         570       580       590
                  ....*....|....*....|....*....|....*...
gi 564333452  558 -AQLKQAVTLGQDLAAYTTYEVYPTfAVTTRGDAYGAF 594
Cdd:TIGR01648 542 nQQNWGAQPIGGDYAGYYGYEVYNN-AVTDNQDFYQTY 578
 
Name Accession Description Interval E-value
hnRNP-R-Q TIGR01648
heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the ...
2-594 0e+00

heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q, and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.


Pssm-ID: 273732 [Multi-domain]  Cd Length: 578  Bit Score: 901.29  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452    2 ESNHKSG----DGLSGTQKEAALRALVQRTGYSLVQENGQRKYGGPPPGWDTTPPERGCEIFIGKLPRDLFEDELIPLCE 77
Cdd:TIGR01648   1 RSREKQGskvqEGTKGTPDEAALKALLERTGYTLVQENGQRKYGGPPPGWSGVQPGRGCEVFVGKIPRDLYEDELVPLFE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452   78 KIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRLLGVCASVDNCRLFVGGIPKTKKREEILSEMK 157
Cdd:TIGR01648  81 KAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISVDNCRLFVGGIPKNKKREEILEEFS 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  158 KVTEGVVDVIVYPSAADKTKNRGFAFVEYESHRAAAMARRRLLPGRIQLWGHPIAVDWAEPEVEVDEDTMSSVKILYVRN 237
Cdd:TIGR01648 161 KVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRN 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  238 LMLSTSEEMIEKEFNSIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSYVRYTRGTG 317
Cdd:TIGR01648 241 LMTTTTEEIIEKSFSEFKPGKVERVKKIRDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTG 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  318 GRNTMLQEYTYPLSHVYDPTTTYLGAPVFYTPQAYAaiPSLHFPATKGHLSNRALIRTPSvreiymnvpvGAAGVRGLGG 397
Cdd:TIGR01648 321 GRGKERQAARQSLGQVYDPASRSLAYEDYYYHPPYA--PSLHFPRMPGPIRGRGRGGAPS----------RAAGGRGYPP 388
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  398 RGYLAYTGLGRGYQVKGDKRQDKLYDLLPGMELTPMNTISLKPQGVKLAPQILEEICQKNNWGQPvyqlhsAIGQDQRQL 477
Cdd:TIGR01648 389 YGYEAYYGDYYGYHDYRGKYEDKYYGYDPGMELTPMNPVRGKPGGRGGRPAIPPPRGRKNGAPPP------AIGQDGRQL 462
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  478 FLYKVTIPALASQNPAIHPFTPPKLSAYVDEAKRYAAEHTLQTLGIPTEGGDAGTTAPTATSATvFPGYAVPSATAPVST 557
Cdd:TIGR01648 463 FLYKITIPAGYSQRPAPHPLGPPRGSAFVRGARGGPAQYQQRGRGSRTSRGNGRGGTAGGKRKA-FDGYAQPDATARQTN 541
                         570       580       590
                  ....*....|....*....|....*....|....*...
gi 564333452  558 -AQLKQAVTLGQDLAAYTTYEVYPTfAVTTRGDAYGAF 594
Cdd:TIGR01648 542 nQQNWGAQPIGGDYAGYYGYEVYNN-AVTDNQDFYQTY 578
RRM3_ACF cd12498
RNA recognition motif 3 in vertebrate APOBEC-1 complementation factor (ACF); This subgroup ...
223-305 2.17e-56

RNA recognition motif 3 in vertebrate APOBEC-1 complementation factor (ACF); This subgroup corresponds to the RRM3 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. ACF contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1.


Pssm-ID: 240942 [Multi-domain]  Cd Length: 83  Bit Score: 184.09  E-value: 2.17e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452 223 DEDTMSSVKILYVRNLMLSTSEEMIEKEFNSIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK 302
Cdd:cd12498    1 DEDTMSSVKILYVRNLMLSTTEETIEKEFNSIKPGAVERVKKIRDYAFVHFSNREDAVDAMNALNGKVIDGSPIEVTLAK 80

                 ...
gi 564333452 303 PVD 305
Cdd:cd12498   81 PVD 83
DND1_DSRM pfam14709
double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead ...
446-522 4.95e-26

double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead end protein 1 (DND1_HUMAN) homologous to double strand RNA binding domains (PF00035, PF00333)


Pssm-ID: 317152  Cd Length: 81  Bit Score: 101.29  E-value: 4.95e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564333452  446 APQILEEICQKNNWGQPVYQLHSA-IGQDQRQLFLYKVTIPALASQNP-AIHPFTPPKLSAYVDEAKRYAAEHTLQTLG 522
Cdd:pfam14709   3 AVQLLEELCQKNKWGSPVYELHSHtAGPDGKLLFLYKVVIPGIPTSFPgVIWIFMPGKLCSTKEEAKEAAAEQVLQALG 81
RRM smart00360
RNA recognition motif;
58-126 4.15e-18

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 78.40  E-value: 4.15e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452    58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFN-GNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRL 126
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKEtGKSKGFAFVEFESEEDAEKALEALNGKELDGRPL 71
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
51-129 5.38e-13

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 223796 [Multi-domain]  Cd Length: 306  Bit Score: 69.98  E-value: 5.38e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  51 PPERGCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIrNGRLLGV 129
Cdd:COG0724  111 SKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDrETGKSRGFAFVEFESEESAEKAIEELNGKEL-EGRPLRV 189
 
Name Accession Description Interval E-value
hnRNP-R-Q TIGR01648
heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the ...
2-594 0e+00

heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q, and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.


Pssm-ID: 273732 [Multi-domain]  Cd Length: 578  Bit Score: 901.29  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452    2 ESNHKSG----DGLSGTQKEAALRALVQRTGYSLVQENGQRKYGGPPPGWDTTPPERGCEIFIGKLPRDLFEDELIPLCE 77
Cdd:TIGR01648   1 RSREKQGskvqEGTKGTPDEAALKALLERTGYTLVQENGQRKYGGPPPGWSGVQPGRGCEVFVGKIPRDLYEDELVPLFE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452   78 KIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRLLGVCASVDNCRLFVGGIPKTKKREEILSEMK 157
Cdd:TIGR01648  81 KAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISVDNCRLFVGGIPKNKKREEILEEFS 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  158 KVTEGVVDVIVYPSAADKTKNRGFAFVEYESHRAAAMARRRLLPGRIQLWGHPIAVDWAEPEVEVDEDTMSSVKILYVRN 237
Cdd:TIGR01648 161 KVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRN 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  238 LMLSTSEEMIEKEFNSIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSYVRYTRGTG 317
Cdd:TIGR01648 241 LMTTTTEEIIEKSFSEFKPGKVERVKKIRDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTG 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  318 GRNTMLQEYTYPLSHVYDPTTTYLGAPVFYTPQAYAaiPSLHFPATKGHLSNRALIRTPSvreiymnvpvGAAGVRGLGG 397
Cdd:TIGR01648 321 GRGKERQAARQSLGQVYDPASRSLAYEDYYYHPPYA--PSLHFPRMPGPIRGRGRGGAPS----------RAAGGRGYPP 388
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  398 RGYLAYTGLGRGYQVKGDKRQDKLYDLLPGMELTPMNTISLKPQGVKLAPQILEEICQKNNWGQPvyqlhsAIGQDQRQL 477
Cdd:TIGR01648 389 YGYEAYYGDYYGYHDYRGKYEDKYYGYDPGMELTPMNPVRGKPGGRGGRPAIPPPRGRKNGAPPP------AIGQDGRQL 462
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  478 FLYKVTIPALASQNPAIHPFTPPKLSAYVDEAKRYAAEHTLQTLGIPTEGGDAGTTAPTATSATvFPGYAVPSATAPVST 557
Cdd:TIGR01648 463 FLYKITIPAGYSQRPAPHPLGPPRGSAFVRGARGGPAQYQQRGRGSRTSRGNGRGGTAGGKRKA-FDGYAQPDATARQTN 541
                         570       580       590
                  ....*....|....*....|....*....|....*...
gi 564333452  558 -AQLKQAVTLGQDLAAYTTYEVYPTfAVTTRGDAYGAF 594
Cdd:TIGR01648 542 nQQNWGAQPIGGDYAGYYGYEVYNN-AVTDNQDFYQTY 578
RRM3_ACF cd12498
RNA recognition motif 3 in vertebrate APOBEC-1 complementation factor (ACF); This subgroup ...
223-305 2.17e-56

RNA recognition motif 3 in vertebrate APOBEC-1 complementation factor (ACF); This subgroup corresponds to the RRM3 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. ACF contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1.


Pssm-ID: 240942 [Multi-domain]  Cd Length: 83  Bit Score: 184.09  E-value: 2.17e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452 223 DEDTMSSVKILYVRNLMLSTSEEMIEKEFNSIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK 302
Cdd:cd12498    1 DEDTMSSVKILYVRNLMLSTTEETIEKEFNSIKPGAVERVKKIRDYAFVHFSNREDAVDAMNALNGKVIDGSPIEVTLAK 80

                 ...
gi 564333452 303 PVD 305
Cdd:cd12498   81 PVD 83
RRM1_ACF cd12486
RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF); This ...
55-132 4.84e-53

RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF); This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1.


Pssm-ID: 240930 [Multi-domain]  Cd Length: 78  Bit Score: 175.16  E-value: 4.84e-53
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564333452  55 GCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRLLGVCAS 132
Cdd:cd12486    1 GCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRLLGVCAS 78
RRM2_ACF cd12490
RNA recognition motif 2 in vertebrate APOBEC-1 complementation factor (ACF); This subgroup ...
134-218 8.61e-48

RNA recognition motif 2 in vertebrate APOBEC-1 complementation factor (ACF); This subgroup corresponds to the RRM2 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. ACF contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1.


Pssm-ID: 240934 [Multi-domain]  Cd Length: 85  Bit Score: 161.38  E-value: 8.61e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452 134 DNCRLFVGGIPKTKKREEILSEMKKVTEGVVDVIVYPSAADKTKNRGFAFVEYESHRAAAMARRRLLPGRIQLWGHPIAV 213
Cdd:cd12490    1 DNCRLFVGGIPKTKKREEILAEMKKVTDGVLDVIVYPSAADKAKNRGFAFVEYESHRAAAMARRKLLPGRIQLWGHPIAV 80

                 ....*
gi 564333452 214 DWAEP 218
Cdd:cd12490   81 DWAEP 85
RRM1_hnRNPR_like cd12249
RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar ...
55-132 3.52e-46

RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs.


Pssm-ID: 240695 [Multi-domain]  Cd Length: 78  Bit Score: 156.95  E-value: 3.52e-46
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564333452  55 GCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRLLGVCAS 132
Cdd:cd12249    1 GCEVFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQLHNYEIRPGKRLGVCIS 78
RRM2_RBM46 cd12492
RNA recognition motif 2 found in vertebrate RNA-binding protein 46 (RBM46); This subgroup ...
134-218 5.65e-45

RNA recognition motif 2 found in vertebrate RNA-binding protein 46 (RBM46); This subgroup corresponds to the RRM2 of RBM46, also termed cancer/testis antigen 68 (CT68). It is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 240936 [Multi-domain]  Cd Length: 85  Bit Score: 154.01  E-value: 5.65e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452 134 DNCRLFVGGIPKTKKREEILSEMKKVTEGVVDVIVYPSAADKTKNRGFAFVEYESHRAAAMARRRLLPGRIQLWGHPIAV 213
Cdd:cd12492    1 DNCRLFIGSIPKEKKKEEILEEMKKVTEGVMDVIVYPSATDRTKNRGFAFVEYESHRAAAMARRKLIPGTFQLWGHTIQV 80

                 ....*
gi 564333452 214 DWAEP 218
Cdd:cd12492   81 DWACP 85
RRM2_RBM47 cd12491
RNA recognition motif 2 in vertebrate RNA-binding protein 47 (RBM47); This subgroup ...
135-223 5.17e-43

RNA recognition motif 2 in vertebrate RNA-binding protein 47 (RBM47); This subgroup corresponds to the RRM2 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 240935 [Multi-domain]  Cd Length: 89  Bit Score: 148.68  E-value: 5.17e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452 135 NCRLFVGGIPKTKKREEILSEMKKVTEGVVDVIVYPSAADKTKNRGFAFVEYESHRAAAMARRRLLPGRIQLWGHPIAVD 214
Cdd:cd12491    1 NCRLFIGGIPKMKKREEILEEISKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD 80

                 ....*....
gi 564333452 215 WAEPEVEVD 223
Cdd:cd12491   81 WAEPEIDVD 89
RRM2_hnRNPR_like cd12250
RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar ...
135-216 1.81e-41

RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM2 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains); DND1 harbors only two RRMs.


Pssm-ID: 240696 [Multi-domain]  Cd Length: 82  Bit Score: 144.34  E-value: 1.81e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452 135 NCRLFVGGIPKTKKREEILSEMKKVTEGVVDVIVYPSAADKTKNRGFAFVEYESHRAAAMARRRLLPGRIQLWGHPIAVD 214
Cdd:cd12250    1 NCRLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAMARRKLVPGRILLWGHEVAVD 80

                 ..
gi 564333452 215 WA 216
Cdd:cd12250   81 WA 82
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar ...
230-303 1.64e-39

RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 240697 [Multi-domain]  Cd Length: 72  Bit Score: 138.53  E-value: 1.64e-39
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564333452 230 VKILYVRNLMLSTSEEMIEKEFNSIkpGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP 303
Cdd:cd12251    1 VKVLYVRNLPLSTTEEQLRELFSEY--GEVERVKKIKDYAFVHFEERDDAVKAMEEMNGKELEGSPIEVSLAKP 72
RRM1_RBM47 cd12485
RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47); This subgroup ...
55-132 8.78e-39

RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47); This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 240929 [Multi-domain]  Cd Length: 78  Bit Score: 136.63  E-value: 8.78e-39
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564333452  55 GCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRLLGVCAS 132
Cdd:cd12485    1 GCEVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVRELNNYEIRPGRLLGVCCS 78
RRM1_RBM46 cd12484
RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46); This subgroup ...
55-132 1.50e-36

RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46); This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 240928 [Multi-domain]  Cd Length: 78  Bit Score: 130.79  E-value: 1.50e-36
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564333452  55 GCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRLLGVCAS 132
Cdd:cd12484    1 GCEVFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIRILNNYEIRPGKFIGVCVS 78
RRM3_RBM46 cd12496
RNA recognition motif 3 in vertebrate RNA-binding protein 46 (RBM46); This subgroup ...
230-303 3.04e-36

RNA recognition motif 3 in vertebrate RNA-binding protein 46 (RBM46); This subgroup corresponds to the RRM3 of RBM46, also termed cancer/testis antigen 68 (CT68), is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 240940 [Multi-domain]  Cd Length: 74  Bit Score: 129.78  E-value: 3.04e-36
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564333452 230 VKILYVRNLMLSTSEEMIEKEFNSIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP 303
Cdd:cd12496    1 VKVLYVRNLMISTTEETIKAEFNKFKPGVVERVKKLRDYAFVHFFNREDAVAAMSVMNGKCIDGASIEVTLAKP 74
RRM3_RBM47 cd12497
RNA recognition motif 3 in vertebrate RNA-binding protein 47 (RBM47); This subgroup ...
230-303 2.83e-34

RNA recognition motif 3 in vertebrate RNA-binding protein 47 (RBM47); This subgroup corresponds to the RRM3 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 240941 [Multi-domain]  Cd Length: 74  Bit Score: 124.37  E-value: 2.83e-34
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564333452 230 VKILYVRNLMLSTSEEMIEKEFNSIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP 303
Cdd:cd12497    1 VKILYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRDYAFVHFTSREDAVHAMNNLNGTELEGSCIEVTLAKP 74
RRM1_hnRNPQ cd12483
RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q); ...
55-132 4.44e-28

RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q); This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains.


Pssm-ID: 240927 [Multi-domain]  Cd Length: 79  Bit Score: 107.01  E-value: 4.44e-28
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564333452  55 GCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRLLGVCAS 132
Cdd:cd12483    1 GTEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDpLTGLNRGYAFVTFCTKEAAQEAVKLYNNHEIRPGKHIGVCIS 79
RRM1_hnRNPR cd12482
RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R); ...
55-132 4.72e-28

RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R); This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains.


Pssm-ID: 240926 [Multi-domain]  Cd Length: 79  Bit Score: 106.97  E-value: 4.72e-28
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564333452  55 GCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRLLGVCAS 132
Cdd:cd12482    1 GTEVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDpLSGQNRGYAFITFCGKEAAQEAVKLCDNYEIRPGKHLGVCIS 79
RRM1_DND1 cd12487
RNA recognition motif 1 found in vertebrate dead end protein homolog 1 (DND1); This subgroup ...
55-132 5.55e-28

RNA recognition motif 1 found in vertebrate dead end protein homolog 1 (DND1); This subgroup corresponds to the RRM1 of DND1, also termed RNA-binding motif, single-stranded-interacting protein 4, an RNA-binding protein that is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. For instance, DND1 binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle regulator and tumor suppressor, LATS2 (large tumor suppressor, homolog 2 of Drosophila). It helps maintain their protein expression through blocking the inhibitory function of microRNAs (miRNA) from these transcripts. DND1 may also impose another level of translational regulation to modulate expression of critical factors in embryonic stem (ES) cells. DND1 interacts specifically with apolipoprotein B editing complex 3 (APOBEC3), a multi-functional protein inhibiting retroviral replication. The DND1-APOBEC3 interaction may play a role in maintaining viability of germ cells and for preventing germ cell tumor development. DND1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 240931 [Multi-domain]  Cd Length: 78  Bit Score: 106.81  E-value: 5.55e-28
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564333452  55 GCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRLLGVCAS 132
Cdd:cd12487    1 GSEVFIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMTFSGLNRGFAYAKYSDRRGASAAIATLHNYELPEGCCLLVCRS 78
RRM2_hnRNPR cd12488
RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R); ...
135-218 4.17e-26

RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R); This subgroup corresponds to the RRM2 of hnRNP R, a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. It contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif. hnRNP R binds RNA through its RRM domains.


Pssm-ID: 240932 [Multi-domain]  Cd Length: 85  Bit Score: 101.73  E-value: 4.17e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452 135 NCRLFVGGIPKTKKREEILSEMKKVTEGVVDVIVYPSAADKTKNRGFAFVEYESHRAAAMARRRLLPGRIQLWGHPIAVD 214
Cdd:cd12488    2 NNRLFVGSIPKNKTKENILEEFSKVTEGLVDVILYHQPDDKKKNRGFCFLEYEDHKSAAQARRRLMSGKVKVWGNVVTVE 81

                 ....
gi 564333452 215 WAEP 218
Cdd:cd12488   82 WADP 85
DND1_DSRM pfam14709
double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead ...
446-522 4.95e-26

double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead end protein 1 (DND1_HUMAN) homologous to double strand RNA binding domains (PF00035, PF00333)


Pssm-ID: 317152  Cd Length: 81  Bit Score: 101.29  E-value: 4.95e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564333452  446 APQILEEICQKNNWGQPVYQLHSA-IGQDQRQLFLYKVTIPALASQNP-AIHPFTPPKLSAYVDEAKRYAAEHTLQTLG 522
Cdd:pfam14709   3 AVQLLEELCQKNKWGSPVYELHSHtAGPDGKLLFLYKVVIPGIPTSFPgVIWIFMPGKLCSTKEEAKEAAAEQVLQALG 81
RRM2_hnRNPQ cd12489
RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q); ...
135-218 8.93e-26

RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q); This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains.


Pssm-ID: 240933 [Multi-domain]  Cd Length: 85  Bit Score: 100.96  E-value: 8.93e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452 135 NCRLFVGGIPKTKKREEILSEMKKVTEGVVDVIVYPSAADKTKNRGFAFVEYESHRAAAMARRRLLPGRIQLWGHPIAVD 214
Cdd:cd12489    2 NNRLFVGSIPKSKTKEQIVEEFSKVTEGLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQARRRLMSGKVKVWGNVVTVE 81

                 ....
gi 564333452 215 WAEP 218
Cdd:cd12489   82 WADP 85
RRM3_hnRNPR cd12494
RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R); ...
230-303 2.96e-23

RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R); This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains.


Pssm-ID: 240938 [Multi-domain]  Cd Length: 72  Bit Score: 93.17  E-value: 2.96e-23
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564333452 230 VKILYVRNLMLSTSEEMIEKEFNSIkpGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP 303
Cdd:cd12494    1 VKVLFVRNLATTVTEEILEKSFSEF--GKLERVKKLKDYAFVHFEERDAAVRAMDEMNGKEIEGEEIEIVLAKP 72
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
58-509 1.81e-22

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 101.04  E-value: 1.81e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452   58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNNyeirngrllgvcASVDNCR 137
Cdd:TIGR01628  91 IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNG------------MLLNDKE 158
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  138 LFVGGIPKTKKREEILSE------MKKVTEGVVD-----------VIVYPSAADKTKN--RGFAFVEYESHRAAAMARRR 198
Cdd:TIGR01628 159 VYVGRFIKKHEREAAPLKkftnlyVKNLDPSVNEdklrelfakfgEITSAAVMKDGSGrsRGFAFVNFEKHEDAAKAVEE 238
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  199 LLPGRIQLWGHP--IAVDWAEPEVE-------------VDEDTMSSVKILYVRNLMLSTSEEMIEKEFNSIkpGAVERVK 263
Cdd:TIGR01628 239 MNGKKIGLAKEGkkLYVGRAQKRAEreaelrrkfeelqQERKMKAQGVNLYVKNLDDTVTDEKLRELFSEC--GEITSAK 316
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  264 KIRD-------YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKdsyvRYTRGTGGRNTMLQEytYPLSHVYDP 336
Cdd:TIGR01628 317 VMLDekgvsrgFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQ----RRAHLQDQFMQLQPR--MRQLPMGSP 390
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  337 TTTYLGAPVFYTPQAYAAIPSlhfpatkghlsnralirTPSVREIYMNVPVGAAGVRGLGGRGY--LAYTGLGRGYQVKG 414
Cdd:TIGR01628 391 MGGAMGQPPYYGQGPQQQFNG-----------------QPLGWPRMSMMPTPMGPGGPLRPNGLapMNAVRAPSRNAQNA 453
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  415 DKRQDKlydllPGMELTPMNTISLKPQGVKLaPQILeeICQKNNWGQPVYQLHSAIGQDQRQ-----LFLYKVTI-PALA 488
Cdd:TIGR01628 454 AQKPPM-----QPVMYPPNYQSLPLSQDLPQ-PQST--ASQGGQNKKLAQVLASATPQMQKQvlgerLFPLVEAIePALA 525
                         490       500       510
                  ....*....|....*....|....*....|..
gi 564333452  489 S----------QNPAIHPF-TPPKLSAYVDEA 509
Cdd:TIGR01628 526 AkitgmllemdNSELLHLLeSPELLKSKVDEA 557
RRM3_hnRNPQ cd12495
RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q); ...
230-303 2.17e-21

RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q); This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains.


Pssm-ID: 240939 [Multi-domain]  Cd Length: 72  Bit Score: 88.13  E-value: 2.17e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564333452 230 VKILYVRNLMLSTSEEMIEKEFNSIkpGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP 303
Cdd:cd12495    1 VKVLFVRNLANTVTEEILEKAFGQF--GKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKELEGENIEIVFAKP 72
RRM smart00360
RNA recognition motif;
58-126 4.15e-18

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 78.40  E-value: 4.15e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452    58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFN-GNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRL 126
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKEtGKSKGFAFVEFESEEDAEKALEALNGKELDGRPL 71
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
58-130 8.65e-18

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 240668 [Multi-domain]  Cd Length: 72  Bit Score: 77.73  E-value: 8.65e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIrNGRLLGVC 130
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALNGKEL-DGRKLKVS 72
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
58-123 3.32e-16

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C-terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 333819 [Multi-domain]  Cd Length: 70  Bit Score: 73.01  E-value: 3.32e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564333452   58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRN 123
Cdd:pfam00076   1 LFVGNLPPDVTEEDLKDLFSKFGPIKSIRLVRDRTGRSKGFAFVEFESEEDAEKAIEALNGKELGG 66
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
233-298 8.87e-16

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 240668 [Multi-domain]  Cd Length: 72  Bit Score: 71.95  E-value: 8.87e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564333452 233 LYVRNLMLSTSEEMIEKEFNSIkpGAVERVKKIRD-------YAFVHFSNREDAVEAMKALNGKVLDGSPIEV 298
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKF--GEIESVRIVRDkdgkskgFAFVEFESPEDAEKALEALNGKELDGRKLKV 71
RRM smart00360
RNA recognition motif;
233-298 9.84e-16

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 71.86  E-value: 9.84e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564333452   233 LYVRNLMLSTSEEMIEKEFNSIkpGAVERVKKIRD--------YAFVHFSNREDAVEAMKALNGKVLDGSPIEV 298
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKF--GKVESVRLVRDketgkskgFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM1_2_CELF1-6_like cd12361
RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant ...
59-118 1.62e-14

RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA; This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain.


Pssm-ID: 240807 [Multi-domain]  Cd Length: 77  Bit Score: 68.34  E-value: 1.62e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564333452  59 FIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFN-GNNRGYAFVTFSNKQEAKNAIKQLNN 118
Cdd:cd12361    3 FVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDtGQSKGCAFVKFSSREEAQKAIEALHG 63
RRM_HP0827_like cd12399
RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; This ...
58-129 5.71e-14

RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.


Pssm-ID: 240845 [Multi-domain]  Cd Length: 78  Bit Score: 66.87  E-value: 5.71e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIrNGRLLGV 129
Cdd:cd12399    2 LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDrETGRSRGFGFVEMETAEEANAAIEKLNGTDF-GGRTLTV 73
RRM_RBMX_like cd12382
RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA ...
55-129 1.39e-13

RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins; This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G.


Pssm-ID: 240828 [Multi-domain]  Cd Length: 80  Bit Score: 66.09  E-value: 1.39e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564333452  55 GCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIrNGRLLGV 129
Cdd:cd12382    1 GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDpETGESRGFGFVTFESVEDADAAIRDLNGKEL-EGRVIKV 75
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3 ...
58-129 2.67e-13

RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.


Pssm-ID: 240844 [Multi-domain]  Cd Length: 75  Bit Score: 64.95  E-value: 2.67e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFN-GNNRGYAFVTFSNKQEAKNAIKQLNNYEIrNGRLLGV 129
Cdd:cd12398    1 VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDtGKPKGYGFCEFEDIETAASAIRNLNGYEF-NGRALRV 72
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
51-129 5.38e-13

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 223796 [Multi-domain]  Cd Length: 306  Bit Score: 69.98  E-value: 5.38e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  51 PPERGCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIrNGRLLGV 129
Cdd:COG0724  111 SKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDrETGKSRGFAFVEFESEESAEKAIEELNGKEL-EGRPLRV 189
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins; This ...
233-300 1.32e-12

RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 240786 [Multi-domain]  Cd Length: 67  Bit Score: 62.83  E-value: 1.32e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564333452 233 LYVRNLMLSTSEEMIEKEFNSIkpGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTL 300
Cdd:cd12340    2 LYVRPFPPDTSESAIREIFSPY--GAVKEVKMISNFAFVEFESLESAIRAKDSVHGKVLNNNPLYVTY 67
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
58-293 2.31e-12

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 69.45  E-value: 2.31e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452   58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFN-GNNRGYAFVTFSNKQEAKNAIKQLNNYEIrNGRLLGVCASV--- 133
Cdd:TIGR01628   3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVtRRSLGYGYVNFQNPADAERALETMNFKRL-GGKPIRIMWSQrdp 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  134 -----DNCRLFVGGIPK---TKKREEILSEMKKVTEGVVdvivypsAADKT-KNRGFAFVEYESHRAAAMARRRLlpGRI 204
Cdd:TIGR01628  82 slrrsGVGNIFVKNLDKsvdNKALFDTFSKFGNILSCKV-------ATDENgKSRGYGFVHFEKEESAKAAIQKV--NGM 152
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  205 QLWGHPIAVDWAEPEVEVDEDTMSSVKILYVRNLMLSTSEEMIEKEFNS---IKPGAVERVK--KIRDYAFVHFSNREDA 279
Cdd:TIGR01628 153 LLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKfgeITSAAVMKDGsgRSRGFAFVNFEKHEDA 232
                         250
                  ....*....|....
gi 564333452  280 VEAMKALNGKVLDG 293
Cdd:TIGR01628 233 AKAVEEMNGKKIGL 246
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
233-297 9.53e-12

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C-terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 333819 [Multi-domain]  Cd Length: 70  Bit Score: 60.30  E-value: 9.53e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564333452  233 LYVRNLMLSTSEEMIEKEFNSIkpGAVERVKKIRD-------YAFVHFSNREDAVEAMKALNGKVLDGSPIE 297
Cdd:pfam00076   1 LFVGNLPPDVTEEDLKDLFSKF--GPIKSIRLVRDrtgrskgFAFVEFESEEDAEKAIEALNGKELGGRTLR 70
RRM1_RRM2_RBM5_like cd12313
RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins; This ...
231-301 9.54e-12

RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins; This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 240759 [Multi-domain]  Cd Length: 84  Bit Score: 61.03  E-value: 9.54e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452 231 KILYVRNLMLSTSEEMIEKEFNSIKPGAVERVKKIRD--------YAFVHFSNREDAVEAMKALNGK---VLDGSPIEVT 299
Cdd:cd12313    3 NTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDkltgtsrgFAFVEFPSLEDATQWMDALNNLdpfVIDGRVVRVS 82

                 ..
gi 564333452 300 LA 301
Cdd:cd12313   83 YA 84
RRM1_Hu_like cd12375
RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar ...
63-126 1.31e-11

RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 240821 [Multi-domain]  Cd Length: 77  Bit Score: 60.44  E-value: 1.31e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564333452  63 LPRDLFEDELIPLCEKIGKIYEMRMMMDFN-GNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRL 126
Cdd:cd12375    8 LPQDMTQEELRSLFEAIGPIESCKIVRDRItGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRL 72
RRM5_RBM19_like cd12318
RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins; This ...
231-300 1.38e-11

RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins; This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 240764 [Multi-domain]  Cd Length: 82  Bit Score: 60.31  E-value: 1.38e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452 231 KILYVRNLMLSTSEEMIEKEFNSI-KPGAVERVKKiRD-----------YAFVHFSNREDAVEAMKALNGKVLDGSPIEV 298
Cdd:cd12318    1 TTLFVKNLNFKTTEETLKKHFEKCgGVRSVTIAKK-KDpkgpgkllsmgYGFVEFKSKEAAQKALKRLQGTVLDGHALEL 79

                 ..
gi 564333452 299 TL 300
Cdd:cd12318   80 KL 81
RRM_RBMX_like cd12382
RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA ...
233-302 1.67e-11

RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins; This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G.


Pssm-ID: 240828 [Multi-domain]  Cd Length: 80  Bit Score: 59.93  E-value: 1.67e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564333452 233 LYVRNLMLSTSEEMIEKEFNsiKPGAVERVKKIRD--------YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK 302
Cdd:cd12382    4 LFVSGLSTRTTEKELEALFS--KFGRVEEVLLMKDpetgesrgFGFVTFESVEDADAAIRDLNGKELEGRVIKVEKAK 79
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
231-306 3.30e-11

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 223796 [Multi-domain]  Cd Length: 306  Bit Score: 64.58  E-value: 3.30e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452 231 KILYVRNLMLSTSEEMIEKEFnsIKPGAVERVKKIRD--------YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK 302
Cdd:COG0724  116 NTLFVGNLPYDVTEEDLRELF--KKFGPVKRVRLVRDretgksrgFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ 193

                 ....
gi 564333452 303 PVDK 306
Cdd:COG0724  194 PASQ 197
sex-lethal TIGR01659
sex-lethal family splicing factor; This model describes the sex-lethal family of splicing ...
48-186 7.50e-11

sex-lethal family splicing factor; This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).


Pssm-ID: 273740 [Multi-domain]  Cd Length: 346  Bit Score: 63.88  E-value: 7.50e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452   48 DTTPPERGCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDF-NGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRL 126
Cdd:TIGR01659 100 DNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYkTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRL 179
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564333452  127 LGVCA-----SVDNCRLFVGGIPKTKKREEILSEMKKVTEGVVDVIVypsaADKT--KNRGFAFVEY 186
Cdd:TIGR01659 180 KVSYArpggeSIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNIL----RDKLtgTPRGVAFVRF 242
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; ...
58-130 1.09e-10

RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 240730 [Multi-domain]  Cd Length: 73  Bit Score: 57.65  E-value: 1.09e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRnGRLLGVC 130
Cdd:cd12284    1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDpETGRSKGYGFIQFADAEDAKKALEQLNGFELA-GRPIKVG 73
RRM1_CELF3_4_5_6 cd12632
RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and ...
58-116 1.15e-10

RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins; This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region.


Pssm-ID: 241076 [Multi-domain]  Cd Length: 87  Bit Score: 57.80  E-value: 1.15e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQL 116
Cdd:cd12632    8 LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDkYTGMHKGCAFLTYCARESALKAQSAL 67
ELAV_HUD_SF TIGR01661
ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing ...
54-299 1.17e-10

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).


Pssm-ID: 273741 [Multi-domain]  Cd Length: 352  Bit Score: 63.04  E-value: 1.17e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452   54 RGCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNgrllgvcaS 132
Cdd:TIGR01661  88 KGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDnVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSG--------C 159
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  133 VDNCRLFVGGIPKTKKREEILSEMKKV----TEGVVDVIVYPSAADKTKNRGFAFVEYE-----SHRAAAMARRRLLPGR 203
Cdd:TIGR01661 160 TEPITVKFANNPSSSNSKGLLSQLEAVqnpqTTRVPLSTILTAAGIGPMHHAAARFRPSagdftAVLAHQQQQHAVAQQH 239
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  204 IQLWGHPIAVDWAEPEVEVDEDTMSS---VKILYVRNLMLSTSEEMIEKEFNSIkpGAVERVKKIRD--------YAFVH 272
Cdd:TIGR01661 240 AAQRASPPATDGQTAGLAAGAQISASdgaGYCIFVYNLSPDTDETVLWQLFGPF--GAVQNVKIIRDlttnqckgYGFVS 317
                         250       260
                  ....*....|....*....|....*..
gi 564333452  273 FSNREDAVEAMKALNGKVLDGSPIEVT 299
Cdd:TIGR01661 318 MTNYDEAAMAILSLNGYTLGNRVLQVS 344
RRM_SR140 cd12223
RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins; This subgroup ...
233-304 1.39e-10

RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins; This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain).


Pssm-ID: 240669 [Multi-domain]  Cd Length: 84  Bit Score: 57.66  E-value: 1.39e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452 233 LYVRNLMLSTSEEMIEKEF------NSIK---PGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP 303
Cdd:cd12223    4 LYVGNLNPKVTEEVLCQEFgrfgplASVKimwPRTEEERRRNRNCGFVAFMNRADAERALDELDGKDVMGYELKLGWGKA 83

                 .
gi 564333452 304 V 304
Cdd:cd12223   84 V 84
RRM1_TIA1_like cd12352
RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This ...
233-301 3.21e-10

RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 240798 [Multi-domain]  Cd Length: 72  Bit Score: 56.16  E-value: 3.21e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564333452 233 LYVRNLMLSTSEEMIEKEFNSIkpGAVERVKKIRD-----YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA 301
Cdd:cd12352    1 LYVGNLDRTVTEDLLAELFSQI--GPIKSCKLIREhgndpYAFVEYYDHRSAAAALQTMNGRLILGQEIKVNWA 72
RRM_eIF3B cd12278
RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and ...
77-119 3.38e-10

RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins; This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain.


Pssm-ID: 240724 [Multi-domain]  Cd Length: 84  Bit Score: 56.43  E-value: 3.38e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 564333452  77 EKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNNY 119
Cdd:cd12278   31 FGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNGY 73
RRM1_2_CoAA_like cd12343
RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and ...
233-298 4.07e-10

RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins; This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region.


Pssm-ID: 240789 [Multi-domain]  Cd Length: 66  Bit Score: 55.70  E-value: 4.07e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564333452 233 LYVRNLMLSTSEEMIEKEFNsiKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV 298
Cdd:cd12343    2 LFVGNLPDATTSEELRALFE--KYGTVTECDVVKNYGFVHMEEEEDAEDAIKALNGYEFMGKRINV 65
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; ...
233-298 4.47e-10

RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 240730 [Multi-domain]  Cd Length: 73  Bit Score: 55.73  E-value: 4.47e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564333452 233 LYVRNLMLSTSEEMIEKEFNSIkpGAVERVKKIRD--------YAFVHFSNREDAVEAMKALNGKVLDGSPIEV 298
Cdd:cd12284    1 LYVGNLHFNITEDDLRGIFEPF--GEIEFVQLQRDpetgrskgYGFIQFADAEDAKKALEQLNGFELAGRPIKV 72
RRM_HP0827_like cd12399
RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; This ...
233-303 4.67e-10

RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.


Pssm-ID: 240845 [Multi-domain]  Cd Length: 78  Bit Score: 55.70  E-value: 4.67e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564333452 233 LYVRNLMLSTSEEMIEKEFNSIkpGAVERVKKIRD--------YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP 303
Cdd:cd12399    2 LYVGNLPYNVTEEDLKDLFGQF--GEVTSARVITDretgrsrgFGFVEMETAEEANAAIEKLNGTDFGGRTLTVNEARP 78
RRM3_I_PABPs cd12380
RNA recognition motif 3 found in type I polyadenylate-binding proteins; This subfamily ...
58-130 7.33e-10

RNA recognition motif 3 found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 240826 [Multi-domain]  Cd Length: 80  Bit Score: 55.27  E-value: 7.33e-10
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gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIrNGRLLGVC 130
Cdd:cd12380    4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELNGKEV-NGKKLYVG 75
RRM1_2_CoAA_like cd12343
RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and ...
58-129 8.64e-10

RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins; This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region.


Pssm-ID: 240789 [Multi-domain]  Cd Length: 66  Bit Score: 54.54  E-value: 8.64e-10
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gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMmdfngNNrgYAFVTFSNKQEAKNAIKQLNNYEIrNGRLLGV 129
Cdd:cd12343    2 LFVGNLPDATTSEELRALFEKYGTVTECDVV-----KN--YGFVHMEEEEDAEDAIKALNGYEF-MGKRINV 65
RRM3_CELF1-6 cd12362
RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, ...
58-126 1.26e-09

RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins; This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts.


Pssm-ID: 240808 [Multi-domain]  Cd Length: 73  Bit Score: 54.57  E-value: 1.26e-09
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gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGN-NRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRL 126
Cdd:cd12362    1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGqSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRL 70
RRM2_Bruno_like cd12636
RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins; This ...
53-124 1.30e-09

RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins; This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region.


Pssm-ID: 241080 [Multi-domain]  Cd Length: 81  Bit Score: 54.82  E-value: 1.30e-09
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gi 564333452  53 ERgcEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNG 124
Cdd:cd12636    1 ER--KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAMHHSQTMEG 70
RRM3_TIA1_like cd12354
RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and ...
56-127 1.47e-09

RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 240800 [Multi-domain]  Cd Length: 73  Bit Score: 54.16  E-value: 1.47e-09
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gi 564333452  56 CEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDfngnnRGYAFVTFSNKQEAKNAIKQLNNYEIrNGRLL 127
Cdd:cd12354    1 TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD-----KGYAFVRFDTHEAAATAIVAVNGTSI-NGQTV 66
RRM1_RBM28_like cd12413
RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily ...
233-303 1.64e-09

RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 240859 [Multi-domain]  Cd Length: 79  Bit Score: 54.54  E-value: 1.64e-09
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gi 564333452 233 LYVRNLMLSTSEEMIEKEFNSIKP---GAVERVK---KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP 303
Cdd:cd12413    2 LFVRNLPYDTTDEQLEEFFSEVGPikrCFVVKDKgskKCRGFGYVTFALEEDAKRALEEKKKTKFGGRKIHVEFAKK 78
RRM2_RBM28_like cd12414
RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily ...
233-301 2.10e-09

RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 240860 [Multi-domain]  Cd Length: 76  Bit Score: 53.80  E-value: 2.10e-09
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gi 564333452 233 LYVRNLMLSTSEEMIEKEFNSIkpGAVERVK-------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA 301
Cdd:cd12414    2 LIVRNLPFKCTEADLKKLFSPF--GFVWEVTiprkpdgKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRPVAVDWA 75
RRM_CIRBP_RBM3 cd12449
RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein ...
233-301 2.23e-09

RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins; This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain.


Pssm-ID: 240895 [Multi-domain]  Cd Length: 80  Bit Score: 54.08  E-value: 2.23e-09
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gi 564333452 233 LYVRNLMLSTSEEMIEKEFNsiKPGAVERVKKIRD--------YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA 301
Cdd:cd12449    3 LFIGGLSFDTNEQSLEQVFS--KYGQISEVVVVKDretqrsrgFGFVTFENPDDAKDAMMAMNGKSVDGRQIRVDQA 77
RRM4_I_PABPs cd12381
RNA recognition motif 4 in type I polyadenylate-binding proteins; This subfamily corresponds ...
233-301 3.40e-09

RNA recognition motif 4 in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 240827 [Multi-domain]  Cd Length: 79  Bit Score: 53.39  E-value: 3.40e-09
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gi 564333452 233 LYVRNLMLSTSEEMIEKEFNSIkpGAVERVKKIRD-------YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA 301
Cdd:cd12381    4 LYVKNLDDSIDDERLREEFSPF--GTITSAKVMTDekgrskgFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVALA 77
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
57-126 3.43e-09

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 240744 [Multi-domain]  Cd Length: 78  Bit Score: 53.41  E-value: 3.43e-09
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gi 564333452  57 EIFIGKLPRDLFEDELIPLCEKIGKIYEMRM----MMDFNGNNRGYAFVTFSNKQEAKNAIkQLNNYEIRNGRL 126
Cdd:cd12298    2 EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIpkkqDEKQGRLNNGFAFVTFKDASSAENAL-QLNGTELGGRKI 74
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in ...
233-299 4.90e-09

RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 240762 [Multi-domain]  Cd Length: 74  Bit Score: 52.68  E-value: 4.90e-09
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gi 564333452 233 LYVRNLMLSTSEEMIEKEFNSIkpGAVERV--------KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVT 299
Cdd:cd12316    2 LFVRNLPFTTTEEELRELFEAF--GEISEVhlpldketKRSKGFAFVSFMFPEHAVKAYSELDGSIFQGRLLHVL 74
RRM_NCBP2 cd12240
RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar ...
233-308 5.16e-09

RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins; This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC.


Pssm-ID: 240686 [Multi-domain]  Cd Length: 78  Bit Score: 52.93  E-value: 5.16e-09
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gi 564333452 233 LYVRNLMLSTSEEMIEKEFNsiKPGAVERV--------KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEvtlakpV 304
Cdd:cd12240    1 LYVGNLSFYTTEEQIYELFS--RCGDIKRIimgldrftKTPCGFCFVEYYTREDAENAVKYLNGTKLDDRIIR------V 72

                 ....
gi 564333452 305 DKDS 308
Cdd:cd12240   73 DWDA 76
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
50-304 6.69e-09

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 58.39  E-value: 6.69e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452   50 TPPERGCE-IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGN-NRGYAFVTFSNKQEAKNAIkQLNnyeirnGRLL 127
Cdd:TIGR01622 108 TEDERDRRtVFVQQLAARARERDLYEFFSKVGKVRDVQIIKDRNSRrSKGVGYVEFYDVDSVQAAL-ALT------GQKL 180
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  128 GvcasvdncrlfvgGIPktkkreeilsemkkvtegvvdVIVYPSAADKtkNRGFAfveyeshraaamarrrllpgriqlw 207
Cdd:TIGR01622 181 L-------------GIP---------------------VIVQLSEAEK--NRAAR------------------------- 199
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452  208 ghpiavdwAEPEVEVDEDTMSSVKILYVRNLMLSTSEEMIEKEFNSIkpGAVERVKKIRD--------YAFVHFSNREDA 279
Cdd:TIGR01622 200 --------AATETSGHHPNSIPFHRLYVGNLHFNITEQDLRQIFEPF--GEIEFVQLQKDpetgrskgYGFIQFRDAEQA 269
                         250       260
                  ....*....|....*....|....*
gi 564333452  280 VEAMKALNGKVLDGSPIEVTLAKPV 304
Cdd:TIGR01622 270 KEALEKMNGFELAGRPIKVGLGNDF 294
RRM_RBM18 cd12355
RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins; This ...
58-117 6.79e-09

RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.


Pssm-ID: 240801 [Multi-domain]  Cd Length: 80  Bit Score: 52.66  E-value: 6.79e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNG----NNRGYAFVTFSNKQEAKNAIKQLN 117
Cdd:cd12355    2 LWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGplkgQPRGYCFVTFETKEEAEKALKSLN 65
RRM2_U1A_like cd12247
RNA recognition motif 2 in the U1A/U2B"/SNF protein family; This subfamily corresponds to the ...
231-299 8.28e-09

RNA recognition motif 2 in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding.


Pssm-ID: 240693 [Multi-domain]  Cd Length: 72  Bit Score: 52.19  E-value: 8.28e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564333452 231 KILYVRNLMLSTSEEMIEKEFNSIkPGAVE-RVKKIRDYAFVHFSNREDAVEAMKALNG-KVLDGSPIEVT 299
Cdd:cd12247    3 KILFLQNLPEETTKEMLEMLFNQF-PGFKEvRLVPRRGIAFVEFETEEQATVALQALQGfKITPGHAMKIS 72
RRM2_RBM28_like cd12414
RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily ...
57-123 9.18e-09

RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 240860 [Multi-domain]  Cd Length: 76  Bit Score: 52.26  E-value: 9.18e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564333452  57 EIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRN 123
Cdd:cd12414    1 RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKG 67
RRM1_SART3 cd12391
RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and ...
58-125 9.48e-09

RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 240837 [Multi-domain]  Cd Length: 72  Bit Score: 51.89  E-value: 9.48e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQlnNYEIRNGR 125
Cdd:cd12391    2 VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKL--DRELIKGR 67
RRM2_PUF60 cd12371
RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins; This ...
58-130 9.62e-09

RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.


Pssm-ID: 240817 [Multi-domain]  Cd Length: 77  Bit Score: 52.27  E-value: 9.62e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDF-NGNNRGYAFVTFSNKQEAKNAIKQLNNYEIrNGRLLGVC 130
Cdd:cd12371    3 IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPeTGKHKGYGFIEYENPQSAQDAIASMNLFDL-GGQQLRVG 75
RRM4_MRD1 cd12319
RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and ...
233-301 1.14e-08

RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 240765 [Multi-domain]  Cd Length: 84  Bit Score: 52.16  E-value: 1.14e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452 233 LYVRNLMLSTSEEMIEKEFNSIKPGAVERVKKIRD-----------YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA 301
Cdd:cd12319    3 LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDpkrpgqtlsmgFGFVGFKTKEQAQAALKAMDGFVLDGHTLVVKFS 82
RRM_CSTF2_CSTF2T cd12671
RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation ...
58-129 1.52e-08

RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins; This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64.


Pssm-ID: 241115 [Multi-domain]  Cd Length: 75  Bit Score: 51.34  E-value: 1.52e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDF-NGNNRGYAFVTFSNKQEAKNAIKQLNNYEIrNGRLLGV 129
Cdd:cd12671    1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDReTGKPKGYGFCEYKDQETALSAMRNLNGYEL-NGRQLRV 72
RRM6_RBM19_RRM5_MRD1 cd12320
RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 ...
71-118 1.71e-08

RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 240766 [Multi-domain]  Cd Length: 76  Bit Score: 51.46  E-value: 1.71e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 564333452  71 ELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNN 118
Cdd:cd12320   16 ELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKS 63
RRM2_SXL cd12651
RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins; This subfamily ...
58-118 2.05e-08

RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 241095 [Multi-domain]  Cd Length: 79  Bit Score: 51.43  E-value: 2.05e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQLNN 118
Cdd:cd12651    3 LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDkSTGLPRGVAFVRYDKREEAQAAISSLNG 64
RRM2_SART3 cd12392
RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and ...
58-123 2.97e-08

RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 240838 [Multi-domain]  Cd Length: 81  Bit Score: 50.87  E-value: 2.97e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRN 123
Cdd:cd12392    5 LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMDGTEIKE 70
RRM1_FCA cd12633
RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins; This ...
57-118 3.51e-08

RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins; This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain.


Pssm-ID: 241077 [Multi-domain]  Cd Length: 80  Bit Score: 50.73  E-value: 3.51e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564333452  57 EIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQLNN 118
Cdd:cd12633    1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDkRTGHQQGCCFVKYSTRDEADRAIRALHN 63
RRM_SKAR cd12681
RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins; This subgroup ...
232-300 3.93e-08

RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins; This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 241125 [Multi-domain]  Cd Length: 69  Bit Score: 49.96  E-value: 3.93e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333452 232 ILYVRNLMLSTSEEMIEKEFNSIkpGAVERVKKIRD-YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTL 300
Cdd:cd12681    2 RLVVSNLHPSVTEDDIVELFSAI--GALKRARLVRPgVAEVVYVRKDDALTAIDKYNNRELDGQPMKCKL 69
RRM2_TIA1_like cd12353
RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This ...
58-125 4.48e-08

RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 240799 [Multi-domain]  Cd Length: 75  Bit Score: 50.06  E-value: 4.48e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDF-NGNNRGYAFVTFSNKQEAKNAIKQLNNYEIrNGR 125
Cdd:cd12353    2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMqTGKSKGYGFVSFVKKEDAENAIQSMNGQWL-GGR 69
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
233-300 4.90e-08

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 240744 [Multi-domain]  Cd Length: 78  Bit Score: 50.33  E-value: 4.90e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564333452 233 LYVRNLMLSTSEEMIEKEFNsiKPGAVERVK--KIRD---------YAFVHFSNREDAVEAMKaLNGKVLDGSPIEVTL 300
Cdd:cd12298    3 IYVRNLDFKLDEDDLRGIFS--KFGEVESIRipKKQDekqgrlnngFAFVTFKDASSAENALQ-LNGTELGGRKISVSL 78
RRM1_I_PABPs cd12378
RNA recognition motif 1 in type I polyadenylate-binding proteins; This subfamily corresponds ...
232-299 4.99e-08

RNA recognition motif 1 in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 240824 [Multi-domain]  Cd Length: 80  Bit Score: 50.23  E-value: 4.99e-08
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gi 564333452 232 ILYVRNLMLSTSEEMIEKEFNSIKPgaVERVKKIRD--------YAFVHFSNREDAVEAMKALNGKVLDGSPIEVT 299
Cdd:cd12378    1 SLYVGDLHPDVTEAMLYEIFSPAGP--VLSIRVCRDlitrrslgYAYVNFQNPADAERALDTLNFDVIKGKPIRIM 74
RRM3_Hu cd12377
RNA recognition motif 3 in the Hu proteins family; This subfamily corresponds to the RRM3 of ...
58-129 8.02e-08

RNA recognition motif 3 in the Hu proteins family; This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 240823 [Multi-domain]  Cd Length: 78  Bit Score: 49.63  E-value: 8.02e-08
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gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNN-RGYAFVTFSNKQEAKNAIKQLNNYEIrNGRLLGV 129
Cdd:cd12377    4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKcKGYGFVTMTNYEEAYSAIASLNGYRL-GGRVLQV 75
RRM2_DND1 cd12493
RNA recognition motif 2 found in vertebrate dead end protein homolog 1 (DND1); This subgroup ...
136-218 8.45e-08

RNA recognition motif 2 found in vertebrate dead end protein homolog 1 (DND1); This subgroup corresponds to the RRM2 of DND1, also termed RNA-binding motif, single-stranded-interacting protein 4. It is an RNA-binding protein that is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. For instance, DND1 binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle regulator and tumor suppressor, LATS2 (large tumor suppressor, homolog 2 of Drosophila). It helps maintain their protein expression through blocking the inhibitory function of microRNAs (miRNA) from these transcripts. DND1 may also impose another level of translational regulation to modulate expression of critical factors in embryonic stem (ES) cells. Moreover, DND1 interacts specifically with apolipoprotein B editing complex 3 (APOBEC3), a multi-functional protein inhibiting retroviral replication. The DND1-APOBEC3 interaction may play a role in maintaining viability of germ cells and for preventing germ cell tumor development. DND1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 240937 [Multi-domain]  Cd Length: 83  Bit Score: 49.81  E-value: 8.45e-08
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gi 564333452 136 CRLFVGGIPKTKKREEILSEMKKVTEGVVDVIVYPSAadkTKNRG-FAFVEYESHRAAAMARRRLLPGRIQLWGHPIAVD 214
Cdd:cd12493    3 CELSLDGLPVNLNESKLLMVLQELTDGVEDVLLHPSP---GKGKGvVALVKYSSHRAAAMAKKALVEGFRNLYGISVTVE 79

                 ....
gi 564333452 215 WAEP 218
Cdd:cd12493   80 WLKP 83
RRM_RNPS1 cd12365
RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar ...
58-121 8.89e-08

RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins; This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain.


Pssm-ID: 240811 [Multi-domain]  Cd Length: 73  Bit Score: 49.09  E-value: 8.89e-08
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gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQLNNYEI 121
Cdd:cd12365    1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDrEVNLPRGYAYVEFESPEDAEKAIKHMDGGQI 65
RRM2_Hu_like cd12376
RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar ...
58-118 8.93e-08

RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 240822 [Multi-domain]  Cd Length: 79  Bit Score: 49.55  E-value: 8.93e-08
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gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQLNN 118
Cdd:cd12376    3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDqLTGVSRGVGFIRFDKRIEAEEAIKGLNG 64
RRM_eIF3G_like cd12408
RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and ...
235-302 1.15e-07

RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins; This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus.


Pssm-ID: 240854 [Multi-domain]  Cd Length: 77  Bit Score: 49.08  E-value: 1.15e-07
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gi 564333452 235 VRNLMLSTSEEMIEKEFNsiKPGAVERV--------KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK 302
Cdd:cd12408    4 VTNLSEDADEDDLRELFR--PFGPISRVylakdketGQSRGFAFVTFHTREDAERAIEKLNGFGYDNLILSVEWAK 77
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in ...
57-129 1.21e-07

RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 240762 [Multi-domain]  Cd Length: 74  Bit Score: 48.83  E-value: 1.21e-07
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gi 564333452  57 EIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQLNNyEIRNGRLLGV 129
Cdd:cd12316    1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDkETKRSKGFAFVSFMFPEHAVKAYSELDG-SIFQGRLLHV 73
RRM2_CELF3_4_5_6 cd12635
RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and ...
58-117 1.28e-07

RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins; This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region.


Pssm-ID: 241079 [Multi-domain]  Cd Length: 81  Bit Score: 48.97  E-value: 1.28e-07
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gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLN 117
Cdd:cd12635    4 LFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALH 63
RRM_CIRBP_RBM3 cd12449
RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein ...
57-129 1.32e-07

RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins; This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain.


Pssm-ID: 240895 [Multi-domain]  Cd Length: 80  Bit Score: 49.08  E-value: 1.32e-07
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gi 564333452  57 EIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGN-NRGYAFVTFSNKQEAKNAIKQLNNYEIrNGRLLGV 129
Cdd:cd12449    2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQrSRGFGFVTFENPDDAKDAMMAMNGKSV-DGRQIRV 74
RRM_snRNP35 cd12237
RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11 ...
231-298 1.49e-07

RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins; This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain.


Pssm-ID: 240683 [Multi-domain]  Cd Length: 93  Bit Score: 49.18  E-value: 1.49e-07
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gi 564333452 231 KILYVRNLMLSTSEEMIEKEFNsiKPGAVERVKKIRD--------YAFVHFSNREDAVEAMKALNGKVLDGSPIEV 298
Cdd:cd12237    4 LTLFVGRLSLQTTEETLREVFS--RYGDIRRLRLVRDivtgfskgYAFVEYEHERDALRAYRDAHKLVIDGSEIFV 77
RRM_NIFK_like cd12307
RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) ...
58-129 1.50e-07

RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins; This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 240753 [Multi-domain]  Cd Length: 74  Bit Score: 48.72  E-value: 1.50e-07
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gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFN-GNNRGYAFVTFSNKQEAKNAIKQLNNYeIRNGRLLGV 129
Cdd:cd12307    2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKtGKSKGYAFVEFESPEVAKIVAETMNNY-LLFERLLKC 73
RRM_SRSF3_like cd12373
RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; ...
233-303 1.65e-07

RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 240819 [Multi-domain]  Cd Length: 73  Bit Score: 48.39  E-value: 1.65e-07
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gi 564333452 233 LYVRNLMLSTSEEMIEKEFnsIKPGAVERVKKIRD---YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP 303
Cdd:cd12373    2 VYVGNLGPRATKRELEDEF--EKYGPLRSVWVARNppgFAFVEFEDPRDAEDAVRALDGRRICGNRVRVELSRG 73
RRM_snRNP70 cd12236
RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar ...
58-127 1.67e-07

RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins; This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function.


Pssm-ID: 240682 [Multi-domain]  Cd Length: 91  Bit Score: 49.17  E-value: 1.67e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDF-NGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRLL 127
Cdd:cd12236    4 LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKkTGKPRGYAFIEFEHERDMKAAYKYADGKKIDGRRVL 74
RRM_RBM24_RBM38_like cd12384
RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins; ...
56-129 1.90e-07

RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins; This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 240830 [Multi-domain]  Cd Length: 76  Bit Score: 48.38  E-value: 1.90e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564333452  56 CEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQLNnyEIRNGRLLGV 129
Cdd:cd12384    1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDrQTGKSRGYGFVTFKDKESAERACKDPN--PIIDGRKANV 73
RRM_Srp1p_AtRSp31_like cd12233
RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis ...
242-302 2.20e-07

RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins; This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus.


Pssm-ID: 240679 [Multi-domain]  Cd Length: 70  Bit Score: 48.21  E-value: 2.20e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564333452 242 TSEEMIEKEFnsiKP-GAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK 302
Cdd:cd12233   12 TREEDIEKLF---EPfGPLVRCDIRKTFAFVEFEDSEDATKALEALHGSRIDGSVLTVEFVK 70
RRM1_SXL cd12649
RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins; This subfamily ...
60-126 2.31e-07

RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 241093 [Multi-domain]  Cd Length: 81  Bit Score: 48.16  E-value: 2.31e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564333452  60 IGKLPRDLFEDELIPLCEKIGKIYEMRMMMDF-NGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRL 126
Cdd:cd12649    5 INYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKrTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRI 72
RRM2_I_PABPs cd12379
RNA recognition motif 2 found in type I polyadenylate-binding proteins; This subfamily ...
58-130 2.58e-07

RNA recognition motif 2 found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 240825 [Multi-domain]  Cd Length: 77  Bit Score: 47.93  E-value: 2.58e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIrNGRLLGVC 130
Cdd:cd12379    5 IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVNGMLL-NDKKVFVG 76
RRM2_gar2 cd12448
RNA recognition motif 2 in yeast protein gar2 and similar proteins; This subfamily corresponds ...
58-126 2.73e-07

RNA recognition motif 2 in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 240894 [Multi-domain]  Cd Length: 73  Bit Score: 47.75  E-value: 2.73e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFN-GNNRGYAFVTFSNKQEAKNAIKQLNNYEI--RNGRL 126
Cdd:cd12448    1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDsGRPKGFGYVEFSSQEAAQAALDALGGTDLlgRPVRL 72
RRM_SCAF4_SCAF8 cd12227
RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and ...
58-122 3.19e-07

RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins; This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs.


Pssm-ID: 240673 [Multi-domain]  Cd Length: 77  Bit Score: 47.72  E-value: 3.19e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMmdfngNNRGYAFVTFSNKQEAKNAIKQLNNYEIR 122
Cdd:cd12227    5 LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMI-----PPRGCAYVCMETRQDAHRALQKLRNVKLA 64
RRM_TRA2 cd12363
RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar ...
233-298 3.31e-07

RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins; This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.


Pssm-ID: 240809 [Multi-domain]  Cd Length: 78  Bit Score: 47.62  E-value: 3.31e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564333452 233 LYVRNLMLSTSEEMIEKEFNsiKPGAVERVKKIRD--------YAFVHFSNREDAVEAMKALNGKVLDGSPIEV 298
Cdd:cd12363    2 LGVFGLSLYTTERDLREVFS--RYGPIEKVQVVYDqktgrsrgFGFVYFESVEDAKEAKERLNGMEIDGRRIRV 73
RRM2_Hrp1p cd12330
RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) ...
58-115 3.34e-07

RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.


Pssm-ID: 240776 [Multi-domain]  Cd Length: 75  Bit Score: 47.75  E-value: 3.34e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFN-GNNRGYAFVTFSNKQEAKNAIKQ 115
Cdd:cd12330    2 IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDtGRSRGFGFVTFDSESAVERVFSA 60
RRM_Aly_REF_like cd12418
RNA recognition motif in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF ...
233-300 3.50e-07

RNA recognition motif in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion.


Pssm-ID: 240864 [Multi-domain]  Cd Length: 75  Bit Score: 47.59  E-value: 3.50e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564333452 233 LYVRNLMLSTSEEMIEKEFnsikpGAVERVKKIR-DY---------AFVHFSNREDAVEAMKALNGKVLDGSPIEVTL 300
Cdd:cd12418    3 LRVSNLHYDVTEEDLEELF-----GRVGEVKKVKiNYdrsgrsegtADVVFEKREDAERAIKQFNGVLLDGQPMQVEL 75
RRM1_gar2 cd12447
RNA recognition motif 1 in yeast protein gar2 and similar proteins; This subfamily corresponds ...
233-301 3.99e-07

RNA recognition motif 1 in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 240893 [Multi-domain]  Cd Length: 76  Bit Score: 47.38  E-value: 3.99e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564333452 233 LYVRNLMLSTSEEMIEKEFNSIkpGAVERVKKIRD--------YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA 301
Cdd:cd12447    2 LFVGNLSWSVDDEWLKAEFEKF--GTVVGARVITDretgrsrgFGYVDFESPEDAKKAIEAMDGKELDGRPINVDFS 76
RRM3_Spen cd12310
RNA recognition motif 3 in the Spen (split end) protein family; This subfamily corresponds to ...
233-302 4.05e-07

RNA recognition motif 3 in the Spen (split end) protein family; This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 240756 [Multi-domain]  Cd Length: 72  Bit Score: 47.20  E-value: 4.05e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564333452 233 LYVRNLMLSTSEEMIEKEFNSIkpGAVERVK--KIRDYAFVHFSNREDAVEAMKALNGKVL--DGSPIEVTLAK 302
Cdd:cd12310    1 LWVGGLGPWTSLAELEREFDRF--GAIRRIDydPGRNYAYIEYESIEAAQAAKEALRGFPLggPGRRLRVDFAD 72
RRM_PPIE cd12347
RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins; This subfamily ...
58-129 4.19e-07

RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins; This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A.


Pssm-ID: 240793 [Multi-domain]  Cd Length: 73  Bit Score: 47.22  E-value: 4.19e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564333452  58 IFIGKLPRDLFEDEL----IPLcekiGKIYEMRMMMDF-NGNNRGYAFVTFSNKQEAKNAIKQLNNYEIrNGRLLGV 129
Cdd:cd12347    1 LYVGGLAEEVDEKVLhaafIPF----GDIKDIQIPLDYeTQKHRGFAFVEFEEPEDAAAAIDNMNESEL-FGRTIRV 72
RRM1_RBM19 cd12564
RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup ...
63-136 4.79e-07

RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 241008 [Multi-domain]  Cd Length: 76  Bit Score: 47.30  E-value: 4.79e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564333452  63 LPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRLlgvcaSVDNC 136
Cdd:cd12564    8 LPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFNNSFIDTSKI-----TVEIC 76
RRM2_PUB1 cd12619
RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein ...
58-117 5.10e-07

RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 241063 [Multi-domain]  Cd Length: 75  Bit Score: 47.12  E-value: 5.10e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFN-GNNRGYAFVTFSNKQEAKNAIKQLN 117
Cdd:cd12619    2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKsGRSRGYGFVSFRSQQDAENAINEMN 62
RRM3_RBM28_like cd12415
RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily ...
58-130 5.31e-07

RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 240861 [Multi-domain]  Cd Length: 82  Bit Score: 47.21  E-value: 5.31e-07
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gi 564333452  58 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQLNNYE----IRNGRLLGVC 130
Cdd:cd12415    3 VFIRNLPFDATEEELKELFSQFGEVKYARIVKDkLTGHSKGTAFVKFKTKESAQKCLEAADNAEdsglSLDGRRLIVT 80
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
138-189 5.65e-07

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 240668 [Multi-domain]  Cd Length: 72  Bit Score: 46.91  E-value: 5.65e-07
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                 ....*....|....*....|....*....|....*....|....*....|..
gi 564333452 138 LFVGGIPKTKKREEILSEMKKVTEgVVDVIVYPSaaDKTKNRGFAFVEYESH 189
Cdd:cd00590</