RNA recognition motif (RRM)-containing protein [Arabidopsis thaliana]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | |||
| LA_like_plant | cd08030 | La-motif domain of plant proteins similar to the La autoantigen; This domain is found in plant ... |
9-98 | 1.20e-43 | |||
La-motif domain of plant proteins similar to the La autoantigen; This domain is found in plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. : Pssm-ID: 153399 Cd Length: 90 Bit Score: 146.77 E-value: 1.20e-43
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| RRM2_La_like | cd12292 | RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 ... |
277-350 | 2.67e-24 | |||
RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 or PIP7S) and similar proteins; This subfamily corresponds to the RRM2 of La and LARP7. La is 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. LARP7 is an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP), 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. LARP7 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. Both La and LARP7 contain an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). : Pssm-ID: 409734 [Multi-domain] Cd Length: 74 Bit Score: 95.08 E-value: 2.67e-24
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| RRM_SF super family | cl17169 | RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ... |
116-187 | 1.08e-10 | |||
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). The actual alignment was detected with superfamily member cd12291: Pssm-ID: 473069 [Multi-domain] Cd Length: 73 Bit Score: 57.22 E-value: 1.08e-10
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| Name | Accession | Description | Interval | E-value | ||||
| LA_like_plant | cd08030 | La-motif domain of plant proteins similar to the La autoantigen; This domain is found in plant ... |
9-98 | 1.20e-43 | ||||
La-motif domain of plant proteins similar to the La autoantigen; This domain is found in plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Pssm-ID: 153399 Cd Length: 90 Bit Score: 146.77 E-value: 1.20e-43
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| LA | smart00715 | Domain in the RNA-binding Lupus La protein; unknown function; |
7-99 | 1.03e-24 | ||||
Domain in the RNA-binding Lupus La protein; unknown function; Pssm-ID: 128955 [Multi-domain] Cd Length: 80 Bit Score: 96.53 E-value: 1.03e-24
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| RRM2_La_like | cd12292 | RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 ... |
277-350 | 2.67e-24 | ||||
RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 or PIP7S) and similar proteins; This subfamily corresponds to the RRM2 of La and LARP7. La is 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. LARP7 is an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP), 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. LARP7 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. Both La and LARP7 contain an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Pssm-ID: 409734 [Multi-domain] Cd Length: 74 Bit Score: 95.08 E-value: 2.67e-24
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| La | pfam05383 | La domain; This presumed domain is found at the N-terminus of La RNA-binding proteins as well ... |
13-58 | 2.48e-17 | ||||
La domain; This presumed domain is found at the N-terminus of La RNA-binding proteins as well as other proteins. The function of this region is uncertain. Pssm-ID: 461635 Cd Length: 59 Bit Score: 75.54 E-value: 2.48e-17
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| RRM1_La | cd12291 | RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily ... |
116-187 | 1.08e-10 | ||||
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: 57.22 E-value: 1.08e-10
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| RRM_3 | pfam08777 | RNA binding motif; This domain is found in protein La which functions as an RNA chaperone ... |
289-363 | 3.01e-06 | ||||
RNA binding motif; This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif. Pssm-ID: 400913 [Multi-domain] Cd Length: 102 Bit Score: 45.44 E-value: 3.01e-06
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| LHP1 | COG5193 | La protein, small RNA-binding pol III transcript stabilizing protein and related ... |
11-171 | 2.05e-03 | ||||
La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis]; Pssm-ID: 227520 [Multi-domain] Cd Length: 438 Bit Score: 40.03 E-value: 2.05e-03
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| Name | Accession | Description | Interval | E-value | ||||
| LA_like_plant | cd08030 | La-motif domain of plant proteins similar to the La autoantigen; This domain is found in plant ... |
9-98 | 1.20e-43 | ||||
La-motif domain of plant proteins similar to the La autoantigen; This domain is found in plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Pssm-ID: 153399 Cd Length: 90 Bit Score: 146.77 E-value: 1.20e-43
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| LA | smart00715 | Domain in the RNA-binding Lupus La protein; unknown function; |
7-99 | 1.03e-24 | ||||
Domain in the RNA-binding Lupus La protein; unknown function; Pssm-ID: 128955 [Multi-domain] Cd Length: 80 Bit Score: 96.53 E-value: 1.03e-24
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| RRM2_La_like | cd12292 | RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 ... |
277-350 | 2.67e-24 | ||||
RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 or PIP7S) and similar proteins; This subfamily corresponds to the RRM2 of La and LARP7. La is 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. LARP7 is an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP), 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. LARP7 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. Both La and LARP7 contain an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Pssm-ID: 409734 [Multi-domain] Cd Length: 74 Bit Score: 95.08 E-value: 2.67e-24
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| LA_like_fungal | cd08029 | La-motif domain of fungal proteins similar to the La autoantigen; This domain is found in ... |
12-98 | 1.81e-19 | ||||
La-motif domain of fungal proteins similar to the La autoantigen; This domain is found in fungal proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Pssm-ID: 153398 Cd Length: 76 Bit Score: 81.96 E-value: 1.81e-19
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| LAM | cd07323 | LA motif RNA-binding domain; This domain is found at the N-terminus of La RNA-binding proteins ... |
11-98 | 3.53e-18 | ||||
LA motif RNA-binding domain; This domain is found at the N-terminus of La RNA-binding proteins as well as in other related proteins. Typically, the domain co-occurs with an RNA-recognition motif (RRM), and together these domains function to bind primary transcripts of RNA polymerase III in the La autoantigen (Lupus La protein, LARP3, or Sjoegren syndrome type B antigen, SS-B). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Pssm-ID: 153396 Cd Length: 75 Bit Score: 78.34 E-value: 3.53e-18
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| LARP_6 | cd08033 | La RNA-binding domain of La-related protein 6; This domain is found in animal and plant ... |
10-98 | 2.20e-17 | ||||
La RNA-binding domain of La-related protein 6; This domain is found in animal and plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Pssm-ID: 153402 Cd Length: 77 Bit Score: 76.17 E-value: 2.20e-17
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| La | pfam05383 | La domain; This presumed domain is found at the N-terminus of La RNA-binding proteins as well ... |
13-58 | 2.48e-17 | ||||
La domain; This presumed domain is found at the N-terminus of La RNA-binding proteins as well as other proteins. The function of this region is uncertain. Pssm-ID: 461635 Cd Length: 59 Bit Score: 75.54 E-value: 2.48e-17
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| RRM1_La | cd12291 | RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily ... |
116-187 | 1.08e-10 | ||||
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: 57.22 E-value: 1.08e-10
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| LARP_7 | cd08032 | La RNA-binding domain of La-related protein 7; LARP7 is a component of the 7SK snRNP, a key ... |
16-98 | 1.53e-09 | ||||
La RNA-binding domain of La-related protein 7; LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation. Pssm-ID: 153401 Cd Length: 82 Bit Score: 54.18 E-value: 1.53e-09
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| LARP_3 | cd08028 | La RNA-binding domain of La-related protein 3; This domain is found at the N-terminus of the ... |
11-98 | 4.74e-07 | ||||
La RNA-binding domain of La-related protein 3; This domain is found at the N-terminus of the La autoantigen and similar proteins, and co-occurs with an RNA-recognition motif (RRM). Together these domains function to bind primary transcripts of RNA polymerase III at their 3' terminus and protect them from exonucleolytic degradation. Binding is specific for the 3'-terminal UUU-OH motif. The La autoantigen is also called Lupus La protein, LARP3, or Sjoegren syndrome type B antigen (SS-B). Pssm-ID: 153397 Cd Length: 82 Bit Score: 47.29 E-value: 4.74e-07
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| RRM1_Crp79 | cd21619 | RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ... |
115-176 | 2.65e-06 | ||||
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: 44.82 E-value: 2.65e-06
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| RRM_3 | pfam08777 | RNA binding motif; This domain is found in protein La which functions as an RNA chaperone ... |
289-363 | 3.01e-06 | ||||
RNA binding motif; This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif. Pssm-ID: 400913 [Multi-domain] Cd Length: 102 Bit Score: 45.44 E-value: 3.01e-06
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| RRM_SF | cd00590 | RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ... |
124-176 | 4.94e-05 | ||||
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Pssm-ID: 409669 [Multi-domain] Cd Length: 72 Bit Score: 41.11 E-value: 4.94e-05
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| RRM1_NUCLs | cd12450 | RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ... |
116-185 | 1.26e-04 | ||||
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: 40.08 E-value: 1.26e-04
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| LARP_1_2 | cd08034 | La RNA-binding domain proteins similar to La-related proteins 1 and 2; This domain is found in ... |
16-58 | 2.87e-04 | ||||
La RNA-binding domain proteins similar to La-related proteins 1 and 2; This domain is found in proteins similar to vertebrate La-related proteins 1 and 2 (LARP1, LARP2). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Pssm-ID: 153403 Cd Length: 73 Bit Score: 38.95 E-value: 2.87e-04
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| RRM6_RBM19_RRM5_MRD1 | cd12320 | RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA ... |
121-187 | 5.32e-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: 38.37 E-value: 5.32e-04
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| LHP1 | COG5193 | La protein, small RNA-binding pol III transcript stabilizing protein and related ... |
11-171 | 2.05e-03 | ||||
La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis]; Pssm-ID: 227520 [Multi-domain] Cd Length: 438 Bit Score: 40.03 E-value: 2.05e-03
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| RRM1_GRSF1 | cd12730 | RNA recognition motif 1 (RRM1) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ... |
124-186 | 2.34e-03 | ||||
RNA recognition motif 1 (RRM1) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; This subgroup corresponds to the RRM1 of GRSF-1, a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic alpha-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity. Pssm-ID: 410129 [Multi-domain] Cd Length: 79 Bit Score: 36.70 E-value: 2.34e-03
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| LARP_1 | cd08037 | La RNA-binding domain of La-related protein 1; This domain is found in vertebrate La-related ... |
16-58 | 2.49e-03 | ||||
La RNA-binding domain of La-related protein 1; This domain is found in vertebrate La-related protein 1 (LARP1). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Pssm-ID: 153406 Cd Length: 73 Bit Score: 36.42 E-value: 2.49e-03
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| RRM_DAZL | cd12672 | RNA recognition motif (RRM) found in vertebrate deleted in azoospermia-like (DAZL) proteins; ... |
126-189 | 2.53e-03 | ||||
RNA recognition motif (RRM) found in vertebrate deleted in azoospermia-like (DAZL) proteins; This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. Pssm-ID: 410073 [Multi-domain] Cd Length: 82 Bit Score: 36.68 E-value: 2.53e-03
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| RRM_SF | cd00590 | RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ... |
284-332 | 2.63e-03 | ||||
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Pssm-ID: 409669 [Multi-domain] Cd Length: 72 Bit Score: 36.11 E-value: 2.63e-03
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| RRM3_Spen | cd12310 | RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family; This subfamily ... |
282-329 | 3.72e-03 | ||||
RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family; This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. Pssm-ID: 409750 [Multi-domain] Cd Length: 72 Bit Score: 35.72 E-value: 3.72e-03
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| RRM_hnRNPH_ESRPs_RBM12_like | cd12254 | RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ... |
129-171 | 5.09e-03 | ||||
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins; The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Pssm-ID: 409699 [Multi-domain] Cd Length: 73 Bit Score: 35.61 E-value: 5.09e-03
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| RRM3_hnRNPH_CRSF1_like | cd12506 | RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H ... |
112-171 | 7.10e-03 | ||||
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H protein family, G-rich sequence factor 1 (GRSF-1) and similar proteins; This subfamily corresponds to the RRM3 of hnRNP H proteins and GRSF-1. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. These proteins have similar RNA binding affinities and specifically recognize the sequence GGGA. They can either stimulate or repress splicing upon binding to a GGG motif. hnRNP H binds to the RNA substrate in the presence or absence of these proteins, whereas hnRNP F binds to the nuclear mRNA only in the presence of cap-binding proteins. hnRNP H and hnRNP H2 are almost identical; both have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. hnRNP H3 may be involved in the splicing arrest induced by heat shock. Most family members contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. For instance, members in this family can regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. The family also includes a cytoplasmic poly(A)+ mRNA binding protein, GRSF-1, which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 also contains three potential RRMs responsible for the RNA binding, and two auxiliary domains (an acidic alpha-helical domain and an N-terminal alanine-rich region) that may play a role in protein-protein interactions and provide binding specificity. Pssm-ID: 409929 [Multi-domain] Cd Length: 75 Bit Score: 35.04 E-value: 7.10e-03
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| RRM6_RBM19 | cd12571 | RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19) and similar proteins; ... |
121-187 | 7.47e-03 | ||||
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Pssm-ID: 409985 [Multi-domain] Cd Length: 79 Bit Score: 35.10 E-value: 7.47e-03
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