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Conserved domains on  [gi|225452763|ref|XP_002283061|]
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binding partner of ACD11 1 [Vitis vinifera]

Protein Classification

RNA-binding protein; RNA-binding protein 43( domain architecture ID 10011002)

RNA-binding protein containing an RNA recognition motif (RRM)| RNA-binding protein 43 (RBM43) is an RNA-binding protein containing an RNA recognition motif (RRM)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03121 PLN03121
nucleic acid binding protein; Provisional
 1-262 1.93e-143

nucleic acid binding protein; Provisional


:

Pssm-ID: 215589 [Multi-domain]  Cd Length: 243  Bit Score: 401.88  E-value: 1.93e-143
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225452763   1 MYPGAYTAEVTCLSPKATEKDVYDFFIHCGMIEHLEIIRSGECARTAYVTFRDFYALETAVLLSGATIVDQRVCISGWGI 80
Cdd:PLN03121   1 MYPGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWGQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225452763  81 YADESDPWSNSSW--------NYEINSMATTPREAVTVAQEVVTTMIAKGYVLGKDALIKAKAFDEAHGVSAAAAAKIAE 152
Cdd:PLN03121  81 YEDEFDFWNRPSWdtedisthNYETNQFASTPGEAVTVAQEVVKTMLAKGYVLGKDALSKAKAFDESHQVSATAAAKVAE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225452763 153 LSKRIGLTDKIYAGVEAVRSVDEKYHVSefsksaankiyggveaaravedryqllEFTKSAAVVTGKTTVAAANAFVNSS 232
Cdd:PLN03121 161 LSKRIGLTDKIFAGMEAVRSVDEKYHVS---------------------------EFTKSAATATGRTAAAAANAVVNSS 213

                        250       260       270
                 ....*....|....*....|....*....|
gi 225452763 233 YFAKGALWVSGILTRAANAAADLGNKGNKM 262
Cdd:PLN03121 214 YFSKGALWVSDALTRAAKAAADLGAHGSNQ 243
 
Name Accession Description Interval E-value
PLN03121 PLN03121
nucleic acid binding protein; Provisional
 1-262 1.93e-143

nucleic acid binding protein; Provisional


Pssm-ID: 215589 [Multi-domain]  Cd Length: 243  Bit Score: 401.88  E-value: 1.93e-143
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225452763   1 MYPGAYTAEVTCLSPKATEKDVYDFFIHCGMIEHLEIIRSGECARTAYVTFRDFYALETAVLLSGATIVDQRVCISGWGI 80
Cdd:PLN03121   1 MYPGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWGQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225452763  81 YADESDPWSNSSW--------NYEINSMATTPREAVTVAQEVVTTMIAKGYVLGKDALIKAKAFDEAHGVSAAAAAKIAE 152
Cdd:PLN03121  81 YEDEFDFWNRPSWdtedisthNYETNQFASTPGEAVTVAQEVVKTMLAKGYVLGKDALSKAKAFDESHQVSATAAAKVAE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225452763 153 LSKRIGLTDKIYAGVEAVRSVDEKYHVSefsksaankiyggveaaravedryqllEFTKSAAVVTGKTTVAAANAFVNSS 232
Cdd:PLN03121 161 LSKRIGLTDKIFAGMEAVRSVDEKYHVS---------------------------EFTKSAATATGRTAAAAANAVVNSS 213

                        250       260       270
                 ....*....|....*....|....*....|
gi 225452763 233 YFAKGALWVSGILTRAANAAADLGNKGNKM 262
Cdd:PLN03121 214 YFSKGALWVSDALTRAAKAAADLGAHGSNQ 243
RRM_Vip1_like cd12269
RNA recognition motif (RRM) found in a group of uncharacterized plant proteins similar to ...
 9-76 3.64e-30

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: 107.62  E-value: 3.64e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 225452763   9 EVTCLSPKATEKDVYDFFIHCGMIEHLEIIRSGECARTAYVTFRDFYALETAVLLSGATIVDQRVCIS 76
Cdd:cd12269    2 EVTNVSPLATERDLHEFFSFSGDIEHIEIQREGEQSRIAFVTFKDPYALETAVLLSGATIVDQRVTIT 69
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 10-68 4.19e-04

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: 37.98  E-value: 4.19e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 225452763   10 VTCLSPKATEKDVYDFFIHCGMIEHLEIIRS--GECARTAYVTFRDFYALETAV-LLSGATI 68
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDetGRSKGFAFVEFEDEEDAEKAIeALNGKEL 64
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 13-75 3.07e-03

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: 38.75  E-value: 3.07e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 225452763   13 LSPKATEKDVYDFFIHCGMIEHLEII---RSGECARTAYVTFRDFYALETAVLLSGATIVDQRVCI 75
Cdd:TIGR01622 122 LAARARERDLYEFFSKVGKVRDVQIIkdrNSRRSKGVGYVEFYDVDSVQAALALTGQKLLGIPVIV 187
 
Name Accession Description Interval E-value
PLN03121 PLN03121
nucleic acid binding protein; Provisional
 1-262 1.93e-143

nucleic acid binding protein; Provisional


Pssm-ID: 215589 [Multi-domain]  Cd Length: 243  Bit Score: 401.88  E-value: 1.93e-143
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225452763   1 MYPGAYTAEVTCLSPKATEKDVYDFFIHCGMIEHLEIIRSGECARTAYVTFRDFYALETAVLLSGATIVDQRVCISGWGI 80
Cdd:PLN03121   1 MYPGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWGQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225452763  81 YADESDPWSNSSW--------NYEINSMATTPREAVTVAQEVVTTMIAKGYVLGKDALIKAKAFDEAHGVSAAAAAKIAE 152
Cdd:PLN03121  81 YEDEFDFWNRPSWdtedisthNYETNQFASTPGEAVTVAQEVVKTMLAKGYVLGKDALSKAKAFDESHQVSATAAAKVAE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225452763 153 LSKRIGLTDKIYAGVEAVRSVDEKYHVSefsksaankiyggveaaravedryqllEFTKSAAVVTGKTTVAAANAFVNSS 232
Cdd:PLN03121 161 LSKRIGLTDKIFAGMEAVRSVDEKYHVS---------------------------EFTKSAATATGRTAAAAANAVVNSS 213

                        250       260       270
                 ....*....|....*....|....*....|
gi 225452763 233 YFAKGALWVSGILTRAANAAADLGNKGNKM 262
Cdd:PLN03121 214 YFSKGALWVSDALTRAAKAAADLGAHGSNQ 243
PLN03120 PLN03120
nucleic acid binding protein; Provisional
 7-259 2.36e-67

nucleic acid binding protein; Provisional


Pssm-ID: 215588  Cd Length: 260  Bit Score: 209.51  E-value: 2.36e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225452763   7 TAEVTCLSPKATEKDVYDFFIHCGMIEHLEIIRSGECARTAYVTFRDFYALETAVLLSGATIVDQRVCISGwgiyADESD 86
Cdd:PLN03120   6 TVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALLLSGATIVDQSVTITP----AEDYQ 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225452763  87 PWSNSSWNYEINSMATTPREAVTVAQEVVTTMIAKGYVLGKDALIKAKAFDEAHGVSAAAAAKIAELSKRIGLTDKIYAG 166
Cdd:PLN03120  82 LPPEALAPLSSNSPASGAESAVKKAEDVVSSMLAKGFILGKDAVNKAKAFDEKHQLTSTASAKVASLDKKIGLSEKLSAG 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225452763 167 V----EAVRSVDEKYHVSefsksaankiyggveaaravedryqllEFTKSAAVVTGKTTVAAANAFVNSSYFAKGALWVS 242
Cdd:PLN03120 162 TavvnEKVKEVDQKYQVS---------------------------EKTKSALAAAEQKVSSAGSAIMKNRYVLTGASWVT 214

                        250
                 ....*....|....*..
gi 225452763 243 GILTRAANAAADLGNKG 259
Cdd:PLN03120 215 GAFNKVAKAAEEVGQKT 231
RRM_Vip1_like cd12269
RNA recognition motif (RRM) found in a group of uncharacterized plant proteins similar to ...
 9-76 3.64e-30

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: 107.62  E-value: 3.64e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 225452763   9 EVTCLSPKATEKDVYDFFIHCGMIEHLEIIRSGECARTAYVTFRDFYALETAVLLSGATIVDQRVCIS 76
Cdd:cd12269    2 EVTNVSPLATERDLHEFFSFSGDIEHIEIQREGEQSRIAFVTFKDPYALETAVLLSGATIVDQRVTIT 69
RRM_Vip1 cd12268
RNA recognition motif (RRM) found in fission yeast protein Vip1 and similar proteins; This ...
 10-76 2.48e-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: 55.23  E-value: 2.48e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 225452763  10 VTCLSPKATEKDVYDFFIHCGMIEHLEIIRSGEcARTAYVTFRDFYALETAVLLSGATIVDQRVCIS 76
Cdd:cd12268    3 VSNISPKTTEKQISDFFSFCGKISNLDLTNDGE-SQTATITFEKPSAAKTALLLDNALLGGKVIQVT 68
RRM1_RBM39_like cd12283
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar ...
 7-65 3.48e-08

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: 49.54  E-value: 3.48e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 225452763   7 TAEVTCLSPKATEKDVYDFFIHCGMIEHLEIIR---SGECARTAYVTFRDFYALETAVLLSG 65
Cdd:cd12283    1 TVFVMQLSLKARERDLYEFFSKAGKVRDVRLIMdrnSRRSKGVAYVEFYDVESVPLALALTG 62
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 10-76 3.96e-07

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


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 46.51  E-value: 3.96e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225452763  10 VTCLSPKATEKDVYDFFIHCGMIEHLEIIR--SGECARTAYVTFRDFYALETAV-LLSGATIVDQRVCIS 76
Cdd:cd00590    3 VGNLPPDTTEEDLRELFSKFGEVVSVRIVRdrDGKSKGFAFVEFESPEDAEKALeALNGTELGGRPLKVS 72
RRM2_Nop12p_like cd12670
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 12 (Nop12p) and similar ...
 13-65 5.41e-05

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: 40.51  E-value: 5.41e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 225452763  13 LSPKATEKDVYDFFIHCGMIEHLEIIRSGECART---AYVTFRDFYALETAVLLSG 65
Cdd:cd12670    7 LAFEAEEEGLWRYFGKCGAIESVRIVRDPKTNVGkgfAYVQFKDENAVEKALLLNE 62
RRM_SRSF11_SREK1 cd12259
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11), ...
 10-70 9.18e-05

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: 39.99  E-value: 9.18e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 225452763  10 VTCLSPKATEKDVYDFFIHCGMIEHLEIIRSGE-----CARTAYVTFRDFYALETAVLLSGATIVD 70
Cdd:cd12259    4 VTNVSPQATEEQMRTLFGFIGKIEELRLYPSEDdlapvLSKVCFVKYEDPEDVAVALHLTNTVFID 69
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 10-68 4.19e-04

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: 37.98  E-value: 4.19e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 225452763   10 VTCLSPKATEKDVYDFFIHCGMIEHLEIIRS--GECARTAYVTFRDFYALETAV-LLSGATI 68
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDetGRSKGFAFVEFEDEEDAEKAIeALNGKEL 64
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 13-75 3.07e-03

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: 38.75  E-value: 3.07e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 225452763   13 LSPKATEKDVYDFFIHCGMIEHLEII---RSGECARTAYVTFRDFYALETAVLLSGATIVDQRVCI 75
Cdd:TIGR01622 122 LAARARERDLYEFFSKVGKVRDVQIIkdrNSRRSKGVGYVEFYDVDSVQAALALTGQKLLGIPVIV 187
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
 13-76 4.03e-03

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


Pssm-ID: 409739 [Multi-domain]  Cd Length: 78  Bit Score: 35.31  E-value: 4.03e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225452763  13 LSPKATEKDVYDFFIHCGMIEHLEIIRSGECART------AYVTFRDFYALETAVLLSGATIVDQRVCIS 76
Cdd:cd12298    8 LDFELDEEALRGIFEKFGEIESINIPKKQKNRKGrhnngfAFVTFEDADSAESALQLNGTLLDNRKISVS 77
RRM1_PHIP1 cd12271
RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting ...
 16-75 7.73e-03

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


Pssm-ID: 409714 [Multi-domain]  Cd Length: 72  Bit Score: 34.22  E-value: 7.73e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 225452763  16 KATEKDVYDFFIHCGMIEHLEIIR---SGECARTAYVTFRDFYALETAVLLSGATIVDQRVCI 75
Cdd:cd12271    9 YSTEAEIRSYFSSCGEVRSVDLMRfpdSGNFRGIAFITFKTEEAAKRALALDGEMLGNRFLKV 71
 
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.
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