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Conserved domains on  [gi|1907105663|ref|XP_036014760|]
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RNA-binding protein 26 isoform X3 [Mus musculus]

Protein Classification

RNA-binding protein 26( domain architecture ID 10246263)

RNA-binding protein 26 (RBM26) represents a cutaneous lymphoma (CL)-associated antigen

Gene Symbol:  RBM26
Gene Ontology:  GO:0003723
PubMed:  22278943|18515081

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM1_RBM26 cd12516
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26); This ...
 744-819 3.31e-51

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26); This subgroup corresponds to the RRM1 of RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, which represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions.


:

Pssm-ID: 409938 [Multi-domain]  Cd Length: 76  Bit Score: 174.43  E-value: 3.31e-51
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907105663  744 NTKLELRKVPPELNNISKLNEHFSRFGTLVNLQVAYNGDPEGALIQFATYEEAKKAISSTEAVLNNRFIKVYWHRE 819
Cdd:cd12516      1 NTKLELRKVPPELNNISKLNEHFSKFGTIVNLQVAYQGDPEGALIQFATHEEAKRAISSTEAVLNNRFIKVYWHRE 76
RRM2_RBM26_like cd12258
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 26 (RBM26) and similar ...
 1099-1170 7.37e-40

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM2 of RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, which represents a cutaneous lymphoma (CL)-associated antigen. RBM26 contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions.


:

Pssm-ID: 409703 [Multi-domain]  Cd Length: 72  Bit Score: 141.66  E-value: 7.37e-40
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907105663 1099 VDHRPRALEISAFTESDREDLLPHFAQYGEIEDCQIDDASLHAIITFKTRAEAEAAAIHGARFKGQDLKLAW 1170
Cdd:cd12258      1 VDRRPRQLEVTGFTESDKDDLLPHFAQFGEVEDVQVDEEGLHLIITFKTRKEAEIAAVHGARFKGQSLQLAW 72
PWI super family cl47670
PWI domain;
214-279 2.53e-09

PWI domain;


The actual alignment was detected with superfamily member pfam01480:

Pssm-ID: 460224 [Multi-domain]  Cd Length: 71  Bit Score: 54.82  E-value: 2.53e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907105663  214 EALKSWLSKTLEPICDADPSALAKYVLALVKKD-KSEKELKalciDQLDVFLQKETQIFVEKLFDAV 279
Cdd:pfam01480    1 EVLKPWIEKKITEILGFEDDVVVEYVVNLLEEKfPDPKELQ----IQLTGFLDKDAAKFVKELWKLL 63
Mplasa_alph_rch super family cl37461
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 933-1054 2.92e-05

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


The actual alignment was detected with superfamily member TIGR04523:

Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 48.48  E-value: 2.92e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105663  933 NNEAQKKKQEALKLQQDVRKRKQEI---------LEKHIETQKMLISKLEKNKTMKSEDKAEIMKTLEILTKNITKLKDE 1003
Cdd:TIGR04523  362 QRELEEKQNEIEKLKKENQSYKQEIknlesqindLESKIQNQEKLNQQKDEQIKKLQQEKELLEKEIERLKETIIKNNSE 441

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907105663 1004 VKS-TSPGRCLPKSIK---TKTQMQKELLDTELDLYKKMQAGEE--VTELRRKYTEL 1054
Cdd:TIGR04523  442 IKDlTNQDSVKELIIKnldNTRESLETQLKVLSRSINKIKQNLEqkQKELKSKEKEL 498
ZnF_C3H1 smart00356
zinc finger;
497-517 1.00e-03

zinc finger;


:

Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 37.61  E-value: 1.00e-03
                            10        20
                    ....*....|....*....|.
gi 1907105663   497 CRDYdEKGFCMRGDMCPFDHG 517
Cdd:smart00356    7 CKFF-KRGYCPRGDRCKFAHP 26
 
Name Accession Description Interval E-value
RRM1_RBM26 cd12516
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26); This ...
 744-819 3.31e-51

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26); This subgroup corresponds to the RRM1 of RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, which represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions.


Pssm-ID: 409938 [Multi-domain]  Cd Length: 76  Bit Score: 174.43  E-value: 3.31e-51
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907105663  744 NTKLELRKVPPELNNISKLNEHFSRFGTLVNLQVAYNGDPEGALIQFATYEEAKKAISSTEAVLNNRFIKVYWHRE 819
Cdd:cd12516      1 NTKLELRKVPPELNNISKLNEHFSKFGTIVNLQVAYQGDPEGALIQFATHEEAKRAISSTEAVLNNRFIKVYWHRE 76
RRM2_RBM26_like cd12258
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 26 (RBM26) and similar ...
 1099-1170 7.37e-40

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM2 of RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, which represents a cutaneous lymphoma (CL)-associated antigen. RBM26 contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions.


Pssm-ID: 409703 [Multi-domain]  Cd Length: 72  Bit Score: 141.66  E-value: 7.37e-40
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907105663 1099 VDHRPRALEISAFTESDREDLLPHFAQYGEIEDCQIDDASLHAIITFKTRAEAEAAAIHGARFKGQDLKLAW 1170
Cdd:cd12258      1 VDRRPRQLEVTGFTESDKDDLLPHFAQFGEVEDVQVDEEGLHLIITFKTRKEAEIAAVHGARFKGQSLQLAW 72
PWI pfam01480
PWI domain;
214-279 2.53e-09

PWI domain;


Pssm-ID: 460224 [Multi-domain]  Cd Length: 71  Bit Score: 54.82  E-value: 2.53e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907105663  214 EALKSWLSKTLEPICDADPSALAKYVLALVKKD-KSEKELKalciDQLDVFLQKETQIFVEKLFDAV 279
Cdd:pfam01480    1 EVLKPWIEKKITEILGFEDDVVVEYVVNLLEEKfPDPKELQ----IQLTGFLDKDAAKFVKELWKLL 63
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 933-1054 2.92e-05

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 48.48  E-value: 2.92e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105663  933 NNEAQKKKQEALKLQQDVRKRKQEI---------LEKHIETQKMLISKLEKNKTMKSEDKAEIMKTLEILTKNITKLKDE 1003
Cdd:TIGR04523  362 QRELEEKQNEIEKLKKENQSYKQEIknlesqindLESKIQNQEKLNQQKDEQIKKLQQEKELLEKEIERLKETIIKNNSE 441

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907105663 1004 VKS-TSPGRCLPKSIK---TKTQMQKELLDTELDLYKKMQAGEE--VTELRRKYTEL 1054
Cdd:TIGR04523  442 IKDlTNQDSVKELIIKnldNTRESLETQLKVLSRSINKIKQNLEqkQKELKSKEKEL 498
RRM smart00360
RNA recognition motif;
1115-1168 4.66e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 42.58  E-value: 4.66e-05
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907105663  1115 DREDLLPHFAQYGEIEDCQI--DDASLH----AIITFKTRAEAEAA--AIHGARFKGQDLKL 1168
Cdd:smart00360   12 TEEELRELFSKFGKVESVRLvrDKETGKskgfAFVEFESEEDAEKAleALNGKELDGRPLKV 73
RRM smart00360
RNA recognition motif;
752-814 5.51e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 42.58  E-value: 5.51e-05
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907105663   752 VPPELNNiSKLNEHFSRFGTLVNLQVAYNGDPEG----ALIQFATYEEAKKAISS-TEAVLNNRFIKV 814
Cdd:smart00360    7 LPPDTTE-EELRELFSKFGKVESVRLVRDKETGKskgfAFVEFESEEDAEKALEAlNGKELDGRPLKV 73
HEC1 COG5185
Chromosome segregation protein NDC80, interacts with SMC proteins [Cell cycle control, cell ...
 932-1045 2.72e-04

Chromosome segregation protein NDC80, interacts with SMC proteins [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 444066 [Multi-domain]  Cd Length: 594  Bit Score: 44.95  E-value: 2.72e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105663  932 DNNEAQKKKQEAL-KLQQDVRKRKQEILEKhIETQKMLISKLEKNKTMKS-------------------EDKAEIMKTLE 991
Cdd:COG5185    272 ENAESSKRLNENAnNLIKQFENTKEKIAEY-TKSIDIKKATESLEEQLAAaeaeqeleeskretetgiqNLTAEIEQGQE 350

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1907105663  992 ILTKNITKLKDEVKSTSPGRCLPKSIKTKTQMQKELLDTELDLYKKMQAGEEVT 1045
Cdd:COG5185    351 SLTENLEAIKEEIENIVGEVELSKSSEELDSFKDTIESTKESLDEIPQNQRGYA 404
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 752-813 2.93e-04

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


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 40.29  E-value: 2.93e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907105663  752 VPPELNNiSKLNEHFSRFGTLVNLQVAY--NGDPEG-ALIQFATYEEAKKAISST-EAVLNNRFIK 813
Cdd:pfam00076    6 LPPDTTE-EDLKDLFSKFGPIKSIRLVRdeTGRSKGfAFVEFEDEEDAEKAIEALnGKELGGRELK 70
Nup35_RRM_2 pfam14605
Nup53/35/40-type RNA recognition motif;
1103-1154 3.96e-04

Nup53/35/40-type RNA recognition motif;


Pssm-ID: 373156  Cd Length: 53  Bit Score: 39.54  E-value: 3.96e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1907105663 1103 PRALEISAFTESDREDLLPHFAQYGEIEDCQIDDASLHAIITFKTRAEAEAA 1154
Cdd:pfam14605    1 STWIVVSGYPAELAYLVRRHFADFGEIVKHYFPPETNSMYLKYASRKDAEQA 52
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 934-1068 6.74e-04

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.


Pssm-ID: 426784 [Multi-domain]  Cd Length: 1161  Bit Score: 44.19  E-value: 6.74e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105663  934 NEAQKKKQEALKLQQDVRKRKQEILEKHIETQKMLISKLEKNKTMKSEDKAEI-------MKTLEILTKNITKLKDEVKS 1006
Cdd:pfam02463  166 RLKRKKKEALKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKleleeeyLLYLDYLKLNEERIDLLQEL 245

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907105663 1007 TSPGRCLPKSIKTKTQMQKELLDTELDLYKKMQAGEEVTELRRKYTELQLEAAKRGILSSGR 1068
Cdd:pfam02463  246 LRDEQEEIESSKQEIEKEEEKLAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLER 307
ZnF_C3H1 smart00356
zinc finger;
497-517 1.00e-03

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 37.61  E-value: 1.00e-03
                            10        20
                    ....*....|....*....|.
gi 1907105663   497 CRDYdEKGFCMRGDMCPFDHG 517
Cdd:smart00356    7 CKFF-KRGYCPRGDRCKFAHP 26
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
1115-1167 1.61e-03

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 38.54  E-value: 1.61e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907105663 1115 DREDLLPHFAQYGEIEDCQI--DDASL----HAIITFKTRAEAEAA--AIHGARFKGQDLK 1167
Cdd:COG0724     14 TEEDLRELFSEYGEVTSVKLitDRETGrsrgFGFVEMPDDEEAQAAieALNGAELMGRTLK 74
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
496-517 8.19e-03

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 34.86  E-value: 8.19e-03
                           10        20
                   ....*....|....*....|..
gi 1907105663  496 RCRDYDEKGFCMRGDMCPFDHG 517
Cdd:pfam00642    5 LCRFFLRTGYCKYGDRCKFAHG 26
 
Name Accession Description Interval E-value
RRM1_RBM26 cd12516
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26); This ...
 744-819 3.31e-51

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26); This subgroup corresponds to the RRM1 of RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, which represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions.


Pssm-ID: 409938 [Multi-domain]  Cd Length: 76  Bit Score: 174.43  E-value: 3.31e-51
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907105663  744 NTKLELRKVPPELNNISKLNEHFSRFGTLVNLQVAYNGDPEGALIQFATYEEAKKAISSTEAVLNNRFIKVYWHRE 819
Cdd:cd12516      1 NTKLELRKVPPELNNISKLNEHFSKFGTIVNLQVAYQGDPEGALIQFATHEEAKRAISSTEAVLNNRFIKVYWHRE 76
RRM_RBM27 cd12517
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 27 (RBM27); This subgroup ...
 744-819 2.76e-43

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 27 (RBM27); This subgroup corresponds to the RRM of RBM27 which contains a single RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although the specific function of the RRM in RBM27 remains unclear, it shows high sequence similarity with RRM1of RBM26, which functions as a cutaneous lymphoma (CL)-associated antigen.


Pssm-ID: 409939 [Multi-domain]  Cd Length: 76  Bit Score: 151.74  E-value: 2.76e-43
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907105663  744 NTKLELRKVPPELNNISKLNEHFSRFGTLVNLQVAYNGDPEGALIQFATYEEAKKAISSTEAVLNNRFIKVYWHRE 819
Cdd:cd12517      1 NTKLEVRKIPQELNNITQLNEHFSKFGTIVNIQVAFGGDPEAALIQYTTNEEARRAISSTEAVLNNRFIRVLWHRE 76
RRM2_RBM26_like cd12258
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 26 (RBM26) and similar ...
 1099-1170 7.37e-40

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM2 of RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, which represents a cutaneous lymphoma (CL)-associated antigen. RBM26 contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions.


Pssm-ID: 409703 [Multi-domain]  Cd Length: 72  Bit Score: 141.66  E-value: 7.37e-40
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907105663 1099 VDHRPRALEISAFTESDREDLLPHFAQYGEIEDCQIDDASLHAIITFKTRAEAEAAAIHGARFKGQDLKLAW 1170
Cdd:cd12258      1 VDRRPRQLEVTGFTESDKDDLLPHFAQFGEVEDVQVDEEGLHLIITFKTRKEAEIAAVHGARFKGQSLQLAW 72
RRM1_RBM26_like cd12257
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar ...
 744-817 2.17e-35

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear.


Pssm-ID: 409702 [Multi-domain]  Cd Length: 72  Bit Score: 128.83  E-value: 2.17e-35
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907105663  744 NTKLELRKVPPELNNISKLNEHFSRFGTLVNLQVAYNgdPEGALIQFATYEEAKKAISSTEAVLNNRFIKVYWH 817
Cdd:cd12257      1 KTTLEVRNIPPELNNITKLREHFSKFGTIVNIQVNYN--PESALVQFSTSEEANKAYRSPEAVFNNRFIKVFWH 72
PWI pfam01480
PWI domain;
214-279 2.53e-09

PWI domain;


Pssm-ID: 460224 [Multi-domain]  Cd Length: 71  Bit Score: 54.82  E-value: 2.53e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907105663  214 EALKSWLSKTLEPICDADPSALAKYVLALVKKD-KSEKELKalciDQLDVFLQKETQIFVEKLFDAV 279
Cdd:pfam01480    1 EVLKPWIEKKITEILGFEDDVVVEYVVNLLEEKfPDPKELQ----IQLTGFLDKDAAKFVKELWKLL 63
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 1115-1168 5.35e-07

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


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 48.05  E-value: 5.35e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907105663 1115 DREDLLPHFAQYGEIEDCQIDDASL-----HAIITFKTRAEAEAA--AIHGARFKGQDLKL 1168
Cdd:cd00590     11 TEEDLRELFSKFGEVVSVRIVRDRDgkskgFAFVEFESPEDAEKAleALNGTELGGRPLKV 71
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 747-814 1.59e-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: 43.81  E-value: 1.59e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907105663  747 LELRKVPPELNNiSKLNEHFSRFGTLVNLQVAYNGDPEG---ALIQFATYEEAKKAISS-TEAVLNNRFIKV 814
Cdd:cd00590      1 LFVGNLPPDTTE-EDLRELFSKFGEVVSVRIVRDRDGKSkgfAFVEFESPEDAEKALEAlNGTELGGRPLKV 71
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 933-1054 2.92e-05

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 48.48  E-value: 2.92e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105663  933 NNEAQKKKQEALKLQQDVRKRKQEI---------LEKHIETQKMLISKLEKNKTMKSEDKAEIMKTLEILTKNITKLKDE 1003
Cdd:TIGR04523  362 QRELEEKQNEIEKLKKENQSYKQEIknlesqindLESKIQNQEKLNQQKDEQIKKLQQEKELLEKEIERLKETIIKNNSE 441

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907105663 1004 VKS-TSPGRCLPKSIK---TKTQMQKELLDTELDLYKKMQAGEE--VTELRRKYTEL 1054
Cdd:TIGR04523  442 IKDlTNQDSVKELIIKnldNTRESLETQLKVLSRSINKIKQNLEqkQKELKSKEKEL 498
RRM_RBM22 cd12224
RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This ...
 1117-1172 3.04e-05

RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines.


Pssm-ID: 409671 [Multi-domain]  Cd Length: 74  Bit Score: 43.04  E-value: 3.04e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907105663 1117 EDLLPHFAQYGEIEDCQIDDASLHAIITFKTRAEAEAAAIHGAR---FKGQDLKLAWNK 1172
Cdd:cd12224     16 KDLRDHFYQFGEIRSITVVARQQCAFVQFTTRQAAERAAERTFNkliIKGRRLKVKWGR 74
RRM smart00360
RNA recognition motif;
1115-1168 4.66e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 42.58  E-value: 4.66e-05
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907105663  1115 DREDLLPHFAQYGEIEDCQI--DDASLH----AIITFKTRAEAEAA--AIHGARFKGQDLKL 1168
Cdd:smart00360   12 TEEELRELFSKFGKVESVRLvrDKETGKskgfAFVEFESEEDAEKAleALNGKELDGRPLKV 73
RRM_MCM3A_like cd12443
RNA recognition motif (RRM) found in 80 kDa MCM3-associated protein (Map80) and similar ...
 745-799 5.02e-05

RNA recognition motif (RRM) found in 80 kDa MCM3-associated protein (Map80) and similar proteins; This subfamily corresponds to the RRM of Map80, also termed germinal center-associated nuclear protein (GANP), involved in the nuclear localization pathway of MCM3, a protein necessary for the initiation of DNA replication and also involves in controls that ensure DNA replication is initiated once per cell cycle. Map80 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409877 [Multi-domain]  Cd Length: 75  Bit Score: 42.69  E-value: 5.02e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1907105663  745 TKLELRKVPPELNNISKLNEHFSRFGTLVNLQVayNGDPEGALIQFATYEEAKKA 799
Cdd:cd12443      1 TAIVCKNIPEELNDKEILRRHFSKFGKVARVFC--NPRKNLAIVHFKDHESAALA 53
RRM smart00360
RNA recognition motif;
752-814 5.51e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 42.58  E-value: 5.51e-05
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907105663   752 VPPELNNiSKLNEHFSRFGTLVNLQVAYNGDPEG----ALIQFATYEEAKKAISS-TEAVLNNRFIKV 814
Cdd:smart00360    7 LPPDTTE-EELRELFSKFGKVESVRLVRDKETGKskgfAFVEFESEEDAEKALEAlNGKELDGRPLKV 73
RRM1_RBM26_like cd12257
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar ...
 1115-1170 2.02e-04

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear.


Pssm-ID: 409702 [Multi-domain]  Cd Length: 72  Bit Score: 41.01  E-value: 2.02e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907105663 1115 DREDLLPHFAQYGEIEDCQIDDASLHAIITFKTRAEAEAA-----AIHGARFkgqdLKLAW 1170
Cdd:cd12257     15 NITKLREHFSKFGTIVNIQVNYNPESALVQFSTSEEANKAyrspeAVFNNRF----IKVFW 71
HEC1 COG5185
Chromosome segregation protein NDC80, interacts with SMC proteins [Cell cycle control, cell ...
 932-1045 2.72e-04

Chromosome segregation protein NDC80, interacts with SMC proteins [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 444066 [Multi-domain]  Cd Length: 594  Bit Score: 44.95  E-value: 2.72e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105663  932 DNNEAQKKKQEAL-KLQQDVRKRKQEILEKhIETQKMLISKLEKNKTMKS-------------------EDKAEIMKTLE 991
Cdd:COG5185    272 ENAESSKRLNENAnNLIKQFENTKEKIAEY-TKSIDIKKATESLEEQLAAaeaeqeleeskretetgiqNLTAEIEQGQE 350

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1907105663  992 ILTKNITKLKDEVKSTSPGRCLPKSIKTKTQMQKELLDTELDLYKKMQAGEEVT 1045
Cdd:COG5185    351 SLTENLEAIKEEIENIVGEVELSKSSEELDSFKDTIESTKESLDEIPQNQRGYA 404
RRM1_2_CELF1-6_like cd12361
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding ...
 1111-1158 2.85e-04

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


Pssm-ID: 409796 [Multi-domain]  Cd Length: 77  Bit Score: 40.68  E-value: 2.85e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907105663 1111 FTEsdrEDLLPHFAQYGEIEDCQI-DDASLH-----AIITFKTRAEAEAA--AIHG 1158
Cdd:cd12361     11 ASE---EDVRPLFEQFGNIEEVQIlRDKQTGqskgcAFVTFSTREEALRAieALHN 63
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 752-813 2.93e-04

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


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 40.29  E-value: 2.93e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907105663  752 VPPELNNiSKLNEHFSRFGTLVNLQVAY--NGDPEG-ALIQFATYEEAKKAISST-EAVLNNRFIK 813
Cdd:pfam00076    6 LPPDTTE-EDLKDLFSKFGPIKSIRLVRdeTGRSKGfAFVEFEDEEDAEKAIEALnGKELGGRELK 70
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 933-1060 3.29e-04

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 45.01  E-value: 3.29e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105663  933 NNEAQKKKQEalKLQQDVRKRKQEILE--KHIETQKMLISKLEKN-KTMKSEDK---AEIMK------TLEILTKNITKL 1000
Cdd:TIGR04523  576 TQKSLKKKQE--EKQELIDQKEKEKKDliKEIEEKEKKISSLEKElEKAKKENEklsSIIKNikskknKLKQEVKQIKET 653

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907105663 1001 KDEVKSTSPgrclpkSIKTKTQMQKELLD----------TELDL-YKK----MQAGEEVTELRRKYTELQLEAAK 1060
Cdd:TIGR04523  654 IKEIRNKWP------EIIKKIKESKTKIDdiielmkdwlKELSLhYKKyitrMIRIKDLPKLEEKYKEIEKELKK 722
Nup35_RRM_2 pfam14605
Nup53/35/40-type RNA recognition motif;
1103-1154 3.96e-04

Nup53/35/40-type RNA recognition motif;


Pssm-ID: 373156  Cd Length: 53  Bit Score: 39.54  E-value: 3.96e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1907105663 1103 PRALEISAFTESDREDLLPHFAQYGEIEDCQIDDASLHAIITFKTRAEAEAA 1154
Cdd:pfam14605    1 STWIVVSGYPAELAYLVRRHFADFGEIVKHYFPPETNSMYLKYASRKDAEQA 52
RRM3_RAVER cd12390
RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...
 751-799 4.30e-04

RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.


Pssm-ID: 409824 [Multi-domain]  Cd Length: 91  Bit Score: 40.30  E-value: 4.30e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1907105663  751 KVPPELNNISKLNEHFSRFGTLVNLQVAY-NGDPEG-ALIQFATYEEAKKA 799
Cdd:cd12390      9 RLPKDFRDGSELRKLFSQVGKPTFCQLAMgNGVPRGfAFVEFASAEDAEEA 59
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 934-1068 6.74e-04

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.


Pssm-ID: 426784 [Multi-domain]  Cd Length: 1161  Bit Score: 44.19  E-value: 6.74e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105663  934 NEAQKKKQEALKLQQDVRKRKQEILEKHIETQKMLISKLEKNKTMKSEDKAEI-------MKTLEILTKNITKLKDEVKS 1006
Cdd:pfam02463  166 RLKRKKKEALKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKleleeeyLLYLDYLKLNEERIDLLQEL 245

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907105663 1007 TSPGRCLPKSIKTKTQMQKELLDTELDLYKKMQAGEEVTELRRKYTELQLEAAKRGILSSGR 1068
Cdd:pfam02463  246 LRDEQEEIESSKQEIEKEEEKLAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLER 307
ZnF_C3H1 smart00356
zinc finger;
497-517 1.00e-03

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 37.61  E-value: 1.00e-03
                            10        20
                    ....*....|....*....|.
gi 1907105663   497 CRDYdEKGFCMRGDMCPFDHG 517
Cdd:smart00356    7 CKFF-KRGYCPRGDRCKFAHP 26
DR0291 COG1579
Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ...
 915-1060 1.19e-03

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];


Pssm-ID: 441187 [Multi-domain]  Cd Length: 236  Bit Score: 41.83  E-value: 1.19e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105663  915 AALKAAQKTLSVSTPAVDNNEAQKKKQEA-LKLQQDVRKRKQE------------ILEKHIETQKMLISKLEknktmksE 981
Cdd:COG1579     38 DELAALEARLEAAKTELEDLEKEIKRLELeIEEVEARIKKYEEqlgnvrnnkeyeALQKEIESLKRRISDLE-------D 110

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105663  982 DKAEIMKTLEILTKNITKLKDEVKstspgrclpksiktktQMQKEL--LDTELDlykkmqagEEVTELRRKYTELQLEAA 1059
Cdd:COG1579    111 EILELMERIEELEEELAELEAELA----------------ELEAELeeKKAELD--------EELAELEAELEELEAERE 166


                   .
gi 1907105663 1060 K 1060
Cdd:COG1579    167 E 167
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 1115-1167 1.20e-03

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


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 38.75  E-value: 1.20e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105663 1115 DREDLLPHFAQYGEIEDCQI-----DDASLHAIITFKTRAEAEAA--AIHGARFKGQDLK 1167
Cdd:pfam00076   11 TEEDLKDLFSKFGPIKSIRLvrdetGRSKGFAFVEFEDEEDAEKAieALNGKELGGRELK 70
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
1115-1167 1.61e-03

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 38.54  E-value: 1.61e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907105663 1115 DREDLLPHFAQYGEIEDCQI--DDASL----HAIITFKTRAEAEAA--AIHGARFKGQDLK 1167
Cdd:COG0724     14 TEEDLRELFSEYGEVTSVKLitDRETGrsrgFGFVEMPDDEEAQAAieALNGAELMGRTLK 74
RRM2_CELF3_4_5_6 cd12635
RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, ...
 1115-1160 2.41e-03

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


Pssm-ID: 410043 [Multi-domain]  Cd Length: 81  Bit Score: 38.16  E-value: 2.41e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1907105663 1115 DREDLLPHFAQYGEIEDCQI----DDASLH-AIITFKTRAEAEAA--AIHGAR 1160
Cdd:cd12635     14 SEDDVRRLFEPFGSIEECTIlrgpDGNSKGcAFVKFSSHAEAQAAinALHGSQ 66
RRM_NOL8 cd12226
RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This ...
 1115-1172 3.03e-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: 3.03e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907105663 1115 DREDLLPHFAQYGEIEDCQI---DDASLH--AIITFKTRAEAEA---AAIHGARFKGQDLKLAWNK 1172
Cdd:cd12226     12 TEDDLERRFSRFGTVSDVEIirkKDAPDRgfAYIDLRTSEAALQkclSTLNGVKWKGSRLKIQLAK 77
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 760-816 4.59e-03

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


Pssm-ID: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 37.15  E-value: 4.59e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907105663  760 SKLNEHFSRFGTLVNLQVAYNGDPEG---ALIQFATYEEAKKAISSTEAV-LNNRFIKVYW 816
Cdd:cd12414     14 DDLKKLFSKFGKVLEVTIPKKPDGKLrgfAFVQFTNVADAAKAIKGMNGKkIKGRPVAVDW 74
RRM1_hnRNPA_hnRNPD_like cd12325
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and ...
 1113-1154 5.21e-03

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins; This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs.


Pssm-ID: 409763 [Multi-domain]  Cd Length: 72  Bit Score: 36.73  E-value: 5.21e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1907105663 1113 ESDREDLLPHFAQYGEIEDCQI--DDASLH----AIITFKTRAEAEAA 1154
Cdd:cd12325      9 ETTEESLREYFSKYGEVVDCVVmkDPATGRsrgfGFVTFKDPSSVDAV 56
RRM_SR140 cd12223
RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This ...
 1112-1174 5.42e-03

RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain).


Pssm-ID: 409670 [Multi-domain]  Cd Length: 84  Bit Score: 37.27  E-value: 5.42e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907105663 1112 TESDREDLLPHFAQYGEIEDCQI-----DD----ASLHAIITFKTRAEAEAA--AIHGARFKGQDLKLAWNKPI 1174
Cdd:cd12223     11 PSVTEEVLLREFGRFGPLASVKImwprtEEerrrNRNCGFVAFMSRADAERAmrELNGKDVMGYELKLGWGKAV 84
RRM_RBM8 cd12324
RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; ...
 1113-1170 5.71e-03

RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain).


Pssm-ID: 409762 [Multi-domain]  Cd Length: 88  Bit Score: 37.21  E-value: 5.71e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907105663 1113 ESDREDLLPHFAQYGEIEDCQIddaSL---------HAIITFKTRAEAEAA--AIHGARFKGQDLKLAW 1170
Cdd:cd12324     17 EAQEEDIHDKFAEFGEIKNLHL---NLdrrtgfvkgYALVEYETKKEAQAAieGLNGKELLGQTISVDW 82
RRM3_TIA1_like cd12354
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...
 1117-1170 6.24e-03

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 409790 [Multi-domain]  Cd Length: 71  Bit Score: 36.49  E-value: 6.24e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907105663 1117 EDLLPHFAQYGEIEDCQIDDASLHAIITFKTRAEAEAA--AIHGARFKGQDLKLAW 1170
Cdd:cd12354     15 ALLQQTFSPFGQILEVRVFPDKGYAFIRFDSHEAATHAivSVNGTIINGQAVKCSW 70
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 933-1060 7.01e-03

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 40.81  E-value: 7.01e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907105663  933 NNEAQKKKQEALKLQ----QDVRKRKQEILEKHIETQKMlISKLEKNKTMKSEDKAEIMKTLEILTKNITKLKDEVKSTS 1008
Cdd:TIGR02168  801 LREALDELRAELTLLneeaANLRERLESLERRIAATERR-LEDLEEQIEELSEDIESLAAEIEELEELIEELESELEALL 879

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907105663 1009 pgrclpksiKTKTQMQKELLDTELDLYKKM----QAGEEVTELRRKYTELQLEAAK 1060
Cdd:TIGR02168  880 ---------NERASLEEALALLRSELEELSeelrELESKRSELRRELEELREKLAQ 926
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
496-517 8.19e-03

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 34.86  E-value: 8.19e-03
                           10        20
                   ....*....|....*....|..
gi 1907105663  496 RCRDYDEKGFCMRGDMCPFDHG 517
Cdd:pfam00642    5 LCRFFLRTGYCKYGDRCKFAHG 26
 
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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