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Conserved domains on  [gi|612149808|ref|NP_001127835|]
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RNA-binding protein 20 [Homo sapiens]

Protein Classification

RRM_RBM20 and ZnF_U1 domain-containing protein( domain architecture ID 10190584)

RRM_RBM20 and ZnF_U1 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM_RBM20 cd12685
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 20 (RBM20); This subfamily ...
 518-593 2.06e-50

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 20 (RBM20); This subfamily corresponds to the RRM of RBM20, an alternative splicing regulator associated with dilated cardiomyopathy (DCM). It contains only one copy of RNA-recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


:

Pssm-ID: 410086 [Multi-domain]  Cd Length: 76  Bit Score: 172.04  E-value: 2.06e-50
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 612149808  518 RVVHICNLPEGSCTENDVINLGLPFGKVTNYILMKSTNQAFLEMAYTEAAQAMVQYYQEKSAVINGEKLLIRMSKR 593
Cdd:cd12685     1 RVVHICNLPEGSCTENDVINLGLPFGKVTNYILMRSTNQAFLEMAYTEAAQAMVQYYQEKPAMINEEKLLIRMSKR 76
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
 1159-1193 5.03e-06

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.


:

Pssm-ID: 197732 [Multi-domain]  Cd Length: 35  Bit Score: 44.17  E-value: 5.03e-06
                            10        20        30
                    ....*....|....*....|....*....|....*
gi 612149808   1159 TGFYCKLCGLFYTSEETAKmSHCRSAVHYRNLQKY 1193
Cdd:smart00451    2 GGFYCKLCNVTFTDEISVE-AHLKGKKHKKNVKKR 35
PTZ00395 super family cl33180
Sec24-related protein; Provisional
 185-362 4.25e-04

Sec24-related protein; Provisional


The actual alignment was detected with superfamily member PTZ00395:

Pssm-ID: 185594 [Multi-domain]  Cd Length: 1560  Bit Score: 44.68  E-value: 4.25e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808  185 NLPNQPPSAMVMHPFTGVMPQT-PGQPAVILGIGKTGpAPATAGFYEYGKASSGQTYGPETDGQPGFLPSSASTS--GSV 261
Cdd:PTZ00395  284 NIASHTPNDNIMHAANNPLNNTnDAQRNAIQGDLVRG-APNDKNSFDRGNEKTYQIYGGFHDGSPNAASAGAPFNglGNQ 362

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808  262 TYEGHYSHTGQDGQAAFSKdfyGPNSQGSHVASGFpaeqAGGLKSEVGPllqgTNSQWE-SPHGFSGQSKPDLTAGPMWP 340
Cdd:PTZ00395  363 ADGGHINQVHPDARGAWAG---GPHSNASYNCAAY----SNAAQSNAAQ----SNAGFSnAGYSNPGNSNPGYNNAPNSN 431

                         170       180
                  ....*....|....*....|..
gi 612149808  341 PPHNQPyelydPEEPTSDRTPP 362
Cdd:PTZ00395  432 TPYNNP-----PNSNTPYSNPP 448
PTZ00121 super family cl31754
MAEBL; Provisional
 682-941 2.24e-03

MAEBL; Provisional


The actual alignment was detected with superfamily member PTZ00121:

Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 42.44  E-value: 2.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808  682 ARREEERDPAPWRD-----NGDDKR--DRMDPWAHDRKHHPRQLDKAElDERPEGGRPHREKYPRSGSPNLPHSVSSYKS 754
Cdd:PTZ00121 1569 AKKAEEDKNMALRKaeeakKAEEARieEVMKLYEEEKKMKAEEAKKAE-EAKIKAEELKKAEEEKKKVEQLKKKEAEEKK 1647

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808  755 REDgyyrKEPKAKSDKYLKQQQDApgRSRRKDEARLRESRHPHPDDSGKEDGLGPKvtrAPEGAKAKQNEKNKTKRTDRD 834
Cdd:PTZ00121 1648 KAE----ELKKAEEENKIKAAEEA--KKAEEDKKKAEEAKKAEEDEKKAAEALKKE---AEEAKKAEELKKKEAEEKKKA 1718

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808  835 QEGADDRKENTMAENEAGKEEQEgmeespqsvgrQEKEAEFSDPENTRTKKEQDWESeseaegeswyptnmEELVTVDEV 914
Cdd:PTZ00121 1719 EELKKAEEENKIKAEEAKKEAEE-----------DKKKAEEAKKDEEEKKKIAHLKK--------------EEEKKAEEI 1773

                         250       260
                  ....*....|....*....|....*..
gi 612149808  915 GEEEDFIVEPDIPELEEIVPIDQKDKI 941
Cdd:PTZ00121 1774 RKEKEAVIEEELDEEDEKRRMEVDKKI 1800
 
Name Accession Description Interval E-value
RRM_RBM20 cd12685
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 20 (RBM20); This subfamily ...
 518-593 2.06e-50

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 20 (RBM20); This subfamily corresponds to the RRM of RBM20, an alternative splicing regulator associated with dilated cardiomyopathy (DCM). It contains only one copy of RNA-recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410086 [Multi-domain]  Cd Length: 76  Bit Score: 172.04  E-value: 2.06e-50
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 612149808  518 RVVHICNLPEGSCTENDVINLGLPFGKVTNYILMKSTNQAFLEMAYTEAAQAMVQYYQEKSAVINGEKLLIRMSKR 593
Cdd:cd12685     1 RVVHICNLPEGSCTENDVINLGLPFGKVTNYILMRSTNQAFLEMAYTEAAQAMVQYYQEKPAMINEEKLLIRMSKR 76
hnRNP-L_PTB TIGR01649
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
 516-608 9.69e-14

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: 75.24  E-value: 9.69e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808   516 AGRVVHICNLPEGScTENDVINLGLPFGKVTNYILMKSTNQAFLEMAYTEAAQAMVQYYQEKSAVINGEKLLIRMSKRYK 595
Cdd:TIGR01649    1 PSPVVHVRNLPQDV-VEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQE 79

                           90
                   ....*....|...
gi 612149808   596 elqLKKPGKAVAA 608
Cdd:TIGR01649   80 ---IKRDGNSDFD 89
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
 1159-1193 5.03e-06

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.


Pssm-ID: 197732 [Multi-domain]  Cd Length: 35  Bit Score: 44.17  E-value: 5.03e-06
                            10        20        30
                    ....*....|....*....|....*....|....*
gi 612149808   1159 TGFYCKLCGLFYTSEETAKmSHCRSAVHYRNLQKY 1193
Cdd:smart00451    2 GGFYCKLCNVTFTDEISVE-AHLKGKKHKKNVKKR 35
RRM smart00360
RNA recognition motif;
519-588 2.10e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 43.74  E-value: 2.10e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 612149808    519 VVHICNLPEgSCTENDVINLGLPFGKVTNYILM------KSTNQAFLEMAYTEAAQAMVQYYQEKsaVINGEKLLI 588
Cdd:smart00360    1 TLFVGNLPP-DTTEEELRELFSKFGKVESVRLVrdketgKSKGFAFVEFESEEDAEKALEALNGK--ELDGRPLKV 73
PTZ00395 PTZ00395
Sec24-related protein; Provisional
 185-362 4.25e-04

Sec24-related protein; Provisional


Pssm-ID: 185594 [Multi-domain]  Cd Length: 1560  Bit Score: 44.68  E-value: 4.25e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808  185 NLPNQPPSAMVMHPFTGVMPQT-PGQPAVILGIGKTGpAPATAGFYEYGKASSGQTYGPETDGQPGFLPSSASTS--GSV 261
Cdd:PTZ00395  284 NIASHTPNDNIMHAANNPLNNTnDAQRNAIQGDLVRG-APNDKNSFDRGNEKTYQIYGGFHDGSPNAASAGAPFNglGNQ 362

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808  262 TYEGHYSHTGQDGQAAFSKdfyGPNSQGSHVASGFpaeqAGGLKSEVGPllqgTNSQWE-SPHGFSGQSKPDLTAGPMWP 340
Cdd:PTZ00395  363 ADGGHINQVHPDARGAWAG---GPHSNASYNCAAY----SNAAQSNAAQ----SNAGFSnAGYSNPGNSNPGYNNAPNSN 431

                         170       180
                  ....*....|....*....|..
gi 612149808  341 PPHNQPyelydPEEPTSDRTPP 362
Cdd:PTZ00395  432 TPYNNP-----PNSNTPYSNPP 448
PTZ00121 PTZ00121
MAEBL; Provisional
 682-941 2.24e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 42.44  E-value: 2.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808  682 ARREEERDPAPWRD-----NGDDKR--DRMDPWAHDRKHHPRQLDKAElDERPEGGRPHREKYPRSGSPNLPHSVSSYKS 754
Cdd:PTZ00121 1569 AKKAEEDKNMALRKaeeakKAEEARieEVMKLYEEEKKMKAEEAKKAE-EAKIKAEELKKAEEEKKKVEQLKKKEAEEKK 1647

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808  755 REDgyyrKEPKAKSDKYLKQQQDApgRSRRKDEARLRESRHPHPDDSGKEDGLGPKvtrAPEGAKAKQNEKNKTKRTDRD 834
Cdd:PTZ00121 1648 KAE----ELKKAEEENKIKAAEEA--KKAEEDKKKAEEAKKAEEDEKKAAEALKKE---AEEAKKAEELKKKEAEEKKKA 1718

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808  835 QEGADDRKENTMAENEAGKEEQEgmeespqsvgrQEKEAEFSDPENTRTKKEQDWESeseaegeswyptnmEELVTVDEV 914
Cdd:PTZ00121 1719 EELKKAEEENKIKAEEAKKEAEE-----------DKKKAEEAKKDEEEKKKIAHLKK--------------EEEKKAEEI 1773

                         250       260
                  ....*....|....*....|....*..
gi 612149808  915 GEEEDFIVEPDIPELEEIVPIDQKDKI 941
Cdd:PTZ00121 1774 RKEKEAVIEEELDEEDEKRRMEVDKKI 1800
 
Name Accession Description Interval E-value
RRM_RBM20 cd12685
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 20 (RBM20); This subfamily ...
 518-593 2.06e-50

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 20 (RBM20); This subfamily corresponds to the RRM of RBM20, an alternative splicing regulator associated with dilated cardiomyopathy (DCM). It contains only one copy of RNA-recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410086 [Multi-domain]  Cd Length: 76  Bit Score: 172.04  E-value: 2.06e-50
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 612149808  518 RVVHICNLPEGSCTENDVINLGLPFGKVTNYILMKSTNQAFLEMAYTEAAQAMVQYYQEKSAVINGEKLLIRMSKR 593
Cdd:cd12685     1 RVVHICNLPEGSCTENDVINLGLPFGKVTNYILMRSTNQAFLEMAYTEAAQAMVQYYQEKPAMINEEKLLIRMSKR 76
RRM1_PTBP1_hnRNPL_like cd12421
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
 519-593 5.99e-33

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 RRM1 of the majority of family members that include 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. 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. The 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. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM.


Pssm-ID: 409855 [Multi-domain]  Cd Length: 74  Bit Score: 121.91  E-value: 5.99e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 612149808  519 VVHICNLPEgSCTENDVINLGLPFGKVTNYILMKSTNQAFLEMAYTEAAQAMVQYYQEKSAVINGEKLLIRMSKR 593
Cdd:cd12421     1 VVHIRNLPP-DATEADLVALGLPFGKVTNVLLLKGKNQALVEMEDVESASSMVNYYTTVPPLIRGRPVYVQYSNH 74
RRM2_MATR3 cd12715
RNA recognition motif 2 (RRM2) found in vertebrate matrin-3; This subgroup corresponds to the ...
 518-597 3.62e-24

RNA recognition motif 2 (RRM2) found in vertebrate matrin-3; This subgroup corresponds to the RRM2 of Matrin 3 (MATR3 or P130), a highly conserved inner nuclear matrix protein with a bipartite nuclear localization signal (NLS), two zinc finger domains predicted to bind DNA, and two RNA recognition motifs (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that are known to interact with RNA. MATR3 has been implicated in various biological processes. It is involved in RNA processing by interacting with other nuclear proteins to anchor hyperedited RNAs to the nuclear matrix. It plays a role in mRNA stabilization through maintaining the stability of certain mRNA species. Besides, it modulates the activity of proximal promoters by binding to highly repetitive sequences of matrix/scaffold attachment region (MAR/SAR). The phosphorylation of MATR3 is assumed to cause neuronal death. It is phosphorylated by the protein kinase ATM, which activates the cellular response to double strand breaks in the DNA. Its phosphorylation by protein kinase A (PKA) is responsible for the activation of the N-methyl-d-aspartic acid (NMDA) receptor. Furthermore, MATR3 has been identified as both a Ca2+-dependent CaM-binding protein and a downstream substrate of caspases. Additional research indicates that matrin 3 also binds Rev/Rev responsive element (RRE)-containing viral RNA and functions as a cofactor that mediates the post-transcriptional regulation of HIV-1.


Pssm-ID: 410114 [Multi-domain]  Cd Length: 80  Bit Score: 97.21  E-value: 3.62e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808  518 RVVHICNLPEGSCTENDVINLGLPFGKVTNYILMKSTNQAFLEMAYTEAAQAMVQYYQEKSAVINGEKLLIRMSKRYKEL 597
Cdd:cd12715     1 RVIHLSNLPHSGYSDAAVLKLAEPYGKVKNYILMRMKNQAFLEMESREDAMAMVDHCKKKPLWFQGRCVKVDLSQKYKTL 80
RRM1_2_MATR3_like cd12436
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in the matrin 3 family of nuclear proteins; ...
 518-593 1.02e-21

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in the matrin 3 family of nuclear proteins; This subfamily corresponds to the RRM of the matrin 3 family of nuclear proteins consisting of Matrin 3 (MATR3), nuclear protein 220 (NP220) and similar proteins. MATR3 is a highly conserved inner nuclear matrix protein that has been implicated in various biological processes. NP220 is a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). Both, Matrin 3 and NP220, contain two RNA recognition motif (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Cys2-His2 zinc finger-like motif at the C-terminal region.


Pssm-ID: 409870 [Multi-domain]  Cd Length: 76  Bit Score: 90.10  E-value: 1.02e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 612149808  518 RVVHICNLPEGSCTENDVINLGLPFGKVTNYILMKSTNQAFLEMAYTEAAQAMVQYYQEKSAVINGEKLLIRMSKR 593
Cdd:cd12436     1 RVLYLTGLPVSKYSEEDVLKLAEPFGKVNNVLLIRSKREAFIEMETAEDAQAMLSYCKTKPITIKGKKVKVSVSQK 76
RRM1_PTBP1 cd12777
RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 1 (PTB) ...
 518-598 3.06e-21

RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 1 (PTB); This subgroup corresponds to the RRM1 of PTB, also known as 58 kDa RNA-binding protein PPTB-1 or heterogeneous nuclear ribonucleoprotein I (hnRNP I), an important negative regulator of alternative splicing in mammalian cells. PTB also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTB contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RRM1 and RRM2 are independent from each other and separated by flexible linkers. By contrast, there is an unusual and conserved interdomain interaction between RRM3 and RRM4. It is widely held that only RRMs 3 and 4 are involved in RNA binding and RRM2 mediates PTB homodimer formation. However, new evidence shows that the RRMs 1 and 2 also contribute substantially to RNA binding. Moreover, PTB may not always dimerize to repress splicing. It is a monomer in solution.


Pssm-ID: 410169 [Multi-domain]  Cd Length: 81  Bit Score: 88.88  E-value: 3.06e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808  518 RVVHICNLPeGSCTENDVINLGLPFGKVTNYILMKSTNQAFLEMAYTEAAQAMVQYYQEKSAVINGEKLLIRMSKrYKEL 597
Cdd:cd12777     1 RVIHVRKLP-NDVTEAEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSN-HKEL 78


                  .
gi 612149808  598 Q 598
Cdd:cd12777    79 K 79
RRM1_PTBP1_like cd12688
RNA recognition motif 1 (RRM1) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) ...
 518-598 2.49e-20

RNA recognition motif 1 (RRM1) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins; This subfamily corresponds to the RRM1 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and functions at several 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. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein and negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410089 [Multi-domain]  Cd Length: 81  Bit Score: 86.21  E-value: 2.49e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808  518 RVVHICNLPeGSCTENDVINLGLPFGKVTNYILMKSTNQAFLEMAYTEAAQAMVQYYQEKSAVINGEKLLIRMSKrYKEL 597
Cdd:cd12688     1 RVLHIRKLP-CDVTEAEVISLGLPFGKVTNLLMLKGKNQAFLEMATEEAAVTMVNYYTPVTPHLRSQPIYIQYSN-HKEL 78


                  .
gi 612149808  598 Q 598
Cdd:cd12688    79 K 79
RRM1_PTBP2 cd12778
RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 2 ...
 518-598 7.64e-19

RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 2 (PTBP2); This subgroup corresponds to the RRM1 of PTBP2, also known as neural polypyrimidine tract-binding protein or neurally-enriched homolog of PTB (nPTB), highly homologous to polypyrimidine tract binding protein (PTB) and 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. PTBP2 contains four RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410170 [Multi-domain]  Cd Length: 82  Bit Score: 82.03  E-value: 7.64e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808  518 RVVHICNLPeGSCTENDVINLGLPFGKVTNYILMKSTNQAFLEMAYTEAAQAMVQYYQEKSAVINGEKLLIRMSKrYKEL 597
Cdd:cd12778     2 RVLHIRKLP-GEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYTAVTPHLRNQPIYIQYSN-HKEL 79


                  .
gi 612149808  598 Q 598
Cdd:cd12778    80 K 80
RRM1_ROD1 cd12779
RNA recognition motif 1 (RRM1) found in vertebrate regulator of differentiation 1 (Rod1); This ...
 515-598 1.21e-16

RNA recognition motif 1 (RRM1) found in vertebrate regulator of differentiation 1 (Rod1); This subgroup corresponds to the RRM1 of ROD1 coding protein Rod1, 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 that negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. Rod1 contains four repeats of RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and does have RNA binding activities.


Pssm-ID: 410171 [Multi-domain]  Cd Length: 90  Bit Score: 76.21  E-value: 1.21e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808  515 GAGRVVHICNLPEgSCTENDVINLGLPFGKVTNYILMKSTNQAFLEMAYTEAAQAMVQYYQEKSAVINGEKLLIRMSKrY 594
Cdd:cd12779     3 SPSRVLHIRKIPN-DVTEAEVISLGLPFGKVTNLLMLKGKNQAFLEMASEEAAVTMVNYYTTVTPHLRNQPVYIQYSN-H 80


                  ....
gi 612149808  595 KELQ 598
Cdd:cd12779    81 RELK 84
RRM1_2_NP220 cd12716
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); ...
 519-590 4.43e-16

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); This subgroup corresponds to RRM1 and RRM2 of NP220, also termed zinc finger protein 638 (ZN638), or cutaneous T-cell lymphoma-associated antigen se33-1, or zinc finger matrin-like protein, a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). NP220 contains multiple domains, including MH1, MH2, and MH3, domains homologous to the acidic nuclear protein matrin 3; RS, an arginine/serine-rich domain commonly found in pre-mRNA splicing factors; PstI-HindIII, a domain essential for DNA binding; acidic repeat, a domain with nine repeats of the sequence LVTVDEVIEEEDL; and a Cys2-His2 zinc finger-like motif that is also present in matrin 3. It may be involved in packaging, transferring, or processing transcripts. This subgroup corresponds to the domain of MH2 that contains two tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410115 [Multi-domain]  Cd Length: 76  Bit Score: 73.97  E-value: 4.43e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 612149808  519 VVHICNLPEGSCTENDVINLGLPFGKVTNYILMKSTNQAFLEMAYTEAAQAMVQYYQEKSAVINGEKLLIRM 590
Cdd:cd12716     2 VVLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNFKEAVDSMVKYYETFPVLVGGKRLKISM 73
RRM1_MATR3 cd12714
RNA recognition motif 1 (RRM1) found in vertebrate matrin-3; This subgroup corresponds to the ...
 518-593 1.09e-14

RNA recognition motif 1 (RRM1) found in vertebrate matrin-3; This subgroup corresponds to the RRM1 of Matrin 3 (MATR3 or P130), a highly conserved inner nuclear matrix protein with a bipartite nuclear localization signal (NLS), two zinc finger domains predicted to bind DNA, and two RNA recognition motifs (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that are known to interact with RNA. MATR3 has been implicated in various biological processes. It is involved in RNA processing by interacting with other nuclear proteins to anchor hyperedited RNAs to the nuclear matrix. It plays a role in mRNA stabilization through maintaining the stability of certain mRNA species. Besides, it modulates the activity of proximal promoters by binding to highly repetitive sequences of matrix/scaffold attachment region (MAR/SAR). The phosphorylation of MATR3 is assumed to cause neuronal death. It is phosphorylated by the protein kinase ATM, which activates the cellular response to double strand breaks in the DNA. Its phosphorylation by protein kinase A (PKA) is responsible for the activation of the N-methyl-d-aspartic acid (NMDA) receptor. Furthermore, MATR3 has been identified as both a Ca2+-dependent CaM-binding protein and a downstream substrate of caspases. Additional research indicates that matrin 3 also binds Rev/Rev responsive element (RRE)-containing viral RNA and functions as a cofactor that mediates the post-transcriptional regulation of HIV-1.


Pssm-ID: 410113 [Multi-domain]  Cd Length: 76  Bit Score: 69.96  E-value: 1.09e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 612149808  518 RVVHICNLPEGSCTENDVINLGLPFGKVTNYILMKSTNQAFLEMAYTEAAQAMVQYYQEKSAVINGEKLLIRMSKR 593
Cdd:cd12714     1 RVVHIMDFQRGKNLRYQLLQLAEPFGIITNHLILNKINEAFIEMATTEEAQAAVDYYMTTPALVFGKPVRVHLSQK 76
hnRNP-L_PTB TIGR01649
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
 516-608 9.69e-14

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: 75.24  E-value: 9.69e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808   516 AGRVVHICNLPEGScTENDVINLGLPFGKVTNYILMKSTNQAFLEMAYTEAAQAMVQYYQEKSAVINGEKLLIRMSKRYK 595
Cdd:TIGR01649    1 PSPVVHVRNLPQDV-VEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQE 79

                           90
                   ....*....|...
gi 612149808   596 elqLKKPGKAVAA 608
Cdd:TIGR01649   80 ---IKRDGNSDFD 89
RRM1_PTBPH3 cd12687
RNA recognition motif 1 (RRM1) found in plant polypyrimidine tract-binding protein homolog 3 ...
 518-592 2.83e-11

RNA recognition motif 1 (RRM1) found in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3); This subfamily corresponds to the RRM1 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that 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. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410088 [Multi-domain]  Cd Length: 75  Bit Score: 60.27  E-value: 2.83e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 612149808  518 RVVHICNL-PEgsCTENDVINLGLPFGKVTNYILMKSTNQAFLEMAYTEAAQAMVQYYQEKSAVINGEKLLIRMSK 592
Cdd:cd12687     1 KVLHVRNVgHE--ISENDLLQLAQPFGVVTKLVMLRAKNQALLQMQDVSAAISALQFYTSVQPSIRGRNVYIQFSS 74
RRM1_PTBPH1_PTBPH2 cd12686
RNA recognition motif 1 (RRM1) found in plant polypyrimidine tract-binding protein homolog 1 ...
 518-593 2.09e-08

RNA recognition motif 1 (RRM1) found in plant polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2); This subfamily corresponds to the RRM1 of PTBPH1 and PTBPH2. Although their biological roles remain unclear, PTBPH1 and PTBPH2 show significant sequence similarity to polypyrimidine tract binding protein (PTB) that 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. Both, PTBPH1 and PTBPH2, contain three RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410087 [Multi-domain]  Cd Length: 81  Bit Score: 52.50  E-value: 2.09e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808  518 RVVHICNLPEgSCTENDVINLGLPFGKVTNYILMKST--NQAFLEMAYTEAAQAMVQYYQEKS--AVINGEKLLIRMSKR 593
Cdd:cd12686     3 KVLHLRNLPW-ECTEEELIELCKPFGTVVNTKCNVGAnkNQAFVEFADLNQAISMVSYYASSSepAQVRGKTVYLQYSNR 81
RRM1_hnRNPL_like cd12689
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) ...
 518-592 6.32e-07

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins; This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. 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 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. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410090 [Multi-domain]  Cd Length: 80  Bit Score: 48.04  E-value: 6.32e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 612149808  518 RVVHICNLPEGsCTENDVINLGLPFGKVTNYILMKSTNQAFLEMAYTEAAQAMVQYYQEKSAVINGEKLLIRMSK 592
Cdd:cd12689     3 PVVHVRGLSEH-VTEADLVEALQNFGPISYVTMMPKKRQALVEFEDIEGAKACVNYAQQNPIYVGGRPAYFNYST 76
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
 1159-1193 5.03e-06

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.


Pssm-ID: 197732 [Multi-domain]  Cd Length: 35  Bit Score: 44.17  E-value: 5.03e-06
                            10        20        30
                    ....*....|....*....|....*....|....*
gi 612149808   1159 TGFYCKLCGLFYTSEETAKmSHCRSAVHYRNLQKY 1193
Cdd:smart00451    2 GGFYCKLCNVTFTDEISVE-AHLKGKKHKKNVKKR 35
RRM smart00360
RNA recognition motif;
519-588 2.10e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 43.74  E-value: 2.10e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 612149808    519 VVHICNLPEgSCTENDVINLGLPFGKVTNYILM------KSTNQAFLEMAYTEAAQAMVQYYQEKsaVINGEKLLI 588
Cdd:smart00360    1 TLFVGNLPP-DTTEEELRELFSKFGKVESVRLVrdketgKSKGFAFVEFESEEDAEKALEALNGK--ELDGRPLKV 73
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 520-589 6.56e-05

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: 42.27  E-value: 6.56e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 612149808  520 VHICNLPEgSCTENDVINLGLPFGKVTNYILM-----KSTNQAFLEMAYTEAAQAMVQYYQEKsaVINGEKLLIR 589
Cdd:cd00590     1 LFVGNLPP-DTTEEDLRELFSKFGEVVSVRIVrdrdgKSKGFAFVEFESPEDAEKALEALNGT--ELGGRPLKVS 72
PTZ00395 PTZ00395
Sec24-related protein; Provisional
 185-362 4.25e-04

Sec24-related protein; Provisional


Pssm-ID: 185594 [Multi-domain]  Cd Length: 1560  Bit Score: 44.68  E-value: 4.25e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808  185 NLPNQPPSAMVMHPFTGVMPQT-PGQPAVILGIGKTGpAPATAGFYEYGKASSGQTYGPETDGQPGFLPSSASTS--GSV 261
Cdd:PTZ00395  284 NIASHTPNDNIMHAANNPLNNTnDAQRNAIQGDLVRG-APNDKNSFDRGNEKTYQIYGGFHDGSPNAASAGAPFNglGNQ 362

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808  262 TYEGHYSHTGQDGQAAFSKdfyGPNSQGSHVASGFpaeqAGGLKSEVGPllqgTNSQWE-SPHGFSGQSKPDLTAGPMWP 340
Cdd:PTZ00395  363 ADGGHINQVHPDARGAWAG---GPHSNASYNCAAY----SNAAQSNAAQ----SNAGFSnAGYSNPGNSNPGYNNAPNSN 431

                         170       180
                  ....*....|....*....|..
gi 612149808  341 PPHNQPyelydPEEPTSDRTPP 362
Cdd:PTZ00395  432 TPYNNP-----PNSNTPYSNPP 448
PTZ00121 PTZ00121
MAEBL; Provisional
 682-941 2.24e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 42.44  E-value: 2.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808  682 ARREEERDPAPWRD-----NGDDKR--DRMDPWAHDRKHHPRQLDKAElDERPEGGRPHREKYPRSGSPNLPHSVSSYKS 754
Cdd:PTZ00121 1569 AKKAEEDKNMALRKaeeakKAEEARieEVMKLYEEEKKMKAEEAKKAE-EAKIKAEELKKAEEEKKKVEQLKKKEAEEKK 1647

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808  755 REDgyyrKEPKAKSDKYLKQQQDApgRSRRKDEARLRESRHPHPDDSGKEDGLGPKvtrAPEGAKAKQNEKNKTKRTDRD 834
Cdd:PTZ00121 1648 KAE----ELKKAEEENKIKAAEEA--KKAEEDKKKAEEAKKAEEDEKKAAEALKKE---AEEAKKAEELKKKEAEEKKKA 1718

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612149808  835 QEGADDRKENTMAENEAGKEEQEgmeespqsvgrQEKEAEFSDPENTRTKKEQDWESeseaegeswyptnmEELVTVDEV 914
Cdd:PTZ00121 1719 EELKKAEEENKIKAEEAKKEAEE-----------DKKKAEEAKKDEEEKKKIAHLKK--------------EEEKKAEEI 1773

                         250       260
                  ....*....|....*....|....*..
gi 612149808  915 GEEEDFIVEPDIPELEEIVPIDQKDKI 941
Cdd:PTZ00121 1774 RKEKEAVIEEELDEEDEKRRMEVDKKI 1800
 
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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