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Conserved domains on  [gi|665391848|ref|NP_001285331|]
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eukaryotic translation initiation factor 4H1, isoform E [Drosophila melanogaster]

Protein Classification

eukaryotic translation initiation factor 4H( domain architecture ID 10189297)

eukaryotic translation initiation factor 4H (eIF-4H), together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RRM_eIF4H cd12401
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4H (eIF-4H) and ...
16-102 9.49e-43

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins; This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation.


:

Pssm-ID: 409835 [Multi-domain]  Cd Length: 84  Bit Score: 142.04  E-value: 9.49e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665391848  16 PTEPPFIAFVGNLPQGLVQGDVIKIFQDFEVKYVRLVKDRETDQFKGFCYVEFETLDNLERALECDGrikLDDLSAPLRI 95
Cdd:cd12401    1 PTEPPFTAYVGNLPFNTVQGDLDAIFKDLKVRSVRLVRDRETDKFKGFCYVEFEDLESLKEALEYDG---ALFEDRPLRV 77

                 ....*..
gi 665391848  96 DIADRRK 102
Cdd:cd12401   78 DIAEGRK 84
 
Name Accession Description Interval E-value
RRM_eIF4H cd12401
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4H (eIF-4H) and ...
16-102 9.49e-43

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins; This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation.


Pssm-ID: 409835 [Multi-domain]  Cd Length: 84  Bit Score: 142.04  E-value: 9.49e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665391848  16 PTEPPFIAFVGNLPQGLVQGDVIKIFQDFEVKYVRLVKDRETDQFKGFCYVEFETLDNLERALECDGrikLDDLSAPLRI 95
Cdd:cd12401    1 PTEPPFTAYVGNLPFNTVQGDLDAIFKDLKVRSVRLVRDRETDKFKGFCYVEFEDLESLKEALEYDG---ALFEDRPLRV 77

                 ....*..
gi 665391848  96 DIADRRK 102
Cdd:cd12401   78 DIAEGRK 84
RRM smart00360
RNA recognition motif;
24-88 7.42e-14

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 65.69  E-value: 7.42e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 665391848    24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALECDGRIKLDD 88
Cdd:smart00360   3 FVGNLPPDTTEEELRELFSKFgKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDG 68
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
24-79 3.79e-11

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 58.57  E-value: 3.79e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALE 79
Cdd:COG0724    5 YVGNLPYSVTEEDLRELFSEYgEVTSVKLITDRETGRSRGFGFVEMPDDEEAQAAIE 61
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
24-84 2.16e-10

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: 55.70  E-value: 2.16e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 665391848   24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDrETDQFKGFCYVEFETLDNLERALE-CDGRI 84
Cdd:pfam00076   2 FVGNLPPDTTEEDLKDLFSKFgPIKSIRLVRD-ETGRSKGFAFVEFEDEEDAEKAIEaLNGKE 63
 
Name Accession Description Interval E-value
RRM_eIF4H cd12401
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4H (eIF-4H) and ...
16-102 9.49e-43

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins; This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation.


Pssm-ID: 409835 [Multi-domain]  Cd Length: 84  Bit Score: 142.04  E-value: 9.49e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665391848  16 PTEPPFIAFVGNLPQGLVQGDVIKIFQDFEVKYVRLVKDRETDQFKGFCYVEFETLDNLERALECDGrikLDDLSAPLRI 95
Cdd:cd12401    1 PTEPPFTAYVGNLPFNTVQGDLDAIFKDLKVRSVRLVRDRETDKFKGFCYVEFEDLESLKEALEYDG---ALFEDRPLRV 77

                 ....*..
gi 665391848  96 DIADRRK 102
Cdd:cd12401   78 DIAEGRK 84
RRM_eIF4B cd12402
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and ...
19-102 5.05e-16

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins; This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation.


Pssm-ID: 409836 [Multi-domain]  Cd Length: 81  Bit Score: 71.87  E-value: 5.05e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665391848  19 PPFIAFVGNLPQGLVQGDVIKIFQDFEVKYVRLVKDRETDQFKGFCYVEFETLDNLERALECDGRiklDDLSAPLRIDIA 98
Cdd:cd12402    1 PPYTAYLGNLPYDVTEDDIEDFFRGLNISSVRLPRENGPGRLRGFGYVEFEDRESLIQALSLNEE---SLKNRRIRVDVA 77

                 ....
gi 665391848  99 DRRK 102
Cdd:cd12402   78 GQAQ 81
RRM smart00360
RNA recognition motif;
24-88 7.42e-14

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 65.69  E-value: 7.42e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 665391848    24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALECDGRIKLDD 88
Cdd:smart00360   3 FVGNLPPDTTEEELRELFSKFgKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDG 68
RRM2_PHIP1 cd12272
RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana phragmoplastin interacting ...
23-82 3.65e-12

RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA.


Pssm-ID: 409715 [Multi-domain]  Cd Length: 73  Bit Score: 60.88  E-value: 3.65e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 665391848  23 AFVGNLPQGLVQGDVIKIF-QDFEVKYVRLVKDRETDQFKGFCYVEFETLDNLERALECDG 82
Cdd:cd12272    2 VYIGNLAWDIDEDDLRELFaECCEITNVRLHTDKETGEFKGYGHVEFADEESLDAALKLAG 62
RRM2_RBM34 cd12395
RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
24-82 6.26e-12

RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.


Pssm-ID: 409829 [Multi-domain]  Cd Length: 73  Bit Score: 60.20  E-value: 6.26e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 665391848  24 FVGNLPQGLVQGDVIKIFQD-FEVKYVRLVKDRETDQFKGFCYVEFETLDNLERALECDG 82
Cdd:cd12395    3 FVGNLPFDIEEEELRKHFEDcGDVEAVRIVRDRETGIGKGFGYVLFKDKDSVDLALKLNG 62
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
24-96 1.07e-11

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: 59.60  E-value: 1.07e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDREtDQFKGFCYVEFETLDNLERALECDGRIKLDDlsAPLRID 96
Cdd:cd00590    2 FVGNLPPDTTEEDLRELFSKFgEVVSVRIVRDRD-GKSKGFAFVEFESPEDAEKALEALNGTELGG--RPLKVS 72
RRM1_NUCLs cd12450
RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ...
24-101 1.58e-11

RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409884 [Multi-domain]  Cd Length: 78  Bit Score: 59.34  E-value: 1.58e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALECDGRiklDDLSAPLRIDIADRR 101
Cdd:cd12450    3 FVGNLSWSATQDDLENFFSDCgEVVDVRIAMDRDDGRSKGFGHVEFASAESAQKALEKSGQ---DLGGREIRLDLANER 78
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
24-79 3.79e-11

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 58.57  E-value: 3.79e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALE 79
Cdd:COG0724    5 YVGNLPYSVTEEDLRELFSEYgEVTSVKLITDRETGRSRGFGFVEMPDDEEAQAAIE 61
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
24-84 2.16e-10

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: 55.70  E-value: 2.16e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 665391848   24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDrETDQFKGFCYVEFETLDNLERALE-CDGRI 84
Cdd:pfam00076   2 FVGNLPPDTTEEDLKDLFSKFgPIKSIRLVRD-ETGRSKGFAFVEFEDEEDAEKAIEaLNGKE 63
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
24-96 3.55e-10

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409882 [Multi-domain]  Cd Length: 73  Bit Score: 55.49  E-value: 3.55e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALECDGRIKLDdlSAPLRID 96
Cdd:cd12448    2 FVGNLPFSATQDALYEAFSQHgSIVSVRLPTDRETGQPKGFGYVDFSTIDSAEAAIDALGGEYID--GRPIRLD 73
RRM_Nop6 cd12400
RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and ...
21-79 2.43e-09

RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins; This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing.


Pssm-ID: 409834 [Multi-domain]  Cd Length: 74  Bit Score: 52.99  E-value: 2.43e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 665391848  21 FIAFVGNLPQGLVQGDVIKIFQD-FEVKYVRLVKDRETDQFKGFCYVEFETLDNLERALE 79
Cdd:cd12400    1 YILFVGNLPYDTTAEDLKEHFKKaGEPPSVRLLTDKKTGKSKGCAFVEFDNQKALQKALK 60
RRM_ist3_like cd12411
RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ...
24-87 3.38e-09

RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well.


Pssm-ID: 409845 [Multi-domain]  Cd Length: 89  Bit Score: 52.98  E-value: 3.38e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFE-------TLDNLERALECDGRIKLD 87
Cdd:cd12411   13 YIGGLPYELTEGDILCVFSQYgEIVDINLVRDKKTGKSKGFAFLAYEdqrstilAVDNLNGIKLLGRTIRVD 84
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
24-79 4.93e-08

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409726 [Multi-domain]  Cd Length: 78  Bit Score: 49.55  E-value: 4.93e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALE 79
Cdd:cd12284    2 YVGSLHFNITEDMLRGIFEPFgKIEFVQLQKDPETGRSKGYGFIQFRDAEDAKKALE 58
RRM1_Nop4p cd12674
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
24-101 4.99e-08

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM1 of Nop4p (also known as 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 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410075 [Multi-domain]  Cd Length: 80  Bit Score: 49.39  E-value: 4.99e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERAL------ECDGRIklddlsapLRID 96
Cdd:cd12674    4 FVRNLPFDVTLESLTDFFSDIgPVKHAVVVTDPETKKSRGYGFVSFSTHDDAEEALaklknrKLSGHI--------LKLD 75

                 ....*
gi 665391848  97 IADRR 101
Cdd:cd12674   76 FAKPR 80
RRM1_RRM2_RBM5_like cd12313
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar ...
36-96 7.41e-08

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409752 [Multi-domain]  Cd Length: 85  Bit Score: 49.19  E-value: 7.41e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 665391848  36 DVIKIFQDFE---VKYVRLVKDRETDQFKGFCYVEFETLDNLERALEcdgriKLDDLSAPLRID 96
Cdd:cd12313   18 DILSALQAHAdlpIKDVRLIRDKLTGTSRGFAFVEFSSLEDATQVMD-----ALQNLLPPFKID 76
RRM1_FCA cd12633
RNA recognition motif 1 (RRM1) found in plant flowering time control protein FCA and similar ...
24-99 1.12e-07

RNA recognition motif 1 (RRM1) found in plant flowering time control protein FCA and similar proteins; This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain.


Pssm-ID: 241077 [Multi-domain]  Cd Length: 80  Bit Score: 48.42  E-value: 1.12e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALEC-DGRIKLDDLSAPLRIDIAD 99
Cdd:cd12633    3 FVGSVPRTITEQEVRPMFEEHgNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAlHNQRTLPGGASPVQVRYAD 80
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
24-83 1.32e-07

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


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 48.32  E-value: 1.32e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALEC------DGR 83
Cdd:cd21608    3 YVGNLSWDTTEDDLRDLFSEFgEVESAKVITDRETGRSRGFGFVTFSTAEAAEAAIDAlngkelDGR 69
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
24-98 1.77e-07

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.


Pssm-ID: 409832 [Multi-domain]  Cd Length: 77  Bit Score: 47.90  E-value: 1.77e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665391848  24 FVGNLPQGLVQGDVIKIF-QDFEVKYVRLVKDRETDQFKGFCYVEFETLDNLERAL------ECDGRiklddlsaPLRID 96
Cdd:cd12398    4 FVGNIPYDATEEQLKEIFsEVGPVVSFRLVTDRETGKPKGYGFCEFRDAETALSAVrnlngyELNGR--------PLRVD 75

                 ..
gi 665391848  97 IA 98
Cdd:cd12398   76 FA 77
RRM1_2_CELF1-6_like cd12361
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding ...
24-93 3.84e-07

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: 46.85  E-value: 3.84e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALE-CDGRIKLDDLSAPL 93
Cdd:cd12361    3 FVGMIPKTASEEDVRPLFEQFgNIEEVQILRDKQTGQSKGCAFVTFSTREEALRAIEaLHNKKTMPGCSSPL 74
RRM2_NUCLs cd12451
RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This ...
45-82 5.23e-07

RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409885 [Multi-domain]  Cd Length: 79  Bit Score: 46.64  E-value: 5.23e-07
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 665391848  45 EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALECDG 82
Cdd:cd12451   29 EVTNVRIPTDRETGELKGFAYIEFSTKEAKEKALELNG 66
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
24-101 5.63e-07

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 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: 409847 [Multi-domain]  Cd Length: 79  Bit Score: 46.43  E-value: 5.63e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALECDGRIKLDdlSAPLRIDIADRR 101
Cdd:cd12413    3 FVRNLPYDTTDEQLEELFSDVgPVKRCFVVKDKGKDKCRGFGYVTFALAEDAQRALEEVKGKKFG--GRKIKVELAKKK 79
RRM1_RBM39_like cd12283
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar ...
24-84 5.89e-07

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409725 [Multi-domain]  Cd Length: 73  Bit Score: 46.45  E-value: 5.89e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALECDGRI 84
Cdd:cd12283    3 FVMQLSLKARERDLYEFFSKAgKVRDVRLIMDRNSRRSKGVAYVEFYDVESVPLALALTGQR 64
RRM1_SART3 cd12391
RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells ...
24-81 5.99e-07

RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409825 [Multi-domain]  Cd Length: 72  Bit Score: 46.07  E-value: 5.99e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDReTDQFKGFCYVEFETLDNLERALECD 81
Cdd:cd12391    3 FVSNLDYSVPEDKIREIFSGCgEITDVRLVKNY-KGKSKGYCYVEFKDEESAQKALKLD 60
RRM1_gar2 cd12447
RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This ...
24-87 1.16e-06

RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409881 [Multi-domain]  Cd Length: 76  Bit Score: 45.50  E-value: 1.16e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDFE-VKYVRLVKDRETDQFKGFCYVEFETLDNLERAL------ECDGR-IKLD 87
Cdd:cd12447    3 FVGGLSWNVDDPWLKKEFEKYGgVISARVITDRGSGRSKGYGYVDFATPEAAQKALaamsgkEIDGRqINVD 74
RRM2_Nop12p_like cd12670
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 12 (Nop12p) and similar ...
24-83 2.85e-06

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 12 (Nop12p) and similar proteins; This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410071 [Multi-domain]  Cd Length: 77  Bit Score: 44.36  E-value: 2.85e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALECDGR 83
Cdd:cd12670    3 FVGNLAFEAEEEGLWRYFGKCgAIESVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLNEK 63
RRM1_PHIP1 cd12271
RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting ...
23-82 4.53e-06

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


Pssm-ID: 409714 [Multi-domain]  Cd Length: 72  Bit Score: 43.85  E-value: 4.53e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 665391848  23 AFVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALECDG 82
Cdd:cd12271    1 VYVGGIPYYSTEAEIRSYFSSCgEVRSVDLMRFPDSGNFRGIAFITFKTEEAAKRALALDG 61
RRM3_RBM28_like cd12415
RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
24-87 8.26e-06

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 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: 409849 [Multi-domain]  Cd Length: 83  Bit Score: 43.36  E-value: 8.26e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALE------CDGRIKLD 87
Cdd:cd12415    4 FIRNLSFDTTEEDLKEFFSKFgEVKYARIVLDKDTGHSKGTAFVQFKTKESADKCIEaandesEDGGLVLD 74
RRM_SNP1_like cd21615
RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ...
16-106 1.01e-05

RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ribonucleoprotein SNP1 and similar proteins; SNP1, also called U1 snRNP protein SNP1, or U1 small nuclear ribonucleoprotein 70 kDa homolog, or U1 70K, or U1 snRNP 70 kDa homolog, interacts with mRNA and is involved in nuclear mRNA splicing. It is a component of the spliceosome, where it is associated with snRNP U1 by binding stem loop I of U1 snRNA. Members in this family contain an N-terminal U1snRNP70 domain and an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410194 [Multi-domain]  Cd Length: 118  Bit Score: 44.23  E-value: 1.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665391848  16 PTEPPFIA--------FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERA-LECDGRIK 85
Cdd:cd21615    6 PEEDPHIAdgdpyktlFVGRLDYSLTELELQKKFSKFgEIEKIRIVRDKETGKSRGYAFIVFKSESDAKNAfKEGNGLRG 85
                         90       100
                 ....*....|....*....|...
gi 665391848  86 LDDLSAPLRIDIADRR--KNDRP 106
Cdd:cd21615   86 LKINDRTCIVDIERGRtvKNWKP 108
RRM2_FCA cd12637
RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar ...
24-99 1.38e-05

RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar proteins; This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain.


Pssm-ID: 410045 [Multi-domain]  Cd Length: 81  Bit Score: 42.75  E-value: 1.38e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALEC-DGRIKLDDLSAPLRIDIAD 99
Cdd:cd12637    3 FVGSLPKTATEQEVRDLFEAYgEVEEVYLMKDPVTQQGTGCAFVKFAYKEEALAAIRSlNGTVTFDGCSRPVEVRFAE 80
RRM_SLIRP cd12242
RNA recognition motif (RRM) found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and ...
23-84 1.41e-05

RNA recognition motif (RRM) found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins; This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities.


Pssm-ID: 409688 [Multi-domain]  Cd Length: 73  Bit Score: 42.34  E-value: 1.41e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 665391848  23 AFVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALECDGRI 84
Cdd:cd12242    2 LFVSNLPWTTGSSELKEYFSQFgKVKRCNLPFDKETGFHKGFGFVSFENEDGLRNALQKQKHI 64
RRM2_U2AF65 cd12231
RNA recognition motif 2 (RRM2) found in U2 large nuclear ribonucleoprotein auxiliary factor ...
24-72 1.83e-05

RNA recognition motif 2 (RRM2) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs.


Pssm-ID: 409678 [Multi-domain]  Cd Length: 77  Bit Score: 42.25  E-value: 1.83e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLD 72
Cdd:cd12231    4 FIGGLPNYLNEDQVKELLQSFgKLKAFNLVKDSATGLSKGYAFCEYVDDN 53
RRM_II_PABPs cd12306
RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to ...
24-82 2.12e-05

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


Pssm-ID: 409747 [Multi-domain]  Cd Length: 73  Bit Score: 41.91  E-value: 2.12e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALECDG 82
Cdd:cd12306    3 YVGNVDYGTTPEELQAHFKSCgTINRVTILCDKFTGQPKGFAYIEFVDKSSVENALLLNE 62
RRM_RNPS1 cd12365
RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and ...
40-78 2.17e-05

RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins; This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain.


Pssm-ID: 409800 [Multi-domain]  Cd Length: 73  Bit Score: 41.77  E-value: 2.17e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 665391848  40 IFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERAL 78
Cdd:cd12365   18 IFSVYgTVKNVDLPIDREPNLPRGYAYVEFESPEDAEKAI 57
RRM2_hnRNPD_like cd12329
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, ...
24-79 2.41e-05

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins; This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, 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. It 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 memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 240775 [Multi-domain]  Cd Length: 75  Bit Score: 41.97  E-value: 2.41e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALE 79
Cdd:cd12329    3 FVGGLSPETTEEKIREYFGKFgNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILE 59
RRM2_MRD1 cd12566
RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 ...
24-84 2.96e-05

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


Pssm-ID: 409982 [Multi-domain]  Cd Length: 79  Bit Score: 41.63  E-value: 2.96e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERA-LECDGRI 84
Cdd:cd12566    6 FLRNLPYSTKEDDLQKLFSKFgEVSEVHVPIDKKTKKSKGFAYVLFLDPEDAVQAyNELDGKV 68
RRM2_PUF60 cd12371
RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
24-79 5.31e-05

RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.


Pssm-ID: 409806 [Multi-domain]  Cd Length: 77  Bit Score: 40.73  E-value: 5.31e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALE 79
Cdd:cd12371    4 YVASVHPDLSEDDIKSVFEAFgKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60
RRM2_Nop13p_fungi cd12397
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar ...
24-98 6.18e-05

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar proteins; This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409831 [Multi-domain]  Cd Length: 76  Bit Score: 40.89  E-value: 6.18e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALEcdGRIKLDDLSAPLRIDIA 98
Cdd:cd12397    2 FVGNLSFETTEEDLRKHFAPAgKIRKVRMATFEDSGKCKGFAFVDFKEIESATNAVK--GPINHSLNGRDLRVEYG 75
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
25-79 6.79e-05

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins; This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus.


Pssm-ID: 409842 [Multi-domain]  Cd Length: 76  Bit Score: 40.57  E-value: 6.79e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 665391848  25 VGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALE 79
Cdd:cd12408    4 VTNLSEDATEEDLRELFRPFgPISRVYLAKDKETGQSKGFAFVTFETREDAERAIE 59
RRM2_MSI cd12323
RNA recognition motif 2 (RRM2) found in RNA-binding protein Musashi homologs Musashi-1, ...
24-79 6.87e-05

RNA recognition motif 2 (RRM2) found in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins; This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function.


Pssm-ID: 240769 [Multi-domain]  Cd Length: 74  Bit Score: 40.50  E-value: 6.87e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALE 79
Cdd:cd12323    3 FVGGLSANTTEDDVKKYFSQFgKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCE 59
RRM1_SECp43_like cd12344
RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and ...
39-79 7.89e-05

RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins; This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs.


Pssm-ID: 409780 [Multi-domain]  Cd Length: 82  Bit Score: 40.37  E-value: 7.89e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 665391848  39 KIFQ--DFEVKYVRLVKDRETDQFKGFCYVEFETLDNLERALE 79
Cdd:cd12344   18 SCFAktGEEVVSVKIIRNKQTGKSAGYCFVEFATQEAAEQALE 60
RRM_NIFK_like cd12307
RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) ...
22-80 1.05e-04

RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins; This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409748 [Multi-domain]  Cd Length: 74  Bit Score: 39.86  E-value: 1.05e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 665391848  22 IAFVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEF----------ETLDNL---ERALEC 80
Cdd:cd12307    1 VVYIGHLPHGFYEPELRKYFSQFgTVTRLRLSRSKKTGKSKGYAFVEFedpevakivaETMNNYllfERLLKC 73
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
24-84 1.06e-04

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


Pssm-ID: 409755 [Multi-domain]  Cd Length: 74  Bit Score: 40.02  E-value: 1.06e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERAL-ECDGRI 84
Cdd:cd12316    3 FVRNLPFTATEDELRELFEAFgKISEVHIPLDKQTKRSKGFAFVLFVIPEDAVKAYqELDGSI 65
RRM1_PSRP2_like cd21609
RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 ...
24-88 1.48e-04

RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins; PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). The family also includes Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (AtCP31A). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. Members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410188 [Multi-domain]  Cd Length: 80  Bit Score: 39.71  E-value: 1.48e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALEcdgriKLDD 88
Cdd:cd21609    3 YVGNIPRNVTSEELAKIFEEAgTVEIAEVMYDRYTGRSRGFGFVTMGSVEDAKAAIE-----KLNG 63
RRM1_2_CID8_like cd12225
RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting ...
25-82 2.14e-04

RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear.


Pssm-ID: 409672 [Multi-domain]  Cd Length: 76  Bit Score: 39.37  E-value: 2.14e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 665391848  25 VGNLPQGLVQGDVIKIFQ-DFEVKYVRLVKDRETDQFkgfCYVEFETLDNLERALECDG 82
Cdd:cd12225    5 VGGIDGSLSEDELADYFSnCGEVTQVRLCGDRVHTRF---AWVEFATDASALSALNLDG 60
RRM_RBM8 cd12324
RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; ...
22-79 2.51e-04

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: 39.13  E-value: 2.51e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 665391848  22 IAFVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALE 79
Cdd:cd12324    8 IIFVTGVHEEAQEEDIHDKFAEFgEIKNLHLNLDRRTGFVKGYALVEYETKKEAQAAIE 66
RRM_ZCRB1 cd12393
RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ...
24-77 2.57e-04

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.


Pssm-ID: 409827 [Multi-domain]  Cd Length: 76  Bit Score: 38.80  E-value: 2.57e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERA 77
Cdd:cd12393    5 YVSNLPFSLTNNDLHQIFSKYgKVVKVTILKDKETRKSKGVAFVLFLDRESAHNA 59
RRM2_NCL cd12404
RNA recognition motif 2 (RRM2) found in vertebrate nucleolin; This subfamily corresponds to ...
24-83 3.04e-04

RNA recognition motif 2 (RRM2) found in vertebrate nucleolin; This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop.


Pssm-ID: 409838 [Multi-domain]  Cd Length: 77  Bit Score: 38.95  E-value: 3.04e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDfeVKYVRLVKDRETDQfKGFCYVEFETLDNLERAL------ECDGR 83
Cdd:cd12404    7 FVKNLPYSTTQDELKEVFED--AVDIRIPMGRDGRS-KGIAYIEFKSEAEAEKALeekqgtEVDGR 69
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
24-82 4.00e-04

RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.


Pssm-ID: 409833 [Multi-domain]  Cd Length: 75  Bit Score: 38.27  E-value: 4.00e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERAL-ECDG 82
Cdd:cd12399    2 YVGNLPYSASEEQLKSLFGQFgAVFDVKLPMDRETKRPRGFGFVELQEEESAEKAIaKLDG 62
RRM3_TIA1_like cd12354
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...
23-70 4.56e-04

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: 38.03  E-value: 4.56e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 665391848  23 AFVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDretdqfKGFCYVEFET 70
Cdd:cd12354    3 VYVGNITKGLTEALLQQTFSPFgQILEVRVFPD------KGYAFIRFDS 45
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
24-86 6.11e-04

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 38.05  E-value: 6.11e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF----EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALEC-DGRIKL 86
Cdd:cd12355    3 WIGNLDPRLTEYHLLKLLSKYgkikKFDFLFHKTGPLKGQPRGYCFVTFETKEEAEKAIEClNGKLAL 70
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
24-86 7.53e-04

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410198 [Multi-domain]  Cd Length: 78  Bit Score: 37.89  E-value: 7.53e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRE--TDQFKGFCYVEFETLDNLERALECDGRIKL 86
Cdd:cd21619    5 YVGNIDMTINEDALEKIFSRYgQVESVRRPPIHTdkADRTTGFGFIKYTDAESAERAMQQADGILL 70
RRM1_RBM45 cd12366
RNA recognition motif 1 (RRM1) found in RNA-binding protein 45 (RBM45) and similar proteins; ...
41-98 8.11e-04

RNA recognition motif 1 (RRM1) found in RNA-binding protein 45 (RBM45) and similar proteins; This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409801 [Multi-domain]  Cd Length: 81  Bit Score: 37.68  E-value: 8.11e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 665391848  41 FQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALE-CDGRIkLDDLSAPLRIDIA 98
Cdd:cd12366   23 FSPFgEIQDIWVVKDKQTKESKGIAYVKFAKSSQAARAMEeMHGKC-LGDDTKPIKVLIA 81
RRM6_RBM19_RRM5_MRD1 cd12320
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA ...
25-79 9.45e-04

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 (RRM5) found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409759 [Multi-domain]  Cd Length: 76  Bit Score: 37.21  E-value: 9.45e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 665391848  25 VGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDREtDQFKGFCYVEFETLDNLERALE 79
Cdd:cd12320    5 VKNVPFEATRKEIRELFSPFgQLKSVRLPKKFD-GSHRGFAFVEFVTKQEAQNAME 59
RRM2_hnRNPA0 cd12579
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) ...
24-77 9.59e-04

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains 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.


Pssm-ID: 409993 [Multi-domain]  Cd Length: 80  Bit Score: 37.51  E-value: 9.59e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERA 77
Cdd:cd12579    3 FVGGLKGDVGEGDLVEHFSQFgTVEKVEVIADKDTGKKRGFGFVYFEDHDSADKA 57
RRM1_La cd12291
RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily ...
36-79 1.04e-03

RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus.


Pssm-ID: 409733 [Multi-domain]  Cd Length: 73  Bit Score: 37.19  E-value: 1.04e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 665391848  36 DVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALE 79
Cdd:cd12291   15 DIQEFFEKKgKVENVRMRRDLDSKEFKGSVFVEFKTEEEAKKFLE 59
RRM2_SART3 cd12392
RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells ...
24-69 1.14e-03

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409826 [Multi-domain]  Cd Length: 81  Bit Score: 37.31  E-value: 1.14e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDReTDQFKGFCYVEFE 69
Cdd:cd12392    6 FVKGLPFSCTKEELEELFKQHgTVKDVRLVTYR-NGKPKGLAYVEYE 51
RRM1_RBM10 cd12753
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 10 (RBM10); This ...
28-83 1.27e-03

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 10 (RBM10); This subgroup corresponds to the RRM1 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 410147 [Multi-domain]  Cd Length: 84  Bit Score: 37.22  E-value: 1.27e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 665391848  28 LPQGLVQGDVIKIFQD--FEVKYVRLVKDRETDQFKGFCYVEFETLDNLERALECDGR 83
Cdd:cd12753    9 LPQSATENDIRGQLQAhgVQPREVRLMRNKSSGQSRGFAFVEFNHLQDATRWMEANQH 66
RRM1_SF3B4 cd12334
RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar ...
24-95 1.35e-03

RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar proteins; This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145.


Pssm-ID: 409771 [Multi-domain]  Cd Length: 74  Bit Score: 36.81  E-value: 1.35e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 665391848  24 FVGNLPQGLVQGDVIKIF-QDFEVKYVRLVKDRETDQFKGFCYVEFETLDNLERALECDGRIKLddLSAPLRI 95
Cdd:cd12334    2 YVGNLDEKVTEELLWELFiQAGPVVNVHMPKDRVTQQHQGYGFVEFLSEEDADYAIKIMNMIKL--YGKPIRV 72
RRM3_PUB1 cd12622
RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated ...
23-73 1.56e-03

RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. 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 RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410033 [Multi-domain]  Cd Length: 74  Bit Score: 36.66  E-value: 1.56e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 665391848  23 AFVGNLPQGLVQGDVIKIFQDFEV-KYVRLVKDretdqfKGFCYVEFETLDN 73
Cdd:cd12622    3 VYVGNLPPEVTQADLIPLFQNFGViEEVRVQRD------KGFGFVKYDTHEE 48
RRM1_RBM5_like cd12561
RNA recognition motif 1 (RRM1) found in RNA-binding protein 5 (RBM5) and similar proteins; ...
25-79 2.65e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein 5 (RBM5) and similar proteins; This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409977 [Multi-domain]  Cd Length: 81  Bit Score: 36.19  E-value: 2.65e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 665391848  25 VGNLPQGLVQGDVIKIFQDFEVKY--VRLVKDRETDQFKGFCYVEFETLDNLERALE 79
Cdd:cd12561    7 LRGLPLSVTEEDIRNALVSHGVQPkdVRLMRRKTTGASRGFAFVEFMSLEEATRWME 63
RRM2_RBM45 cd12367
RNA recognition motif 2 (RRM2) found in RNA-binding protein 45 (RBM45) and similar proteins; ...
29-85 2.96e-03

RNA recognition motif 2 (RRM2) found in RNA-binding protein 45 (RBM45) and similar proteins; This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409802 [Multi-domain]  Cd Length: 74  Bit Score: 35.81  E-value: 2.96e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 665391848  29 PQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALE-CDGRIK 85
Cdd:cd12367    9 PKSYTEEDLREKFKEFgDIEYCSIVKDKNTGESKGFGYVKFLKPSQAALAIEnCDRSFK 67
RRM_snRNP70 cd12236
RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and ...
24-88 3.07e-03

RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins; This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function.


Pssm-ID: 409682 [Multi-domain]  Cd Length: 91  Bit Score: 36.45  E-value: 3.07e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERAL-ECDGRiKLDD 88
Cdd:cd12236    5 FVARLSYDTTESKLRREFEKYgPIKRVRLVRDKKTGKSRGYAFIEFEHERDMKAAYkHADGK-KIDG 70
RRM1_Hu cd12650
RNA recognition motif 1 (RRM1) found in the Hu proteins family; This subfamily corresponds to ...
25-78 3.46e-03

RNA recognition motif 1 (RRM1) found in the Hu proteins family; This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410053 [Multi-domain]  Cd Length: 77  Bit Score: 35.84  E-value: 3.46e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 665391848  25 VGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERAL 78
Cdd:cd12650    5 VNYLPQNMTQDEIRSLFSSIgEIESCKLIRDKVTGQSLGYGFVNYVDPSDAEKAI 59
RRM_Nop15p cd12552
RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins; ...
22-77 3.53e-03

RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins; This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409968 [Multi-domain]  Cd Length: 77  Bit Score: 35.61  E-value: 3.53e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 665391848  22 IAFVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFetlDNLERA 77
Cdd:cd12552    1 IIYVSHLPHGFHEKELKKYFAQFgDLKNVRLARSKKTGNSKHYGFLEF---VNPEDA 54
RRM3_Nop4p cd12676
RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
24-96 4.05e-03

RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM3 of Nop4p (also known as 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 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410077 [Multi-domain]  Cd Length: 107  Bit Score: 36.25  E-value: 4.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEF---ETLDN-LERALE----------CDGRIKLDD 88
Cdd:cd12676    5 FVRNLPFDATEDELYSHFSQFgPLKYARVVKDPATGRSKGTAFVKFknkEDADNcLSAAPEaqstsllekySLEQDITDD 84

                 ....*...
gi 665391848  89 LSAPLRID 96
Cdd:cd12676   85 VSAKFTLD 92
RRM4_RBM12_like cd12514
RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
23-86 4.23e-03

RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; This subfamily corresponds to the RRM4 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B show high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear.


Pssm-ID: 409936 [Multi-domain]  Cd Length: 73  Bit Score: 35.47  E-value: 4.23e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 665391848  23 AFVGNLPQGLVQGDVIKIFQDFEV--KYVRLVKDRETdQFKGFCYVEFETLDNLERALECDGRIKL 86
Cdd:cd12514    2 IRITNLPYDATPVDIQRFFEDHGVrpEDVHLLRNKKG-RGNGEALVTFKSEGDAREVLKLNGKKLG 66
RRM_CIRBP_RBM3 cd12449
RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding ...
24-87 4.71e-03

RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins; This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain.


Pssm-ID: 409883 [Multi-domain]  Cd Length: 80  Bit Score: 35.53  E-value: 4.71e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALEC------DGR-IKLD 87
Cdd:cd12449    4 FVGGLSFDTNEQSLEEVFSKYgQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAmngkslDGRqIRVD 75
RRM2_RBM5 cd12755
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup ...
41-96 6.86e-03

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup corresponds to the RRM2 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.


Pssm-ID: 410149 [Multi-domain]  Cd Length: 86  Bit Score: 35.29  E-value: 6.86e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 665391848  41 FQDFEVKYVRLVKDRETDQFKGFCYVEfetldnLERALECDGRIK-LDDLSAPLRID 96
Cdd:cd12755   26 YASLAVNNIRLIKDKQTQQNRGFAFVQ------LSSALEASQLLQiLQSLHPPLKID 76
RRM1_LARP7 cd12290
RNA recognition motif 1 (RRM1) found in La-related protein 7 (LARP7) and similar proteins; ...
24-79 9.32e-03

RNA recognition motif 1 (RRM1) found in La-related protein 7 (LARP7) and similar proteins; This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus.


Pssm-ID: 409732 [Multi-domain]  Cd Length: 79  Bit Score: 34.61  E-value: 9.32e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF-EVKYVRLVKDRETDQFKGFCYVEFETLDNLERALE 79
Cdd:cd12290    3 YVELLPKNATHEWIEAVFSKYgEVVYVSIPRYKSTGDPKGFAFIEFETSESAQKAVK 59
RRM2_CID8_like cd12460
RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana CTC-interacting domain protein ...
24-82 9.84e-03

RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM2 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear.


Pssm-ID: 409893 [Multi-domain]  Cd Length: 82  Bit Score: 34.68  E-value: 9.84e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 665391848  24 FVGNLPQGLVQGDVIKIFQDF--EVKYVRLVKDrETDQFKgFCYVEFETLDNLERALECDG 82
Cdd:cd12460    8 YCTNIDKKVTQDDVKAFFESLcgEVHRLRLLGD-YVHSTR-IAFVEFVMAESAIAALNCSG 66
 
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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