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Conserved domains on  [gi|45219878|gb|AAH66928|]
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Eukaryotic translation initiation factor 4H [Homo sapiens]

Protein Classification

RRM and RRM_eIF4H domain-containing protein (domain architecture ID 11791481)

RRM and RRM_eIF4H domain-containing protein

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RRM_eIF4H cd12401
RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar ...
41-116 7.34e-48

RNA recognition motif 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: 240847  Cd Length: 76  Bit Score: 155.18  E-value: 7.34e-48
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 45219878  41 PYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIA 116
Cdd:cd12401   1 PFTAFVGNLPFNTVQGDLDAIFKDLSVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALEYDGALFDDRSLRVDIA 76
RRM super family cl25887
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
40-207 6.77e-06

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


The actual alignment was detected with superfamily member TIGR01622:

Pssm-ID: 330708  Cd Length: 494  Bit Score: 46.07  E-value: 6.77e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878    40 PPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-YDGALLGDRSLRVdiae 117
Cdd:TIGR01622 213 PFHRLYVGNLHFNITEQDLRQIFEPFGeIEFVQLQKDPETGRSKGYGFIQFRDAEQAKEALEkMNGFELAGRPIKV---- 288
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878   118 GRKQDKGGFGFRKGGPDDRGFRDDFLGGRGGSRPG--------DRRTGPPMGSRFRDGPPLRGSNM---------DFREP 180
Cdd:TIGR01622 289 GLGNDFTPESDANLAQRFQDQDGSAFSGAGLNTPArsqlmrklARDNEKGTGGLAIPGTDVGGVNMnnysrdglmRKLAP 368
                         170       180
                  ....*....|....*....|....*...
gi 45219878   181 TEEERAQRPRLQ-LKPRTVATPLNQVAN 207
Cdd:TIGR01622 369 TDEPPAVIPETQiLKPKAETSFVPVNVN 396
 
Name Accession Description Interval E-value
RRM_eIF4H cd12401
RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar ...
41-116 7.34e-48

RNA recognition motif 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: 240847  Cd Length: 76  Bit Score: 155.18  E-value: 7.34e-48
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 45219878  41 PYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIA 116
Cdd:cd12401   1 PFTAFVGNLPFNTVQGDLDAIFKDLSVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALEYDGALFDDRSLRVDIA 76
RRM smart00360
RNA recognition motif;
43-113 3.03e-15

RNA recognition motif;


Pssm-ID: 214636  Cd Length: 73  Bit Score: 68.77  E-value: 3.03e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45219878     43 TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-YDGALLGDRSLRV 113
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFgKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEaLNGKELDGRPLKV 73
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
37-121 2.64e-12

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


Pssm-ID: 223796  Cd Length: 306  Bit Score: 64.58  E-value: 2.64e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878  37 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY-DGALLGDRSLRVD 114
Cdd:COG0724 111 SKEENNTLFVGNLPYDVTEEDLRELFKKFGpVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEElNGKELEGRPLRVQ 190

                ....*..
gi 45219878 115 IAEGRKQ 121
Cdd:COG0724 191 KAQPASQ 197
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
45-112 7.30e-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: 278504  Cd Length: 70  Bit Score: 59.15  E-value: 7.30e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878    45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDkDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLR 112
Cdd:pfam00076   2 FVGNLPPDVTEEDLKDLFSKFgPIKSIRLVRD-ETGRSKGFAFVEFESEEDAEKAIeALNGKELGGRTLR 70
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
40-207 6.77e-06

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  Cd Length: 494  Bit Score: 46.07  E-value: 6.77e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878    40 PPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-YDGALLGDRSLRVdiae 117
Cdd:TIGR01622 213 PFHRLYVGNLHFNITEQDLRQIFEPFGeIEFVQLQKDPETGRSKGYGFIQFRDAEQAKEALEkMNGFELAGRPIKV---- 288
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878   118 GRKQDKGGFGFRKGGPDDRGFRDDFLGGRGGSRPG--------DRRTGPPMGSRFRDGPPLRGSNM---------DFREP 180
Cdd:TIGR01622 289 GLGNDFTPESDANLAQRFQDQDGSAFSGAGLNTPArsqlmrklARDNEKGTGGLAIPGTDVGGVNMnnysrdglmRKLAP 368
                         170       180
                  ....*....|....*....|....*...
gi 45219878   181 TEEERAQRPRLQ-LKPRTVATPLNQVAN 207
Cdd:TIGR01622 369 TDEPPAVIPETQiLKPKAETSFVPVNVN 396
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
43-120 7.32e-04

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  Cd Length: 494  Bit Score: 39.90  E-value: 7.32e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 45219878    43 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRK 120
Cdd:TIGR01622 116 TVFVQQLAARARERDLYEFFSKVGkVRDVQIIKDRNSRRSKGVGYVEFYDVDSVQAALALTGQKLLGIPVIVQLSEAEK 194
eIF-4B pfam06273
Plant specific eukaryotic initiation factor 4B; This family consists of several plant specific ...
148-223 3.35e-03

Plant specific eukaryotic initiation factor 4B; This family consists of several plant specific eukaryotic initiation factor 4B proteins.


Pssm-ID: 310698  Cd Length: 502  Bit Score: 37.94  E-value: 3.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878   148 GSRPGDRRTgPPMGSRFRDGP--PLRGSNMD-FREPteeeraQRPRLQLKPR---TVATPLNQVANPNSAIFGGARPREE 221
Cdd:pfam06273 206 GKKPLPSRS-STFGSGFRDSGpePDRWSRGGgVREP------ERPRLVLDPPkgdSVVSETPPAKTSRPNPFGAARPREE 278

                  ..
gi 45219878   222 VV 223
Cdd:pfam06273 279 VL 280
 
Name Accession Description Interval E-value
RRM_eIF4H cd12401
RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar ...
41-116 7.34e-48

RNA recognition motif 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: 240847  Cd Length: 76  Bit Score: 155.18  E-value: 7.34e-48
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 45219878  41 PYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIA 116
Cdd:cd12401   1 PFTAFVGNLPFNTVQGDLDAIFKDLSVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALEYDGALFDDRSLRVDIA 76
RRM_eIF4B cd12402
RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar ...
41-116 4.69e-20

RNA recognition motif 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: 240848  Cd Length: 77  Bit Score: 82.43  E-value: 4.69e-20
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45219878  41 PYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDK-DTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIA 116
Cdd:cd12402   1 PYTAYLGNLPYDVTEEDIKEFFRGLNVSSVRLPREPgDPGRLRGFGYAEFEDRDSLLQALSLNDESLKNRRIRVDIA 77
RRM2_PHIP1 cd12272
RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) ...
43-114 1.53e-17

RNA recognition motif 2 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: 240718  Cd Length: 72  Bit Score: 75.12  E-value: 1.53e-17
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVD 114
Cdd:cd12272   1 TVYIGNLAWDITEDDVREFFKGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALKLDGTVLCGRPIRIA 72
RRM_HP0827_like cd12399
RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; This ...
43-117 1.56e-15

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  Cd Length: 78  Bit Score: 69.56  E-value: 1.56e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-YDGALLGDRSLRVDIAE 117
Cdd:cd12399   1 NLYVGNLPYNVTEEDLKDLFGQFgEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEkLNGTDFGGRTLTVNEAR 77
RRM2_RBM34 cd12395
RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily ...
43-113 1.97e-15

RNA recognition motif 2 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: 240841  Cd Length: 73  Bit Score: 69.11  E-value: 1.97e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKD-LSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRV 113
Cdd:cd12395   1 SVFVGNLPFDIEEEELRKHFEDcGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNGIKLKGRKIRV 72
RRM smart00360
RNA recognition motif;
43-113 3.03e-15

RNA recognition motif;


Pssm-ID: 214636  Cd Length: 73  Bit Score: 68.77  E-value: 3.03e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45219878     43 TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-YDGALLGDRSLRV 113
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFgKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEaLNGKELDGRPLKV 73
RRM1_NUCLs cd12450
RNA recognition motif 1 found in nucleolin-like proteins mainly from plants; This subfamily ...
43-119 4.19e-14

RNA recognition motif 1 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: 240896  Cd Length: 77  Bit Score: 65.80  E-value: 4.19e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDtDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGR 119
Cdd:cd12450   1 TLFVGNLSWSAEQDDLEEFFKECgEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALEKSGEELLGREIRVDLATER 77
RRM_Nop6 cd12400
RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar ...
42-114 1.27e-13

RNA recognition motif 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: 240846  Cd Length: 74  Bit Score: 64.29  E-value: 1.27e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 45219878  42 YTAYVGNLPFNTVQGDIDAIFKD-LSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVD 114
Cdd:cd12400   1 FILFVGNLPYDTTAEDLLAHFKNaGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLHHTLLKGRKINVE 74
RRM_II_PABPs cd12306
RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to ...
45-113 3.37e-13

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: 240752  Cd Length: 73  Bit Score: 63.08  E-value: 3.37e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRV 113
Cdd:cd12306   3 FVGNVDYGTTPEELQEHFKSCgTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLNESEFRGRQIKV 72
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
45-114 7.41e-13

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  Cd Length: 72  Bit Score: 61.94  E-value: 7.41e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDtDKFKGFCYVEFDEVDSLKEALT-YDGALLGDRSLRVD 114
Cdd:cd00590   2 FVGNLPPDTTEEDLRELFSKFgEIESVRIVRDKD-GKSKGFAFVEFESPEDAEKALEaLNGKELDGRKLKVS 72
RRM_ist3_like cd12411
RNA recognition motif in ist3 family; This subfamily corresponds to the RRM of the ist3 family ...
45-114 1.03e-12

RNA recognition motif in ist3 family; This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well.


Pssm-ID: 240857  Cd Length: 89  Bit Score: 61.89  E-value: 1.03e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD 114
Cdd:cd12411  13 YIGGLPYELTEGDILCVFSQYgEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVdNLNGIKLLGRTIRVD 84
RRM1_SART3 cd12391
RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and ...
43-114 1.17e-12

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  Cd Length: 72  Bit Score: 61.52  E-value: 1.17e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDkDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVD 114
Cdd:cd12391   1 TVFVSNLDYSVPEDELRKLFSKCgEITDVRLVKN-YKGKSKGYAYVEFENEESVQEALKLDRELIKGRPMFVS 72
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
37-121 2.64e-12

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


Pssm-ID: 223796  Cd Length: 306  Bit Score: 64.58  E-value: 2.64e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878  37 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY-DGALLGDRSLRVD 114
Cdd:COG0724 111 SKEENNTLFVGNLPYDVTEEDLRELFKKFGpVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEElNGKELEGRPLRVQ 190

                ....*..
gi 45219878 115 IAEGRKQ 121
Cdd:COG0724 191 KAQPASQ 197
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
45-112 7.30e-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: 278504  Cd Length: 70  Bit Score: 59.15  E-value: 7.30e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878    45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDkDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLR 112
Cdd:pfam00076   2 FVGNLPPDVTEEDLKDLFSKFgPIKSIRLVRD-ETGRSKGFAFVEFESEEDAEKAIeALNGKELGGRTLR 70
RRM2_gar2 cd12448
RNA recognition motif 2 in yeast protein gar2 and similar proteins; This subfamily corresponds ...
45-114 9.05e-11

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  Cd Length: 73  Bit Score: 56.23  E-value: 9.05e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY-DGALLGDRSLRVD 114
Cdd:cd12448   2 FVGNLSFDADEDSIYEAFGEYGeISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAlGGTDLLGRPVRLD 73
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3 ...
45-116 1.71e-10

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  Cd Length: 75  Bit Score: 55.71  E-value: 1.71e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIA 116
Cdd:cd12398   2 FVGNIPYDATEEQLIEIFSEVGpVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIrNLNGYEFNGRALRVDFA 75
RRM1_RBM28_like cd12413
RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily ...
43-119 1.37e-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  Cd Length: 79  Bit Score: 53.39  E-value: 1.37e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-YDGALLGDRSLRVDIAEGR 119
Cdd:cd12413   1 TLFVRNLPYDTTDEQLEEFFSEVGpIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEeKKKTKFGGRKIHVEFAKKK 79
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; ...
45-113 3.01e-09

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  Cd Length: 73  Bit Score: 52.26  E-value: 3.01e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-YDGALLGDRSLRV 113
Cdd:cd12284   2 YVGNLHFNITEDDLRGIFEPFgEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEqLNGFELAGRPIKV 72
RRM1_PHIP1 cd12271
RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) ...
44-113 3.98e-09

RNA recognition motif 1 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: 240717  Cd Length: 72  Bit Score: 51.97  E-value: 3.98e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45219878  44 AYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRV 113
Cdd:cd12271   1 VYVGGIPYYSTEDEIRSYFSYCgEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALALDGEDMGGRFLKV 71
RRM_snRNP70 cd12236
RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar ...
43-119 7.88e-09

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  Cd Length: 91  Bit Score: 51.48  E-value: 7.88e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY-DGALLGDRSLRVDIAEGR 119
Cdd:cd12236   3 TLFVARLNYDTTESKLRREFEEYgPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYaDGKKIDGRRVLVDVERGR 81
RRM2_SART3 cd12392
RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and ...
41-117 8.33e-09

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  Cd Length: 81  Bit Score: 51.26  E-value: 8.33e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 45219878  41 PYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKdTDKFKGFCYVEF-DEVDSLKEALTYDGALLGDRSLRVDIAE 117
Cdd:cd12392   2 KHKLFVSGLPFSVTKEELEKLFKKHgVVKSVRLVTNR-SGKPKGLAYVEYeNESSASQAVLKMDGTEIKEKTISVAISN 79
RRM2_PUF60 cd12371
RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins; This ...
45-116 1.36e-08

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  Cd Length: 77  Bit Score: 50.73  E-value: 1.36e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT----YDgalLGDRSLRVDIA 116
Cdd:cd12371   4 YVASVHPDLSEDDIKSVFEAFGkIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIAsmnlFD---LGGQQLRVGKA 77
RRM1_RBM39_like cd12283
RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; ...
43-113 1.67e-08

RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is 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: 240729  Cd Length: 73  Bit Score: 50.30  E-value: 1.67e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRV 113
Cdd:cd12283   1 TVFVMQLSLKVRERDLYEFFSKAgKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGLTGQRLLGQPIMV 72
RRM3_RBM28_like cd12415
RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily ...
43-116 1.68e-08

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  Cd Length: 82  Bit Score: 50.29  E-value: 1.68e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL------TYDGALLGDRSLRVDI 115
Cdd:cd12415   2 TVFIRNLPFDATEEELKELFSQFgEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLeaadnaEDSGLSLDGRRLIVTL 81

                .
gi 45219878 116 A 116
Cdd:cd12415  82 A 82
RRM1_RRM2_RBM5_like cd12313
RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins; This ...
48-114 7.69e-08

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  Cd Length: 84  Bit Score: 48.70  E-value: 7.69e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878  48 NLPFNTVQGDIDAIFKD---LSIRSVRLVRDKDTDKFKGFCYVEFdevDSLKEALTYDGALLGDRSLRVD 114
Cdd:cd12313   9 GLDLLTTEEDILQALSAiasVPIKDVRLIRDKLTGTSRGFAFVEF---PSLEDATQWMDALNNLDPFVID 75
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
45-113 1.41e-07

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  Cd Length: 78  Bit Score: 48.02  E-value: 1.41e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFK---GFCYVEFDEVDSLKEALTYDGALLGDRSLRV 113
Cdd:cd12298   4 YVRNLDFKLDEDDLRGIFSKFgEVESIRIPKKQDEKQGRlnnGFAFVTFKDASSAENALQLNGTELGGRKISV 76
RRM_NCBP2 cd12240
RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar ...
45-114 1.55e-07

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  Cd Length: 78  Bit Score: 47.93  E-value: 1.55e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45219878  45 YVGNLPFNTVQGDIDAIF-KDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY-DGALLGDRSLRVD 114
Cdd:cd12240   2 YVGNLSFYTTEEQIYELFsRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYlNGTKLDDRIIRVD 73
RRM2_Nop13p_fungi cd12397
RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins; This ...
45-117 1.92e-07

RNA recognition motif 2 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: 240843  Cd Length: 73  Bit Score: 47.44  E-value: 1.92e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTydGALLGDRSLRVDIAE 117
Cdd:cd12397   2 FVGNLSFETTEDELRAHFGRVgRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALK--GKHLNGRALRVEYGE 73
RRM_hnRNPH_ESRPs_RBM12_like cd12254
RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ...
45-113 2.30e-07

RNA recognition motif 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: 240700  Cd Length: 73  Bit Score: 47.17  E-value: 2.30e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDLSIR--SVRLVRDKDTdKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRV 113
Cdd:cd12254   3 RLRGLPFSATEEDIRDFFSGLDIPpdGIHIVYDDDG-RPTGEAYVEFASPEDARRALRKHNNKMGGRYIEV 72
RRM_II_PABPN1 cd12550
RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins; ...
45-113 6.27e-07

RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins; This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain.


Pssm-ID: 240994  Cd Length: 76  Bit Score: 45.95  E-value: 6.27e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRV 113
Cdd:cd12550   3 YVGNVDYGATAEELEAHFHGCgSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALALDESLFRGRQIKV 72
RRM1_Nop4p cd12674
RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins; This ...
43-119 7.87e-07

RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM1 of Nop4p (also known as 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 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 241118  Cd Length: 79  Bit Score: 45.98  E-value: 7.87e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-YDGALLGDRSLRVDIAEGR 119
Cdd:cd12674   1 TLFVRNLAFSVTQEDLTDFFSDVApIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAkLKNKKLHGRILRLDIAERR 79
RRM1_2_CID8_like cd12225
RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain ...
43-113 2.15e-06

RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear.


Pssm-ID: 240671  Cd Length: 77  Bit Score: 44.65  E-value: 2.15e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45219878  43 TAYVGNLPFNTVQGDIDAIF-KDLSIRSVRLVRDKDTDKfkGFCYVEFDEVDSLKEALTYDGALLGDRSLRV 113
Cdd:cd12225   2 TIHVGGIDGSLSEDDLKEFFsNCGEVTRVRLCGDRQHSA--RFAFVEFADAESALSALNLSGTLLGGHPLRV 71
RRM_CIRBP_RBM3 cd12449
RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein ...
45-116 3.21e-06

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  Cd Length: 80  Bit Score: 44.07  E-value: 3.21e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIA 116
Cdd:cd12449   4 FIGGLSFDTNEQSLEQVFSKYgQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMmAMNGKSVDGRQIRVDQA 77
RRM_CSTF2_CSTF2T cd12671
RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation ...
45-116 3.67e-06

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  Cd Length: 75  Bit Score: 44.02  E-value: 3.67e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEF-DEVDSLKEALTYDGALLGDRSLRVDIA 116
Cdd:cd12671   2 FVGNIPYEATEEQLKDIFSEVgPVVSFRLVYDRETGKPKGYGFCEYkDQETALSAMRNLNGYELNGRQLRVDNA 75
RRM_ZCRB1 cd12393
RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 ...
43-116 4.69e-06

RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.


Pssm-ID: 240839  Cd Length: 78  Bit Score: 43.84  E-value: 4.69e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 45219878  43 TAYVGNLPFNTVQGDIDAIF-KDLSIRSVRLVRDKDTDKFKGFCYVEF-DEVDSLKEALTYDGALLGDRSLRVDIA 116
Cdd:cd12393   3 TVYVSNLPFSLTNNDLHKIFsKYGKVVKVTIVKDKETRKSKGVAFILFlDREDAHKCVKALNNKELFGRTLKCSIA 78
RRM_RBMX_like cd12382
RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA ...
45-116 5.55e-06

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  Cd Length: 80  Bit Score: 43.37  E-value: 5.55e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 45219878  45 YVGNLPFNTVQGDIDAIF-KDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY-DGALLGDRSLRVDIA 116
Cdd:cd12382   5 FVSGLSTRTTEKELEALFsKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDlNGKELEGRVIKVEKA 78
RRM2_Nop12p_like cd12670
RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins; This ...
45-113 5.95e-06

RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins; This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 241114  Cd Length: 79  Bit Score: 43.33  E-value: 5.95e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGA---LLGDRSLRV 113
Cdd:cd12670   3 FVGNLGFEDVEEGLWRVFGKCgGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLNEKkfpPMLPRELRV 75
RRM2_SREK1 cd12260
RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and ...
43-113 5.95e-06

RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site.


Pssm-ID: 240706  Cd Length: 85  Bit Score: 43.44  E-value: 5.95e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKdlSIRSVRLVR-DKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRV 113
Cdd:cd12260   6 TIYVGNLDPTTTADQLLEFFS--QAGEVKYVRmAGDETQPTRYAFVEFAEQTSVINALKLNGAMFGGRPLKV 75
RRM1_RBM45 cd12366
RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins; This subfamily ...
66-116 6.16e-06

RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins; This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 240812  Cd Length: 81  Bit Score: 43.47  E-value: 6.16e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 45219878  66 SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGD--RSLRVDIA 116
Cdd:cd12366  28 EIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMeEMNGKCLGGdtKPLKVLIA 81
RRM2_NUCLs cd12451
RNA recognition motif 2 in nucleolin-like proteins mainly from plants; This subfamily ...
67-114 6.18e-06

RNA recognition motif 2 in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM2 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: 240897  Cd Length: 79  Bit Score: 43.53  E-value: 6.18e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 45219878  67 IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVD 114
Cdd:cd12451  30 ITRVSIPTDRETGASKGFAYIEFKSVDGVEKALELDGSDLGGGNLVVD 77
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
40-207 6.77e-06

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  Cd Length: 494  Bit Score: 46.07  E-value: 6.77e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878    40 PPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-YDGALLGDRSLRVdiae 117
Cdd:TIGR01622 213 PFHRLYVGNLHFNITEQDLRQIFEPFGeIEFVQLQKDPETGRSKGYGFIQFRDAEQAKEALEkMNGFELAGRPIKV---- 288
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878   118 GRKQDKGGFGFRKGGPDDRGFRDDFLGGRGGSRPG--------DRRTGPPMGSRFRDGPPLRGSNM---------DFREP 180
Cdd:TIGR01622 289 GLGNDFTPESDANLAQRFQDQDGSAFSGAGLNTPArsqlmrklARDNEKGTGGLAIPGTDVGGVNMnnysrdglmRKLAP 368
                         170       180
                  ....*....|....*....|....*...
gi 45219878   181 TEEERAQRPRLQ-LKPRTVATPLNQVAN 207
Cdd:TIGR01622 369 TDEPPAVIPETQiLKPKAETSFVPVNVN 396
RRM_PPIE cd12347
RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins; This subfamily ...
45-113 9.30e-06

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  Cd Length: 73  Bit Score: 42.59  E-value: 9.30e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRV 113
Cdd:cd12347   2 YVGGLAEEVDEKVLHAAFIPFgDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIdNMNESELFGRTIRV 72
RRM1_PUF60 cd12370
RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins; This ...
45-113 1.03e-05

RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM1 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: 240816  Cd Length: 76  Bit Score: 42.80  E-value: 1.03e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRV 113
Cdd:cd12370   4 YVGSISFELGEDTIRQAFSPFgPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALeQMNGVMLGGRNIKV 74
RRM1_gar2 cd12447
RNA recognition motif 1 in yeast protein gar2 and similar proteins; This subfamily corresponds ...
43-116 1.06e-05

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  Cd Length: 76  Bit Score: 42.76  E-value: 1.06e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIA 116
Cdd:cd12447   1 TLFVGNLSWSVDDEWLKAEFEKFgTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIeAMDGKELDGRPINVDFS 76
RRM_II_PABPN1L cd12551
RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2) ...
43-113 2.06e-05

RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2); This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain.


Pssm-ID: 240995  Cd Length: 77  Bit Score: 41.77  E-value: 2.06e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRV 113
Cdd:cd12551   1 SVYVGNVDYGSTAEELEAHFSGCgPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVALDESSFRGRVIKV 72
RRM2_Prp24 cd12297
RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
43-115 2.36e-05

RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM2 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: 240743  Cd Length: 78  Bit Score: 41.78  E-value: 2.36e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKD----LSIR--SVRlvrdkdTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDI 115
Cdd:cd12297   2 TLWVTNFPPSFDQSDIRDLFEQygeiLSIRfpSLR------FNKTRRFCYVQFTSPESAAAAVaLLNGKLGEGYKLVVKI 75
RRM2_hnRNPD_like cd12329
RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP ...
45-99 2.41e-05

RNA recognition motif 2 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  Cd Length: 75  Bit Score: 41.58  E-value: 2.41e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 99
Cdd:cd12329   3 FVGGLSPETTEEKIREYFGKFgNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKIL 58
RRM5_RBM19_like cd12318
RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins; This ...
43-111 2.42e-05

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  Cd Length: 82  Bit Score: 41.82  E-value: 2.42e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFK-----GFCYVEFDEVDSLKEAL-TYDGALLGDRSL 111
Cdd:cd12318   2 TLFVKNLNFKTTEETLKKHFEKCgGVRSVTIAKKKDPKGPGkllsmGYGFVEFKSKEAAQKALkRLQGTVLDGHAL 77
RRM1_RBM34 cd12394
RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily ...
43-114 2.52e-05

RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM1 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: 240840  Cd Length: 91  Bit Score: 41.86  E-value: 2.52e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRL----------------VRDKDTDKfKGFC--YVEFDEVDSLKEALTYDG 103
Cdd:cd12394   2 TVFVGNLPLTTKKKDLKKLFKQFGpIESVRFrsvpvkekklpkkvaaIKKKFHDK-KDNVnaYVVFKEEESAEKALKLNG 80
                        90
                ....*....|.
gi 45219878 104 ALLGDRSLRVD 114
Cdd:cd12394  81 TEFEGHHIRVD 91
RRM1_La cd12291
RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily ...
43-106 3.24e-05

RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus.


Pssm-ID: 240737  Cd Length: 72  Bit Score: 41.42  E-value: 3.24e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTdKFKGFCYVEFDEVDSLK-----EALTYDGALL 106
Cdd:cd12291   1 TVYVKGFPKDATLDDIQEFFEKFgKVNNIRMRRDLDK-KFKGSVFVEFKTEEDAKkflekEKLKYKEKEL 69
RRM_snRNP35 cd12237
RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11 ...
39-120 4.14e-05

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  Cd Length: 93  Bit Score: 41.09  E-value: 4.14e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878  39 EPPYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAltYDGA---LLGDRSLRVD 114
Cdd:cd12237   1 DPYLTLFVGRLSLQTTEETLREVFSRYgDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRA--YRDAhklVIDGSEIFVD 78

                ....*.
gi 45219878 115 IAEGRK 120
Cdd:cd12237  79 FERERT 84
RRM1_Hu_like cd12375
RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar ...
46-116 4.79e-05

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  Cd Length: 77  Bit Score: 40.79  E-value: 4.79e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45219878  46 VGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEF-DEVDSLKEALTYDGALLGDRSLRVDIA 116
Cdd:cd12375   5 VNYLPQDMTQEELRSLFEAIgPIESCKIVRDRITGQSLGYGFVDYvDENDAQKAINTLNGFEIRNKRLKVSYA 77
RRM2_NGR1_NAM8_like cd12613
RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 ...
42-116 5.11e-05

RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins; This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 241057  Cd Length: 80  Bit Score: 40.97  E-value: 5.11e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 45219878  42 YTAYVGNLPFNTVQGDIDAIFKD--LSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY-DGALLGDRSLRVDIA 116
Cdd:cd12613   2 YSIFVGDLSPEVNESDLVSLFQSrfPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIEmQGVYCGGRPMRISTA 79
RRM_SLIRP cd12242
RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and ...
43-113 5.64e-05

RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins; This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities.


Pssm-ID: 240688  Cd Length: 73  Bit Score: 40.75  E-value: 5.64e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRV 113
Cdd:cd12242   1 KLFVGNLPWTVGSKELKEYFSQFgKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQKQKHILEGNKLQV 72
RRM2_NCL cd12404
RNA recognition motif 2 in vertebrate nucleolin; This subfamily corresponds to the RRM2 of ...
43-114 5.66e-05

RNA recognition motif 2 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: 240850  Cd Length: 77  Bit Score: 40.60  E-value: 5.66e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKDlsIRSVRLVRdKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD 114
Cdd:cd12404   5 TLFVKNLPYNITVDELKEVFED--AVDIRLPS-GKDGSSKGIAYIEFKTEAEAEKALeEKQGAEVDGRSIVVD 74
RRM_NIFK_like cd12307
RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) ...
45-113 1.50e-04

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  Cd Length: 74  Bit Score: 39.48  E-value: 1.50e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKE-ALTYDGALLGDRSLRV 113
Cdd:cd12307   3 YIGHLPHGFYEPELRKYFSQFgTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIvAETMNNYLLFERLLKC 73
RRM1_I_PABPs cd12378
RNA recognition motif 1 in type I polyadenylate-binding proteins; This subfamily corresponds ...
45-100 1.90e-04

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  Cd Length: 80  Bit Score: 39.05  E-value: 1.90e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 100
Cdd:cd12378   3 YVGDLHPDVTEAMLYEIFSPAgPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALD 59
RRM1_Hu cd12650
RNA recognition motif 1 in the Hu proteins family; This subfamily corresponds to the RRM1 of ...
46-116 2.26e-04

RNA recognition motif 1 in the Hu proteins family; This subfamily corresponds to the RRM1 of the Hu proteins family which 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. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. 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: 241094  Cd Length: 78  Bit Score: 38.94  E-value: 2.26e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45219878  46 VGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIA 116
Cdd:cd12650   6 VNYLPQNMTQDEIRSLFSSIgEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAInTLNGLRLQNKTIKVSYA 78
RRM2_SECp43_like cd12345
RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar ...
42-116 3.06e-04

RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins; This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs.


Pssm-ID: 240791  Cd Length: 80  Bit Score: 38.41  E-value: 3.06e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 45219878  42 YTAYVGNLPFNTVQGDIDAIFKDL--SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-YDGALLGDRSLRVDIA 116
Cdd:cd12345   2 HSIFVGDLAPDVTDYMLQETFRARypSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTeMNGVYCSSRPMRVSPA 79
RRM3_Nop4p cd12676
RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins; This ...
42-99 3.12e-04

RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM3 of Nop4p (also known as 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 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 241120  Cd Length: 107  Bit Score: 38.76  E-value: 3.12e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 45219878  42 YTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 99
Cdd:cd12676   2 FTLFVRNLPYDATEESLAPHFSKFgSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60
RRM_PPIL4 cd12235
RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar ...
53-114 3.15e-04

RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins; This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus.


Pssm-ID: 240681  Cd Length: 83  Bit Score: 38.40  E-value: 3.15e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 45219878  53 TVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEA-LTYDGALLGDRSLRVD 114
Cdd:cd12235  15 TTDEDLEIIFSRFgKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAyFKMDNVLIDDRRIHVD 78
RRM1_LARP7 cd12290
RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins; This subfamily ...
43-100 4.03e-04

RNA recognition motif 1 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: 240736  Cd Length: 80  Bit Score: 38.11  E-value: 4.03e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 100
Cdd:cd12290   1 TVYVECLPKNATHEWLKAVFSKYGtVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACK 59
RRM2_MRD1 cd12566
RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and ...
45-113 4.46e-04

RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM2 of MRD1 which 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 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: 241010  Cd Length: 79  Bit Score: 38.14  E-value: 4.46e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEF-DEVDSLKEALTYDGALLGDRSLRV 113
Cdd:cd12566   6 FVRNLPYSCKEDDLEKLFSKFgELSEVHVAIDKKSGKSKGFAYVLFlDPEDAVKAYKELDGKVFQGRLIHI 76
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
43-120 7.32e-04

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  Cd Length: 494  Bit Score: 39.90  E-value: 7.32e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 45219878    43 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRK 120
Cdd:TIGR01622 116 TVFVQQLAARARERDLYEFFSKVGkVRDVQIIKDRNSRRSKGVGYVEFYDVDSVQAALALTGQKLLGIPVIVQLSEAEK 194
RRM4_RBM12_like cd12514
RNA recognition motif 4 in RNA-binding protein RBM12, RBM12B and similar proteins; This ...
44-113 8.04e-04

RNA recognition motif 4 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: 240958  Cd Length: 73  Bit Score: 37.31  E-value: 8.04e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45219878  44 AYVGNLPFNTVQGDIDAIFKDLSI--RSVRLVRDKdTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRV 113
Cdd:cd12514   2 IKIKNIPFDVTKGEVLAFFAGIAIaeQGIHILYDK-TGKTLGEAYVEFVSEEDAMRAERLHRKKLKGREILL 72
ELAV_HUD_SF TIGR01661
ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing ...
46-116 8.25e-04

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  Cd Length: 352  Bit Score: 39.54  E-value: 8.25e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45219878    46 VGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEF-DEVDSLKEALTYDGALLGDRSLRVDIA 116
Cdd:TIGR01661   8 VNYLPQTMTQEEIRSLFTSIgEIESCKLVRDKVTGQSLGYGFVNYvRPEDAEKAVNSLNGLRLQNKTIKVSYA 80
RRM1_SECp43_like cd12344
RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar ...
56-99 8.95e-04

RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins; This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs.


Pssm-ID: 240790  Cd Length: 81  Bit Score: 37.24  E-value: 8.95e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 45219878  56 GDID----------AIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 99
Cdd:cd12344   5 GDLEpwmdeayiysAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQAL 58
RRM_Nop15p cd12552
RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins; ...
43-117 1.05e-03

RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins; This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 240996  Cd Length: 77  Bit Score: 37.08  E-value: 1.05e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLK-EALTYDGALLGDRSLRVDIAE 117
Cdd:cd12552   1 VIYIGHLPHGFLEKELKKYFSQFgTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAiAAKSMNNYLLMGKVLQVHVLP 77
RRM2_TIA1_like cd12353
RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This ...
45-112 1.06e-03

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  Cd Length: 75  Bit Score: 36.97  E-value: 1.06e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-YDGALLGDRSLR 112
Cdd:cd12353   3 FVGDLSPEIDTETLRAAFAPFgEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQsMNGQWLGGRAIR 72
RRM_RNPS1 cd12365
RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar ...
45-113 1.17e-03

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  Cd Length: 73  Bit Score: 36.76  E-value: 1.17e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY-DGALLGDRSLRV 113
Cdd:cd12365   2 HVGKLTRNVNKDHLKEIFSNYgTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHmDGGQIDGQEVTV 72
RRM2_RAVER cd12389
RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; ...
45-117 1.32e-03

RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.


Pssm-ID: 240835  Cd Length: 77  Bit Score: 36.48  E-value: 1.32e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878  45 YVGNLPFNTVQGDidaiFKDL-----SIRSVRLVRDKDTDKFKGFCYVEFDEVDS---LKEALtyDGALLGDRSLRVDIA 116
Cdd:cd12389   3 CVGNLPLEFTDEQ----FRELvspfgAVERCFLVYSESTGESKGYGFVEYASKASalkAKNQL--DGKQIGGRKLQVDWA 76

                .
gi 45219878 117 E 117
Cdd:cd12389  77 D 77
RRM6_RBM19_RRM5_MRD1 cd12320
RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 ...
46-99 1.34e-03

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  Cd Length: 76  Bit Score: 36.44  E-value: 1.34e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 45219878  46 VGNLPFNTVQGDIDAIFKDLS-IRSVRLVRdKDTDKFKGFCYVEF---DEVDSLKEAL 99
Cdd:cd12320   5 VRNVPFEATKKELRELFSPFGqVKSVRLPK-KFDGSHRGFAFVEFvtkQEAQNAMEAL 61
RRM1_RRT5 cd12409
RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar ...
45-113 1.34e-03

RNA recognition motif 1 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: 240855  Cd Length: 84  Bit Score: 36.59  E-value: 1.34e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDLSIRSVRLV------RDKDTDKFKGFCYVEFDEVD-SLKEALTYDGALLGDRSLRV 113
Cdd:cd12409   3 YISNLSYSSSEEDLEEFLKDFEPVSVLIPsqtvrgFRSRRVRPLGIAYAEFSSPEqAEKVVKDLNGKVFKNRKLFV 78
RRM_SARFH cd12534
RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar ...
45-116 1.38e-03

RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins; This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 240978  Cd Length: 83  Bit Score: 36.63  E-value: 1.38e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878  45 YVGNLPFNTVQGDIDAIF---------KDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-YDGALLGDRSLRVD 114
Cdd:cd12534   2 FVSNLPPNTTEQDLAEHFgsigiikidKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHAASAAIEwFNNKDFMGNTIKVS 81

                ..
gi 45219878 115 IA 116
Cdd:cd12534  82 LA 83
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in ...
44-113 1.45e-03

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  Cd Length: 74  Bit Score: 36.51  E-value: 1.45e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45219878  44 AYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEV-DSLKEALTYDGALLGDRSLRV 113
Cdd:cd12316   2 LFVRNLPFTTTEEELRELFEAFgEISEVHLPLDKETKRSKGFAFVSFMFPeHAVKAYSELDGSIFQGRLLHV 73
RRM1_Nop13p_fungi cd12396
RNA recognition motif 1 in yeast nucleolar protein 13 (Nop13p) and similar proteins; This ...
45-99 1.78e-03

RNA recognition motif 1 in yeast nucleolar protein 13 (Nop13p) and similar proteins; This subfamily corresponds to the RRM1 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: 240842  Cd Length: 85  Bit Score: 36.36  E-value: 1.78e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDLSIRSV------RL----VRDKDTDKF--KGFCYVEFDEVDSLKEAL 99
Cdd:cd12396   2 WIGNLSFTTTKEMLRQFFVSKSGDRItdeqitRVhmpdSKAKRKGVKqnKGFAYVDFTSQEATKAAI 68
RRM_CFIm68_CFIm59 cd12372
RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), ...
45-99 1.80e-03

RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins; This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping.


Pssm-ID: 240818  Cd Length: 76  Bit Score: 36.12  E-value: 1.80e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDL---SIRSVRLVRDKDTDKFKGFCYVEFDEVDS---LKEAL 99
Cdd:cd12372   2 YVGNLTWWTTDEDLEGALAEAgvvDVKSIKFFEHKANGKSKGFAYVEFASEAAaaaVKEKL 62
RRM2_MSI cd12323
RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and ...
45-98 1.86e-03

RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins; This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function.


Pssm-ID: 240769  Cd Length: 74  Bit Score: 36.26  E-value: 1.86e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEA 98
Cdd:cd12323   3 FVGGLSANTTEDDVKKYFSQFGkVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKV 57
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
45-113 1.92e-03

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  Cd Length: 562  Bit Score: 38.63  E-value: 1.92e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45219878    45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRV 113
Cdd:TIGR01628   4 YVGDLDPDVTEAKLYDLFKPFgPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALeTMNFKRLGGKPIRI 74
RRM3_TIA1_like cd12354
RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and ...
43-90 1.96e-03

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  Cd Length: 73  Bit Score: 36.06  E-value: 1.96e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 45219878  43 TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDkdtdkfKGFCYVEFD 90
Cdd:cd12354   2 TVYVGNLPHGLTEEELQRTFSPFgAIEEVRVFKD------KGYAFVRFD 44
RRM1_Prp24 cd12296
RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
46-115 2.26e-03

RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM1 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: 240742  Cd Length: 71  Bit Score: 36.07  E-value: 2.26e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45219878  46 VGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKdtdkfkGFCY--VEFDEVDSLKEALTYDGALLGDRSLRVDI 115
Cdd:cd12296   5 VKNLPKDTTENKIRQFFKDCgEIREVKIVESE------GGLVavIEFETEDEALAALTKDHKRLGGNEISVSR 71
RRM_TRA2 cd12363
RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar ...
46-118 2.32e-03

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  Cd Length: 78  Bit Score: 36.06  E-value: 2.32e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 45219878  46 VGNLPFNTVQGDIDAIFKD-LSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEA-LTYDGALLGDRSLRVDIAEG 118
Cdd:cd12363   4 VFGLSLYTTERDLREVFSRyGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAkERLNGMEIDGRRIRVDYSIT 78
RRM2_RMB19 cd12502
RNA recognition motif 2 in RNA-binding protein 19 (RBM19) and similar proteins; This subfamily ...
49-113 2.54e-03

RNA recognition motif 2 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: 240946  Cd Length: 72  Bit Score: 35.81  E-value: 2.54e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 45219878  49 LPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKfKGFCYVEFDEVDSLKEALTYDGALLGDRSLRV 113
Cdd:cd12502   8 APFNVKEKHIREFFSPLKPVAIRIVKNDHGRK-TGFAFVDLKSEEDLKKALKRNKDYMGGRYIEL 71
RRM1_HuD cd12770
RNA recognition motif 1 in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the ...
46-116 2.62e-03

RNA recognition motif 1 in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD 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: 241214  Cd Length: 83  Bit Score: 35.86  E-value: 2.62e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45219878  46 VGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEF-DEVDSLKEALTYDGALLGDRSLRVDIA 116
Cdd:cd12770   7 VNYLPQNMTQEEFRSLFGSIgEIESCKLVRDKITGQSLGYGFVNYiDPKDAEKAINTLNGLRLQTKTIKVSYA 79
RRM2_hnRNPA_like cd12328
RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily; This subfamily ...
45-99 2.92e-03

RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily; This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 240774  Cd Length: 73  Bit Score: 35.70  E-value: 2.92e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 99
Cdd:cd12328   3 FVGGLKEDVTEEDLREYFSQYgNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIV 58
RRM2_TIAR cd12617
RNA recognition motif 2 in nucleolysin TIAR and similar proteins; This subgroup corresponds to ...
42-116 2.95e-03

RNA recognition motif 2 in nucleolysin TIAR and similar proteins; This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). 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. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is 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. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 241061  Cd Length: 80  Bit Score: 35.83  E-value: 2.95e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45219878  42 YTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEF-DEVDSLKEALTYDGALLGDRSLRVDIA 116
Cdd:cd12617   2 FHVFVGDLSPEITTEDIKSAFAPFgKISDARVVKDMATGKSKGYGFVSFyNKLDAENAIVHMGGQWLGGRQIRTNWA 78
RRM_RBM24_RBM38_like cd12384
RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins; ...
45-99 3.32e-03

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  Cd Length: 76  Bit Score: 35.28  E-value: 3.32e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 45219878  45 YVGNLPFNTvqgDIDAIFKDLS----IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 99
Cdd:cd12384   4 FVGGLPYHT---TDDSLRKYFSqfgeIEEAVVITDRQTGKSRGYGFVTFKDKESAERAC 59
eIF-4B pfam06273
Plant specific eukaryotic initiation factor 4B; This family consists of several plant specific ...
148-223 3.35e-03

Plant specific eukaryotic initiation factor 4B; This family consists of several plant specific eukaryotic initiation factor 4B proteins.


Pssm-ID: 310698  Cd Length: 502  Bit Score: 37.94  E-value: 3.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878   148 GSRPGDRRTgPPMGSRFRDGP--PLRGSNMD-FREPteeeraQRPRLQLKPR---TVATPLNQVANPNSAIFGGARPREE 221
Cdd:pfam06273 206 GKKPLPSRS-STFGSGFRDSGpePDRWSRGGgVREP------ERPRLVLDPPkgdSVVSETPPAKTSRPNPFGAARPREE 278

                  ..
gi 45219878   222 VV 223
Cdd:pfam06273 279 VL 280
RRM_eIF3G_like cd12408
RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and ...
46-117 3.63e-03

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  Cd Length: 77  Bit Score: 35.21  E-value: 3.63e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 45219878  46 VGNLPFNTVQGDIDAIF-KDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAE 117
Cdd:cd12408   4 VTNLSEDADEDDLRELFrPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIeKLNGFGYDNLILSVEWAK 77
RRM1_HuC cd12772
RNA recognition motif 1 in vertebrate Hu-antigen C (HuC); This subgroup corresponds to the ...
46-116 4.74e-03

RNA recognition motif 1 in vertebrate Hu-antigen C (HuC); This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC 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 AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. 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: 241216  Cd Length: 84  Bit Score: 35.09  E-value: 4.74e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45219878  46 VGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEF-DEVDSLKEALTYDGALLGDRSLRVDIA 116
Cdd:cd12772   8 VNYLPQNMTQEEFKSLFGSIgEIESCKLVRDKITGQSLGYGFVNYvDPNDADKAINTLNGLKLQTKTIKVSYA 80
RRM3_HuD cd12656
RNA recognition motif 3 in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the ...
66-113 4.74e-03

RNA recognition motif 3 in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD 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: 241100  Cd Length: 86  Bit Score: 35.07  E-value: 4.74e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 45219878  66 SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRV 113
Cdd:cd12656  29 AVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIaSLNGYRLGDRVLQV 77
RRM1_RBM5_like cd12561
RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins; This subgroup ...
40-101 4.91e-03

RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins; This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, 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. Both, RBM5 and RBM10, 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: 241005  Cd Length: 81  Bit Score: 35.05  E-value: 4.91e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 45219878  40 PPYTAYVGNLPFNTVQGDI-DAIFK-DLSIRSVRLVRDKDTDKFKGFCYVEFdevDSLKEALTY 101
Cdd:cd12561   1 PNNTIMLRGLPLSVTEEDIrNALVShGVEPKDVRLMRRKTTGASRGFAFVEF---MSLEEATRW 61
RRM3_HuB cd12654
RNA recognition motif 3 in vertebrate Hu-antigen B (HuB); This subgroup corresponds to the ...
66-113 5.92e-03

RNA recognition motif 3 in vertebrate Hu-antigen B (HuB); This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB 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 AU-rich RNA element (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: 241098  Cd Length: 86  Bit Score: 35.07  E-value: 5.92e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 45219878  66 SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRV 113
Cdd:cd12654  29 AVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIaSLNGYRLGDRVLQV 77
RRM2_Hu_like cd12376
RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar ...
45-100 8.16e-03

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  Cd Length: 79  Bit Score: 34.53  E-value: 8.16e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 100
Cdd:cd12376   4 YVSGLPKTMTQKELEQLFSQYgRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60
RRM2_U2AF65 cd12231
RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 ...
45-113 8.59e-03

RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs.


Pssm-ID: 240677  Cd Length: 77  Bit Score: 34.13  E-value: 8.59e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 45219878  45 YVGNLPFNTvqgDIDAIFKDLS----IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRV 113
Cdd:cd12231   4 FIGGLPNYL---SEDQVKELLEsfgkLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIaGLNGMQLGDKKLTV 74
RRM2_SXL cd12651
RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins; This subfamily ...
45-100 8.70e-03

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  Cd Length: 79  Bit Score: 34.49  E-value: 8.70e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 45219878  45 YVGNLPFNTVQGDIDAIF-KDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 100
Cdd:cd12651   4 YVTNLPRQLTEDELRKIFeAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
45-122 8.76e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727  Cd Length: 509  Bit Score: 36.79  E-value: 8.76e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45219878    45 YVGNLPFNTVQGDIDAIFKDlSIRSVRLVRDKDTDKF--------KGFCYVEFDEVDSLKEALTYDGALLGDRSLRVdia 116
Cdd:TIGR01642 179 YVGGIPPEFVEEAVVDFFND-LMIATGYHKAEDGKHVssvninkeKNFAFLEFRTVEEATFAMALDSIIYSNVFLKI--- 254

                  ....*.
gi 45219878   117 eGRKQD 122
Cdd:TIGR01642 255 -RRPHD 259
RRM2_RBM12_like cd12511
RNA recognition motif 2 in RNA-binding protein RBM12, RBM12B and similar proteins; This ...
45-113 9.10e-03

RNA recognition motif 2 in RNA-binding protein RBM12, RBM12B and similar proteins; This subfamily corresponds to the RRM2 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 shows high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear.


Pssm-ID: 240955  Cd Length: 73  Bit Score: 33.98  E-value: 9.10e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 45219878  45 YVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKfKGFCYVEFDEVDSLKEALTYDGALLGDRSLRV 113
Cdd:cd12511   3 FLHGLPYTADEHDVKEFFHGLDVEDVIFLKRHNGRN-NGNAIVKFATFQDAKEALKRHRELMGSRYIEL 70
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.16
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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