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Conserved domains on  [gi|50053795|ref|NP_001408|]
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eukaryotic translation initiation factor 4B isoform 2 [Homo sapiens]

Protein Classification

RRM_eIF4B and PRK12678 domain-containing protein( domain architecture ID 10189300)

RRM_eIF4B and PRK12678 domain-containing protein

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RRM_eIF4B cd12402
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and ...
94-175 2.85e-35

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins; This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation.


:

Pssm-ID: 409836 [Multi-domain]  Cd Length: 81  Bit Score: 127.34  E-value: 2.85e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795  94 PPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPsNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVADQ 173
Cdd:cd12402   1 PPYTAYLGNLPYDVTEDDIEDFFRGLNISSVRLPREN-GPGRLRGFGYVEFEDRESLIQALSLNEESLKNRRIRVDVAGQ 79

                ..
gi 50053795 174 AQ 175
Cdd:cd12402  80 AQ 81
PTZ00108 super family cl36510
DNA topoisomerase 2-like protein; Provisional
372-608 3.91e-04

DNA topoisomerase 2-like protein; Provisional


The actual alignment was detected with superfamily member PTZ00108:

Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 43.50  E-value: 3.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795   372 REREVEERLQKEQEKLQRQLDEPKLERRPRERHP-SWRSEETQERERSRTGSESSQTGTSTTSSRNARRRESEKSLENET 450
Cdd:PTZ00108 1150 KEIAKEQRLKSKTKGKASKLRKPKLKKKEKKKKKsSADKSKKASVVGNSKRVDSDEKRKLDDKPDNKKSNSSGSDQEDDE 1229
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795   451 LNKEEDCHSPTSKPPKPDQPLKVMPAPPPKENAWVKRSS----NPPARSQSSDTEQQSPTSGGGKVAPAQPSEEGPGRKD 526
Cdd:PTZ00108 1230 EQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKEgkpkNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKK 1309
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795   527 ENKVDgmnAPKGQTGNSSRGPGDGGNRDHWKESDRKDGKKDQDSRSAPEPKKPEEnpaSKFSSASKYAALSVDGEDENEG 606
Cdd:PTZ00108 1310 VKKRL---EGSLAALKKKKKSEKKTARKKKSKTRVKQASASQSSRLLRRPRKKKS---DSSSEDDDDSEVDDSEDEDDED 1383

                  ..
gi 50053795   607 ED 608
Cdd:PTZ00108 1384 DE 1385
PRK12678 super family cl36163
transcription termination factor Rho; Provisional
158-273 4.88e-04

transcription termination factor Rho; Provisional


The actual alignment was detected with superfamily member PRK12678:

Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 42.97  E-value: 4.88e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795  158 EESLGNRRIRVDVADQAQDKDRDDRSFGRDRNRDSDKTDTDwRARPATDSFDDYPPRRGDDSFGDKYR---DRYDSDRYR 234
Cdd:PRK12678 166 EEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRR-DRREQGDRREERGRRDGGDRRGRRRRrdrRDARGDDNR 244
                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 50053795  235 DGYRDGYRDGPRRDMDRYGGRDRYDDRGSRDYDRGYDSR 273
Cdd:PRK12678 245 EDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDGGNER 283
 
Name Accession Description Interval E-value
RRM_eIF4B cd12402
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and ...
94-175 2.85e-35

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins; This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation.


Pssm-ID: 409836 [Multi-domain]  Cd Length: 81  Bit Score: 127.34  E-value: 2.85e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795  94 PPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPsNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVADQ 173
Cdd:cd12402   1 PPYTAYLGNLPYDVTEDDIEDFFRGLNISSVRLPREN-GPGRLRGFGYVEFEDRESLIQALSLNEESLKNRRIRVDVAGQ 79

                ..
gi 50053795 174 AQ 175
Cdd:cd12402  80 AQ 81
RRM smart00360
RNA recognition motif;
97-168 1.38e-09

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 54.52  E-value: 1.38e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 50053795     97 TAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPsNPERLKGFGYAEFEDLDSLLS-ALSLNEESLGNRRIRV 168
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFgKVESVRLVRDK-ETGKSKGFAFVEFESEEDAEKaLEALNGKELDGRPLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
99-167 5.83e-09

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: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 52.62  E-value: 5.83e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 50053795    99 FLGNLPYDVTEESIKEFFRGLN-ISAVRLPRepSNPERLKGFGYAEFEDLDSLLS-ALSLNEESLGNRRIR 167
Cdd:pfam00076   2 FVGNLPPDTTEEDLKDLFSKFGpIKSIRLVR--DETGRSKGFAFVEFEDEEDAEKaIEALNGKELGGRELK 70
PTZ00108 PTZ00108
DNA topoisomerase 2-like protein; Provisional
372-608 3.91e-04

DNA topoisomerase 2-like protein; Provisional


Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 43.50  E-value: 3.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795   372 REREVEERLQKEQEKLQRQLDEPKLERRPRERHP-SWRSEETQERERSRTGSESSQTGTSTTSSRNARRRESEKSLENET 450
Cdd:PTZ00108 1150 KEIAKEQRLKSKTKGKASKLRKPKLKKKEKKKKKsSADKSKKASVVGNSKRVDSDEKRKLDDKPDNKKSNSSGSDQEDDE 1229
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795   451 LNKEEDCHSPTSKPPKPDQPLKVMPAPPPKENAWVKRSS----NPPARSQSSDTEQQSPTSGGGKVAPAQPSEEGPGRKD 526
Cdd:PTZ00108 1230 EQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKEgkpkNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKK 1309
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795   527 ENKVDgmnAPKGQTGNSSRGPGDGGNRDHWKESDRKDGKKDQDSRSAPEPKKPEEnpaSKFSSASKYAALSVDGEDENEG 606
Cdd:PTZ00108 1310 VKKRL---EGSLAALKKKKKSEKKTARKKKSKTRVKQASASQSSRLLRRPRKKKS---DSSSEDDDDSEVDDSEDEDDED 1383

                  ..
gi 50053795   607 ED 608
Cdd:PTZ00108 1384 DE 1385
PRK12678 PRK12678
transcription termination factor Rho; Provisional
158-273 4.88e-04

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 42.97  E-value: 4.88e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795  158 EESLGNRRIRVDVADQAQDKDRDDRSFGRDRNRDSDKTDTDwRARPATDSFDDYPPRRGDDSFGDKYR---DRYDSDRYR 234
Cdd:PRK12678 166 EEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRR-DRREQGDRREERGRRDGGDRRGRRRRrdrRDARGDDNR 244
                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 50053795  235 DGYRDGYRDGPRRDMDRYGGRDRYDDRGSRDYDRGYDSR 273
Cdd:PRK12678 245 EDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDGGNER 283
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
83-190 1.61e-03

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


Pssm-ID: 223796 [Multi-domain]  Cd Length: 306  Bit Score: 40.70  E-value: 1.61e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795  83 PNIDRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPsNPERLKGFGYAEFEDLDSLLS-ALSLNEES 160
Cdd:COG0724 103 ESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFgPVKRVRLVRDR-ETGKSRGFAFVEFESEESAEKaIEELNGKE 181
                        90       100       110
                ....*....|....*....|....*....|
gi 50053795 161 LGNRRIRVDVAdQAQDKDRDDRSFGRDRNR 190
Cdd:COG0724 182 LEGRPLRVQKA-QPASQPRSELSNNLDASF 210
 
Name Accession Description Interval E-value
RRM_eIF4B cd12402
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and ...
94-175 2.85e-35

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins; This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation.


Pssm-ID: 409836 [Multi-domain]  Cd Length: 81  Bit Score: 127.34  E-value: 2.85e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795  94 PPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPsNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVADQ 173
Cdd:cd12402   1 PPYTAYLGNLPYDVTEDDIEDFFRGLNISSVRLPREN-GPGRLRGFGYVEFEDRESLIQALSLNEESLKNRRIRVDVAGQ 79

                ..
gi 50053795 174 AQ 175
Cdd:cd12402  80 AQ 81
RRM_eIF4H cd12401
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4H (eIF-4H) and ...
91-172 4.32e-13

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins; This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation.


Pssm-ID: 409835 [Multi-domain]  Cd Length: 84  Bit Score: 65.00  E-value: 4.32e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795  91 PKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREpSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDV 170
Cdd:cd12401   1 PTEPPFTAYVGNLPFNTVQGDLDAIFKDLKVRSVRLVRD-RETDKFKGFCYVEFEDLESLKEALEYDGALFEDRPLRVDI 79

                ..
gi 50053795 171 AD 172
Cdd:cd12401  80 AE 81
RRM_Nop6 cd12400
RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and ...
96-168 1.51e-12

RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins; This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing.


Pssm-ID: 409834 [Multi-domain]  Cd Length: 74  Bit Score: 63.01  E-value: 1.51e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 50053795  96 YTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNpERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRV 168
Cdd:cd12400   1 YILFVGNLPYDTTAEDLKEHFKKAgEPPSVRLLTDKKT-GKSKGCAFVEFDNQKALQKALKLHHTSLGGRKINV 73
RRM2_RBM34 cd12395
RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
97-168 4.05e-11

RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.


Pssm-ID: 409829 [Multi-domain]  Cd Length: 73  Bit Score: 59.05  E-value: 4.05e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 50053795  97 TAFLGNLPYDVTEESIKEFFRG-LNISAVRLPREPSNPERlKGFGYAEFEDLDSLLSALSLNEESLGNRRIRV 168
Cdd:cd12395   1 SVFVGNLPFDIEEEELRKHFEDcGDVEAVRIVRDRETGIG-KGFGYVLFKDKDSVDLALKLNGSKLRGRKLRV 72
RRM smart00360
RNA recognition motif;
97-168 1.38e-09

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 54.52  E-value: 1.38e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 50053795     97 TAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPsNPERLKGFGYAEFEDLDSLLS-ALSLNEESLGNRRIRV 168
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFgKVESVRLVRDK-ETGKSKGFAFVEFESEEDAEKaLEALNGKELDGRPLKV 73
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
99-169 3.46e-09

RNA recognition motif 2 (RRM2) found 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: 409882 [Multi-domain]  Cd Length: 73  Bit Score: 53.57  E-value: 3.46e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 50053795  99 FLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNpERLKGFGYAEFEDLDSLLSALSLNE-ESLGNRRIRVD 169
Cdd:cd12448   2 FVGNLPFSATQDALYEAFSQHgSIVSVRLPTDRET-GQPKGFGYVDFSTIDSAEAAIDALGgEYIDGRPIRLD 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
99-167 5.83e-09

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: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 52.62  E-value: 5.83e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 50053795    99 FLGNLPYDVTEESIKEFFRGLN-ISAVRLPRepSNPERLKGFGYAEFEDLDSLLS-ALSLNEESLGNRRIR 167
Cdd:pfam00076   2 FVGNLPPDTTEEDLKDLFSKFGpIKSIRLVR--DETGRSKGFAFVEFEDEEDAEKaIEALNGKELGGRELK 70
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
99-169 1.58e-08

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: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 51.51  E-value: 1.58e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 50053795  99 FLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNpeRLKGFGYAEFEDLDSLLS-ALSLNEESLGNRRIRVD 169
Cdd:cd00590   2 FVGNLPPDTTEEDLRELFSKFgEVVSVRIVRDRDG--KSKGFAFVEFESPEDAEKaLEALNGTELGGRPLKVS 72
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
96-171 2.73e-08

RNA recognition motif (RRM) found 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: 409832 [Multi-domain]  Cd Length: 77  Bit Score: 50.98  E-value: 2.73e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 50053795  96 YTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNpERLKGFGYAEFEDLDSLLSALSL-NEESLGNRRIRVDVA 171
Cdd:cd12398   1 RSVFVGNIPYDATEEQLKEIFSEVgPVVSFRLVTDRET-GKPKGYGFCEFRDAETALSAVRNlNGYELNGRPLRVDFA 77
RRM1_SART3 cd12391
RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells ...
97-145 1.68e-07

RNA recognition motif 1 (RRM1) found 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: 409825 [Multi-domain]  Cd Length: 72  Bit Score: 48.76  E-value: 1.68e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 50053795  97 TAFLGNLPYDVTEESIKEFFRGL-NISAVRLPRepSNPERLKGFGYAEFE 145
Cdd:cd12391   1 TVFVSNLDYSVPEDKIREIFSGCgEITDVRLVK--NYKGKSKGYCYVEFK 48
RRM1_NUCLs cd12450
RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ...
97-173 3.17e-07

RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409884 [Multi-domain]  Cd Length: 78  Bit Score: 48.17  E-value: 3.17e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 50053795  97 TAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNpERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVADQ 173
Cdd:cd12450   1 TLFVGNLSWSATQDDLENFFSDCgEVVDVRIAMDRDD-GRSKGFGHVEFASAESAQKALEKSGQDLGGREIRLDLANE 77
RRM2_PHIP1 cd12272
RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana phragmoplastin interacting ...
97-169 9.47e-07

RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA.


Pssm-ID: 409715 [Multi-domain]  Cd Length: 73  Bit Score: 46.63  E-value: 9.47e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 50053795  97 TAFLGNLPYDVTEESIKEFF-RGLNISAVRLPREPSNPErLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVD 169
Cdd:cd12272   1 TVYIGNLAWDIDEDDLRELFaECCEITNVRLHTDKETGE-FKGYGHVEFADEESLDAALKLAGTKLCGRPIRVD 73
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
102-171 4.56e-06

RNA recognition motif 2 (RRM2) found 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: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 44.85  E-value: 4.56e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 50053795 102 NLPYDVTEESIKEFFRGL-NISAVRLPREPSNpeRLKGFGYAEFEDLDSLLSA-LSLNEESLGNRRIRVDVA 171
Cdd:cd12414   6 NLPFKCTEDDLKKLFSKFgKVLEVTIPKKPDG--KLRGFAFVQFTNVADAAKAiKGMNGKKIKGRPVAVDWA 75
RRM_CSTF2_CSTF2T cd12671
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage ...
97-171 2.04e-05

RNA recognition motif (RRM) found 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: 410072 [Multi-domain]  Cd Length: 85  Bit Score: 43.27  E-value: 2.04e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 50053795  97 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRL--PREPSNPerlKGFGYAEFEDLDSLLSALSL-NEESLGNRRIRVDVA 171
Cdd:cd12671   8 SVFVGNIPYEATEEQLKDIFSEVGpVVSFRLvyDRETGKP---KGYGFCEYQDQETALSAMRNlNGYELNGRALRVDNA 83
RRM2_hnRNPD_like cd12329
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, ...
99-171 5.67e-05

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins; This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 240775 [Multi-domain]  Cd Length: 75  Bit Score: 41.58  E-value: 5.67e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 50053795  99 FLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERlKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVA 171
Cdd:cd12329   3 FVGGLSPETTEEKIREYFGKFgNIVEIELPMDKKTNKR-RGFCFITFDSEEPVKKILETQFHVIGGKKVEVKKA 75
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
99-171 7.26e-05

RNA recognition motif (RRM) found 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: 409833 [Multi-domain]  Cd Length: 75  Bit Score: 41.35  E-value: 7.26e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 50053795  99 FLGNLPYDVTEESIKEFFRGLN-ISAVRLP--REPSNPerlKGFGYAEFEDLDSLLSA-LSLNEESLGNRRIRVDVA 171
Cdd:cd12399   2 YVGNLPYSASEEQLKSLFGQFGaVFDVKLPmdRETKRP---RGFGFVELQEEESAEKAiAKLDGTDFMGRTIRVNEA 75
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
97-173 8.10e-05

RNA recognition motif 1 (RRM1) found 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: 409847 [Multi-domain]  Cd Length: 79  Bit Score: 41.42  E-value: 8.10e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795  97 TAFLGNLPYDVTEESIKEFFRglNISAVR---LPREPsNPERLKGFGYAEFEDLDSLLSA-LSLNEESLGNRRIRVDVAD 172
Cdd:cd12413   1 TLFVRNLPYDTTDEQLEELFS--DVGPVKrcfVVKDK-GKDKCRGFGYVTFALAEDAQRAlEEVKGKKFGGRKIKVELAK 77

                .
gi 50053795 173 Q 173
Cdd:cd12413  78 K 78
RRM_II_PABPs cd12306
RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to ...
99-168 9.58e-05

RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are 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. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only.


Pssm-ID: 409747 [Multi-domain]  Cd Length: 73  Bit Score: 40.75  E-value: 9.58e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 50053795  99 FLGNLPYDVTEESIKEFFRGL-NISAVRLPREPsNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRV 168
Cdd:cd12306   3 YVGNVDYGTTPEELQAHFKSCgTINRVTILCDK-FTGQPKGFAYIEFVDKSSVENALLLNESEFRGRQIKV 72
RRM_hnRNPH_ESRPs_RBM12_like cd12254
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ...
102-168 1.05e-04

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins; The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409699 [Multi-domain]  Cd Length: 73  Bit Score: 40.62  E-value: 1.05e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 50053795 102 NLPYDVTEESIKEFFRGLNISA--VRLPREPSNpeRLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRV 168
Cdd:cd12254   6 GLPFSATEEDIRDFFSGLDIPPdgIHIVYDDDG--RPTGEAYVEFASEEDAQRALRRHKGKMGGRYIEV 72
RRM5_RBM19_like cd12318
RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar ...
97-145 1.64e-04

RNA recognition motif 5 (RRM5) found 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: 409757 [Multi-domain]  Cd Length: 80  Bit Score: 40.29  E-value: 1.64e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 50053795  97 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPR--EPSNPERLKGFGYAEFE 145
Cdd:cd12318   2 TLFVKNLNFKTTEEALKKHFEKCGpIRSVTIAKkkDPKGPLLSMGYGFVEFK 53
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
99-145 1.99e-04

RNA recognition motif 3 (RRM3) found 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: 409755 [Multi-domain]  Cd Length: 74  Bit Score: 40.02  E-value: 1.99e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 50053795  99 FLGNLPYDVTEESIKEFFRGL-NISAVRLPREpSNPERLKGFGYAEFE 145
Cdd:cd12316   3 FVRNLPFTATEDELRELFEAFgKISEVHIPLD-KQTKRSKGFAFVLFV 49
RRM1_RRT5 cd12409
RNA recognition motif 1 (RRM1) found in yeast regulator of rDNA transcription protein 5 (RRT5) ...
102-168 2.19e-04

RNA recognition motif 1 (RRM1) found in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins; This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409843 [Multi-domain]  Cd Length: 84  Bit Score: 40.34  E-value: 2.19e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 50053795 102 NLPYDVTEESIKEFFRGLNISAVRLPREP-----SNPERLKGFGYAEFEDLDSLLSALSL-NEESLGNRRIRV 168
Cdd:cd12409   6 NLSYSTTEEELEELLKDYKPVSVLIPSYTvrgfrSRKHRPLGIAYAEFSSVEEAEKVVKDlNGKVFKGRKLFV 78
RRM3_RBM28_like cd12415
RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
97-171 2.53e-04

RNA recognition motif 3 (RRM3) found 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: 409849 [Multi-domain]  Cd Length: 83  Bit Score: 39.89  E-value: 2.53e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795  97 TAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNpERLKGFGYAEFEDLDS-------LLSALSLNEESLGNRRIRV 168
Cdd:cd12415   2 TVFIRNLSFDTTEEDLKEFFSKFgEVKYARIVLDKDT-GHSKGTAFVQFKTKESadkcieaANDESEDGGLVLDGRKLIV 80

                ...
gi 50053795 169 DVA 171
Cdd:cd12415  81 SLA 83
RRM_CIRBP_RBM3 cd12449
RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding ...
99-173 3.67e-04

RNA recognition motif (RRM) found 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: 409883 [Multi-domain]  Cd Length: 80  Bit Score: 39.39  E-value: 3.67e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 50053795  99 FLGNLPYDVTEESIKEFFRGL-NISAVRLPREpSNPERLKGFGYAEFEDLDSLLSA-LSLNEESLGNRRIRVDVADQ 173
Cdd:cd12449   4 FVGGLSFDTNEQSLEEVFSKYgQISEVVVVKD-RETQRSRGFGFVTFENPDDAKDAmMAMNGKSLDGRQIRVDQAGK 79
PTZ00108 PTZ00108
DNA topoisomerase 2-like protein; Provisional
372-608 3.91e-04

DNA topoisomerase 2-like protein; Provisional


Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 43.50  E-value: 3.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795   372 REREVEERLQKEQEKLQRQLDEPKLERRPRERHP-SWRSEETQERERSRTGSESSQTGTSTTSSRNARRRESEKSLENET 450
Cdd:PTZ00108 1150 KEIAKEQRLKSKTKGKASKLRKPKLKKKEKKKKKsSADKSKKASVVGNSKRVDSDEKRKLDDKPDNKKSNSSGSDQEDDE 1229
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795   451 LNKEEDCHSPTSKPPKPDQPLKVMPAPPPKENAWVKRSS----NPPARSQSSDTEQQSPTSGGGKVAPAQPSEEGPGRKD 526
Cdd:PTZ00108 1230 EQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKEgkpkNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKK 1309
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795   527 ENKVDgmnAPKGQTGNSSRGPGDGGNRDHWKESDRKDGKKDQDSRSAPEPKKPEEnpaSKFSSASKYAALSVDGEDENEG 606
Cdd:PTZ00108 1310 VKKRL---EGSLAALKKKKKSEKKTARKKKSKTRVKQASASQSSRLLRRPRKKKS---DSSSEDDDDSEVDDSEDEDDED 1383

                  ..
gi 50053795   607 ED 608
Cdd:PTZ00108 1384 DE 1385
RRM2_hnRNPH_CRSF1_like cd12504
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H ...
100-168 4.44e-04

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family; This subfamily corresponds to the RRM2 of hnRNP H protein family which includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9). They represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing, having similar RNA binding affinities and specifically recognizing the sequence GGGA. They can either stimulate or repress splicing upon binding to a GGG motif. hnRNP H binds to the RNA substrate in the presence or absence of these proteins, whereas hnRNP F binds to the nuclear mRNA only in the presence of cap-binding proteins. Furthermore, hnRNP H and hnRNP H2 are almost identical; both have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. hnRNP H3 may be involved in the splicing arrest induced by heat shock. Most family members contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. Members in this family can regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. The family also includes a cytoplasmic poly(A)+ mRNA binding protein, GRSF-1, which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 also contains three potential RRMs responsible for the RNA binding, and two auxiliary domains (an acidic alpha-helical domain and an N-terminal alanine-rich region) that may play a role in protein-protein interactions and provide binding specificity.


Pssm-ID: 409927 [Multi-domain]  Cd Length: 77  Bit Score: 39.26  E-value: 4.44e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 50053795 100 LGNLPYDVTEESIKEFFRGLNI--SAVRLPREPSNpeRLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRV 168
Cdd:cd12504   5 LRGLPYGCTKEEIAQFFSGLEIvpNGITLPMDRRG--RSTGEAFVQFASQEIAEQALGKHKEKIGHRYIEI 73
PRK12678 PRK12678
transcription termination factor Rho; Provisional
158-273 4.88e-04

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 42.97  E-value: 4.88e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795  158 EESLGNRRIRVDVADQAQDKDRDDRSFGRDRNRDSDKTDTDwRARPATDSFDDYPPRRGDDSFGDKYR---DRYDSDRYR 234
Cdd:PRK12678 166 EEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRR-DRREQGDRREERGRRDGGDRRGRRRRrdrRDARGDDNR 244
                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 50053795  235 DGYRDGYRDGPRRDMDRYGGRDRYDDRGSRDYDRGYDSR 273
Cdd:PRK12678 245 EDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDGGNER 283
RRM2_PUF60 cd12371
RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
99-171 5.51e-04

RNA recognition motif 2 (RRM2) found 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: 409806 [Multi-domain]  Cd Length: 77  Bit Score: 38.81  E-value: 5.51e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 50053795  99 FLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSnPERLKGFGYAEFEDLDSLLSA-LSLNEESLGNRRIRVDVA 171
Cdd:cd12371   4 YVASVHPDLSEDDIKSVFEAFgKIKSCSLAPDPE-TGKHKGYGFIEYENPQSAQDAiASMNLFDLGGQYLRVGRA 77
RRM_PPIE cd12347
RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This ...
99-171 5.81e-04

RNA recognition motif (RRM) found 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: 409783 [Multi-domain]  Cd Length: 75  Bit Score: 38.74  E-value: 5.81e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 50053795  99 FLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNpERLKGFGYAEFEDLDSLLSA-LSLNEESLGNRRIRVDVA 171
Cdd:cd12347   2 YVGGLAEEVDEKVLHAAFIPFgDIVDIQIPLDYET-EKHRGFAFVEFEEAEDAAAAiDNMNESELFGRTIRVNLA 75
RRM2_NCL cd12404
RNA recognition motif 2 (RRM2) found in vertebrate nucleolin; This subfamily corresponds to ...
97-145 6.24e-04

RNA recognition motif 2 (RRM2) found in vertebrate nucleolin; This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop.


Pssm-ID: 409838 [Multi-domain]  Cd Length: 77  Bit Score: 38.57  E-value: 6.24e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 50053795  97 TAFLGNLPYDVTEESIKEFFRglNISAVRLPrePSNPERLKGFGYAEFE 145
Cdd:cd12404   5 TLFVKNLPYSTTQDELKEVFE--DAVDIRIP--MGRDGRSKGIAYIEFK 49
RRM2_Nop13p_fungi cd12397
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar ...
99-171 9.87e-04

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar proteins; This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409831 [Multi-domain]  Cd Length: 76  Bit Score: 38.19  E-value: 9.87e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 50053795  99 FLGNLPYDVTEESIKEFF-RGLNISAVRLPR-EPSNpeRLKGFGYAEFEDLDSLLSA-LSLNEESLGNRRIRVDVA 171
Cdd:cd12397   2 FVGNLSFETTEEDLRKHFaPAGKIRKVRMATfEDSG--KCKGFAFVDFKEIESATNAvKGPINHSLNGRDLRVEYG 75
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
97-168 1.31e-03

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410198 [Multi-domain]  Cd Length: 78  Bit Score: 37.89  E-value: 1.31e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 50053795  97 TAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSN-PERLKGFGYAEFEDLDSLLSA-LSLNEESLGNRRIRV 168
Cdd:cd21619   3 TIYVGNIDMTINEDALEKIFSRYgQVESVRRPPIHTDkADRTTGFGFIKYTDAESAERAmQQADGILLGRRRLVV 77
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
99-171 1.59e-03

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 37.53  E-value: 1.59e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 50053795  99 FLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNpERLKGFGYAEFEDLDSLLSA-LSLNEESLGNRRIRVDVA 171
Cdd:cd21608   3 YVGNLSWDTTEDDLRDLFSEFgEVESAKVITDRET-GRSRGFGFVTFSTAEAAEAAiDALNGKELDGRSIVVNEA 76
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
83-190 1.61e-03

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


Pssm-ID: 223796 [Multi-domain]  Cd Length: 306  Bit Score: 40.70  E-value: 1.61e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795  83 PNIDRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPsNPERLKGFGYAEFEDLDSLLS-ALSLNEES 160
Cdd:COG0724 103 ESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFgPVKRVRLVRDR-ETGKSRGFAFVEFESEESAEKaIEELNGKE 181
                        90       100       110
                ....*....|....*....|....*....|
gi 50053795 161 LGNRRIRVDVAdQAQDKDRDDRSFGRDRNR 190
Cdd:COG0724 182 LEGRPLRVQKA-QPASQPRSELSNNLDASF 210
RRM3_RBM12 cd12512
RNA recognition motif 3 (RRM3) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
87-168 1.73e-03

RNA recognition motif 3 (RRM3) found in RNA-binding protein 12 (RBM12) and similar proteins; This subfamily corresponds to the RRM3 of RBM12. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. The biological role of RBM12 remains unclear.


Pssm-ID: 409934 [Multi-domain]  Cd Length: 101  Bit Score: 38.29  E-value: 1.73e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795  87 RSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNI--SAVRLPREPSNpeRLKGFGYAEFEDLDSLLSALSLNEESLGNR 164
Cdd:cd12512   1 RSRSPHEKGFCVYLKGLPYEAENKHVIEFFKKLDIveDSIYIAYGPNG--RATGEGFVEFRNEIDYKAALCRHKQYMGNR 78

                ....
gi 50053795 165 RIRV 168
Cdd:cd12512  79 FIQV 82
RRM4_RBM12_like cd12514
RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
98-168 1.86e-03

RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; This subfamily corresponds to the RRM4 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B show high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear.


Pssm-ID: 409936 [Multi-domain]  Cd Length: 73  Bit Score: 37.39  E-value: 1.86e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 50053795  98 AFLGNLPYDVTEESIKEFFRGLNIS--AVRLPREPSNpeRLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRV 168
Cdd:cd12514   2 IRITNLPYDATPVDIQRFFEDHGVRpeDVHLLRNKKG--RGNGEALVTFKSEGDAREVLKLNGKKLGKREAVV 72
RRM2_hnRNPH_hnRNPH2_hnRNPF cd12731
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP H, hnRNP ...
100-175 1.87e-03

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP H, hnRNP H2, hnRNP F and similar proteins; This subgroup corresponds to the RRM2 of hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and hnRNP F. These represent a group of nuclear RNA binding proteins that play important roles in the regulation of alternative splicing decisions. hnRNP H and hnRNP F are two closely related proteins, both of which bind to the RNA sequence DGGGD. They are present in a complex with the tissue-specific splicing factor Fox2, and regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts. The presence of Fox 2 can allows hnRNP H and hnRNP F to better compete with the SR protein ASF/SF2 for binding to FGFR2 exon IIIc. Thus, hnRNP H and hnRNP F can function as potent silencers of FGFR2 exon IIIc inclusion through an interaction with the exonic GGG motifs. Furthermore, hnRNP H and hnRNP H2 are almost identical; both have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize.


Pssm-ID: 410130 [Multi-domain]  Cd Length: 90  Bit Score: 37.68  E-value: 1.87e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 50053795 100 LGNLPYDVTEESIKEFFRGLNI--SAVRLPREPSNpeRLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVADQAQ 175
Cdd:cd12731  13 LRGLPFGCSKEEIVQFFSGLEIvpNGITLPVDFQG--RSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAE 88
RRM2_GRSF1 cd12505
RNA recognition motif 2 (RRM2) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
100-168 3.04e-03

RNA recognition motif 2 (RRM2) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; This subfamily corresponds to the RRM2 of GRSF-1, a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic alpha-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity.


Pssm-ID: 409928 [Multi-domain]  Cd Length: 77  Bit Score: 36.73  E-value: 3.04e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 50053795 100 LGNLPYDVTEESIKEFFRGLNISAVRLPREPSNpERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRV 168
Cdd:cd12505   6 LRGLPYSCTEADIAHFFSGLDIVDITFVMDLRG-GRKTGEAFVQFASPEMAAQALLKHKEEIGNRYIEI 73
RRM_G3BP cd12229
RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, ...
99-145 3.91e-03

RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins; This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif).


Pssm-ID: 409676 [Multi-domain]  Cd Length: 81  Bit Score: 36.62  E-value: 3.91e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 50053795  99 FLGNLPYDVTEESIKEFF-RGLNISAVRLPREPSNpERLKGFGYAEFE 145
Cdd:cd12229   7 FVGNLPHDITEDELKEFFsRFGNVLELRINSKGGG-GRLPNFGFVVFD 53
RRM_7 pfam16367
RNA recognition motif;
99-145 4.39e-03

RNA recognition motif;


Pssm-ID: 435303 [Multi-domain]  Cd Length: 91  Bit Score: 36.56  E-value: 4.39e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 50053795    99 FLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPER---LKGFGYAEFE 145
Cdd:pfam16367   5 FVGGLPWDITEAELTATFGRFGPLLVDWPGKPESPSYfpdVKGYVFLVFE 54
RRM2_RBM12 cd12747
RNA recognition motif 2 (RRM2) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
95-171 5.27e-03

RNA recognition motif 2 (RRM2) found in RNA-binding protein 12 (RBM12) and similar proteins; This subgroup corresponds to the RRM2 of RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), which is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. The biological role of RBM12 remains unclear.


Pssm-ID: 410141 [Multi-domain]  Cd Length: 75  Bit Score: 35.92  E-value: 5.27e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 50053795  95 PYTAFLGnLPYDVTEESIKEFFRGLNISAVRLPREPSNpeRLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVA 171
Cdd:cd12747   2 LYVHLHG-MPFSATEADVRDFFHGLRIDAIHMLKDHLG--RNNGNALVKFYSPQDTFEALKRNRMMMGQRYIEVSPA 75
RRM2_hnRNPAB cd12584
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) ...
92-145 5.33e-03

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop.


Pssm-ID: 409997 [Multi-domain]  Cd Length: 80  Bit Score: 36.08  E-value: 5.33e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 50053795  92 KSPPYTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERlKGFGYAEFE 145
Cdd:cd12584   1 KDPVKKIFVGGLNPETTEEKIREYFGEFgEIEAIELPMDPKTNKR-RGFVFITFK 54
RRM2_RMB19 cd12502
RNA recognition motif 2 (RRM2) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
96-168 6.90e-03

RNA recognition motif 2 (RRM2) found in RNA-binding protein 19 (RBM19) and similar proteins; This subfamily corresponds to the RRM2 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 and is also 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: 409925 [Multi-domain]  Cd Length: 72  Bit Score: 35.47  E-value: 6.90e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 50053795  96 YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPRepSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRV 168
Cdd:cd12502   1 FTVKLRGAPFNVKEKQIREFFSPLKPVAIRIVK--NAHGNKTGYVFVDFKSEEDVEKALKRNKDYMGGRYIEV 71
RRM1_PHIP1 cd12271
RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting ...
98-168 7.73e-03

RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA.


Pssm-ID: 409714 [Multi-domain]  Cd Length: 72  Bit Score: 35.38  E-value: 7.73e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 50053795  98 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPeRLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRV 168
Cdd:cd12271   1 VYVGGIPYYSTEAEIRSYFSSCGeVRSVDLMRFPDSG-NFRGIAFITFKTEEAAKRALALDGEMLGNRFLKV 71
RRM1_LARP7 cd12290
RNA recognition motif 1 (RRM1) found in La-related protein 7 (LARP7) and similar proteins; ...
103-145 8.42e-03

RNA recognition motif 1 (RRM1) found in La-related protein 7 (LARP7) and similar proteins; This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus.


Pssm-ID: 409732 [Multi-domain]  Cd Length: 79  Bit Score: 35.38  E-value: 8.42e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 50053795 103 LPYDVTEESIKEFFRGL-NISAVRLPREPSNpERLKGFGYAEFE 145
Cdd:cd12290   7 LPKNATHEWIEAVFSKYgEVVYVSIPRYKST-GDPKGFAFIEFE 49
PRK12678 PRK12678
transcription termination factor Rho; Provisional
159-295 9.51e-03

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 39.12  E-value: 9.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795  159 ESLGNRRIRVDVADQAQDKDRDDRsfgRDRNRDSDKTDTDWRARPATDSFDDYPPRRGDDSFGDKYRDRYDSDRYRDGYR 238
Cdd:PRK12678 155 EARADAAERTEEEERDERRRRGDR---EDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRR 231
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 50053795  239 DGYRDGPRRDMDRYGGRDRYDDrgSRDYDRGYDSRIGSGRRafgsgyRRDDDYRGGG 295
Cdd:PRK12678 232 RRDRRDARGDDNREDRGDRDGD--DGEGRGGRRGRRFRDRD------RRGRRGGDGG 280
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
102-168 9.98e-03

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: 409739 [Multi-domain]  Cd Length: 78  Bit Score: 35.31  E-value: 9.98e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50053795 102 NLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLK--GFGYAEFEDLDSLLSALSLNEESLGNRRIRV 168
Cdd:cd12298   7 NLDFELDEEALRGIFEKFgEIESINIPKKQKNRKGRHnnGFAFVTFEDADSAESALQLNGTLLDNRKISV 76
RRM2_RBM12B cd12746
RNA recognition motif 2 (RRM2) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
99-175 9.98e-03

RNA recognition motif 2 (RRM2) found in RNA-binding protein 12B (RBM12B) and similar proteins; This subgroup corresponds to the RRM2 of RBM12B which contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Its biological role remains unclear.


Pssm-ID: 410140 [Multi-domain]  Cd Length: 86  Bit Score: 35.49  E-value: 9.98e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 50053795  99 FLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNpeRLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVADQAQ 175
Cdd:cd12746   6 FLRGMPYSATEDDVRNFFSGLKVDGVIFLKHPNG--RNNGNGLVKFATKEDASEGLKRHRQYMGSRFIEVTRTTEEQ 80
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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