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Conserved domains on  [gi|1720417259|ref|XP_030111075|]
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zinc finger protein 638 isoform X9 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RRM1_2_NP220 cd12716
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); ...
879-953 3.07e-36

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: 132.13  E-value: 3.07e-36
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720417259  879 SVVFISNLPNKGYSTEEIYNLAKPFGALKDILVLSSHKKAYIEIN-KKSADSMVKFYTCFPISMDGNQLSISMAPE 953
Cdd:cd12716      1 CVVLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNfKEAVDSMVKYYETFPVLVGGKRLKISMAEK 76
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
676-751 6.90e-28

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).


The actual alignment was detected with superfamily member cd12716:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 76  Bit Score: 108.25  E-value: 6.90e-28
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720417259  676 SILLVSELPEDGFTEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSVKVCVPGK 751
Cdd:cd12716      1 CVVLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNFKEAVDSMVKYYETFPVLVGGKRLKISMAEK 76
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
983-1041 4.76e-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).


The actual alignment was detected with superfamily member cd12715:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 80  Bit Score: 52.14  E-value: 4.76e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720417259  983 RFVHLDNLPEDGLQ--CVLCVGHQFGKVDRYMFMSNKNKVILQLESPESALSMYNFLKQNP 1041
Cdd:cd12715      1 RVIHLSNLPHSGYSdaAVLKLAEPYGKVKNYILMRMKNQAFLEMESREDAMAMVDHCKKKP 61
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
1886-1918 1.67e-07

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: 49.17  E-value: 1.67e-07
                            10        20        30
                    ....*....|....*....|....*....|...
gi 1720417259  1886 GFFCPICSLFYSGEKAMANHCKSTRHKQNTEKF 1918
Cdd:smart00451    3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKKR 35
hnRNP-L_PTB super family cl25888
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
880-1180 5.35e-04

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).


The actual alignment was detected with superfamily member TIGR01649:

Pssm-ID: 273733 [Multi-domain]  Cd Length: 481  Bit Score: 44.81  E-value: 5.35e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  880 VVFISNLPNKgySTE-EIYNLAKPFGALKDILVLSSHKKAYIEI-NKKSADSMVKFYTCFPISMDGNQLSISMApEHVDL 957
Cdd:TIGR01649    4 VVHVRNLPQD--VVEaDLVEALIPFGPVSYVMMLPGKRQALVEFeDEESAKACVNFATSVPIYIRGQPAFFNYS-TSQEI 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  958 KdeealfTTLIQENDPeANIDKIYnRFVHLDNLPEDGLQCVLCVGHQFGKVDRYMFMSNKNKV--ILQLESPESALSMYN 1035
Cdd:TIGR01649   81 K------RDGNSDFDS-AGPNKVL-RVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNVFqaLVEFESVNSAQHAKA 152
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259 1036 FLkqNPQNIgeHVLTCTL----SPKTDSEVQRKNDlelgKGSTFS-PDLKNSPvDESEVQTAADSSSV----KPSEVEEE 1106
Cdd:TIGR01649  153 AL--NGADI--YNGCCTLkieyAKPTRLNVKYNDD----DSRDYTnPDLPGRR-DPGLDQTHRQRQPAllgqHPSSYGHD 223
                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1720417259 1107 TTSNIGTETSVHQEELGKEEPKQALcesdfAIQTLELEAQGAEVSIEIPLVASTPANIELFSENIDESALNQQM 1180
Cdd:TIGR01649  224 GYSSHGGPLAPLAGGDRMGPPHGPP-----SRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDR 292
PTZ00121 super family cl31754
MAEBL; Provisional
740-877 2.03e-03

MAEBL; Provisional


The actual alignment was detected with superfamily member PTZ00121:

Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 43.21  E-value: 2.03e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  740 KGKSVKVCVPGKKKPQNK----EMKKKPSDIKKSSASALKKETDASKTMETVSSSSSAKSGQIKSSTvkvNKCAAKSGKK 815
Cdd:PTZ00121  1297 KAEEKKKADEAKKKAEEAkkadEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAE---EKAEAAEKKK 1373
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720417259  816 SLEAKKSGNIKNKDSNKPvtvPANSEIKASSEDKatgKSAEESPSGTLEATEKEPVNKESEE 877
Cdd:PTZ00121  1374 EEAKKKADAAKKKAEEKK---KADEAKKKAEEDK---KKADELKKAAAAKKKADEAKKKAEE 1429
 
Name Accession Description Interval E-value
RRM1_2_NP220 cd12716
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); ...
879-953 3.07e-36

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: 132.13  E-value: 3.07e-36
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720417259  879 SVVFISNLPNKGYSTEEIYNLAKPFGALKDILVLSSHKKAYIEIN-KKSADSMVKFYTCFPISMDGNQLSISMAPE 953
Cdd:cd12716      1 CVVLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNfKEAVDSMVKYYETFPVLVGGKRLKISMAEK 76
RRM1_2_NP220 cd12716
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); ...
676-751 6.90e-28

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: 108.25  E-value: 6.90e-28
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720417259  676 SILLVSELPEDGFTEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSVKVCVPGK 751
Cdd:cd12716      1 CVVLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNFKEAVDSMVKYYETFPVLVGGKRLKISMAEK 76
RRM2_MATR3 cd12715
RNA recognition motif 2 (RRM2) found in vertebrate matrin-3; This subgroup corresponds to the ...
983-1041 4.76e-08

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: 52.14  E-value: 4.76e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720417259  983 RFVHLDNLPEDGLQ--CVLCVGHQFGKVDRYMFMSNKNKVILQLESPESALSMYNFLKQNP 1041
Cdd:cd12715      1 RVIHLSNLPHSGYSdaAVLKLAEPYGKVKNYILMRMKNQAFLEMESREDAMAMVDHCKKKP 61
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
1886-1918 1.67e-07

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: 49.17  E-value: 1.67e-07
                            10        20        30
                    ....*....|....*....|....*....|...
gi 1720417259  1886 GFFCPICSLFYSGEKAMANHCKSTRHKQNTEKF 1918
Cdd:smart00451    3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKKR 35
RRM smart00360
RNA recognition motif;
678-746 1.48e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 44.51  E-value: 1.48e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1720417259   678 LLVSELPEDgFTEEDIRKAFLPFGKISDVLLVP------CRNEAYLEMELRKAVTSIMKYIETMplVIKGKSVKV 746
Cdd:smart00360    2 LFVGNLPPD-TTEEELRELFSKFGKVESVRLVRdketgkSKGFAFVEFESEEDAEKALEALNGK--ELDGRPLKV 73
hnRNP-L_PTB TIGR01649
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
983-1047 5.31e-04

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: 44.81  E-value: 5.31e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720417259  983 RFVHLDNLPEDGLQC-VLCVGHQFGKVDRYMFMSNKNKVILQLESPESALSMYNFLKQNPQNIGEH 1047
Cdd:TIGR01649    3 PVVHVRNLPQDVVEAdLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQ 68
hnRNP-L_PTB TIGR01649
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
880-1180 5.35e-04

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: 44.81  E-value: 5.35e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  880 VVFISNLPNKgySTE-EIYNLAKPFGALKDILVLSSHKKAYIEI-NKKSADSMVKFYTCFPISMDGNQLSISMApEHVDL 957
Cdd:TIGR01649    4 VVHVRNLPQD--VVEaDLVEALIPFGPVSYVMMLPGKRQALVEFeDEESAKACVNFATSVPIYIRGQPAFFNYS-TSQEI 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  958 KdeealfTTLIQENDPeANIDKIYnRFVHLDNLPEDGLQCVLCVGHQFGKVDRYMFMSNKNKV--ILQLESPESALSMYN 1035
Cdd:TIGR01649   81 K------RDGNSDFDS-AGPNKVL-RVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNVFqaLVEFESVNSAQHAKA 152
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259 1036 FLkqNPQNIgeHVLTCTL----SPKTDSEVQRKNDlelgKGSTFS-PDLKNSPvDESEVQTAADSSSV----KPSEVEEE 1106
Cdd:TIGR01649  153 AL--NGADI--YNGCCTLkieyAKPTRLNVKYNDD----DSRDYTnPDLPGRR-DPGLDQTHRQRQPAllgqHPSSYGHD 223
                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1720417259 1107 TTSNIGTETSVHQEELGKEEPKQALcesdfAIQTLELEAQGAEVSIEIPLVASTPANIELFSENIDESALNQQM 1180
Cdd:TIGR01649  224 GYSSHGGPLAPLAGGDRMGPPHGPP-----SRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDR 292
zf-C2H2_jaz pfam12171
Zinc-finger double-stranded RNA-binding; This domain family is found in archaea and eukaryotes, ...
1887-1912 1.58e-03

Zinc-finger double-stranded RNA-binding; This domain family is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localize in the nucleus, particularly the nucleolus. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localization.


Pssm-ID: 432381 [Multi-domain]  Cd Length: 27  Bit Score: 37.53  E-value: 1.58e-03
                           10        20
                   ....*....|....*....|....*.
gi 1720417259 1887 FFCPICSLFYSGEKAMANHCKSTRHK 1912
Cdd:pfam12171    2 FYCVLCDKYFKSENALQNHLKSKKHK 27
hnRNP-L_PTB TIGR01649
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
680-744 1.85e-03

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


Pssm-ID: 273733 [Multi-domain]  Cd Length: 481  Bit Score: 42.88  E-value: 1.85e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1720417259  680 VSELPEDgFTEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSV 744
Cdd:TIGR01649    7 VRNLPQD-VVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPA 70
PTZ00121 PTZ00121
MAEBL; Provisional
740-877 2.03e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 43.21  E-value: 2.03e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  740 KGKSVKVCVPGKKKPQNK----EMKKKPSDIKKSSASALKKETDASKTMETVSSSSSAKSGQIKSSTvkvNKCAAKSGKK 815
Cdd:PTZ00121  1297 KAEEKKKADEAKKKAEEAkkadEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAE---EKAEAAEKKK 1373
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720417259  816 SLEAKKSGNIKNKDSNKPvtvPANSEIKASSEDKatgKSAEESPSGTLEATEKEPVNKESEE 877
Cdd:PTZ00121  1374 EEAKKKADAAKKKAEEKK---KADEAKKKAEEDK---KKADELKKAAAAKKKADEAKKKAEE 1429
 
Name Accession Description Interval E-value
RRM1_2_NP220 cd12716
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); ...
879-953 3.07e-36

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: 132.13  E-value: 3.07e-36
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720417259  879 SVVFISNLPNKGYSTEEIYNLAKPFGALKDILVLSSHKKAYIEIN-KKSADSMVKFYTCFPISMDGNQLSISMAPE 953
Cdd:cd12716      1 CVVLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNfKEAVDSMVKYYETFPVLVGGKRLKISMAEK 76
RRM1_2_NP220 cd12716
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); ...
676-751 6.90e-28

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: 108.25  E-value: 6.90e-28
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720417259  676 SILLVSELPEDGFTEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSVKVCVPGK 751
Cdd:cd12716      1 CVVLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNFKEAVDSMVKYYETFPVLVGGKRLKISMAEK 76
RRM1_2_MATR3_like cd12436
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in the matrin 3 family of nuclear proteins; ...
676-751 1.99e-20

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: 87.01  E-value: 1.99e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720417259  676 SILLVSELPEDGFTEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSVKVCVPGK 751
Cdd:cd12436      1 RVLYLTGLPVSKYSEEDVLKLAEPFGKVNNVLLIRSKREAFIEMETAEDAQAMLSYCKTKPITIKGKKVKVSVSQK 76
RRM2_MATR3 cd12715
RNA recognition motif 2 (RRM2) found in vertebrate matrin-3; This subgroup corresponds to the ...
677-753 8.38e-13

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: 65.63  E-value: 8.38e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720417259  677 ILLVSELPEDGFTEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSVKVCVPGKKK 753
Cdd:cd12715      2 VIHLSNLPHSGYSDAAVLKLAEPYGKVKNYILMRMKNQAFLEMESREDAMAMVDHCKKKPLWFQGRCVKVDLSQKYK 78
RRM1_2_MATR3_like cd12436
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in the matrin 3 family of nuclear proteins; ...
879-951 2.41e-09

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: 55.43  E-value: 2.41e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1720417259  879 SVVFISNLPNKGYSTEEIYNLAKPFGALKDILVLSSHKKAYIEINKKS-ADSMVKFYTCFPISMDGNQLSISMA 951
Cdd:cd12436      1 RVLYLTGLPVSKYSEEDVLKLAEPFGKVNNVLLIRSKREAFIEMETAEdAQAMLSYCKTKPITIKGKKVKVSVS 74
RRM1_PTBP1_hnRNPL_like cd12421
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
683-744 1.46e-08

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: 53.35  E-value: 1.46e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720417259  683 LPEDGfTEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSV 744
Cdd:cd12421      7 LPPDA-TEADLVALGLPFGKVTNVLLLKGKNQALVEMEDVESASSMVNYYTTVPPLIRGRPV 67
RRM2_MATR3 cd12715
RNA recognition motif 2 (RRM2) found in vertebrate matrin-3; This subgroup corresponds to the ...
983-1041 4.76e-08

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: 52.14  E-value: 4.76e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720417259  983 RFVHLDNLPEDGLQ--CVLCVGHQFGKVDRYMFMSNKNKVILQLESPESALSMYNFLKQNP 1041
Cdd:cd12715      1 RVIHLSNLPHSGYSdaAVLKLAEPYGKVKNYILMRMKNQAFLEMESREDAMAMVDHCKKKP 61
RRM2_MATR3 cd12715
RNA recognition motif 2 (RRM2) found in vertebrate matrin-3; This subgroup corresponds to the ...
880-957 9.71e-08

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: 50.99  E-value: 9.71e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1720417259  880 VVFISNLPNKGYSTEEIYNLAKPFGALKDILVLSSHKKAYIEI-NKKSADSMVKFYTCFPISMDGNQLSISMAPEHVDL 957
Cdd:cd12715      2 VIHLSNLPHSGYSDAAVLKLAEPYGKVKNYILMRMKNQAFLEMeSREDAMAMVDHCKKKPLWFQGRCVKVDLSQKYKTL 80
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
1886-1918 1.67e-07

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: 49.17  E-value: 1.67e-07
                            10        20        30
                    ....*....|....*....|....*....|...
gi 1720417259  1886 GFFCPICSLFYSGEKAMANHCKSTRHKQNTEKF 1918
Cdd:smart00451    3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKKR 35
RRM1_PTBP1 cd12777
RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 1 (PTB) ...
677-746 2.70e-07

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: 49.98  E-value: 2.70e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  677 ILLVSELPEDgFTEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSVKV 746
Cdd:cd12777      2 VIHVRKLPND-VTEAEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI 70
RRM_RBM20 cd12685
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 20 (RBM20); This subfamily ...
676-746 2.36e-06

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: 47.23  E-value: 2.36e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720417259  676 SILLVSELPEDGFTEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSVKV 746
Cdd:cd12685      1 RVVHICNLPEGSCTENDVINLGLPFGKVTNYILMRSTNQAFLEMAYTEAAQAMVQYYQEKPAMINEEKLLI 71
RRM_RBM20 cd12685
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 20 (RBM20); This subfamily ...
879-951 7.08e-06

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: 45.69  E-value: 7.08e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1720417259  879 SVVFISNLPNKGYSTEEIYNLAKPFGALKDILVLSSHKKAYIEIN-KKSADSMVKFYTCFPISMDGNQLSISMA 951
Cdd:cd12685      1 RVVHICNLPEGSCTENDVINLGLPFGKVTNYILMRSTNQAFLEMAyTEAAQAMVQYYQEKPAMINEEKLLIRMS 74
RRM1_PTBP1_hnRNPL_like cd12421
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
985-1045 7.17e-06

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: 45.64  E-value: 7.17e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720417259  985 VHLDNLPEDGLQC-VLCVGHQFGKVDRYMFMSNKNKVILQLESPESALSMYNFLKQNPQNIG 1045
Cdd:cd12421      2 VHIRNLPPDATEAdLVALGLPFGKVTNVLLLKGKNQALVEMEDVESASSMVNYYTTVPPLIR 63
RRM smart00360
RNA recognition motif;
678-746 1.48e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 44.51  E-value: 1.48e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1720417259   678 LLVSELPEDgFTEEDIRKAFLPFGKISDVLLVP------CRNEAYLEMELRKAVTSIMKYIETMplVIKGKSVKV 746
Cdd:smart00360    2 LFVGNLPPD-TTEEELRELFSKFGKVESVRLVRdketgkSKGFAFVEFESEEDAEKALEALNGK--ELDGRPLKV 73
RRM1_ROD1 cd12779
RNA recognition motif 1 (RRM1) found in vertebrate regulator of differentiation 1 (Rod1); This ...
673-746 3.44e-05

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: 44.24  E-value: 3.44e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1720417259  673 SSNSILLVSELPEDgFTEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSVKV 746
Cdd:cd12779      3 SPSRVLHIRKIPND-VTEAEVISLGLPFGKVTNLLMLKGKNQAFLEMASEEAAVTMVNYYTTVTPHLRNQPVYI 75
RRM1_PTBP1_hnRNPL_like cd12421
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
880-946 3.61e-05

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: 43.72  E-value: 3.61e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1720417259  880 VVFISNLPNKgySTE-EIYNLAKPFGALKDILVLSSHKKAYIEI-NKKSADSMVKFYTCFPISMDGNQL 946
Cdd:cd12421      1 VVHIRNLPPD--ATEaDLVALGLPFGKVTNVLLLKGKNQALVEMeDVESASSMVNYYTTVPPLIRGRPV 67
RRM1_PTBP1_like cd12688
RNA recognition motif 1 (RRM1) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) ...
677-746 4.48e-05

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: 43.45  E-value: 4.48e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  677 ILLVSELPEDgFTEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSVKV 746
Cdd:cd12688      2 VLHIRKLPCD-VTEAEVISLGLPFGKVTNLLMLKGKNQAFLEMATEEAAVTMVNYYTPVTPHLRSQPIYI 70
RRM1_PTBP1 cd12777
RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 1 (PTB) ...
880-958 9.02e-05

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: 42.66  E-value: 9.02e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  880 VVFISNLPNKgYSTEEIYNLAKPFGALKDILVLSSHKKAYIEIN-KKSADSMVKFYTCFPISMDGNQLSISMApEHVDLK 958
Cdd:cd12777      2 VIHVRKLPND-VTEAEVISLGLPFGKVTNLLMLKGKNQAFIEMNtEEAANTMVNYYTSVTPVLRGQPIYIQFS-NHKELK 79
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
678-746 1.67e-04

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: 41.50  E-value: 1.67e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1720417259  678 LLVSELPEDgFTEEDIRKAFLPFGKISDVLLVP-----CRNEAYLEMELRKAVTSIMKYIETMplVIKGKSVKV 746
Cdd:cd00590      1 LFVGNLPPD-TTEEDLRELFSKFGEVVSVRIVRdrdgkSKGFAFVEFESPEDAEKALEALNGT--ELGGRPLKV 71
RRM1_hnRNPL_like cd12689
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) ...
680-744 2.52e-04

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: 41.49  E-value: 2.52e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1720417259  680 VSELPEdGFTEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSV 744
Cdd:cd12689      7 VRGLSE-HVTEADLVEALQNFGPISYVTMMPKKRQALVEFEDIEGAKACVNYAQQNPIYVGGRPA 70
RRM1_PTBP2 cd12778
RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 2 ...
982-1036 3.41e-04

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: 41.20  E-value: 3.41e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1720417259  982 NRFVHLDNLPEDGLQC-VLCVGHQFGKVDRYMFMSNKNKVILQLESPESALSMYNF 1036
Cdd:cd12778      1 SRVLHIRKLPGEVTETeVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNY 56
RRM1_PTBPH3 cd12687
RNA recognition motif 1 (RRM1) found in plant polypyrimidine tract-binding protein homolog 3 ...
689-746 3.53e-04

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: 41.01  E-value: 3.53e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1720417259  689 TEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSVKV 746
Cdd:cd12687     13 SENDLLQLAQPFGVVTKLVMLRAKNQALLQMQDVSAAISALQFYTSVQPSIRGRNVYI 70
RRM1_PTBP2 cd12778
RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 2 ...
677-735 3.95e-04

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: 40.82  E-value: 3.95e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1720417259  677 ILLVSELPEDgFTEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETM 735
Cdd:cd12778      3 VLHIRKLPGE-VTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYTAV 60
hnRNP-L_PTB TIGR01649
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
983-1047 5.31e-04

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: 44.81  E-value: 5.31e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720417259  983 RFVHLDNLPEDGLQC-VLCVGHQFGKVDRYMFMSNKNKVILQLESPESALSMYNFLKQNPQNIGEH 1047
Cdd:TIGR01649    3 PVVHVRNLPQDVVEAdLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQ 68
hnRNP-L_PTB TIGR01649
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
880-1180 5.35e-04

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: 44.81  E-value: 5.35e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  880 VVFISNLPNKgySTE-EIYNLAKPFGALKDILVLSSHKKAYIEI-NKKSADSMVKFYTCFPISMDGNQLSISMApEHVDL 957
Cdd:TIGR01649    4 VVHVRNLPQD--VVEaDLVEALIPFGPVSYVMMLPGKRQALVEFeDEESAKACVNFATSVPIYIRGQPAFFNYS-TSQEI 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  958 KdeealfTTLIQENDPeANIDKIYnRFVHLDNLPEDGLQCVLCVGHQFGKVDRYMFMSNKNKV--ILQLESPESALSMYN 1035
Cdd:TIGR01649   81 K------RDGNSDFDS-AGPNKVL-RVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNVFqaLVEFESVNSAQHAKA 152
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259 1036 FLkqNPQNIgeHVLTCTL----SPKTDSEVQRKNDlelgKGSTFS-PDLKNSPvDESEVQTAADSSSV----KPSEVEEE 1106
Cdd:TIGR01649  153 AL--NGADI--YNGCCTLkieyAKPTRLNVKYNDD----DSRDYTnPDLPGRR-DPGLDQTHRQRQPAllgqHPSSYGHD 223
                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1720417259 1107 TTSNIGTETSVHQEELGKEEPKQALcesdfAIQTLELEAQGAEVSIEIPLVASTPANIELFSENIDESALNQQM 1180
Cdd:TIGR01649  224 GYSSHGGPLAPLAGGDRMGPPHGPP-----SRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDR 292
RRM1_PTBP2 cd12778
RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 2 ...
880-935 6.44e-04

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: 40.43  E-value: 6.44e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1720417259  880 VVFISNLPNKGYSTEEIyNLAKPFGALKDILVLSSHKKAYIEI-NKKSADSMVKFYT 935
Cdd:cd12778      3 VLHIRKLPGEVTETEVI-ALGLPFGKVTNILMLKGKNQAFLELaTEEAAITMVNYYT 58
RRM1_PTBP1_like cd12688
RNA recognition motif 1 (RRM1) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) ...
983-1036 1.41e-03

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: 39.21  E-value: 1.41e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1720417259  983 RFVHLDNLPEDGLQC-VLCVGHQFGKVDRYMFMSNKNKVILQLESPESALSMYNF 1036
Cdd:cd12688      1 RVLHIRKLPCDVTEAeVISLGLPFGKVTNLLMLKGKNQAFLEMATEEAAVTMVNY 55
RRM1_PTBP1_like cd12688
RNA recognition motif 1 (RRM1) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) ...
880-958 1.46e-03

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: 39.21  E-value: 1.46e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  880 VVFISNLPnkGYSTE-EIYNLAKPFGALKDILVLSSHKKAYIEIN-KKSADSMVKFYTCFPISMDGNQLSISMApEHVDL 957
Cdd:cd12688      2 VLHIRKLP--CDVTEaEVISLGLPFGKVTNLLMLKGKNQAFLEMAtEEAAVTMVNYYTPVTPHLRSQPIYIQYS-NHKEL 78

                   .
gi 1720417259  958 K 958
Cdd:cd12688     79 K 79
zf-C2H2_jaz pfam12171
Zinc-finger double-stranded RNA-binding; This domain family is found in archaea and eukaryotes, ...
1887-1912 1.58e-03

Zinc-finger double-stranded RNA-binding; This domain family is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localize in the nucleus, particularly the nucleolus. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localization.


Pssm-ID: 432381 [Multi-domain]  Cd Length: 27  Bit Score: 37.53  E-value: 1.58e-03
                           10        20
                   ....*....|....*....|....*.
gi 1720417259 1887 FFCPICSLFYSGEKAMANHCKSTRHK 1912
Cdd:pfam12171    2 FYCVLCDKYFKSENALQNHLKSKKHK 27
RRM1_ROD1 cd12779
RNA recognition motif 1 (RRM1) found in vertebrate regulator of differentiation 1 (Rod1); This ...
982-1036 1.83e-03

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: 39.23  E-value: 1.83e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1720417259  982 NRFVHLDNLPEDGLQC-VLCVGHQFGKVDRYMFMSNKNKVILQLESPESALSMYNF 1036
Cdd:cd12779      5 SRVLHIRKIPNDVTEAeVISLGLPFGKVTNLLMLKGKNQAFLEMASEEAAVTMVNY 60
hnRNP-L_PTB TIGR01649
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
680-744 1.85e-03

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


Pssm-ID: 273733 [Multi-domain]  Cd Length: 481  Bit Score: 42.88  E-value: 1.85e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1720417259  680 VSELPEDgFTEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSV 744
Cdd:TIGR01649    7 VRNLPQD-VVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPA 70
RRM1_PTBP1 cd12777
RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 1 (PTB) ...
983-1036 1.97e-03

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: 38.81  E-value: 1.97e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1720417259  983 RFVHLDNLPEDGLQC-VLCVGHQFGKVDRYMFMSNKNKVILQLESPESALSMYNF 1036
Cdd:cd12777      1 RVIHVRKLPNDVTEAeVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNY 55
PTZ00121 PTZ00121
MAEBL; Provisional
740-877 2.03e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 43.21  E-value: 2.03e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  740 KGKSVKVCVPGKKKPQNK----EMKKKPSDIKKSSASALKKETDASKTMETVSSSSSAKSGQIKSSTvkvNKCAAKSGKK 815
Cdd:PTZ00121  1297 KAEEKKKADEAKKKAEEAkkadEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAE---EKAEAAEKKK 1373
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720417259  816 SLEAKKSGNIKNKDSNKPvtvPANSEIKASSEDKatgKSAEESPSGTLEATEKEPVNKESEE 877
Cdd:PTZ00121  1374 EEAKKKADAAKKKAEEKK---KADEAKKKAEEDK---KKADELKKAAAAKKKADEAKKKAEE 1429
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
881-949 3.18e-03

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: 38.03  E-value: 3.18e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1720417259  881 VFISNLPnKGYSTEEIYNLAKPFGALKDILVLSSHKK-----AYIE-INKKSADSMVKFYTCFPIsmDGNQLSIS 949
Cdd:cd00590      1 LFVGNLP-PDTTEEDLRELFSKFGEVVSVRIVRDRDGkskgfAFVEfESPEDAEKALEALNGTEL--GGRPLKVS 72
RRM1_MATR3 cd12714
RNA recognition motif 1 (RRM1) found in vertebrate matrin-3; This subgroup corresponds to the ...
699-746 4.39e-03

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: 37.99  E-value: 4.39e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1720417259  699 PFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSVKV 746
Cdd:cd12714     24 PFGIITNHLILNKINEAFIEMATTEEAQAAVDYYMTTPALVFGKPVRV 71
RRM1_ROD1 cd12779
RNA recognition motif 1 (RRM1) found in vertebrate regulator of differentiation 1 (Rod1); This ...
880-960 4.69e-03

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: 38.08  E-value: 4.69e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  880 VVFISNLPNKgYSTEEIYNLAKPFGALKDILVLSSHKKAYIEI-NKKSADSMVKFYTCFPISMDGNQLSISMApEHVDLK 958
Cdd:cd12779      7 VLHIRKIPND-VTEAEVISLGLPFGKVTNLLMLKGKNQAFLEMaSEEAAVTMVNYYTTVTPHLRNQPVYIQYS-NHRELK 84

                   ..
gi 1720417259  959 DE 960
Cdd:cd12779     85 TD 86
RRM_NOL8 cd12226
RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This ...
689-724 5.74e-03

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


Pssm-ID: 409673 [Multi-domain]  Cd Length: 77  Bit Score: 37.56  E-value: 5.74e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1720417259  689 TEEDIRKAFLPFGKISDVLLV-----PCRNEAYLEMELRKA 724
Cdd:cd12226     12 TEDDLERRFSRFGTVSDVEIIrkkdaPDRGFAYIDLRTSEA 52
PTZ00121 PTZ00121
MAEBL; Provisional
740-878 5.77e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 42.05  E-value: 5.77e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  740 KGKSVKVCVPGKKKPQnkEMKKKPSDIKKsSASALKKETDASKTMETVSSSSSAKsgqiksSTVKVNKCAAKSGKKSLEA 819
Cdd:PTZ00121  1386 KAEEKKKADEAKKKAE--EDKKKADELKK-AAAAKKKADEAKKKAEEKKKADEAK------KKAEEAKKADEAKKKAEEA 1456
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1720417259  820 KKSGNIKNKDSNKPVTVPANSEIKASSEDKATGKSAEESPSGTLEATEKEPVNKESEEM 878
Cdd:PTZ00121  1457 KKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEA 1515
PRK13808 PRK13808
adenylate kinase; Provisional
749-873 8.69e-03

adenylate kinase; Provisional


Pssm-ID: 172341 [Multi-domain]  Cd Length: 333  Bit Score: 40.64  E-value: 8.69e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  749 PGKKKPQNKEMKKKPSDIKKSSASALKKETDASKTMETVSSSSSAKSGQIKSSTVKVNKCAAKSGKKSLEAKKSGNIKNK 828
Cdd:PRK13808   207 AAKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKKTAKKALKKAAKAVKKAAKKAAKAAAKAAKGAA 286
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1720417259  829 DSNKPvTVPANSEIKASSEDKATGKSAEESPSGTLEATEKEPVNK 873
Cdd:PRK13808   287 KATKG-KAKAKKKAGKKAAAGSKAKATAKAPKRGAKGKKAKKVTK 330
 
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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