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Conserved domains on  [gi|18421342|ref|NP_568522|]
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RNA binding (RRM/RBD/RNP motifs) family protein [Arabidopsis thaliana]

Protein Classification

PLN03120 family protein( domain architecture ID 11477442)

PLN03120 family protein

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PLN03120 PLN03120
nucleic acid binding protein; Provisional
1-267 5.31e-131

nucleic acid binding protein; Provisional


:

Pssm-ID: 215588  Cd Length: 260  Bit Score: 371.30  E-value: 5.31e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18421342    1 MQTTRSVQVNNVSDLATEREIHEFFSFSGDIEHIEIQKEFGQSRIAFVTFTDPKALEIALLLSGATIVDQIVTITRAENY 80
Cdd:PLN03120   1 VMQVRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAEDY 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18421342   81 vqrretqevRMLDNAMPLGLQESTTqtktnmdGNSRAYVSKAQDVVATVLAKGSALGQDAVNKAKAFDEKHQLRANASAK 160
Cdd:PLN03120  81 ---------QLPPEALAPLSSNSPA-------SGAESAVKKAEDVVSSMLAKGFILGKDAVNKAKAFDEKHQLTSTASAK 144
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18421342  161 VSSFDKRVGLTEKLSVGISAVNEKVKSVDQKLQVSDKTMAAIFAAERKLNDTGSAVKSSRYVTAGAAWFSGAFSKVARVG 240
Cdd:PLN03120 145 VASLDKKIGLSEKLSAGTAVVNEKVKEVDQKYQVSEKTKSALAAAEQKVSSAGSAIMKNRYVLTGASWVTGAFNKVAKAA 224
                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 18421342  241 QVAGSKTKEKFNLA---------VSNMSSKDTPIAV 267
Cdd:PLN03120 225 EEVGQKTKEKVGAAeeeqqvvdaYANIHLSESPKAV 260
 
Name Accession Description Interval E-value
PLN03120 PLN03120
nucleic acid binding protein; Provisional
1-267 5.31e-131

nucleic acid binding protein; Provisional


Pssm-ID: 215588  Cd Length: 260  Bit Score: 371.30  E-value: 5.31e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18421342    1 MQTTRSVQVNNVSDLATEREIHEFFSFSGDIEHIEIQKEFGQSRIAFVTFTDPKALEIALLLSGATIVDQIVTITRAENY 80
Cdd:PLN03120   1 VMQVRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAEDY 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18421342   81 vqrretqevRMLDNAMPLGLQESTTqtktnmdGNSRAYVSKAQDVVATVLAKGSALGQDAVNKAKAFDEKHQLRANASAK 160
Cdd:PLN03120  81 ---------QLPPEALAPLSSNSPA-------SGAESAVKKAEDVVSSMLAKGFILGKDAVNKAKAFDEKHQLTSTASAK 144
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18421342  161 VSSFDKRVGLTEKLSVGISAVNEKVKSVDQKLQVSDKTMAAIFAAERKLNDTGSAVKSSRYVTAGAAWFSGAFSKVARVG 240
Cdd:PLN03120 145 VASLDKKIGLSEKLSAGTAVVNEKVKEVDQKYQVSEKTKSALAAAEQKVSSAGSAIMKNRYVLTGASWVTGAFNKVAKAA 224
                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 18421342  241 QVAGSKTKEKFNLA---------VSNMSSKDTPIAV 267
Cdd:PLN03120 225 EEVGQKTKEKVGAAeeeqqvvdaYANIHLSESPKAV 260
RRM_Vip1_like cd12269
RNA recognition motif (RRM) found in a group of uncharacterized plant proteins similar to ...
7-75 1.29e-38

RNA recognition motif (RRM) found in a group of uncharacterized plant proteins similar to fission yeast Vip1; This subfamily corresponds to the Vip1-like, uncharacterized proteins found in plants. Although their biological roles remain unclear, these proteins show high sequence similarity to the fission yeast Vip1. Like Vip1 protein, members in this family contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409712 [Multi-domain]  Cd Length: 69  Bit Score: 129.58  E-value: 1.29e-38
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18421342   7 VQVNNVSDLATEREIHEFFSFSGDIEHIEIQKEFGQSRIAFVTFTDPKALEIALLLSGATIVDQIVTIT 75
Cdd:cd12269   1 VEVTNVSPLATERDLHEFFSFSGDIEHIEIQREGEQSRIAFVTFKDPYALETAVLLSGATIVDQRVTIT 69
RRM smart00360
RNA recognition motif;
9-74 1.42e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 47.59  E-value: 1.42e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18421342      9 VNNVSDLATEREIHEFFSFSGDIEHIEI--QKEFGQSR-IAFVTFTDPKALEIAL-LLSGATIVDQIVTI 74
Cdd:smart00360   4 VGNLPPDTTEEELRELFSKFGKVESVRLvrDKETGKSKgFAFVEFESEEDAEKALeALNGKELDGRPLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
9-67 4.03e-05

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: 40.68  E-value: 4.03e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18421342     9 VNNVSDLATEREIHEFFSFSGDIEHIEI-QKEFGQSR-IAFVTFTDPKALEIAL-LLSGATI 67
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGPIKSIRLvRDETGRSKgFAFVEFEDEEDAEKAIeALNGKEL 64
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
5-89 7.56e-05

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: 43.75  E-value: 7.56e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18421342     5 RSVQVNNVSDLATEREIHEFFSFSGDIEHIEIQKEFGQSR---IAFVTFTDPKALEIALLLSGATIVDQ--IVTITRAEN 79
Cdd:TIGR01622 115 RTVFVQQLAARARERDLYEFFSKVGKVRDVQIIKDRNSRRskgVGYVEFYDVDSVQAALALTGQKLLGIpvIVQLSEAEK 194
                          90
                  ....*....|
gi 18421342    80 YVQRRETQEV 89
Cdd:TIGR01622 195 NRAARAATET 204
 
Name Accession Description Interval E-value
PLN03120 PLN03120
nucleic acid binding protein; Provisional
1-267 5.31e-131

nucleic acid binding protein; Provisional


Pssm-ID: 215588  Cd Length: 260  Bit Score: 371.30  E-value: 5.31e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18421342    1 MQTTRSVQVNNVSDLATEREIHEFFSFSGDIEHIEIQKEFGQSRIAFVTFTDPKALEIALLLSGATIVDQIVTITRAENY 80
Cdd:PLN03120   1 VMQVRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAEDY 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18421342   81 vqrretqevRMLDNAMPLGLQESTTqtktnmdGNSRAYVSKAQDVVATVLAKGSALGQDAVNKAKAFDEKHQLRANASAK 160
Cdd:PLN03120  81 ---------QLPPEALAPLSSNSPA-------SGAESAVKKAEDVVSSMLAKGFILGKDAVNKAKAFDEKHQLTSTASAK 144
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18421342  161 VSSFDKRVGLTEKLSVGISAVNEKVKSVDQKLQVSDKTMAAIFAAERKLNDTGSAVKSSRYVTAGAAWFSGAFSKVARVG 240
Cdd:PLN03120 145 VASLDKKIGLSEKLSAGTAVVNEKVKEVDQKYQVSEKTKSALAAAEQKVSSAGSAIMKNRYVLTGASWVTGAFNKVAKAA 224
                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 18421342  241 QVAGSKTKEKFNLA---------VSNMSSKDTPIAV 267
Cdd:PLN03120 225 EEVGQKTKEKVGAAeeeqqvvdaYANIHLSESPKAV 260
PLN03121 PLN03121
nucleic acid binding protein; Provisional
2-238 6.38e-61

nucleic acid binding protein; Provisional


Pssm-ID: 215589 [Multi-domain]  Cd Length: 243  Bit Score: 192.72  E-value: 6.38e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18421342    2 QTTRSVQVNNVSDLATEREIHEFFSFSGDIEHIEIQKEFGQSRIAFVTFTDPKALEIALLLSGATIVDQIVTITRAENYV 81
Cdd:PLN03121   3 PGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWGQYE 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18421342   82 qrretQEVRMLDNAMPLGLQESTTQTKTN-MDGNSRAYVSKAQDVVATVLAKGSALGQDAVNKAKAFDEKHQLRANASAK 160
Cdd:PLN03121  83 -----DEFDFWNRPSWDTEDISTHNYETNqFASTPGEAVTVAQEVVKTMLAKGYVLGKDALSKAKAFDESHQVSATAAAK 157
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 18421342  161 VSSFDKRVGLTEKLSVGIsavnEKVKSVDQKLQVSDKTMAAIFAAERKLNDTGSAVKSSRYVTAGAAWFSGAFSKVAR 238
Cdd:PLN03121 158 VAELSKRIGLTDKIFAGM----EAVRSVDEKYHVSEFTKSAATATGRTAAAAANAVVNSSYFSKGALWVSDALTRAAK 231
RRM_Vip1_like cd12269
RNA recognition motif (RRM) found in a group of uncharacterized plant proteins similar to ...
7-75 1.29e-38

RNA recognition motif (RRM) found in a group of uncharacterized plant proteins similar to fission yeast Vip1; This subfamily corresponds to the Vip1-like, uncharacterized proteins found in plants. Although their biological roles remain unclear, these proteins show high sequence similarity to the fission yeast Vip1. Like Vip1 protein, members in this family contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409712 [Multi-domain]  Cd Length: 69  Bit Score: 129.58  E-value: 1.29e-38
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18421342   7 VQVNNVSDLATEREIHEFFSFSGDIEHIEIQKEFGQSRIAFVTFTDPKALEIALLLSGATIVDQIVTIT 75
Cdd:cd12269   1 VEVTNVSPLATERDLHEFFSFSGDIEHIEIQREGEQSRIAFVTFKDPYALETAVLLSGATIVDQRVTIT 69
RRM_SRSF11_SREK1 cd12259
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11), ...
7-76 8.24e-11

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11), splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM domain of SRSF11 (SRp54 or p54), SREK1 ( SFRS12 or SRrp86) and similar proteins, a group of proteins containing regions rich in serine-arginine dipeptides (SR protein family). These are involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SR proteins have been identified as crucial regulators of alternative splicing. Different SR proteins display different substrate specificity, have distinct functions in alternative splicing of different pre-mRNAs, and can even negatively regulate splicing. All SR family members are characterized by the presence of one or two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and the C-terminal regions rich in serine and arginine dipeptides (SR domains). The RRM domain is responsible for RNA binding and specificity in both alternative and constitutive splicing. In contrast, SR domains are thought to be protein-protein interaction domains that are often interchangeable.


Pssm-ID: 409704 [Multi-domain]  Cd Length: 76  Bit Score: 56.94  E-value: 8.24e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18421342   7 VQVNNVSDLATEREIHEFFSFSGDIEHIEIQKEFG-----QSRIAFVTFTDPKALEIALLLSGATIVDQIVTITR 76
Cdd:cd12259   2 VQVTNVSPQATEEQMRTLFGFIGKIEELRLYPSEDdlapvLSKVCFVKYEDPEDVAVALHLTNTVFIDRALIVIP 76
RRM_Vip1 cd12268
RNA recognition motif (RRM) found in fission yeast protein Vip1 and similar proteins; This ...
7-75 4.43e-10

RNA recognition motif (RRM) found in fission yeast protein Vip1 and similar proteins; This subfamily corresponds to Vip1, an RNA-binding protein encoded by gene vip1 from fission yeast Schizosaccharomyces pombe. Its biological role remains unclear. Vip1 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 240714 [Multi-domain]  Cd Length: 68  Bit Score: 54.46  E-value: 4.43e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18421342   7 VQVNNVSDLATEREIHEFFSFSGDIEHIEIQKEfGQSRIAFVTFTDPKALEIALLLSGATIVDQIVTIT 75
Cdd:cd12268   1 VYVSNISPKTTEKQISDFFSFCGKISNLDLTND-GESQTATITFEKPSAAKTALLLDNALLGGKVIQVT 68
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
7-74 4.81e-08

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


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 49.20  E-value: 4.81e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18421342   7 VQVNNVSDLATEREIHEFFSFSGDIEHIEIQKE-FGQSR-IAFVTFTDPKALEIAL-LLSGATIVDQIVTI 74
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDrDGKSKgFAFVEFESPEDAEKALeALNGTELGGRPLKV 71
RRM smart00360
RNA recognition motif;
9-74 1.42e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 47.59  E-value: 1.42e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18421342      9 VNNVSDLATEREIHEFFSFSGDIEHIEI--QKEFGQSR-IAFVTFTDPKALEIAL-LLSGATIVDQIVTI 74
Cdd:smart00360   4 VGNLPPDTTEEELRELFSKFGKVESVRLvrDKETGKSKgFAFVEFESEEDAEKALeALNGKELDGRPLKV 73
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
5-76 1.37e-05

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: 42.25  E-value: 1.37e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 18421342   5 RSVQVNNVSDLATEREIHEFFSFSGDIEHIEIQK--EFGQSRI----AFVTFTDPKALEIALLLSGATIVDQIVTITR 76
Cdd:cd12298   1 REIRVRNLDFELDEEALRGIFEKFGEIESINIPKkqKNRKGRHnngfAFVTFEDADSAESALQLNGTLLDNRKISVSL 78
RRM2_SREK1 cd12260
RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 ...
2-79 3.70e-05

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: 41.14  E-value: 3.70e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18421342   2 QTTRSVQVNNVSDLATEREIHEFFSFSGDIEHIEIQKEFGQ-SRIAFVTFTDPKALEIALLLSGATIVDQIVTITRAEN 79
Cdd:cd12260   2 EIRRTVYVGNLDPSTTADQLLEFFSQAGEVKYVRMAGDETQpTRYAFVEFAEQTSVINALKLNGKMFGGRPLKVNHSNN 80
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
9-67 4.03e-05

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: 40.68  E-value: 4.03e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18421342     9 VNNVSDLATEREIHEFFSFSGDIEHIEI-QKEFGQSR-IAFVTFTDPKALEIAL-LLSGATI 67
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGPIKSIRLvRDETGRSKgFAFVEFEDEEDAEKAIeALNGKEL 64
RRM1_RBM39_like cd12283
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar ...
6-64 4.87e-05

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: 40.68  E-value: 4.87e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18421342   6 SVQVNNVSDLATEREIHEFFSFSGDIEHIEIQKEFGQSR---IAFVTFTDPKALEIALLLSG 64
Cdd:cd12283   1 TVFVMQLSLKARERDLYEFFSKAGKVRDVRLIMDRNSRRskgVAYVEFYDVESVPLALALTG 62
RRM_II_PABPs cd12306
RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to ...
6-67 5.31e-05

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


Pssm-ID: 409747 [Multi-domain]  Cd Length: 73  Bit Score: 40.36  E-value: 5.31e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18421342   6 SVQVNNVSDLATEREIHEFFSFSGDIEHIEI--QKEFGQSR-IAFVTFTDPKALEIALLLSGATI 67
Cdd:cd12306   1 SIYVGNVDYGTTPEELQAHFKSCGTINRVTIlcDKFTGQPKgFAYIEFVDKSSVENALLLNESEF 65
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
5-89 7.56e-05

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: 43.75  E-value: 7.56e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18421342     5 RSVQVNNVSDLATEREIHEFFSFSGDIEHIEIQKEFGQSR---IAFVTFTDPKALEIALLLSGATIVDQ--IVTITRAEN 79
Cdd:TIGR01622 115 RTVFVQQLAARARERDLYEFFSKVGKVRDVQIIKDRNSRRskgVGYVEFYDVDSVQAALALTGQKLLGIpvIVQLSEAEK 194
                          90
                  ....*....|
gi 18421342    80 YVQRRETQEV 89
Cdd:TIGR01622 195 NRAARAATET 204
RRM_SRSF11 cd12518
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11) and ...
7-78 1.31e-04

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11) and similar proteins; This subgroup corresponds to the RRM of SRSF11, also termed arginine-rich 54 kDa nuclear protein (SRp54 or p54), which belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family). It is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SRSF11 has been identified as a tau exon 10 splicing repressor. It interacts with a purine-rich element in exon 10, and suppresses exon 10 inclusion by antagonizing Tra2beta, an SR-domain-containing protein that enhances exon 10 inclusion. SRSF11 is a unique SR family member and may regulate the alternative splicing in a tissue- and substrate-dependent manner. It can directly interact with the U2 auxiliary factor 65-kDa subunit (U2AF65), a protein associated with the 3' splice site. In addition, unlike the typical SR proteins, SRSF11 associates with other SR proteins but not with the U1 small nuclear ribonucleoprotein U1-70K or the U2 auxiliary factor 35-kDa subunit (U2AF35). SREK1 has unique properties in regulating alternative splicing of different pre-mRNAs; it promotes the use of the distal 5' splice site in E1A pre-mRNA alternative splicing. It also inhibits cryptic splice site selection on the beta-globin pre-mRNA containing competing 5' splice sites. SREK1 contains an RNA recognition motif (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and one serine-arginine (SR)-rich domains (SR domains).


Pssm-ID: 409940 [Multi-domain]  Cd Length: 80  Bit Score: 39.64  E-value: 1.31e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 18421342   7 VQVNNVSDLATEREIHEFFSFSGDIEHIEIQKEFGQ-----SRIAFVTFTDPKALEIALLLSGATIVDQ-IVTITRAE 78
Cdd:cd12518   2 IQVTNVSPSASSEQMRTLFGFLGKIDELRLFPPDDSplpvtSRVCFVKFHEPDSAVVAQHLTNTVFVDRaLIVVPYAE 79
RRM1_SREK1 cd12519
RNA recognition motif 1 (RRM1) found in splicing regulatory glutamine/lysine-rich protein 1 ...
7-74 1.56e-04

RNA recognition motif 1 (RRM1) found in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subgroup corresponds to the RRM1 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), and 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 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 generally contains two 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; 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: 409941 [Multi-domain]  Cd Length: 80  Bit Score: 39.62  E-value: 1.56e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18421342   7 VQVNNVSDLATEREIHEFFSFSGDIEHIEIQKEFG-----QSRIAFVTFTDPKALEIALLLSGATIVDQIVTI 74
Cdd:cd12519   2 IQVTNLSAAVTSDQMRTLFSFLGDIEELRLYPPDNaplafSSKVCYVKYREPSSVGVAQHLTNTVFIDRALIV 74
RRM_RBM7_like cd12336
RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This ...
5-74 1.92e-04

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: 39.21  E-value: 1.92e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18421342   5 RSVQVNNVSDLATEREIHEFFSFSGDIEHIEIQKEF-GQSR-IAFVTFTDPKALEIAL-LLSGATIVDQIVTI 74
Cdd:cd12336   2 RTLFVGNLDPRVTEEILYELFLQAGPLEGVKIPKDPnGKPKnFAFVTFKHEVSVPYAIqLLNGIRLFGREIRI 74
RRM1_SRSF5 cd12595
RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 5 ...
7-77 2.04e-04

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 5 (SRSF5); This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain.


Pssm-ID: 410008 [Multi-domain]  Cd Length: 70  Bit Score: 38.77  E-value: 2.04e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18421342   7 VQVNNVSDLATEREIHEFFSFSGDIEHIEIQKEFGqsriaFVTFTDPKALEIALL-LSGATIVDQIVTITRA 77
Cdd:cd12595   2 VFIGRLNPAAREKDVERFFKGYGRIRDIDLKRGFG-----FVEFEDPRDADDAVYeLDGKELCNERVTIEHA 68
RRM1_PHIP1 cd12271
RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting ...
16-74 2.24e-04

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: 38.85  E-value: 2.24e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18421342  16 ATEREIHEFFSFSGDIEHIEIQ--KEFGQSR-IAFVTFTDPKALEIALLLSGATIVDQIVTI 74
Cdd:cd12271  10 STEAEIRSYFSSCGEVRSVDLMrfPDSGNFRgIAFITFKTEEAAKRALALDGEMLGNRFLKV 71
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
9-54 2.36e-04

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


Pssm-ID: 409755 [Multi-domain]  Cd Length: 74  Bit Score: 38.86  E-value: 2.36e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 18421342   9 VNNVSDLATEREIHEFFSFSGDIE--HIEIQKEFGQSR-IAFVTFTDPK 54
Cdd:cd12316   4 VRNLPFTATEDELRELFEAFGKISevHIPLDKQTKRSKgFAFVLFVIPE 52
RRM_Nop6 cd12400
RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and ...
9-62 5.38e-04

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: 37.59  E-value: 5.38e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 18421342   9 VNNVSDLATEREIHEFFSFSGDIEHIEI--QKEFGQSR-IAFVTFTDPKALEIALLL 62
Cdd:cd12400   5 VGNLPYDTTAEDLKEHFKKAGEPPSVRLltDKKTGKSKgCAFVEFDNQKALQKALKL 61
RRM2_4_MRN1 cd12262
RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar ...
4-51 7.33e-04

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: 37.38  E-value: 7.33e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 18421342   4 TRSVQVNNVSDLATEREIHEFFSFSGDIEHIEIQKEFGqsrIAFVTFT 51
Cdd:cd12262   3 SRNVYVGNLDDSLTEEEIRGILEKYGEIESIKILKEKN---CAFVNYL 47
RRM2_MRN1 cd12523
RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This ...
2-50 7.81e-04

RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 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: 409943 [Multi-domain]  Cd Length: 78  Bit Score: 37.41  E-value: 7.81e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 18421342   2 QTTRSVQVNNVSDLATEREIHEFFSFSGDIEHIEIQKEFGqsrIAFVTF 50
Cdd:cd12523   1 GASRNVYLGNLPESITEEELREDLEKFGPIDQIKIVKEKN---IAFVHF 46
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
6-60 1.10e-03

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: 36.72  E-value: 1.10e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 18421342   6 SVQVNNVSDLATEREIHEFFSFSGDIEHIEI--QKEFGQSR-IAFVTFTDPKALEIAL 60
Cdd:cd12408   1 TIRVTNLSEDATEEDLRELFRPFGPISRVYLakDKETGQSKgFAFVTFETREDAERAI 58
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
9-60 1.72e-03

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


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 36.38  E-value: 1.72e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 18421342   9 VNNVSDLATEREIHEFFSFSGDIEHIEI--QKEFGQSR-IAFVTFTDPKALEIAL 60
Cdd:cd21608   4 VGNLSWDTTEDDLRDLFSEFGEVESAKVitDRETGRSRgFGFVTFSTAEAAEAAI 58
RRM_G3BP cd12229
RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, ...
9-60 1.75e-03

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


Pssm-ID: 409676 [Multi-domain]  Cd Length: 81  Bit Score: 36.62  E-value: 1.75e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 18421342   9 VNNVSDLATEREIHEFFSFSGDIEHIEIQKEFGQSRI---AFVTFTDPKALEIAL 60
Cdd:cd12229   8 VGNLPHDITEDELKEFFSRFGNVLELRINSKGGGGRLpnfGFVVFDDPEAVQKIL 62
RRM1_2_CID8_like cd12225
RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting ...
5-66 1.92e-03

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: 36.29  E-value: 1.92e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18421342   5 RSVQVNNVSDLATEREIHEFFSFSGDIEHIEIQKEFGQSRIAFVTFTDPKALEIALLLSGAT 66
Cdd:cd12225   1 RTIHVGGIDGSLSEDELADYFSNCGEVTQVRLCGDRVHTRFAWVEFATDASALSALNLDGTT 62
RRM1_PUB1 cd12614
RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated ...
7-77 2.09e-03

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: 36.26  E-value: 2.09e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18421342   7 VQVNNVSDLATEREIHEFFSFSGDIEHIEI--QKEFGQSRIAFVTFTDPKALEIALL-LSGATIVDQIVTITRA 77
Cdd:cd12614   1 LYVGNLDPRVTEDLLQEIFAVTGPVENCKIipDKNSKGVNYGFVEYYDRRSAEIAIQtLNGRQIFGQEIKVNWA 74
RRM1_Prp24 cd12296
RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
6-76 2.37e-03

RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM1 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409737 [Multi-domain]  Cd Length: 71  Bit Score: 35.71  E-value: 2.37e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18421342   6 SVQVNNVSDLATEREIHEFFSFSGDIEHIEIqKEFGQSRIAFVTFTDPKALEIALLLSGATIVDQIVTITR 76
Cdd:cd12296   2 TVLVKNLPKSITENKIRQFFKDCGEIREVKI-LESGNGLVAVIEFETEDEALAALTKDHKRIGGNEISVSR 71
RRM2_CID8_like cd12460
RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana CTC-interacting domain protein ...
2-65 2.38e-03

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: 36.22  E-value: 2.38e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18421342   2 QTTRSVQVNNVSDLATEREIHEFF-SFSGDIEHIEIQKEFGQS-RIAFVTFTDPKALEIALLLSGA 65
Cdd:cd12460   2 MCARTIYCTNIDKKVTQDDVKAFFeSLCGEVHRLRLLGDYVHStRIAFVEFVMAESAIAALNCSGA 67
RRM1_SRSF1_like cd12338
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and ...
7-60 3.75e-03

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins; This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues.


Pssm-ID: 409775 [Multi-domain]  Cd Length: 72  Bit Score: 35.42  E-value: 3.75e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 18421342   7 VQVNNVSDLATEREIHEFFSFSGDIEHIEIQKEFGQSRIAFVTFTDPKALEIAL 60
Cdd:cd12338   2 IYVGNLPGDIRERDIEDLFYKYGPILAIDLKNRRRGPPFAFVEFEDPRDAEDAI 55
RRM1_SRSF9 cd12598
RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 9 ...
7-60 3.82e-03

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 9 (SRSF9); This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides.


Pssm-ID: 241042 [Multi-domain]  Cd Length: 72  Bit Score: 35.16  E-value: 3.82e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 18421342   7 VQVNNVSDLATEREIHEFFSFSGDIEHIEIQKEFGQSRIAFVTFTDPKALEIAL 60
Cdd:cd12598   2 IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAV 55
RRM2_RBM34 cd12395
RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
6-67 6.50e-03

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: 34.78  E-value: 6.50e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18421342   6 SVQVNNVSDLATEREIHEFFSFSGDIEHIEI--QKEFGQSR-IAFVTFTDPKALEIALLLSGATI 67
Cdd:cd12395   1 SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIvrDRETGIGKgFGYVLFKDKDSVDLALKLNGSKL 65
RRM2_Nop12p_like cd12670
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 12 (Nop12p) and similar ...
6-64 6.99e-03

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: 34.73  E-value: 6.99e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18421342   6 SVQVNNVSDLATEREIHEFFSFSGDIEHIEIQKE----FGQSrIAFVTFTDPKALEIALLLSG 64
Cdd:cd12670   1 CVFVGNLAFEAEEEGLWRYFGKCGAIESVRIVRDpktnVGKG-FAYVQFKDENAVEKALLLNE 62
 
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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