EMBRYO DEFECTIVE 140 [Arabidopsis thaliana]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||
| RNA14 super family | cl34906 | Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and ... |
53-567 | 8.92e-25 | ||||||||
Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]; The actual alignment was detected with superfamily member COG5107: Pssm-ID: 227438 [Multi-domain] Cd Length: 660 Bit Score: 109.72 E-value: 8.92e-25
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| RRM | smart00360 | RNA recognition motif; |
652-692 | 3.52e-07 | ||||||||
RNA recognition motif; : Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 47.97 E-value: 3.52e-07
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| cdk7 super family | cl31015 | CDK-activating kinase assembly factor MAT1; All proteins in this family for which functions ... |
576-670 | 3.92e-03 | ||||||||
CDK-activating kinase assembly factor MAT1; All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] The actual alignment was detected with superfamily member TIGR00570: Pssm-ID: 129661 [Multi-domain] Cd Length: 309 Bit Score: 39.79 E-value: 3.92e-03
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| Name | Accession | Description | Interval | E-value | ||||||||
| RNA14 | COG5107 | Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and ... |
53-567 | 8.92e-25 | ||||||||
Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]; Pssm-ID: 227438 [Multi-domain] Cd Length: 660 Bit Score: 109.72 E-value: 8.92e-25
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| RRM | smart00360 | RNA recognition motif; |
652-692 | 3.52e-07 | ||||||||
RNA recognition motif; Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 47.97 E-value: 3.52e-07
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| RRM_Nop6 | cd12400 | RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and ... |
654-692 | 3.72e-07 | ||||||||
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: 47.99 E-value: 3.72e-07
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| RRM | COG0724 | RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]; |
654-692 | 3.17e-06 | ||||||||
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440488 [Multi-domain] Cd Length: 85 Bit Score: 45.47 E-value: 3.17e-06
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| cdk7 | TIGR00570 | CDK-activating kinase assembly factor MAT1; All proteins in this family for which functions ... |
576-670 | 3.92e-03 | ||||||||
CDK-activating kinase assembly factor MAT1; All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 129661 [Multi-domain] Cd Length: 309 Bit Score: 39.79 E-value: 3.92e-03
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| Suf | pfam05843 | Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of ... |
455-557 | 8.02e-03 | ||||||||
Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster Suppressor of forked [Su(f)] protein shares homology with the yeast RNA14 protein and the 77-kDa subunit of human cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilization and an important role of the GU-rich sequence for this regulation to occur. Pssm-ID: 428647 [Multi-domain] Cd Length: 291 Bit Score: 38.90 E-value: 8.02e-03
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| Name | Accession | Description | Interval | E-value | ||||||||
| RNA14 | COG5107 | Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and ... |
53-567 | 8.92e-25 | ||||||||
Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]; Pssm-ID: 227438 [Multi-domain] Cd Length: 660 Bit Score: 109.72 E-value: 8.92e-25
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| RRM | smart00360 | RNA recognition motif; |
652-692 | 3.52e-07 | ||||||||
RNA recognition motif; Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 47.97 E-value: 3.52e-07
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| RRM_Nop6 | cd12400 | RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and ... |
654-692 | 3.72e-07 | ||||||||
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: 47.99 E-value: 3.72e-07
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| RRM | COG0724 | RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]; |
654-692 | 3.17e-06 | ||||||||
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440488 [Multi-domain] Cd Length: 85 Bit Score: 45.47 E-value: 3.17e-06
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| RRM3_RBM28_like | cd12415 | RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; ... |
652-692 | 4.93e-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: 44.90 E-value: 4.93e-06
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| RRM2_gar2 | cd12448 | RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ... |
654-692 | 8.15e-06 | ||||||||
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: 44.32 E-value: 8.15e-06
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| RRM_CSTF2_RNA15_like | cd12398 | RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ... |
651-692 | 1.70e-05 | ||||||||
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: 43.27 E-value: 1.70e-05
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| RRM_eIF4B | cd12402 | RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and ... |
652-692 | 3.03e-05 | ||||||||
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: 42.59 E-value: 3.03e-05
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| RRM2_RBM34 | cd12395 | RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; ... |
652-689 | 4.90e-05 | ||||||||
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: 41.71 E-value: 4.90e-05
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| RRM2_PHIP1 | cd12272 | RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana phragmoplastin interacting ... |
652-690 | 5.44e-05 | ||||||||
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: 42.00 E-value: 5.44e-05
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| RRM_snRNP70 | cd12236 | RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and ... |
652-692 | 8.27e-05 | ||||||||
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: 41.84 E-value: 8.27e-05
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| RRM1_NUCLs | cd12450 | RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ... |
652-692 | 9.21e-05 | ||||||||
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: 41.23 E-value: 9.21e-05
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| RRM_SF | cd00590 | RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ... |
654-692 | 2.88e-04 | ||||||||
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Pssm-ID: 409669 [Multi-domain] Cd Length: 72 Bit Score: 39.57 E-value: 2.88e-04
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| RRM2_NsCP33_like | cd21608 | RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ... |
654-692 | 3.12e-04 | ||||||||
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: 39.84 E-value: 3.12e-04
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| RRM_CSTF2_CSTF2T | cd12671 | RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage ... |
652-692 | 4.06e-04 | ||||||||
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins; This subgroup 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. Pssm-ID: 410072 [Multi-domain] Cd Length: 85 Bit Score: 39.80 E-value: 4.06e-04
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| RRM1_RBM34 | cd12394 | RNA recognition motif 1 (RRM1) found in RNA-binding protein 34 (RBM34) and similar proteins; ... |
651-692 | 4.14e-04 | ||||||||
RNA recognition motif 1 (RRM1) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM1 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: 409828 [Multi-domain] Cd Length: 91 Bit Score: 39.89 E-value: 4.14e-04
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| RRM5_RBM19_like | cd12318 | RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar ... |
651-695 | 5.89e-04 | ||||||||
RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins; This subfamily corresponds to the RRM5 of RBM19 and RRM4 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). Pssm-ID: 409757 [Multi-domain] Cd Length: 80 Bit Score: 39.13 E-value: 5.89e-04
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| RRM_eIF3G_like | cd12408 | RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ... |
655-692 | 7.86e-04 | ||||||||
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: 38.64 E-value: 7.86e-04
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| RRM2_Nop12p_like | cd12670 | RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 12 (Nop12p) and similar ... |
654-683 | 1.40e-03 | ||||||||
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: 37.81 E-value: 1.40e-03
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| RRM1_RBM39_like | cd12283 | RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar ... |
652-692 | 1.50e-03 | ||||||||
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: 37.60 E-value: 1.50e-03
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| RRM3_Nop4p | cd12676 | RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ... |
650-692 | 2.17e-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: 38.18 E-value: 2.17e-03
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| cdk7 | TIGR00570 | CDK-activating kinase assembly factor MAT1; All proteins in this family for which functions ... |
576-670 | 3.92e-03 | ||||||||
CDK-activating kinase assembly factor MAT1; All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 129661 [Multi-domain] Cd Length: 309 Bit Score: 39.79 E-value: 3.92e-03
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| RRM1_2_CELF1-6_like | cd12361 | RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding ... |
654-692 | 4.44e-03 | ||||||||
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: 36.45 E-value: 4.44e-03
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| RRM2_Nop13p_fungi | cd12397 | RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar ... |
654-690 | 4.53e-03 | ||||||||
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: 36.65 E-value: 4.53e-03
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| RRM1_SART3 | cd12391 | RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells ... |
652-682 | 7.08e-03 | ||||||||
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: 35.67 E-value: 7.08e-03
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| SF-CC1 | TIGR01622 | splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ... |
577-692 | 7.67e-03 | ||||||||
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Pssm-ID: 273721 [Multi-domain] Cd Length: 494 Bit Score: 39.52 E-value: 7.67e-03
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| Suf | pfam05843 | Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of ... |
455-557 | 8.02e-03 | ||||||||
Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster Suppressor of forked [Su(f)] protein shares homology with the yeast RNA14 protein and the 77-kDa subunit of human cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilization and an important role of the GU-rich sequence for this regulation to occur. Pssm-ID: 428647 [Multi-domain] Cd Length: 291 Bit Score: 38.90 E-value: 8.02e-03
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