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Conserved domains on  [gi|15238140|ref|NP_196597|]
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RNA-binding (RRM/RBD/RNP motifs) family protein [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RRM_II_PABPs cd12306
RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to ...
90-161 8.11e-47

RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only.


:

Pssm-ID: 409747 [Multi-domain]  Cd Length: 73  Bit Score: 148.99  E-value: 8.11e-47
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVS 161
Cdd:cd12306   1 SIYVGNVDYGTTPEELQAHFKSCGTINRVTILCDKFtGQPKGFAYIEFVDKSSVENALLLNESEFRGRQIKVT 73
PIN_SF super family cl28905
PIN (PilT N terminus) domain: Superfamily; The PIN (PilT N terminus) domain belongs to a large ...
6-70 5.67e-03

PIN (PilT N terminus) domain: Superfamily; The PIN (PilT N terminus) domain belongs to a large nuclease superfamily, and were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. The PIN domain superfamily includes: the FEN-like PIN domain family such as the PIN domains of Flap endonuclease-1 (FEN1), exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease, 5'-3' exonucleases of DNA polymerase I and bacteriophage T4- and T5-5' nucleases; the VapC-like PIN domain family which includes toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1; the LabA-like PIN domain family which includes the PIN domains of Synechococcus elongatus LabA (low-amplitude and bright); the PRORP-Zc3h12a-like PIN domain family which includes the PIN domains of RNase P (PRORP), ribonuclease Zc3h12a; and Bacillus subtilis YacP/Rae1-like PIN domains. It also includes the Mut7-C PIN domain family, which is not represented here as it is a shortened version of the PIN fold and lacks a core strand and helix (H3 and S3). The Mut7-C PIN domain family includes the C-terminus of Caenorhabditis elegans exonuclease Mut-7.


The actual alignment was detected with superfamily member cd18739:

Pssm-ID: 475124  Cd Length: 124  Bit Score: 35.77  E-value: 5.67e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140   6 HEVYGGEIPEVGDTDVPDPDIDMSAA-----DEDAVTELAEMKRRLKEMEEEAAALREMQAKVEKEMGAT 70
Cdd:cd18739  37 YEVYVGAVRSAGETDLDGVREDLDWVepldfDEEVAREAAQIQAELLEAGEPINPPDLMIAATARSLGAT 106
 
Name Accession Description Interval E-value
RRM_II_PABPs cd12306
RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to ...
90-161 8.11e-47

RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only.


Pssm-ID: 409747 [Multi-domain]  Cd Length: 73  Bit Score: 148.99  E-value: 8.11e-47
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVS 161
Cdd:cd12306   1 SIYVGNVDYGTTPEELQAHFKSCGTINRVTILCDKFtGQPKGFAYIEFVDKSSVENALLLNESEFRGRQIKVT 73
RRM smart00360
RNA recognition motif;
90-160 1.51e-19

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 79.17  E-value: 1.51e-19
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140     90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKEtGKSKGFAFVEFESEEDAEKALEaLNGKELDGRPLKV 73
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
90-164 1.32e-18

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 76.68  E-value: 1.32e-18
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKVSPKR 164
Cdd:COG0724   3 KIYVGNLPYSVTEEDLRELFSEYGEVTSVKLITDREtGRSRGFGFVEMPDDEEAQAAIEaLNGAELMGRTLKVNEAR 79
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
91-159 9.25e-16

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


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 69.18  E-value: 9.25e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140    91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLK 159
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEaLNGKELGGRELK 70
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
43-162 6.28e-11

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


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 61.09  E-value: 6.28e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140    43 KRRLKEMEEEAAALREMQAKVEKEMGATQDpasmaanqEGKEEVDARSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILM 122
Cdd:TIGR01622  77 RRRGDSYRRRRDDRRSRREKPRARDGTPEP--------LTEDERDRRTVFVQQLAARARERDLYEFFSKVGKVRDVQIIK 148
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 15238140   123 DKF-GQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVSP 162
Cdd:TIGR01622 149 DRNsRRSKGVGYVEFYDVDSVQAALALTGQKLLGIPVIVQL 189
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
91-184 3.43e-04

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 39.64  E-value: 3.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140   91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEAL-QLNESELHGRQLKVSP--KRTN 166
Cdd:PLN03134  37 LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDReTGRSRGFGFVNFNDEGAATAAIsEMDGKELNGRHIRVNPanDRPS 116
                         90
                 ....*....|....*...
gi 15238140  167 VPGMKQYHPGRFNPSMGY 184
Cdd:PLN03134 117 APRAYGGGGGYSGGGGGY 134
PIN_VapC4-5_FitB-like cd18739
uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily; ...
6-70 5.67e-03

uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily; The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350306  Cd Length: 124  Bit Score: 35.77  E-value: 5.67e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140   6 HEVYGGEIPEVGDTDVPDPDIDMSAA-----DEDAVTELAEMKRRLKEMEEEAAALREMQAKVEKEMGAT 70
Cdd:cd18739  37 YEVYVGAVRSAGETDLDGVREDLDWVepldfDEEVAREAAQIQAELLEAGEPINPPDLMIAATARSLGAT 106
 
Name Accession Description Interval E-value
RRM_II_PABPs cd12306
RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to ...
90-161 8.11e-47

RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only.


Pssm-ID: 409747 [Multi-domain]  Cd Length: 73  Bit Score: 148.99  E-value: 8.11e-47
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVS 161
Cdd:cd12306   1 SIYVGNVDYGTTPEELQAHFKSCGTINRVTILCDKFtGQPKGFAYIEFVDKSSVENALLLNESEFRGRQIKVT 73
RRM_II_PABPN1 cd12550
RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins; ...
90-164 6.33e-36

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: 409966 [Multi-domain]  Cd Length: 76  Bit Score: 121.45  E-value: 6.33e-36
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVSPKR 164
Cdd:cd12550   1 SVYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFsGHPKGFAYIEFADKESVRTALALDESLFRGRQIKVMPKR 76
RRM_II_PABPN1L cd12551
RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2) ...
90-165 8.06e-31

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: 409967 [Multi-domain]  Cd Length: 77  Bit Score: 108.38  E-value: 8.06e-31
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVSPKRT 165
Cdd:cd12551   1 SVYVGNVDYGSTADELEAHFNGCGPINRVTILCDKFsGHPKGYAYIEFATRSSVQAAVALDESSFRGRVIKVLPKRT 77
RRM2_RBM34 cd12395
RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
90-161 7.88e-22

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


Pssm-ID: 409829 [Multi-domain]  Cd Length: 73  Bit Score: 84.86  E-value: 7.88e-22
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVS 161
Cdd:cd12395   1 SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDReTGIGKGFGYVLFKDKDSVDLALKLNGSKLRGRKLRVK 73
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
91-161 2.65e-21

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


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 83.49  E-value: 2.65e-21
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKVS 161
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKSKGFAFVEFESPEDAEKALEaLNGTELGGRPLKVS 72
RRM smart00360
RNA recognition motif;
90-160 1.51e-19

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 79.17  E-value: 1.51e-19
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140     90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKEtGKSKGFAFVEFESEEDAEKALEaLNGKELDGRPLKV 73
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
90-164 1.32e-18

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 76.68  E-value: 1.32e-18
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKVSPKR 164
Cdd:COG0724   3 KIYVGNLPYSVTEEDLRELFSEYGEVTSVKLITDREtGRSRGFGFVEMPDDEEAQAAIEaLNGAELMGRTLKVNEAR 79
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
91-159 9.25e-16

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


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 69.18  E-value: 9.25e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140    91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLK 159
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEaLNGKELGGRELK 70
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
91-162 1.16e-15

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


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 68.73  E-value: 1.16e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKVSP 162
Cdd:cd21608   2 LYVGNLSWDTTEDDLRDLFSEFGEVESAKVITDREtGRSRGFGFVTFSTAEAAEAAIDaLNGKELDGRSIVVNE 75
RRM_Nop6 cd12400
RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and ...
91-160 1.22e-15

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


Pssm-ID: 409834 [Multi-domain]  Cd Length: 74  Bit Score: 68.79  E-value: 1.22e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKV 160
Cdd:cd12400   3 LFVGNLPYDTTAEDLKEHFKKAGEPPSVRLLTDKkTGKSKGCAFVEFDNQKALQKALKLHHTSLGGRKINV 73
RRM1_NUCLs cd12450
RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ...
90-160 4.02e-15

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


Pssm-ID: 409884 [Multi-domain]  Cd Length: 78  Bit Score: 67.43  E-value: 4.02e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKV 160
Cdd:cd12450   1 TLFVGNLSWSATQDDLENFFSDCGEVVDVRIAMDRdDGRSKGFGHVEFASAESAQKALEKSGQDLGGREIRL 72
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
89-160 1.38e-14

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


Pssm-ID: 409832 [Multi-domain]  Cd Length: 77  Bit Score: 66.00  E-value: 1.38e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12398   1 RSVFVGNIPYDATEEQLKEIFSEVGPVVSFRLVTDReTGKPKGYGFCEFRDAETALSAVRnLNGYELNGRPLRV 74
RRM2_SREK1 cd12260
RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 ...
89-160 5.08e-14

RNA recognition motif 2 (RRM2) found 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: 409705 [Multi-domain]  Cd Length: 85  Bit Score: 65.02  E-value: 5.08e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKfGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKV 160
Cdd:cd12260   5 RTVYVGNLDPSTTADQLLEFFSQAGEVKYVRMAGDE-TQPTRYAFVEFAEQTSVINALKLNGKMFGGRPLKV 75
RRM2_NUCLs cd12451
RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This ...
90-162 7.29e-14

RNA recognition motif 2 (RRM2) found 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: 409885 [Multi-domain]  Cd Length: 79  Bit Score: 64.35  E-value: 7.29e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15238140  90 SVYVGNVDYAC----TPEEVQLHFQTCGTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVSP 162
Cdd:cd12451   1 TIFVKGFDASLgedtIRDELREHFGECGEVTNVRIPTDReTGELKGFAYIEFSTKEAKEKALELNGSDIAGGNLVVDE 78
RRM_DAZL_BOULE cd12412
RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and ...
91-162 1.52e-13

RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE; This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 409846 [Multi-domain]  Cd Length: 81  Bit Score: 63.40  E-value: 1.52e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQL-NESELHGRQLKVSP 162
Cdd:cd12412   5 IFVGGIDWDTTEEELREFFSKFGKVKDVKIIKDRAGVSKGYGFVTFETQEDAEKIQKWgANLVFKGKKLNVGP 77
RRM2_SART3 cd12392
RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells ...
87-161 9.88e-13

RNA recognition motif 2 (RRM2) found 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: 409826 [Multi-domain]  Cd Length: 81  Bit Score: 61.19  E-value: 9.88e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15238140  87 DARSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFV-EVEAVQEALQLNESELHGRQLKVS 161
Cdd:cd12392   1 EKNKLFVKGLPFSCTKEELEELFKQHGTVKDVRLVTYRNGKPKGLAYVEYEnEADASQAVLKTDGTEIKDHTISVA 76
RRM1_SART3 cd12391
RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells ...
90-161 1.15e-12

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


Pssm-ID: 409825 [Multi-domain]  Cd Length: 72  Bit Score: 61.09  E-value: 1.15e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVS 161
Cdd:cd12391   1 TVFVSNLDYSVPEDKIREIFSGCGEITDVRLVKNYKGKSKGYCYVEFKDEESAQKALKLDRQPVEGRPMFVS 72
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
91-163 2.14e-12

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


Pssm-ID: 409833 [Multi-domain]  Cd Length: 75  Bit Score: 60.23  E-value: 2.14e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEAL-QLNESELHGRQLKVSPK 163
Cdd:cd12399   1 LYVGNLPYSASEEQLKSLFGQFGAVFDVKLPMDReTKRPRGFGFVELQEEESAEKAIaKLDGTDFMGRTIRVNEA 75
RRM2_CID8_like cd12460
RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana CTC-interacting domain protein ...
85-165 2.49e-12

RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM2 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: 409893 [Multi-domain]  Cd Length: 82  Bit Score: 60.49  E-value: 2.49e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  85 EVDARSVYVGNVDYACTPEEVQLHFQT-CGTVNRVTILMDKFGQPKgFAYVEFVEVEAVQEALQLNESELHGRQLKVSPK 163
Cdd:cd12460   1 EMCARTIYCTNIDKKVTQDDVKAFFESlCGEVHRLRLLGDYVHSTR-IAFVEFVMAESAIAALNCSGALLGSLPIRVSPS 79

                ..
gi 15238140 164 RT 165
Cdd:cd12460  80 KT 81
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
91-161 2.65e-12

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


Pssm-ID: 409882 [Multi-domain]  Cd Length: 73  Bit Score: 60.11  E-value: 2.65e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMD-KFGQPKGFAYVEFVEVEAVQEALQLNESE-LHGRQLKVS 161
Cdd:cd12448   1 LFVGNLPFSATQDALYEAFSQHGSIVSVRLPTDrETGQPKGFGYVDFSTIDSAEAAIDALGGEyIDGRPIRLD 73
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
89-161 3.16e-12

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


Pssm-ID: 409739 [Multi-domain]  Cd Length: 78  Bit Score: 59.97  E-value: 3.16e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTI----LMDKFGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVS 161
Cdd:cd12298   1 REIRVRNLDFELDEEALRGIFEKFGEIESINIpkkqKNRKGRHNNGFAFVTFEDADSAESALQLNGTLLDNRKISVS 77
RRM_RBM7_like cd12336
RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This ...
89-161 3.40e-12

RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization.


Pssm-ID: 409773 [Multi-domain]  Cd Length: 75  Bit Score: 59.62  E-value: 3.40e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQL-NESELHGRQLKVS 161
Cdd:cd12336   2 RTLFVGNLDPRVTEEILYELFLQAGPLEGVKIPKDPNGKPKNFAFVTFKHEVSVPYAIQLlNGIRLFGREIRIK 75
RRM2_Nop12p_like cd12670
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 12 (Nop12p) and similar ...
90-161 4.42e-12

RNA recognition motif 2 (RRM2) found 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: 410071 [Multi-domain]  Cd Length: 77  Bit Score: 59.38  E-value: 4.42e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMD-KFGQPKGFAYVEFVEVEAVQEALQLNESE-LHGRQLKVS 161
Cdd:cd12670   1 CVFVGNLAFEAEEEGLWRYFGKCGAIESVRIVRDpKTNVGKGFAYVQFKDENAVEKALLLNEKPtMKGRKLRVS 74
RRM_ZCRB1 cd12393
RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ...
90-161 1.06e-11

RNA recognition motif (RRM) found 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: 409827 [Multi-domain]  Cd Length: 76  Bit Score: 58.45  E-value: 1.06e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFG-QPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKVS 161
Cdd:cd12393   3 TVYVSNLPFSLTNNDLHQIFSKYGKVVKVTILKDKETrKSKGVAFVLFLDRESAHNAVRaMNNKELFGRTLKCS 76
RRM1_2_CID8_like cd12225
RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting ...
89-165 2.91e-11

RNA recognition motif 1 and 2 (RRM1, RRM2) found 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: 409672 [Multi-domain]  Cd Length: 76  Bit Score: 57.47  E-value: 2.91e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKfgQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVSPKRT 165
Cdd:cd12225   1 RTIHVGGIDGSLSEDELADYFSNCGEVTQVRLCGDR--VHTRFAWVEFATDASALSALNLDGTTLGGHPLRVSPSKT 75
RRM1_PSRP2_like cd21609
RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 ...
91-161 2.98e-11

RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins; PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). The family also includes Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (AtCP31A). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. Members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410188 [Multi-domain]  Cd Length: 80  Bit Score: 57.43  E-value: 2.98e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKVS 161
Cdd:cd21609   2 LYVGNIPRNVTSEELAKIFEEAGTVEIAEVMYDRYtGRSRGFGFVTMGSVEDAKAAIEkLNGTEVGGREIKVN 74
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
43-162 6.28e-11

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


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 61.09  E-value: 6.28e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140    43 KRRLKEMEEEAAALREMQAKVEKEMGATQDpasmaanqEGKEEVDARSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILM 122
Cdd:TIGR01622  77 RRRGDSYRRRRDDRRSRREKPRARDGTPEP--------LTEDERDRRTVFVQQLAARARERDLYEFFSKVGKVRDVQIIK 148
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 15238140   123 DKF-GQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVSP 162
Cdd:TIGR01622 149 DRNsRRSKGVGYVEFYDVDSVQAALALTGQKLLGIPVIVQL 189
RRM1_HRB1_GBP2 cd21605
RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, ...
90-160 6.93e-11

RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410184 [Multi-domain]  Cd Length: 77  Bit Score: 56.15  E-value: 6.93e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKfGQPKGFAYVEFVEVEAVQEAL-QLNESELHGRQLKV 160
Cdd:cd21605   3 SIFVGNLPFDCTWEDLKDHFSQVGEVIRADIVTSR-GRHRGMGTVEFTNKEDVDRAIsKFDHTMFMGREIFV 73
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
79-212 7.11e-11

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


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 60.98  E-value: 7.11e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140    79 NQEGKEEVDARSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQlnesELHGRQL 158
Cdd:TIGR01628 276 QQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVT----EMHGRML 351
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15238140   159 KVSP-----------KRT--------NVPGMKQYHPGR-FNPSMG---YRFRRP--FVPPYfysPYGYGKAPRFRRPMR 212
Cdd:TIGR01628 352 GGKPlyvalaqrkeqRRAhlqdqfmqLQPRMRQLPMGSpMGGAMGqppYYGQGPqqQFNGQ---PLGWPRMSMMPTPMG 427
RRM1_RBM39_like cd12283
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar ...
90-160 1.12e-10

RNA recognition motif 1 (RRM1) found 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: 409725 [Multi-domain]  Cd Length: 73  Bit Score: 55.70  E-value: 1.12e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMD-KFGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKV 160
Cdd:cd12283   1 TVFVMQLSLKARERDLYEFFSKAGKVRDVRLIMDrNSRRSKGVAYVEFYDVESVPLALALTGQRLLGQPIMV 72
RRM_CSTF2_CSTF2T cd12671
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage ...
88-160 1.37e-10

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


Pssm-ID: 410072 [Multi-domain]  Cd Length: 85  Bit Score: 55.98  E-value: 1.37e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15238140  88 ARSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12671   6 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDReTGKPKGYGFCEYQDQETALSAMRnLNGYELNGRALRV 80
RRM_RBM11 cd12593
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 11 (RBM11); This subfamily ...
89-161 3.01e-10

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 11 (RBM11); This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization.


Pssm-ID: 410006 [Multi-domain]  Cd Length: 75  Bit Score: 54.42  E-value: 3.01e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15238140  89 RSVYVGNVDyACTPEEV--QLHFQTcGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKVS 161
Cdd:cd12593   2 RTVFVGNLH-SNVNEEIlyELFLQA-GPLTKVTIAKDKEGKPKSFGFVCFKHAESVPYAIAlLNGIRLYGRPIKLQ 75
RRM2_PHIP1 cd12272
RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana phragmoplastin interacting ...
90-161 3.49e-10

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


Pssm-ID: 409715 [Multi-domain]  Cd Length: 73  Bit Score: 54.33  E-value: 3.49e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVS 161
Cdd:cd12272   1 TVYIGNLAWDIDEDDLRELFAECCEITNVRLHTDKeTGEFKGYGHVEFADEESLDAALKLAGTKLCGRPIRVD 73
RRM_eIF4B cd12402
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and ...
92-160 6.96e-10

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


Pssm-ID: 409836 [Multi-domain]  Cd Length: 81  Bit Score: 53.76  E-value: 6.96e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  92 YVGNVDYACTPEEVQLHFQTCGTVNrVTILMD-KFGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKV 160
Cdd:cd12402   6 YLGNLPYDVTEDDIEDFFRGLNISS-VRLPREnGPGRLRGFGYVEFEDRESLIQALSLNEESLKNRRIRV 74
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
88-160 9.80e-10

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


Pssm-ID: 410198 [Multi-domain]  Cd Length: 78  Bit Score: 53.30  E-value: 9.80e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15238140  88 ARSVYVGNVDYACTPEEVQLHFQTCGTVNRV---TILMDKFGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd21619   1 SNTIYVGNIDMTINEDALEKIFSRYGQVESVrrpPIHTDKADRTTGFGFIKYTDAESAERAMQqADGILLGRRRLVV 77
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
92-162 1.27e-09

RNA recognition motif 2 (RRM2) found 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: 409726 [Multi-domain]  Cd Length: 78  Bit Score: 53.01  E-value: 1.27e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  92 YVGNVDYACTPEEVQLHFQTCGTVNRVTILMD-KFGQPKGFAYVEFVEVEAVQEAL-QLNESELHGRQLKVSP 162
Cdd:cd12284   2 YVGSLHFNITEDMLRGIFEPFGKIEFVQLQKDpETGRSKGYGFIQFRDAEDAKKALeQLNGFELAGRPMKVGH 74
RRM3_RBM28_like cd12415
RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
89-162 2.00e-09

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


Pssm-ID: 409849 [Multi-domain]  Cd Length: 83  Bit Score: 52.60  E-value: 2.00e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEALQLNESE-------LHGRQLKV 160
Cdd:cd12415   1 KTVFIRNLSFDTTEEDLKEFFSKFGEVKYARIVLDKdTGHSKGTAFVQFKTKESADKCIEAANDEsedgglvLDGRKLIV 80

                ..
gi 15238140 161 SP 162
Cdd:cd12415  81 SL 82
RRM2_Nop13p_fungi cd12397
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar ...
91-160 2.23e-09

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


Pssm-ID: 409831 [Multi-domain]  Cd Length: 76  Bit Score: 52.45  E-value: 2.23e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTilMDKF---GQPKGFAYVEFVEVEAVQEALQLNES-ELHGRQLKV 160
Cdd:cd12397   1 LFVGNLSFETTEEDLRKHFAPAGKIRKVR--MATFedsGKCKGFAFVDFKEIESATNAVKGPINhSLNGRDLRV 72
RRM_PPIE cd12347
RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This ...
91-162 2.61e-09

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


Pssm-ID: 409783 [Multi-domain]  Cd Length: 75  Bit Score: 51.84  E-value: 2.61e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMD-KFGQPKGFAYVEFVEVEAVQEAL-QLNESELHGRQLKVSP 162
Cdd:cd12347   1 LYVGGLAEEVDEKVLHAAFIPFGDIVDIQIPLDyETEKHRGFAFVEFEEAEDAAAAIdNMNESELFGRTIRVNL 74
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
91-160 3.16e-09

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


Pssm-ID: 409755 [Multi-domain]  Cd Length: 74  Bit Score: 51.96  E-value: 3.16e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12316   2 LFVRNLPFTATEDELRELFEAFGKISEVHIPLDKqTKRSKGFAFVLFVIPEDAVKAYQeLDGSIFQGRLLHV 73
RRM2_Hrp1p cd12330
RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 ...
91-160 4.07e-09

RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.


Pssm-ID: 409767 [Multi-domain]  Cd Length: 78  Bit Score: 51.56  E-value: 4.07e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKV 160
Cdd:cd12330   2 IFVGGLAPDVTEEEFKEYFEQFGTVVDAVVMLDHdTGRSRGFGFVTFDSESAVEKVLSKGFHELGGKKVEV 72
RRM3_I_PABPs cd12380
RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This ...
91-160 4.55e-09

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


Pssm-ID: 409814 [Multi-domain]  Cd Length: 80  Bit Score: 51.41  E-value: 4.55e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12380   4 VYVKNFGEDVDDDELKELFEKYGKITSAKVMKDDSGKSKGFGFVNFENHEAAQKAVEeLNGKELNGKKLYV 74
RRM2_MRD1 cd12566
RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 ...
91-162 7.76e-09

RNA recognition motif 2 (RRM2) found 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: 409982 [Multi-domain]  Cd Length: 79  Bit Score: 50.88  E-value: 7.76e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMD-KFGQPKGFAYVEFVEVE-AVQEALQLNESELHGRQLKVSP 162
Cdd:cd12566   5 LFLRNLPYSTKEDDLQKLFSKFGEVSEVHVPIDkKTKKSKGFAYVLFLDPEdAVQAYNELDGKVFQGRLIHILP 78
RRM_RBM7 cd12592
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 7 (RBM7); This subfamily ...
89-160 7.90e-09

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 7 (RBM7); This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus.


Pssm-ID: 410005 [Multi-domain]  Cd Length: 75  Bit Score: 50.60  E-value: 7.90e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12592   2 RTLFVGNLDTKVTEELLFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNlLNGIKLYGRPLKI 74
RRM_RBM25 cd12446
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 25 and similar proteins; ...
89-161 1.10e-08

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 25 and similar proteins; This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor.


Pssm-ID: 409880 [Multi-domain]  Cd Length: 83  Bit Score: 50.60  E-value: 1.10e-08
                        10        20        30        40        50        60        70
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gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKVS 161
Cdd:cd12446   1 TTVFVGNIPDDVSDDFIRQLLEKCGKVLSWKRVQDPSGKLKAFGFCEFEDPEGALRALRlLNGLELGGKKLLVK 74
RRM_SRSF10_SRSF12 cd12312
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and ...
90-160 1.19e-08

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins; This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 240758 [Multi-domain]  Cd Length: 84  Bit Score: 50.45  E-value: 1.19e-08
                        10        20        30        40        50        60        70
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gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEAL-QLNESELHGRQLKV 160
Cdd:cd12312   2 SLFVRNVADDTRPDDLRREFGRYGPIVDVYIPLDFYtRRPRGFAYIQFEDVRDAEDALyYLDRTRFLGREIEI 74
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
74-161 2.88e-08

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


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 53.00  E-value: 2.88e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140    74 ASMAANQEG--KEEVDARSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEAL-QLN 149
Cdd:TIGR01622 198 ARAATETSGhhPNSIPFHRLYVGNLHFNITEQDLRQIFEPFGEIEFVQLQKDPEtGRSKGYGFIQFRDAEQAKEALeKMN 277
                          90
                  ....*....|..
gi 15238140   150 ESELHGRQLKVS 161
Cdd:TIGR01622 278 GFELAGRPIKVG 289
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
93-160 2.90e-08

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


Pssm-ID: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 49.09  E-value: 2.90e-08
                        10        20        30        40        50        60
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gi 15238140  93 VGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12414   4 VRNLPFKCTEDDLKKLFSKFGKVLEVTIPKKPDGKLRGFAFVQFTNVADAAKAIKgMNGKKIKGRPVAV 72
RRM1_PHIP1 cd12271
RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting ...
91-160 4.10e-08

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


Pssm-ID: 409714 [Multi-domain]  Cd Length: 72  Bit Score: 48.86  E-value: 4.10e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILM-DKFGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKV 160
Cdd:cd12271   1 VYVGGIPYYSTEAEIRSYFSSCGEVRSVDLMRfPDSGNFRGIAFITFKTEEAAKRALALDGEMLGNRFLKV 71
RRM_NCBP2 cd12240
RNA recognition motif (RRM) found in nuclear cap-binding protein subunit 2 (CBP20) and similar ...
91-160 6.05e-08

RNA recognition motif (RRM) 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: 409686 [Multi-domain]  Cd Length: 78  Bit Score: 48.34  E-value: 6.05e-08
                        10        20        30        40        50        60        70
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gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12240   1 LYVGNLSFYTTEEQIYELFSKCGDIKRIIMGLDKFkKTPCGFCFVEYYSREDAENAVKyLNGTKLDDRIIRV 72
RRM1_2_CoAA_like cd12343
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator ...
91-160 6.94e-08

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator/modulator (CoAA) and similar proteins; This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region.


Pssm-ID: 409779 [Multi-domain]  Cd Length: 66  Bit Score: 47.99  E-value: 6.94e-08
                        10        20        30        40        50        60        70
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gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILmdkfgqpKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12343   2 IFVGNLPDAATSEELRALFEKYGKVTECDIV-------KNYAFVHMEKEEDAEDAIKaLNGYEFMGSRINV 65
RRM5_RBM19_like cd12318
RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar ...
90-161 7.64e-08

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


Pssm-ID: 409757 [Multi-domain]  Cd Length: 80  Bit Score: 47.99  E-value: 7.64e-08
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gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTIL----MDKFGQPKGFAYVEFVEVEAVQEAL-QLNESEL--HGRQLKVS 161
Cdd:cd12318   2 TLFVKNLNFKTTEEALKKHFEKCGPIRSVTIAkkkdPKGPLLSMGYGFVEFKSPEAAQKALkQLQGTVLdgHALELKIS 80
RRM1_hnRNPA_hnRNPD_like cd12325
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and ...
91-163 9.05e-08

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins; This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes 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. 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). 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. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is 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. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP 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 members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs.


Pssm-ID: 409763 [Multi-domain]  Cd Length: 72  Bit Score: 47.90  E-value: 9.05e-08
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gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQLNESELHGRQlkVSPK 163
Cdd:cd12325   1 LFVGGLSWETTEESLREYFSKYGEVVDCVVMKDPAtGRSRGFGFVTFKDPSSVDAVLAARPHTLDGRT--IDPK 72
RRM_hnRNPH_ESRPs_RBM12_like cd12254
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ...
91-160 1.21e-07

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


Pssm-ID: 409699 [Multi-domain]  Cd Length: 73  Bit Score: 47.55  E-value: 1.21e-07
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gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCG-TVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKV 160
Cdd:cd12254   2 VRLRGLPFSATEEDIRDFFSGLDiPPDGIHIVYDDDGRPTGEAYVEFASEEDAQRALRRHKGKMGGRYIEV 72
RRM_eIF4H cd12401
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4H (eIF-4H) and ...
91-160 1.31e-07

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


Pssm-ID: 409835 [Multi-domain]  Cd Length: 84  Bit Score: 47.67  E-value: 1.31e-07
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gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCgTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKV 160
Cdd:cd12401   8 AYVGNLPFNTVQGDLDAIFKDL-KVRSVRLVRDReTDKFKGFCYVEFEDLESLKEALEYDGALFEDRPLRV 77
RRM2_hnRNPM_like cd12386
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) ...
91-160 1.89e-07

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins; This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity.


Pssm-ID: 409820 [Multi-domain]  Cd Length: 74  Bit Score: 46.97  E-value: 1.89e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVE-VEAVQEALQLNESELHGRQLKV 160
Cdd:cd12386   1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIREDKDGKSRGMGVVQFEHpIEAVQAISMFNGQMLFDRPMRV 71
RRM4_RBM12_like cd12514
RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
91-161 2.05e-07

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


Pssm-ID: 409936 [Multi-domain]  Cd Length: 73  Bit Score: 47.02  E-value: 2.05e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNR-VTILMDKFGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVS 161
Cdd:cd12514   2 IRITNLPYDATPVDIQRFFEDHGVRPEdVHLLRNKKGRGNGEALVTFKSEGDAREVLKLNGKKLGKREAVVE 73
RRM1_hnRNPAB cd12757
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) ...
85-164 2.13e-07

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop.


Pssm-ID: 410151 [Multi-domain]  Cd Length: 80  Bit Score: 46.89  E-value: 2.13e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  85 EVDARSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMD-KFGQPKGFAYVEFVEVEAVQEALQLNESELHGRQlkVSPK 163
Cdd:cd12757   1 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDpNTGRSRGFGFILFKDAASVDKVLEQKEHRLDGRV--IDPK 78

                .
gi 15238140 164 R 164
Cdd:cd12757  79 K 79
RRM1_RBM34 cd12394
RNA recognition motif 1 (RRM1) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
89-160 2.42e-07

RNA recognition motif 1 (RRM1) found 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: 409828 [Multi-domain]  Cd Length: 91  Bit Score: 47.20  E-value: 2.42e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTV----------------NRVTILMDKFgQPKG---FAYVEFVEVEAVQEALQLN 149
Cdd:cd12394   1 RTVFVGNLPVTVKKKALKKLFKEFGKIesvrfrsvavanpklpKKVAVIKKKF-HPKRdsmNAYVVFKEEESAQKALKLN 79
                        90
                ....*....|.
gi 15238140 150 ESELHGRQLKV 160
Cdd:cd12394  80 GTEFEGHHIRV 90
RRM1_gar2 cd12447
RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This ...
90-160 2.57e-07

RNA recognition motif 1 (RRM1) found 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: 409881 [Multi-domain]  Cd Length: 76  Bit Score: 46.66  E-value: 2.57e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12447   1 TLFVGGLSWNVDDPWLKKEFEKYGGVISARVITDRGsGRSKGYGYVDFATPEAAQKALAaMSGKEIDGRQINV 73
RRM1_hnRNPR_like cd12249
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
91-162 2.61e-07

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


Pssm-ID: 409695 [Multi-domain]  Cd Length: 78  Bit Score: 46.81  E-value: 2.61e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQ-LNESELH-GRQLKVSP 162
Cdd:cd12249   4 VFVGKIPRDVFEDELVPLFEKCGKIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKtLNNYEIRpGKLLGVCI 77
RRM1_CID8_like cd12459
RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana CTC-interacting domain protein ...
89-165 3.33e-07

RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM1 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: 409892 [Multi-domain]  Cd Length: 80  Bit Score: 46.64  E-value: 3.33e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKfGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVSPKRT 165
Cdd:cd12459   3 RTVYVSDIDQQVTEEQLAALFSNCGQVVDCRICGDP-NSVLRFAFIEFTDEEGARAALSLSGTMLGFYPVRVLPSKT 78
RRM_TUT1 cd12279
RNA recognition motif (RRM) found in speckle targeted PIP5K1A-regulated poly(A) polymerase ...
89-163 4.08e-07

RNA recognition motif (RRM) found in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins; This subfamily corresponds to the RRM of Star-PAP, also termed RNA-binding motif protein 21 (RBM21), which is a ubiquitously expressed U6 snRNA-specific terminal uridylyltransferase (U6-TUTase) essential for cell proliferation. Although it belongs to the well-characterized poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both, the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes. Star-PAP predominantly localizes at nuclear speckles and catalyzes RNA-modifying nucleotidyl transferase reactions. It functions in mRNA biosynthesis and may be regulated by phosphoinositides. It binds to glutathione S-transferase (GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a nucleotide substrate and possesses PAP activity that is stimulated by PtdIns4,5P2. It contains an N-terminal C2H2-type zinc finger motif followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a split PAP domain linked by a proline-rich region, a PAP catalytic and core domain, a PAP-associated domain, an RS repeat, and a nuclear localization signal (NLS).


Pssm-ID: 409721 [Multi-domain]  Cd Length: 74  Bit Score: 45.87  E-value: 4.08e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTilMDKfgQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVSPK 163
Cdd:cd12279   3 RSVFVSGFKRGTSELELSDYFQAFGPVASVV--MDK--DKGVYAIVEMDSTETVEKVLSQPQHCLNGQRLRVKPR 73
RRM_Aly_REF_like cd12418
RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM ...
91-160 4.88e-07

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


Pssm-ID: 409852 [Multi-domain]  Cd Length: 75  Bit Score: 45.65  E-value: 4.88e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEAL-QLNESELHGRQLKV 160
Cdd:cd12418   3 VRVSNLHPDVTEEDLRELFGRVGPVKSVKINYDRSGRSTGTAYVVFERPEDAEKAIkQFDGVLLDGQPMKV 73
RRM2_PUF60 cd12371
RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
91-161 5.87e-07

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


Pssm-ID: 409806 [Multi-domain]  Cd Length: 77  Bit Score: 45.74  E-value: 5.87e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMD-KFGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKVS 161
Cdd:cd12371   3 IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDpETGKHKGYGFIEYENPQSAQDAIAsMNLFDLGGQYLRVG 75
RRM1_PUF60 cd12370
RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
91-160 6.49e-07

RNA recognition motif 1 (RRM1) found 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: 409805 [Multi-domain]  Cd Length: 76  Bit Score: 45.48  E-value: 6.49e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQP-KGFAYVEFVEVEAVQEAL-QLNESELHGRQLKV 160
Cdd:cd12370   3 VYVGSIYFELGEDTIRQAFAPFGPIKSIDMSWDPVTMKhKGFAFVEYEVPEAAQLALeQMNGVMLGGRNIKV 74
RRM1_Nop13p_fungi cd12396
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 13 (Nop13p) and similar ...
91-158 8.48e-07

RNA recognition motif 1 (RRM1) found 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: 409830 [Multi-domain]  Cd Length: 85  Bit Score: 45.52  E-value: 8.48e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  91 VYVGNVDYACTPEEVQLHFQ-------TCGTVNRVTILMDK-----FGQPKGFAYVEFVEVEAVQEALQLNESELHGRQL 158
Cdd:cd12396   1 VWIGNLSFTTTKEDLRQFFVdksgdriTEEQITRIHMPTSKakpkgKPQNKGFAYVDFSSLEATKAAIALSEKILNGRNL 80
RRM_CFIm68_CFIm59 cd12372
RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or ...
91-162 8.96e-07

RNA recognition motif (RRM) found in 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: 409807 [Multi-domain]  Cd Length: 76  Bit Score: 45.00  E-value: 8.96e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTIlmdKF------GQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKVSP 162
Cdd:cd12372   1 LYVGNLQWWTTDEDLEGACASFGVVDVKEI---KFfehkanGKSKGYAYVEFASPAAAAAVKEkLEKREFNGRPCVVTP 76
RRM_DAZL cd12672
RNA recognition motif (RRM) found in vertebrate deleted in azoospermia-like (DAZL) proteins; ...
90-162 9.27e-07

RNA recognition motif (RRM) found in vertebrate deleted in azoospermia-like (DAZL) proteins; This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 410073 [Multi-domain]  Cd Length: 82  Bit Score: 45.16  E-value: 9.27e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQLNESeLHGRQLKVSP 162
Cdd:cd12672   7 TVFVGGIDIRMDENEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYDDVDIQKIVESQIN-FHGKKLKLGP 78
RRM3_Nop4p cd12676
RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
89-162 1.07e-06

RNA recognition motif 3 (RRM3) found 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: 410077 [Multi-domain]  Cd Length: 107  Bit Score: 45.88  E-value: 1.07e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQ---------LNESE------ 152
Cdd:cd12676   2 RTLFVRNLPFDATEDELYSHFSQFGPLKYARVVKDPAtGRSKGTAFVKFKNKEDADNCLSaapeaqstsLLEKYsleqdi 81
                        90
                ....*....|....*....
gi 15238140 153 ---------LHGRQLKVSP 162
Cdd:cd12676  82 tddvsakftLDGRVLQVTP 100
RRM_CIRBP_RBM3 cd12449
RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding ...
89-160 1.14e-06

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


Pssm-ID: 409883 [Multi-domain]  Cd Length: 80  Bit Score: 45.16  E-value: 1.14e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12449   1 GKLFVGGLSFDTNEQSLEEVFSKYGQISEVVVVKDReTQRSRGFGFVTFENPDDAKDAMMaMNGKSLDGRQIRV 74
RRM1_SF3B4 cd12334
RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar ...
91-161 1.26e-06

RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar proteins; This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145.


Pssm-ID: 409771 [Multi-domain]  Cd Length: 74  Bit Score: 44.52  E-value: 1.26e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKVS 161
Cdd:cd12334   1 VYVGNLDEKVTEELLWELFIQAGPVVNVHMPKDRVtQQHQGYGFVEFLSEEDADYAIKiMNMIKLYGKPIRVN 73
RRM1_CoAA cd12608
RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator ...
91-160 1.31e-06

RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator/modulator (CoAA); This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs.


Pssm-ID: 410020 [Multi-domain]  Cd Length: 69  Bit Score: 44.41  E-value: 1.31e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILmdkfgqpKGFAYVEFVEVEAVQEAL-QLNESELHGRQLKV 160
Cdd:cd12608   3 IFVGNVDEDTSQEELSALFEPYGAVLSCAVM-------KQFAFVHMRGEAAADRAIrELNGRELHGRALVV 66
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
90-147 1.99e-06

RNA recognition motif (RRM) found 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: 409842 [Multi-domain]  Cd Length: 76  Bit Score: 44.04  E-value: 1.99e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQ 147
Cdd:cd12408   1 TIRVTNLSEDATEEDLRELFRPFGPISRVYLAKDKEtGQSKGFAFVTFETREDAERAIE 59
RRM3_NCL cd12405
RNA recognition motif 3 (RRM3) found in vertebrate nucleolin; This subfamily corresponds to ...
88-160 2.12e-06

RNA recognition motif 3 (RRM3) found in vertebrate nucleolin; This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is 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.


Pssm-ID: 409839 [Multi-domain]  Cd Length: 72  Bit Score: 44.09  E-value: 2.12e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15238140  88 ARSVYVGNVDYACTPEEVQLHFQTCGTVNrvtiLMDKFGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12405   1 SKTLVVNNLSYSATEESLQSVFEKATSIR----IPQNNGRPKGYAFVEFESVEDAKEALEsCNNTEIEGRSIRL 70
RRM1_PUB1 cd12614
RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated ...
91-160 2.49e-06

RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410026 [Multi-domain]  Cd Length: 74  Bit Score: 43.96  E-value: 2.49e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12614   1 LYVGNLDPRVTEDLLQEIFAVTGPVENCKIIPDKNSKGVNYGFVEYYDRRSAEIAIQtLNGRQIFGQEIKV 71
RRM3_RBM19 cd12567
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
91-162 3.11e-06

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409983 [Multi-domain]  Cd Length: 79  Bit Score: 43.92  E-value: 3.11e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFG-QPKGFAYVEFVEVE-AVQEALQLNESELHGRQLKVSP 162
Cdd:cd12567   5 LFVRNLPYTCTEEDLEKLFSKYGPLSEVHFPIDSLTkKPKGFAFVTYMIPEhAVKAYAELDGTVFQGRLLHLLP 78
RRM1_Mug28 cd21620
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe meiotically up-regulated ...
89-160 3.97e-06

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe meiotically up-regulated gene 28 protein (Mug28) and similar proteins; Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410199 [Multi-domain]  Cd Length: 84  Bit Score: 43.65  E-value: 3.97e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDK------FGQPKGFAYVEFVEVEAVQEAL-QLNESELHGRQLKV 160
Cdd:cd21620   2 RSLYVGNLPQTCQSEDLIILFEPYGNVCGAHIASRKkvkvswVKPSKLFAFVEFETKEAATTAIvLLNGITYMGCQLKV 80
RRM3_PUB1 cd12622
RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated ...
90-161 4.68e-06

RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. 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 RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410033 [Multi-domain]  Cd Length: 74  Bit Score: 43.21  E-value: 4.68e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVtilmdKFGQPKGFAYVEF-VEVEAVQEALQLNESELHGRQLKVS 161
Cdd:cd12622   2 TVYVGNLPPEVTQADLIPLFQNFGVIEEV-----RVQRDKGFGFVKYdTHEEAALAIQQLNGQPFLGRPIKCS 69
RRM2_NCL cd12404
RNA recognition motif 2 (RRM2) found in vertebrate nucleolin; This subfamily corresponds to ...
87-160 4.93e-06

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


Pssm-ID: 409838 [Multi-domain]  Cd Length: 77  Bit Score: 43.19  E-value: 4.93e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15238140  87 DARSVYVGNVDYACTPEEVQLHFQTCGTVNrvtILMDKFGQPKGFAYVEFVEVEAVQEALQLNE-SELHGRQLKV 160
Cdd:cd12404   2 DARTLFVKNLPYSTTQDELKEVFEDAVDIR---IPMGRDGRSKGIAYIEFKSEAEAEKALEEKQgTEVDGRSIVV 73
RRM1_hnRNPM_like cd12385
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) ...
91-160 4.96e-06

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins; This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity.


Pssm-ID: 409819 [Multi-domain]  Cd Length: 76  Bit Score: 43.17  E-value: 4.96e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15238140  91 VYVGNVDYACTPEEVQLHFQT-CGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12385   2 VFISNIPYDYKWQDLKDLFREkVGEVTYVELFKDENGKSRGCGIVEFKDLESVQKALEtMNRYELKGRKLVV 73
RRM4_I_PABPs cd12381
RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily ...
92-162 5.26e-06

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


Pssm-ID: 409815 [Multi-domain]  Cd Length: 79  Bit Score: 43.03  E-value: 5.26e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140  92 YVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQlnesELHGRQLKVSP 162
Cdd:cd12381   5 YVKNLDDTIDDEKLREEFSPFGTITSAKVMTDEGGRSKGFGFVCFSSPEEATKAVT----EMNGRIIGGKP 71
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
90-161 6.39e-06

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


Pssm-ID: 409847 [Multi-domain]  Cd Length: 79  Bit Score: 42.96  E-value: 6.39e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEAL-QLNESELHGRQLKVS 161
Cdd:cd12413   1 TLFVRNLPYDTTDEQLEELFSDVGPVKRCFVVKDKgKDKCRGFGYVTFALAEDAQRALeEVKGKKFGGRKIKVE 74
RRM_BOULE cd12673
RNA recognition motif (RRM) found in protein BOULE; This subgroup corresponds to the RRM of ...
90-164 7.50e-06

RNA recognition motif (RRM) found in protein BOULE; This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 410074 [Multi-domain]  Cd Length: 81  Bit Score: 42.95  E-value: 7.50e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQLNES-ELHGRQLKVSPKR 164
Cdd:cd12673   4 RIFVGGIDFKTNENDLRKFFAQYGSVKEVKIVNDRAGVSKGYGFITFETQEDAQKILQEAEKlNYKDKKLNIGPAI 79
RRM2_hnRNPM cd12659
RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein M ...
90-160 9.80e-06

RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M); This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif).


Pssm-ID: 410060 [Multi-domain]  Cd Length: 76  Bit Score: 42.34  E-value: 9.80e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEF-VEVEAVQEALQLNESELHGRQLKV 160
Cdd:cd12659   2 TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFeQPIEAVQAISMFNGQLLFDRPMHV 73
RRM_SRSF2_SRSF8 cd12311
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and ...
93-160 1.08e-05

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins; This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain.


Pssm-ID: 409751 [Multi-domain]  Cd Length: 73  Bit Score: 42.26  E-value: 1.08e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  93 VGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEAL-QLNESELHGRQLKV 160
Cdd:cd12311   3 VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYtRESRGFAFVRFYDKRDAEDAIdAMDGAELDGRELRV 72
RRM_FET cd12280
RNA recognition motif (RRM) found in the FET family of RNA-binding proteins; This subfamily ...
91-161 1.35e-05

RNA recognition motif (RRM) found in the FET family of RNA-binding proteins; This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15.


Pssm-ID: 409722 [Multi-domain]  Cd Length: 82  Bit Score: 42.01  E-value: 1.35e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNR--------VTILMDK-FGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12280   1 IFVSGLPPDVTIDELADLFGQIGIIKRykdtwppkIKIYTDKeTGKPKGEATLTYEDPSAAKAAIEwFNGKEFRGNKIKV 80

                .
gi 15238140 161 S 161
Cdd:cd12280  81 S 81
RRM2_CELF3_4_5_6 cd12635
RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, ...
89-157 1.37e-05

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


Pssm-ID: 410043 [Multi-domain]  Cd Length: 81  Bit Score: 42.01  E-value: 1.37e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQlnesELHGRQ 157
Cdd:cd12635   2 RKLFVGMLGKQQSEDDVRRLFEPFGSIEECTILRGPDGNSKGCAFVKFSSHAEAQAAIN----ALHGSQ 66
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
91-164 1.50e-05

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


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 41.90  E-value: 1.50e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFG----QPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKVSPKR 164
Cdd:cd12355   2 LWIGNLDPRLTEYHLLKLLSKYGKIKKFDFLFHKTGplkgQPRGYCFVTFETKEEAEKAIEcLNGKLALGKKLVVRWAH 80
RRM1_hnRPDL cd12758
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP ...
91-164 1.80e-05

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which 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. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 410152 [Multi-domain]  Cd Length: 76  Bit Score: 41.50  E-value: 1.80e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQLNESELHGRQlkVSPKR 164
Cdd:cd12758   2 MFIGGLSWDTSKKDLTEYLSRFGEVVDCTIKTDPVtGRSRGFGFVLFKDAASVDKVLELKEHKLDGKL--IDPKR 74
RRM6_RBM19_RRM5_MRD1 cd12320
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA ...
93-162 2.25e-05

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 (RRM5) found 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: 409759 [Multi-domain]  Cd Length: 76  Bit Score: 41.45  E-value: 2.25e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140  93 VGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKVSP 162
Cdd:cd12320   5 VKNVPFEATRKEIRELFSPFGQLKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEaLKSTHLYGRHLVLEY 75
RRM_THOC4 cd12680
RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This ...
91-161 2.75e-05

RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes.


Pssm-ID: 410081 [Multi-domain]  Cd Length: 75  Bit Score: 41.06  E-value: 2.75e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVE-VEAVQEALQLNESELHGRQLKVS 161
Cdd:cd12680   3 LLVSNLDFGVSDADIKELFAEFGTLKKAAVHYDRSGRSLGTAEVVFERrADALKAMKQYNGVPLDGRPMKIQ 74
RRM_SRSF12 cd12560
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 12 (SRSF12) and ...
90-160 3.18e-05

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins; This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 409976 [Multi-domain]  Cd Length: 84  Bit Score: 41.14  E-value: 3.18e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQ-PKGFAYVEFVEVEAVQEAL-QLNESELHGRQLKV 160
Cdd:cd12560   2 SLFVRNVADATRPEDLRREFGRYGPIVDVYIPLDFYNRrPRGFAYIQFEDVRDAEDALyNLNRKWVCGRQIEI 74
RRM1_Nop4p cd12674
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
89-160 3.22e-05

RNA recognition motif 1 (RRM1) found 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: 410075 [Multi-domain]  Cd Length: 80  Bit Score: 40.91  E-value: 3.22e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMD-KFGQPKGFAYVEFVEVEAVQEAL-QLNESELHGRQLKV 160
Cdd:cd12674   1 TTLFVRNLPFDVTLESLTDFFSDIGPVKHAVVVTDpETKKSRGYGFVSFSTHDDAEEALaKLKNRKLSGHILKL 74
RRM1_TatSF1_like cd12281
RNA recognition motif 1 (RRM1) found in HIV Tat-specific factor 1 (Tat-SF1) and similar ...
90-162 3.27e-05

RNA recognition motif 1 (RRM1) found in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins; This subfamily corresponds to the RRM1 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well.


Pssm-ID: 409723 [Multi-domain]  Cd Length: 92  Bit Score: 41.38  E-value: 3.27e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVN--------RVTILMDKFGQPKGFAYVEFVEVEAVQEALQ-LNESE-LHGRQLK 159
Cdd:cd12281   3 NVYVSGLPLDITVEEFVELFSKCGIIMedpetgepKIKLYRDENGNLKGDALCCYLKEESVELALQlLDGTEiGRGYKIH 82

                ...
gi 15238140 160 VSP 162
Cdd:cd12281  83 VER 85
RRM2_MYEF2 cd12660
RNA recognition motif 2 (RRM2) found in vertebrate myelin expression factor 2 (MEF-2); This ...
90-160 3.35e-05

RNA recognition motif 2 (RRM2) found in vertebrate myelin expression factor 2 (MEF-2); This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity.


Pssm-ID: 410061 [Multi-domain]  Cd Length: 76  Bit Score: 40.77  E-value: 3.35e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVE-VEAVQEALQLNESELHGRQLKV 160
Cdd:cd12660   2 TIFVANLDFKVGWKKLKEVFSMAGTVKRADIKEDKDGKSRGMGTVTFEQaIEAVQAISMFNGQFLFDRPMHV 73
RRM1_RRT5 cd12409
RNA recognition motif 1 (RRM1) found in yeast regulator of rDNA transcription protein 5 (RRT5) ...
90-162 3.48e-05

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


Pssm-ID: 409843 [Multi-domain]  Cd Length: 84  Bit Score: 41.11  E-value: 3.48e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  90 SVYVGNVDYACTPEEV-QLHFQT--------CGTVNRVTilmDKFGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLK 159
Cdd:cd12409   1 RVYISNLSYSTTEEELeELLKDYkpvsvlipSYTVRGFR---SRKHRPLGIAYAEFSSVEEAEKVVKdLNGKVFKGRKLF 77

                ...
gi 15238140 160 VSP 162
Cdd:cd12409  78 VKL 80
RRM1_hnRNPA1 cd12761
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) ...
89-164 4.53e-05

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains 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. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions.


Pssm-ID: 410154 [Multi-domain]  Cd Length: 81  Bit Score: 40.81  E-value: 4.53e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQ-PKGFAYVEFVEVEAVQEALQLNESELHGRQlkVSPKR 164
Cdd:cd12761   3 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKrSRGFGFVTYATVEEVDAAMNARPHKVDGRV--VEPKR 77
RRM1_hnRNPD cd12756
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) ...
91-164 4.57e-05

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically.


Pssm-ID: 410150 [Multi-domain]  Cd Length: 74  Bit Score: 40.37  E-value: 4.57e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQLNESELHGRQlkVSPKR 164
Cdd:cd12756   1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPItGRSRGFGFVLFKESESVDKVMDQKEHKLNGKV--IDPKR 73
RRM_snRNP70 cd12236
RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and ...
89-178 5.37e-05

RNA recognition motif (RRM) found 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: 409682 [Multi-domain]  Cd Length: 91  Bit Score: 40.68  E-value: 5.37e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQL-NESELHGRQLKVSPKRTN 166
Cdd:cd12236   2 KTLFVARLSYDTTESKLRREFEKYGPIKRVRLVRDKKtGKSRGYAFIEFEHERDMKAAYKHaDGKKIDGRRVLVDVERGR 81
                        90
                ....*....|..
gi 15238140 167 VpgMKQYHPGRF 178
Cdd:cd12236  82 T--VKGWKPRRL 91
RRM1_DAZAP1 cd12574
RNA recognition motif 1 (RRM1) found in Deleted in azoospermia-associated protein 1 (DAZAP1) ...
91-172 5.62e-05

RNA recognition motif 1 (RRM1) found in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins; This subfamily corresponds to the RRM1 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated form is predominantly nuclear and the nonacetylated form is in cytoplasm. It also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain.


Pssm-ID: 409988 [Multi-domain]  Cd Length: 82  Bit Score: 40.40  E-value: 5.62e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQLNESELHGRQlkVSPKRTNVPG 169
Cdd:cd12574   2 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTtNQSRGFGFVKFKDPNCVGTVLASRPHNLDGRN--IDPKPCTPRG 79

                ...
gi 15238140 170 MKQ 172
Cdd:cd12574  80 MQP 82
RRM1_U2AF65 cd12230
RNA recognition motif 1 (RRM1) found in U2 large nuclear ribonucleoprotein auxiliary factor ...
88-161 6.76e-05

RNA recognition motif 1 (RRM1) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; The subfamily corresponds to the RRM1 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: 409677 [Multi-domain]  Cd Length: 82  Bit Score: 40.22  E-value: 6.76e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  88 ARSVYVGNVDYACTPEEV------QLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVS 161
Cdd:cd12230   1 ARRLYVGNIPPGITEEELmdffnqAMRAAGLTQAPGNPVLAVQINPDKNFAFVEFRSVEETTAALALDGIIFKGQPLKIR 80
RRM3_HRB1_GBP2 cd21607
RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, ...
91-161 7.04e-05

RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the third RRM motif.


Pssm-ID: 410186 [Multi-domain]  Cd Length: 79  Bit Score: 40.00  E-value: 7.04e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKVS 161
Cdd:cd21607   5 IYCSNLPLSTAESDLYDLFETIGKVNNAELKYDETGDPTGSAVVEYENLDDADVCISkLNNYNYGGCDLKIS 76
RRM2_4_MRN1 cd12262
RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar ...
89-166 8.32e-05

RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409706 [Multi-domain]  Cd Length: 78  Bit Score: 39.69  E-value: 8.32e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDkfgqpKGFAYVEFVEVEAVQEALQlnesELHGRQLKVSPKRTN 166
Cdd:cd12262   4 RNVYVGNLDDSLTEEEIRGILEKYGEIESIKILKE-----KNCAFVNYLNIANAIKAVQ----ELPIKNPKFKKVRIN 72
RRM1_TIA1_like cd12352
RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and ...
92-160 9.71e-05

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


Pssm-ID: 409788 [Multi-domain]  Cd Length: 73  Bit Score: 39.31  E-value: 9.71e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  92 YVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKfGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12352   2 YVGNLDRQVTEDLILQLFSQIGPCKSCKMITEH-GGNDPYCFVEFYEHNHAAAALQaMNGRKILGKEVKV 70
RRM2_hnRNPA_like cd12328
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily; ...
91-161 1.28e-04

RNA recognition motif 2 (RRM2) found 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: 409766 [Multi-domain]  Cd Length: 73  Bit Score: 39.17  E-value: 1.28e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVS 161
Cdd:cd12328   2 LFVGGLKEDVEEEDLREYFSQFGKVESVEIVTDKeTGKKRGFAFVTFDDHDSVDKIVLQKYHTINGHRCEVK 73
RRM1_hnRNPH_GRSF1_like cd12503
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H ...
98-160 1.28e-04

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


Pssm-ID: 409926 [Multi-domain]  Cd Length: 77  Bit Score: 39.29  E-value: 1.28e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15238140  98 YACTPEEVQLHFQTC---GTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKV 160
Cdd:cd12503   9 WSATAEDVLNFFTDCrikGGENGIHFTYTREGRPSGEAFIELESEEDVEKALEKHNEHMGHRYIEV 74
RRM1_2_CELF1-6_like cd12361
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding ...
92-157 1.36e-04

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


Pssm-ID: 409796 [Multi-domain]  Cd Length: 77  Bit Score: 39.14  E-value: 1.36e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15238140  92 YVGNVDYACTPEEVQLHFQTCGTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEALQlnesELHGRQ 157
Cdd:cd12361   3 FVGMIPKTASEEDVRPLFEQFGNIEEVQILRDKqTGQSKGCAFVTFSTREEALRAIE----ALHNKK 65
RRM_SNP1_like cd21615
RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ...
89-165 1.39e-04

RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ribonucleoprotein SNP1 and similar proteins; SNP1, also called U1 snRNP protein SNP1, or U1 small nuclear ribonucleoprotein 70 kDa homolog, or U1 70K, or U1 snRNP 70 kDa homolog, interacts with mRNA and is involved in nuclear mRNA splicing. It is a component of the spliceosome, where it is associated with snRNP U1 by binding stem loop I of U1 snRNA. Members in this family contain an N-terminal U1snRNP70 domain and an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410194 [Multi-domain]  Cd Length: 118  Bit Score: 39.99  E-value: 1.39e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEALQlnesELHGRQLKVSPKRT 165
Cdd:cd21615  19 KTLFVGRLDYSLTELELQKKFSKFGEIEKIRIVRDKeTGKSRGYAFIVFKSESDAKNAFK----EGNGLRGLKINDRT 92
RRM2_PTBP1_hnRNPL_like cd12422
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
91-158 1.60e-04

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins; This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs.


Pssm-ID: 409856 [Multi-domain]  Cd Length: 85  Bit Score: 39.09  E-value: 1.60e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTIlmdkFGQPKGF-AYVEFVEVEAVQEALQLneseLHGRQL 158
Cdd:cd12422   4 VTVTNLLYPVTVDVLHQVFSPYGAVEKIVI----FEKGTGVqALVQFDSVESAEAAKKA----LNGRNI 64
RRM_SRSF3_like cd12373
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and ...
91-160 1.75e-04

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


Pssm-ID: 409808 [Multi-domain]  Cd Length: 73  Bit Score: 38.77  E-value: 1.75e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMdkfgQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12373   2 VYVGNLGPRVTKRELEDAFEKYGPLRNVWVAR----NPPGFAFVEFEDPRDAEDAVRaLDGRRICGSRVRV 68
RRM2_Bruno_like cd12636
RNA recognition motif 2 (RRM2) found in Drosophila melanogaster Bruno protein and similar ...
89-136 1.88e-04

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


Pssm-ID: 410044 [Multi-domain]  Cd Length: 81  Bit Score: 39.09  E-value: 1.88e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEF 136
Cdd:cd12636   2 RKLFVGMLSKKCNESDVRIMFSPYGSIEECTVLRDQNGKSRGCAFVTF 49
RRM3_TIA1_like cd12354
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...
90-161 2.05e-04

RNA recognition motif 2 (RRM2) found 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: 409790 [Multi-domain]  Cd Length: 71  Bit Score: 38.42  E-value: 2.05e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDkfgqpKGFAYVEFVEVE-AVQEALQLNESELHGRQLKVS 161
Cdd:cd12354   2 TVYVGNITKGLTEALLQQTFSPFGQILEVRVFPD-----KGYAFIRFDSHEaATHAIVSVNGTIINGQAVKCS 69
RRM_RNPS1 cd12365
RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and ...
91-161 2.19e-04

RNA recognition motif (RRM) found 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: 409800 [Multi-domain]  Cd Length: 73  Bit Score: 38.30  E-value: 2.19e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKVS 161
Cdd:cd12365   1 LHVGKLTRNVTKDHLKEIFSVYGTVKNVDLPIDRePNLPRGYAYVEFESPEDAEKAIKhMDGGQIDGQEVTVE 73
sex-lethal TIGR01659
sex-lethal family splicing factor; This model describes the sex-lethal family of splicing ...
82-146 2.46e-04

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


Pssm-ID: 273740 [Multi-domain]  Cd Length: 346  Bit Score: 41.16  E-value: 2.46e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15238140    82 GKEEVDARSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEAL 146
Cdd:TIGR01659 187 GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLtGTPRGVAFVRFNKREEAQEAI 252
RRM1_LARP7 cd12290
RNA recognition motif 1 (RRM1) found in La-related protein 7 (LARP7) and similar proteins; ...
91-166 3.00e-04

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


Pssm-ID: 409732 [Multi-domain]  Cd Length: 79  Bit Score: 38.08  E-value: 3.00e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTIlmDKF---GQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKVSPKRTN 166
Cdd:cd12290   2 VYVELLPKNATHEWIEAVFSKYGEVVYVSI--PRYkstGDPKGFAFIEFETSESAQKAVKhFNSPPEARRKPGPFPKTVA 79
RRM_NOL8 cd12226
RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This ...
91-164 3.33e-04

RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells.


Pssm-ID: 409673 [Multi-domain]  Cd Length: 77  Bit Score: 37.94  E-value: 3.33e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEF-VEVEAVQEAL-QLNESELHGRQLKVSPKR 164
Cdd:cd12226   2 LFVGGLSPSITEDDLERRFSRFGTVSDVEIIRKKDAPDRGFAYIDLrTSEAALQKCLsTLNGVKWKGSRLKIQLAK 77
RRM2_Nop4p cd12675
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
102-160 3.38e-04

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM2 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: 410076 [Multi-domain]  Cd Length: 83  Bit Score: 38.23  E-value: 3.38e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140 102 PEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12675  15 PVHLKKLFGRYGKVVEATIPRKKGGKLSGFAFVTMKGRKNAEEALEsVNGLEIDGRPVAV 74
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
91-184 3.43e-04

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 39.64  E-value: 3.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140   91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEAL-QLNESELHGRQLKVSP--KRTN 166
Cdd:PLN03134  37 LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDReTGRSRGFGFVNFNDEGAATAAIsEMDGKELNGRHIRVNPanDRPS 116
                         90
                 ....*....|....*...
gi 15238140  167 VPGMKQYHPGRFNPSMGY 184
Cdd:PLN03134 117 APRAYGGGGGYSGGGGGY 134
RRM2_HRB1_GBP2 cd21606
RNA recognition motif 2 (RRM2) found in Saccharomyces cerevisiae protein HRB1, ...
91-160 3.59e-04

RNA recognition motif 2 (RRM2) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410185 [Multi-domain]  Cd Length: 75  Bit Score: 38.11  E-value: 3.59e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEAL-QLNESELHGRQLKV 160
Cdd:cd21606   4 VFIANLPYSINWQALKDMFKECGDVLRADVELDYNGRSRGFGTVIYATEEEMHRAIdTFNGYELEGRVLEV 74
RRM_TRA2 cd12363
RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and ...
101-160 4.56e-04

RNA recognition motif (RRM) found 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: 409798 [Multi-domain]  Cd Length: 80  Bit Score: 37.59  E-value: 4.56e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15238140 101 TPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEA-LQLNESELHGRQLKV 160
Cdd:cd12363  14 TERDLREVFSRYGPIEKVQVVYDQQtGRSRGFGFVYFESVEDAKEAkERLNGQEIDGRRIRV 75
RRM1_NCL cd12403
RNA recognition motif 1 (RRM1) found in vertebrate nucleolin; This subfamily corresponds to ...
90-160 4.94e-04

RNA recognition motif 1 (RRM1) found in vertebrate nucleolin; This subfamily corresponds to the RRM1 of ubiquitously expressed protein nucleolin, also termed protein C23. Nucleolin is 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. RRM1, together with RRM2, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop.


Pssm-ID: 409837 [Multi-domain]  Cd Length: 75  Bit Score: 37.40  E-value: 4.94e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKV 160
Cdd:cd12403   2 SLFVGNLNSNKSFEELKTAISEFFAKKDLAVVDVRIGSSKKFGYVDFESAEDLEKALELNGKKVLGNEIKL 72
RRM1_RBM23 cd12537
RNA recognition motif 1 (RRM1) found in vertebrate probable RNA-binding protein 23 (RBM23); ...
88-155 5.28e-04

RNA recognition motif 1 (RRM1) found in vertebrate probable RNA-binding protein 23 (RBM23); This subgroup corresponds to the RRM1 of RBM23, also termed RNA-binding region-containing protein 4, or splicing factor SF2, which may function as a pre-mRNA splicing factor. It shows high sequence homology to RNA-binding protein 39 (RBM39 or 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). In contrast to RBM39, RBM23 contains only two RRMs.


Pssm-ID: 409953 [Multi-domain]  Cd Length: 85  Bit Score: 37.68  E-value: 5.28e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15238140  88 ARSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQ-PKGFAYVEFVEVEAVQEALQLNESELHG 155
Cdd:cd12537   1 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRrSKGIAYVEFCEIQSVPLAIGLTGQRLLG 69
RRM1_SECp43_like cd12344
RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and ...
90-147 6.08e-04

RNA recognition motif 1 (RRM1) found 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: 409780 [Multi-domain]  Cd Length: 82  Bit Score: 37.28  E-value: 6.08e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCG-TVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQ 147
Cdd:cd12344   1 TLWMGDLEPWMDEAYISSCFAKTGeEVVSVKIIRNKQtGKSAGYCFVEFATQEAAEQALE 60
RRM2_SXL cd12651
RNA recognition motif 2 (RRM2) found in Drosophila sex-lethal (SXL) and similar proteins; This ...
90-163 6.22e-04

RNA recognition motif 2 (RRM2) found 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: 410054 [Multi-domain]  Cd Length: 81  Bit Score: 37.57  E-value: 6.22e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKVSPK 163
Cdd:cd12651   4 NLYVTNLPRTITEDELDTIFGAYGNIVQKNLLRDKLtGRPRGVAFVRYDKREEAQAAISaLNGTIPEGGTQPLSVR 79
half-pint TIGR01645
poly-U binding splicing factor, half-pint family; The proteins represented by this model ...
91-172 7.21e-04

poly-U binding splicing factor, half-pint family; The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.


Pssm-ID: 130706 [Multi-domain]  Cd Length: 612  Bit Score: 40.05  E-value: 7.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140    91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEAL-QLNESELHGRQLKVSpKRTNVP 168
Cdd:TIGR01645 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPAtGKHKGFAFVEYEVPEAAQLALeQMNGQMLGGRNIKVG-RPSNMP 188

                  ....
gi 15238140   169 GMKQ 172
Cdd:TIGR01645 189 QAQP 192
RRM2_DAZAP1 cd12327
RNA recognition motif 2 (RRM2) found in Deleted in azoospermia-associated protein 1 (DAZAP1) ...
91-160 7.71e-04

RNA recognition motif 2 (RRM2) found in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins; This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain.


Pssm-ID: 409765 [Multi-domain]  Cd Length: 80  Bit Score: 37.10  E-value: 7.71e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQ-PKGFAYVEFVEVEAVQEALQLNESELHGRQLKV 160
Cdd:cd12327   5 VFVGGIPHNCGETELRDYFKRYGVVTEVVMMYDAEKQrSRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEV 75
RRM1_La cd12291
RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily ...
90-161 9.75e-04

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: 409733 [Multi-domain]  Cd Length: 73  Bit Score: 36.80  E-value: 9.75e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRvtILMDKFGQPKGF---AYVEFVEVEAVQEALQLNESELHGRQLKVS 161
Cdd:cd12291   1 TVYVKGFPLDATLDDIQEFFEKKGKVEN--VRMRRDLDSKEFkgsVFVEFKTEEEAKKFLEKEKLKYKGKELTIM 73
RRM_EWS cd12533
RNA recognition motif (RRM) found in vertebrate Ewing Sarcoma Protein (EWS); This subgroup ...
90-161 1.03e-03

RNA recognition motif (RRM) found in vertebrate Ewing Sarcoma Protein (EWS); This subgroup corresponds to the RRM of EWS, also termed Ewing sarcoma breakpoint region 1 protein, a member 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 multifunctional protein and may play roles in transcription and RNA processing. EWS is involved in transcriptional regulation by interacting with the preinitiation complex TFIID and the RNA polymerase II (RNAPII) complexes. It is also associated with splicing factors, such as the U1 snRNP protein U1C, suggesting its implication in pre-mRNA splicing. Additionally, EWS has been shown to regulate DNA damage-induced alternative splicing (AS). Like other members in the FET family, EWS contains an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. EWS specifically binds to poly G and poly U RNA. It also binds to the proximal-element DNA of the macrophage-specific promoter of the CSF-1 receptor gene.


Pssm-ID: 409950 [Multi-domain]  Cd Length: 84  Bit Score: 36.74  E-value: 1.03e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTV--NR------VTILMDK-FGQPKGFAYVEFVEVEAVQEALQL-NESELHGRQLK 159
Cdd:cd12533   2 TIYVQGLNENVTLEELADFFKHCGVVkiNKrtgqpmINIYTDKeTGKPKGDATVSYEDPPAAKAAVEWfDGKDFQGNKLK 81

                ..
gi 15238140 160 VS 161
Cdd:cd12533  82 VS 83
RRM_SLIRP cd12242
RNA recognition motif (RRM) found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and ...
91-160 1.07e-03

RNA recognition motif (RRM) 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: 409688 [Multi-domain]  Cd Length: 73  Bit Score: 36.56  E-value: 1.07e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKV 160
Cdd:cd12242   2 LFVSNLPWTTGSSELKEYFSQFGKVKRCNLPFDKeTGFHKGFGFVSFENEDGLRNALQKQKHIFEGNKVSV 72
RRM1_RRM2_RBM5_like cd12313
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar ...
95-161 1.17e-03

RNA recognition motif 1 (RRM1) and 2 (RRM2) found 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: 409752 [Multi-domain]  Cd Length: 85  Bit Score: 36.86  E-value: 1.17e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15238140  95 NVDYACTPEEVQLHFQ--TCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQLNES-----ELHGRQLKVS 161
Cdd:cd12313   9 GLDVLTTEEDILSALQahADLPIKDVRLIRDKLtGTSRGFAFVEFSSLEDATQVMDALQNllppfKIDGRVVSVS 83
RRM2_CoAA cd12609
RNA recognition motif 2 (RRM2) found in vertebrate RRM-containing coactivator activator ...
91-160 1.24e-03

RNA recognition motif 2 (RRM2) found in vertebrate RRM-containing coactivator activator/modulator (CoAA); This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs.


Pssm-ID: 410021 [Multi-domain]  Cd Length: 68  Bit Score: 36.37  E-value: 1.24e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILmdkfgqpKGFAYVEFV-EVEAVQEALQLNESELHGRQLKV 160
Cdd:cd12609   3 IFVGNVSATCTSDELRGLFEEFGRVVECDKV-------KDYAFVHMErEEEALAAIEALNGKEVKGRRINV 66
RRM1_Hu_like cd12375
RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), ...
101-161 1.38e-03

RNA recognition motif 1 (RRM1) found 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: 409810 [Multi-domain]  Cd Length: 76  Bit Score: 36.23  E-value: 1.38e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140 101 TPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKVS 161
Cdd:cd12375  12 TQEELRSLFGAIGPIESCKLVRDKItGQSLGYGFVNYRDPNDARKAINtLNGLDLENKRLKVS 74
hnRNP-L_PTB TIGR01649
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
113-189 1.39e-03

hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).


Pssm-ID: 273733 [Multi-domain]  Cd Length: 481  Bit Score: 39.03  E-value: 1.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140   113 GTVNRVTILMDKfgqpKGFAYVEFVEVEAVQEAL-QLNESELHGRQLKVSP-KRTNVPGMKQYHPGR-------FNPSMG 183
Cdd:TIGR01649 301 GNVERVKFMKNK----KETALIEMADPYQAQLALtHLNGVKLFGKPLRVCPsKQQNVQPPREGQLDDgltsykdYSSSRN 376

                  ....*.
gi 15238140   184 YRFRRP 189
Cdd:TIGR01649 377 HRFKKP 382
RRM1_hnRNPA3 cd12763
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) ...
89-164 1.40e-03

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains 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: 410156 [Multi-domain]  Cd Length: 81  Bit Score: 36.57  E-value: 1.40e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMD-KFGQPKGFAYVEFVEVEAVQEALQLNESELHGRQlkVSPKR 164
Cdd:cd12763   3 RKLFIGGLSFETTDDSLREHFEQWGTLTDCVVMRDpQTKRSRGFGFVTYSCVEEVDAAMSARPHKVDGRV--VEPKR 77
RRM1_RBM39 cd12536
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39); This ...
88-155 1.47e-03

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39); This subgroup corresponds to the RRM1 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor 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. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs.


Pssm-ID: 409952 [Multi-domain]  Cd Length: 83  Bit Score: 36.57  E-value: 1.47e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15238140  88 ARSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQ-PKGFAYVEFVEVEAVQEALQLNESELHG 155
Cdd:cd12536   1 ARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRrSKGIAYVEFVDVSSVPLAIGLTGQRVLG 69
RRM1_MEI2_like cd12524
RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to ...
89-160 1.61e-03

RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409944 [Multi-domain]  Cd Length: 77  Bit Score: 36.10  E-value: 1.61e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRvtiLMDKFGQpKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12524   2 RTLFVRNINSSVEDEELRALFEQFGEIRT---LYTACKH-RGFIMVSYYDIRAAQSAKRaLQGTELGGRKLDI 70
RRM_CFIm68 cd12643
RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or ...
90-162 1.62e-03

RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins; This subgroup corresponds to the RRM of CFIm68. 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. The family includes CFIm68, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF6), or cleavage and polyadenylation specificity factor 68 kDa subunit (CPSF68), or protein HPBRII-4/7. CFIm68 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. The N-terminal RRM of CFIm68 mediates the interaction with CFIm25. It also serves to enhance RNA binding and facilitate RNA looping.


Pssm-ID: 410048 [Multi-domain]  Cd Length: 77  Bit Score: 36.25  E-value: 1.62e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGtVNRVtiLMDKF------GQPKGFAYVEFVEVEAVQEAL-QLNESELHGRQLKVSP 162
Cdd:cd12643   1 ALYVGNLTWWTTDEDLTEALHSIG-VNDL--LEIKFfenranGQSKGFALIVVGSEASSRKLMdKLPKKELHGQNPVVTP 77
RRM3_NGR1_NAM8_like cd12346
RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), ...
90-164 1.66e-03

RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins; This subfamily corresponds to the RRM3 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: 409782 [Multi-domain]  Cd Length: 72  Bit Score: 36.15  E-value: 1.66e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTIlmdKFGqpKGFAYVEFVEVEAVQEALQlnesELHGRQLKVSPKR 164
Cdd:cd12346   3 TVFVGGLDPNVTEEDLRVLFGPFGEIVYVKI---PPG--KGCGFVQFVNRASAEAAIQ----KLQGTPIGGSRIR 68
RRM_SAFB_like cd12417
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ...
90-160 1.68e-03

RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM.


Pssm-ID: 409851 [Multi-domain]  Cd Length: 74  Bit Score: 36.08  E-value: 1.68e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKG-FAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12417   1 NLWISGLSDTTKAADLKKIFSKYGKVVSAKVVTSARTPGSRcYGYVTMASVEEADLCIKsLNKTELHGRVITV 73
RRM1_hnRNPR cd12482
RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein R ...
91-151 1.80e-03

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


Pssm-ID: 409909 [Multi-domain]  Cd Length: 79  Bit Score: 36.11  E-value: 1.80e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQLNES 151
Cdd:cd12482   4 VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLsGQNRGYAFITFCNKEAAQEAVKLCDN 65
RRM_SRSF10 cd12559
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 10 (SRSF10) and ...
90-160 1.91e-03

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins; This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 409975 [Multi-domain]  Cd Length: 95  Bit Score: 36.57  E-value: 1.91e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  90 SVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQ-PKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12559   7 SLFVRNVADDTRSEDLRREFGRYGPIVDVYVPLDFYTRrPRGFAYVQFEDVRDAEDALHnLDRKWICGRQIEI 79
RRM2_hnRNPH_CRSF1_like cd12504
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H ...
98-164 1.97e-03

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


Pssm-ID: 409927 [Multi-domain]  Cd Length: 77  Bit Score: 35.79  E-value: 1.97e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15238140  98 YACTPEEVQLHFQTCGTV-NRVTILMDKFGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVSPKR 164
Cdd:cd12504  10 YGCTKEEIAQFFSGLEIVpNGITLPMDRRGRSTGEAFVQFASQEIAEQALGKHKEKIGHRYIEIFRSS 77
RRM1_GRSF1 cd12730
RNA recognition motif 1 (RRM1) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
98-160 2.05e-03

RNA recognition motif 1 (RRM1) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; This subgroup corresponds to the RRM1 of GRSF-1, a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic alpha-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity.


Pssm-ID: 410129 [Multi-domain]  Cd Length: 79  Bit Score: 35.93  E-value: 2.05e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15238140  98 YACTPEEVQLHFQTC---GTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKV 160
Cdd:cd12730  11 WSCTAEDVLSFFSDCrirNGEDGIHFLLNRDGKRRGDALIELESEEDVQKALEQHRKYMGQRYVEV 76
RRM1_CELF3_4_5_6 cd12632
RNA recognition motif 1 (RRM1) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, ...
85-170 2.47e-03

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


Pssm-ID: 410041 [Multi-domain]  Cd Length: 87  Bit Score: 35.85  E-value: 2.47e-03
                        10        20        30        40        50        60        70        80
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gi 15238140  85 EVDARSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEAlqlnESELHGRQlkvspk 163
Cdd:cd12632   2 DHDAIKLFIGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYtGMHKGCAFLTYCARESALKA----QSALHEQK------ 71

                ....*..
gi 15238140 164 rtNVPGM 170
Cdd:cd12632  72 --TLPGM 76
RRM3_Hu cd12377
RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to ...
106-163 2.54e-03

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


Pssm-ID: 409811 [Multi-domain]  Cd Length: 76  Bit Score: 35.76  E-value: 2.54e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140 106 QLhFQTCGTVNRVTILMDKFGQP-KGFAYVEFVEV-EAVQEALQLNESELHGRQLKVSPK 163
Cdd:cd12377  18 QL-FGPFGAVQNVKIIRDFTTNKcKGYGFVTMTNYdEAAVAIASLNGYRLGGRVLQVSFK 76
RRM_Rrp7A cd12294
RNA recognition motif in ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar ...
89-174 2.68e-03

RNA recognition motif in ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar proteins; This subfamily corresponds to the RRM of Rrp7A, also termed gastric cancer antigen Zg14, a homolog of yeast ribosomal RNA-processing protein 7 (Rrp7p), and mainly found in Metazoa. Rrp7p is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle. In contrast, the cellular function of Rrp7A remains unclear currently. Rrp7A harbors an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal Rrp7 domain.


Pssm-ID: 409735 [Multi-domain]  Cd Length: 103  Bit Score: 36.14  E-value: 2.68e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTI------------LMDKFGQP---KGF--AYVEFVEVEAVQEALQLNES 151
Cdd:cd12294   1 RTLFVLNVPPYCTEESLKRLFSRCGKVESVELqekpgpaekidsKTSKFFNPqpiKGFkvAYVVFKKPSSLKAALKLKST 80
                        90       100
                ....*....|....*....|....
gi 15238140 152 ELhgrqLKVSPKRTNVP-GMKQYH 174
Cdd:cd12294  81 KP----FVLSTESHPVKtGLEKWI 100
RRM1_Hrp1p cd12577
RNA recognition motif 1 (RRM1) found in yeast nuclear polyadenylated RNA-binding protein 4 ...
91-164 2.68e-03

RNA recognition motif 1 (RRM1) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.


Pssm-ID: 409991 [Multi-domain]  Cd Length: 76  Bit Score: 35.55  E-value: 2.68e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQlNESELHGRQlkVSPKR 164
Cdd:cd12577   1 MFIGGLNWDTTEEGLRDYFSQFGTVVDCTIMKDSAtGRSRGFGFLTFEDPSSVNEVMK-KEHVLDGKI--IDPKR 72
RRM1_MSI cd12576
RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog Musashi-1, ...
92-163 2.70e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins; This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is 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: 409990 [Multi-domain]  Cd Length: 76  Bit Score: 35.50  E-value: 2.70e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  92 YVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQ-PKGFAYVEFVEVEAVQEALQLNESELHGRqlKVSPK 163
Cdd:cd12576   3 FIGGLSWQTTPEGLREYFSKFGEITECMVMRDPTTKrSRGFGFVTFSDPASVDKVLAQGPHELDGK--KIDPK 73
RRM2_hnRNPA0 cd12579
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) ...
91-160 2.80e-03

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A0, 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 A0 contains 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: 409993 [Multi-domain]  Cd Length: 80  Bit Score: 35.58  E-value: 2.80e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKV 160
Cdd:cd12579   2 LFVGGLKGDVGEGDLVEHFSQFGTVEKVEVIADKDtGKKRGFGFVYFEDHDSADKAAVVKFHSINGHRVEV 72
RRM_TDRD10 cd21617
RNA recognition motif (RRM) found in Tudor domain-containing protein 10 (TDRD10) and similar ...
91-160 2.89e-03

RNA recognition motif (RRM) found in Tudor domain-containing protein 10 (TDRD10) and similar proteins; TDRD10 is widely expressed and localized both to the nucleus and cytoplasm and may play general roles like regulation of RNA metabolism. It contains a Tudor domain and a RNA recognition motif (RRM).


Pssm-ID: 410196 [Multi-domain]  Cd Length: 69  Bit Score: 35.09  E-value: 2.89e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNrVTILMDKFgqpKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd21617   2 VYVGNLPLDISEEEILQLFKAFNPVL-VKKIRSGF---KCFAFVDLGSDENVKLAIQqLNGTLFGGRRLVV 68
RRM1_hnRNPM cd12657
RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein M ...
90-160 2.90e-03

RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M); This subgroup corresponds to the RRM1 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif).


Pssm-ID: 410058 [Multi-domain]  Cd Length: 76  Bit Score: 35.64  E-value: 2.90e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  90 SVYVGNVDYACTPEEVQ-LHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12657   1 RVFISNIPFDVKWQTLKdLVKEKVGEVTYVELLMDAEGKSRGCAVVEFKTEESMKKAVEvLNKHSFNGRPLKV 73
RRM2_U2AF65 cd12231
RNA recognition motif 2 (RRM2) found in U2 large nuclear ribonucleoprotein auxiliary factor ...
91-160 3.51e-03

RNA recognition motif 2 (RRM2) 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: 409678 [Multi-domain]  Cd Length: 77  Bit Score: 35.32  E-value: 3.51e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKF-GQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12231   3 LFIGGLPNYLNEDQVKELLQSFGKLKAFNLVKDSAtGLSKGYAFCEYVDDNVTDQAIAgLNGMQLGDKKLLV 74
RRM1_SHARP cd12348
RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
91-160 3.86e-03

RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM1 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409784 [Multi-domain]  Cd Length: 75  Bit Score: 35.28  E-value: 3.86e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEAlQLNESELHGRQLKV 160
Cdd:cd12348   2 LWVGNLPENVREEKIIEHFKRFGRVESVKILPKRGSEGGVAAFVDFVDIKSAQKA-HSAVNKMGGRDLRT 70
RRM2_RBM4 cd12607
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup ...
91-160 3.97e-03

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup corresponds to the RRM2 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4.


Pssm-ID: 410019 [Multi-domain]  Cd Length: 67  Bit Score: 34.94  E-value: 3.97e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDkfgqpkgFAYVEFVEVEAVQEALQ-LNESELHGRQLKV 160
Cdd:cd12607   3 LHVGNISSSCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAMEAIRgLDNTEFQGKRMHV 66
RRM6_RBM19 cd12571
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
93-158 4.06e-03

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409985 [Multi-domain]  Cd Length: 79  Bit Score: 35.10  E-value: 4.06e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140  93 VGNVDYACTPEEVQLHFQTCGTVNRVTI--LMDKFGQPKGFAYVEFV---EVEAVQEALQLNeSELHGRQL 158
Cdd:cd12571   5 VRNIPFQATVKEVRELFSTFGELKTVRLpkKMGGTGQHRGFGFVDFItkqDAKRAFDALCHS-THLYGRRL 74
RRM2_MSI cd12323
RNA recognition motif 2 (RRM2) found in RNA-binding protein Musashi homologs Musashi-1, ...
91-160 4.36e-03

RNA recognition motif 2 (RRM2) found 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 [Multi-domain]  Cd Length: 74  Bit Score: 34.72  E-value: 4.36e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQP-KGFAYVEFVEVEAVQEALQLNESELHGRQLKV 160
Cdd:cd12323   2 IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRhRGFGFVTFESEDVVDKVCEIHFHEINNKMVEC 72
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
91-162 4.74e-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 [Multi-domain]  Cd Length: 562  Bit Score: 37.48  E-value: 4.74e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140    91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKVSP 162
Cdd:TIGR01628  91 IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQkVNGMLLNDKEVYVGR 163
RRM_Srp1p_AtRSp31_like cd12233
RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis ...
101-160 4.75e-03

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


Pssm-ID: 240679 [Multi-domain]  Cd Length: 70  Bit Score: 34.73  E-value: 4.75e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15238140 101 TPEEVQLHFQTCGTVNRVTIlmdkfgqPKGFAYVEFVEVEAVQEAL-QLNESELHGRQLKV 160
Cdd:cd12233  13 REEDIEKLFEPFGPLVRCDI-------RKTFAFVEFEDSEDATKALeALHGSRIDGSVLTV 66
RRM1_hnRNPA_like cd12578
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A subfamily; ...
91-164 5.16e-03

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A subfamily; This subfamily corresponds to the RRM1 in 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: 409992 [Multi-domain]  Cd Length: 78  Bit Score: 34.72  E-value: 5.16e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMD-KFGQPKGFAYVEFVEVEAVQEALQLNESELHGRQlkVSPKR 164
Cdd:cd12578   2 LFIGGLSYETTDDSLRNHFEQWGEITDVVVMKDpATKRSRGFGFVTYSSASEVDAAMNARPHKVDGRV--VEPKR 74
RRM2_I_PABPs cd12379
RNA recognition motif 2 (RRM2) found found in type I polyadenylate-binding proteins; This ...
91-162 5.24e-03

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


Pssm-ID: 409813 [Multi-domain]  Cd Length: 77  Bit Score: 34.86  E-value: 5.24e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQ-LNESELHGRQLKVSP 162
Cdd:cd12379   5 IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAERAIEkVNGMLLNGKKVFVGR 77
PIN_VapC4-5_FitB-like cd18739
uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily; ...
6-70 5.67e-03

uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily; The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350306  Cd Length: 124  Bit Score: 35.77  E-value: 5.67e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140   6 HEVYGGEIPEVGDTDVPDPDIDMSAA-----DEDAVTELAEMKRRLKEMEEEAAALREMQAKVEKEMGAT 70
Cdd:cd18739  37 YEVYVGAVRSAGETDLDGVREDLDWVepldfDEEVAREAAQIQAELLEAGEPINPPDLMIAATARSLGAT 106
RRM1_hnRNPH_hnRNPH2_hnRNPF cd12729
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP H , ...
91-160 5.87e-03

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


Pssm-ID: 410128 [Multi-domain]  Cd Length: 79  Bit Score: 34.75  E-value: 5.87e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  91 VYVGNVDYACTPEEVQLHFQTCGTVNRVT---ILMDKFGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKV 160
Cdd:cd12729   4 VKVRGLPWSCSADEVQNFFSDCKIANGASgihFIYTREGRPSGEAFVELESEEDVKLALKKDRETMGHRYVEV 76
RRM2_Spen cd12309
RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily ...
89-160 5.92e-03

RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 240755 [Multi-domain]  Cd Length: 79  Bit Score: 34.68  E-value: 5.92e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEA-LQLNESELHGRQLKV 160
Cdd:cd12309   3 RTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAkVAMSGQYIGRNQIKI 75
RRM2_RMB19 cd12502
RNA recognition motif 2 (RRM2) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
120-161 5.92e-03

RNA recognition motif 2 (RRM2) found in RNA-binding protein 19 (RBM19) and similar proteins; This subfamily corresponds to the RRM2 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is also essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409925 [Multi-domain]  Cd Length: 72  Bit Score: 34.32  E-value: 5.92e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 15238140 120 ILMDKFGQPKGFAYVEFVEVEAVQEALQLNESELHGRQLKVS 161
Cdd:cd12502  31 IVKNAHGNKTGYVFVDFKSEEDVEKALKRNKDYMGGRYIEVF 72
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
91-180 6.00e-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 [Multi-domain]  Cd Length: 562  Bit Score: 37.09  E-value: 6.00e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140    91 VYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDKFGQPKGFAYVEFVEVEAVQEALQlnesELHGRQLKVSPkrtnvPGM 170
Cdd:TIGR01628 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVE----EMNGKKIGLAK-----EGK 251
                          90
                  ....*....|
gi 15238140   171 KQYhPGRFNP 180
Cdd:TIGR01628 252 KLY-VGRAQK 260
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
89-161 6.22e-03

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


Pssm-ID: 409697 [Multi-domain]  Cd Length: 72  Bit Score: 34.53  E-value: 6.22e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDkfgqpkgFAYVEFVEVEAVQEALQ-LNESELHGRQLKVS 161
Cdd:cd12251   2 KVLYVRNLMLSTTEEKLRELFSEYGKVERVKKIKD-------YAFVHFEERDDAVKAMEeMNGKELEGSEIEVS 68
RRM1_MRN1 cd12520
RNA recognition motif 1 (RRM1) found in RNA-binding protein MRN1 and similar proteins; This ...
89-160 7.19e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM1 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa,which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 240964 [Multi-domain]  Cd Length: 74  Bit Score: 34.34  E-value: 7.19e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15238140  89 RSVYVGNVDYACTPEEVQLHFQTcGTVNRVTILMDKFgqpkgFAYVEFVEVEAVQ---EALQLNESELHGRQLKV 160
Cdd:cd12520   2 RTVYLGNLPPNTTVKELLSHVRS-GPIENVRILPEKN-----CAFISFLDPSAATafhSDAILKRLSIKGVELKI 70
RRM_G3BP cd12229
RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, ...
87-164 8.30e-03

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


Pssm-ID: 409676 [Multi-domain]  Cd Length: 81  Bit Score: 34.31  E-value: 8.30e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238140  87 DARSVYVGNVDYACTPEEVQLHFQTCGTVNRVTILMDK-FGQPKGFAYVEFVEVEAVQEALQLNESELHGRQ-LKVSPKR 164
Cdd:cd12229   2 DNHQLFVGNLPHDITEDELKEFFSRFGNVLELRINSKGgGGRLPNFGFVVFDDPEAVQKILANKPIMFRGEHrLNVEEKK 81
RRM2_GRSF1 cd12505
RNA recognition motif 2 (RRM2) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
98-164 9.06e-03

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


Pssm-ID: 409928 [Multi-domain]  Cd Length: 77  Bit Score: 34.04  E-value: 9.06e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15238140  98 YACTPEEVqLHFQTCGTVNRVTILMDKFGQPK-GFAYVEFVEVEAVQEALQLNESELHGRQLKVSPKR 164
Cdd:cd12505  11 YSCTEADI-AHFFSGLDIVDITFVMDLRGGRKtGEAFVQFASPEMAAQALLKHKEEIGNRYIEIFPSR 77
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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