OCRE domain found in RNA-binding protein RBM5, RBM10, 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), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, and a G-patch/D111 domain.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 954443199 473 PAPNVSQFQYDQTSGYYYDPTTGLYYDSNSQYFYNNTTQQFLYWDSCCQTYLPV 526
Cdd:cd16162    1 PPPDPSTYQYDETSGYYYDPTTGLYYDPNSQYFYNSQTQQYLYWDQTKKTYVPV 54

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).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954443199 252 PCDTLLFRNLPYSVDEVKLTDHLNRTCAMTIQQVLIARNVENGFSRGYAYVQMTNVNDAAQLLTTLTAV-SKLIIDGREI 330
Cdd:cd12313    1 PTNVLILRGLDVLTTEEDILSALQAHADLPIKDVRLIRDKLTGTSRGFAFVEFSSLEDATQVMDALQNLlPPFKIDGRVV 80

                 ....*
gi 954443199 331 LVSYS 335
Cdd:cd12313   81 SVSYA 85

OCRE domain found in RNA-binding protein RBM5, RBM10, 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), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, and a G-patch/D111 domain.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 954443199 473 PAPNVSQFQYDQTSGYYYDPTTGLYYDSNSQYFYNNTTQQFLYWDSCCQTYLPV 526
Cdd:cd16162    1 PPPDPSTYQYDETSGYYYDPTTGLYYDPNSQYFYNSQTQQYLYWDQTKKTYVPV 54

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 954443199  797 ESIGSRLMRNMGWKEGQGLGKSNQGITNPIESERRVQGAGLGAP 840
Cdd:pfam01585   2 SNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGAE 45

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954443199 252 PCDTLLFRNLPYSVDEVKLTDHLNRTCAMTIQQVLIARNVENGFSRGYAYVQMTNVNDAAQLLTTLTAV-SKLIIDGREI 330
Cdd:cd12313    1 PTNVLILRGLDVLTTEEDILSALQAHADLPIKDVRLIRDKLTGTSRGFAFVEFSSLEDATQVMDALQNLlPPFKIDGRVV 80

                 ....*
gi 954443199 331 LVSYS 335
Cdd:cd12313   81 SVSYA 85

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 954443199   255 TLLFRNLPYSVDEVKLTDHLNRTCamTIQQVLIARNVENGFSRGYAYVQMTNVNDAAQLLTTLtavSKLIIDGREILV 332
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFG--KVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL---NGKELDGRPLKV 73

Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.

                           10        20
                   ....*....|....*....|...
gi 954443199   209 GDWICGKCTTNNFKKRDHCFKCG 231
Cdd:smart00547   1 GDWECPACTFLNFASRSKCFACG 23

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954443199 255 TLLFRNLPYSVDEVKLTDHLNRTCamTIQQVLIARNVENGFSRGYAYVQMTNVNDAAQllttltAVSKL---IIDGREIL 331
Cdd:COG0724    3 KIYVGNLPYSVTEEDLRELFSEYG--EVTSVKLITDRETGRSRGFGFVEMPDDEEAQA------AIEALngaELMGRTLK 74

                 ..
gi 954443199 332 VS 333
Cdd:COG0724   75 VN 76

Zn-finger in Ran binding protein and others;

                          10        20
                  ....*....|....*....|....*
gi 954443199  207 RGGDWICGKCTTNNFKKRDHCFKCG 231
Cdd:pfam00641   1 REGDWDCSKCLVQNFATSTKCVACQ 25

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 954443199  259 RNLPYSVDEVKLTDHLnRTCAmTIQQVLIARNvENGFSRGYAYVQMTNVNDAAQllttltAVSKL---IIDGREIL 331
Cdd:pfam00076   4 GNLPPDTTEEDLKDLF-SKFG-PIKSIRLVRD-ETGRSKGFAFVEFEDEEDAEK------AIEALngkELGGRELK 70

OCRE domain found in RNA-binding protein RBM5, RBM10, 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), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, and a G-patch/D111 domain.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 954443199 473 PAPNVSQFQYDQTSGYYYDPTTGLYYDSNSQYFYNNTTQQFLYWDSCCQTYLPV 526
Cdd:cd16162    1 PPPDPSTYQYDETSGYYYDPTTGLYYDPNSQYFYNSQTQQYLYWDQTKKTYVPV 54

OCRE domain found in RNA-binding protein 5 (RBM5) and similar proteins; RBM5 is also called protein G15, H37, putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9. It is a known modulator of apoptosis. It acts 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 of them specifically binds poly(G) RNA. RBM5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 954443199 475 PNVSQFQYDQTSGYYYDPTTGLYYDSNSQYFYNNTTQQFLYWDSCCQTYLPVV 527
Cdd:cd16168    3 PDTSTYQYDESSGYYYDPITGLYYDPNSQYYYNSLTQQYLYWDGEKQTYLPAA 55

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 954443199  797 ESIGSRLMRNMGWKEGQGLGKSNQGITNPIESERRVQGAGLGAP 840
Cdd:pfam01585   2 SNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGAE 45

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 954443199 110 PNSTLVVKGIPLSYNEELVRNAVVEMGVTPI-DVRILRKRESGESRGFGFIEFMSIEEATKYMERSQG---FLEVNGRR 184
Cdd:cd12313    1 PTNVLILRGLDVLTTEEDILSALQAHADLPIkDVRLIRDKLTGTSRGFAFVEFSSLEDATQVMDALQNllpPFKIDGRV 79

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954443199 111 NSTLVVKGIPLSYNEELVRNAVVEMGVTPIDVRILRKRESGESRGFGFIEFMSIEEATKYMERSQGFLEVNGRRMAeLQY 190
Cdd:cd12753    1 SNIIMLRMLPQSATENDIRGQLQAHGVQPREVRLMRNKSSGQSRGFAFVEFNHLQDATRWMEANQHSLTILGQKVS-MHY 79

                 ....
gi 954443199 191 SINK 194
Cdd:cd12753   80 SDPK 83

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup corresponds to the RRM1 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954443199 113 TLVVKGIPLSYNEELVRNAVVEM-GVTPIDVRILrKRESGESRGFGFIEFMSIEEATKYMERSQGFLEVNGRRMAeLQYS 191
Cdd:cd12752    7 TIMLRGLPINITENDIRELIESFeGPQPADVRLM-KRKTGVSRGFAFVEFYHLQDATSWMEANQKKLVIQGKTIA-MHYS 84

                 ...
gi 954443199 192 INK 194
Cdd:cd12752   85 NPR 87

G-patch domain; Yeast Spp2, a G-patch protein and spliceosome component, interacts with the ATP-dependent DExH-box splicing factor Prp2. As this interaction involves the G-patch sequence in Spp2 and is required for the recruitment of Prp2 to the spliceosome before the first catalytic step of splicing, it is proposed that Spp2 might be an accessory factor that confers spliceosome specificity on Prp2.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 954443199  796 VESIGSRLMRNMGWKEGQGLGKSNQGITNPIESERRVQGAGLGA 839
Cdd:pfam12656  14 VEEFGAAMLRGMGWKPGQGIGKNKKGDVKPKEYKRRPGGLGLGA 57

OCRE domain found in angiogenic factor VG5Q and similar proteins; VG5Q, also called angiogenic factor with G patch and FHA domains 1 (AGGF1), or G patch domain-containing protein 7, or vasculogenesis gene on 5q protein, functions as a potent angiogenic factor in promoting angiogenesis through interacting with TWEAK (also known as TNFSF12), which is a member of the tumor necrosis factor (TNF) superfamily that induces angiogenesis in vivo. VG5Q can bind to the surface of endothelial cells and promote cell proliferation, suggesting that it may act in an autocrine fashion. The chromosomal translocation t(5;11) and the E133K variant in VG5Q are associated with Klippel-Trenaunay syndrome (KTS), a disorder characterized by diverse effects in the vascular system. In addition to a forkhead-associated (FHA) domain and a G-patch motif, VG5Q contains an N-terminal OCtamer REpeat (OCRE) domain that is characterized by a 5-fold, imperfectly repeated octameric sequence.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 954443199 473 PAPNVSQFQYDQTSGYYYDPTTGLYYDSNSQYFYNNTTQQFLYWDSCCQTY 523
Cdd:cd16164    1 AAVSQSGFVYDEATGMYYDPSTGYYYDSETQLYYDPNTGTYYYYDEESGSY 51

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).

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 954443199 114 LVVKGIPLSYNEELVRNAVVEMGvTPIDVRILRKReSGESRGFGFIEFMSIEEATKYMERSQGFlEVNGRRM 185
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFG-EVVSVRIVRDR-DGKSKGFAFVEFESPEDAEKALEALNGT-ELGGRPL 69

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954443199 260 NLPYSVDEVKLTDHLNRtcAMTIQQVLIARNVENGFSRGYAYVQMTNVNDAAqllttlTAVSKL---IIDGREILVSYSK 336
Cdd:cd21609    6 NIPRNVTSEELAKIFEE--AGTVEIAEVMYDRYTGRSRGFGFVTMGSVEDAK------AAIEKLngtEVGGREIKVNITE 77

                 ...
gi 954443199 337 IPL 339
Cdd:cd21609   78 KPL 80

OCRE domain found in Zinc-finger and OCRE domain-containing Protein 1 (ZOP1) and similar proteins found in plant; ZOP1 is a novel plant-specific nucleic acid-binding protein required for both RNA-directed DNA methylation (RdDM) and pre-mRNA splicing. It promotes RNA polymerase IV (Pol IV)-dependent siRNA accumulation, DNA methylation, and transcriptional silencing. As a pre-mRNA splicing factor, ZOP1 associates with several typical splicing proteins as well as with RNA polymerase II (RNAP II and Pol II). It also shows both RdDM-dependent and -independent roles in transcriptional silencing. ZOP1 contains an N-terminal C2H2-type ZnF domain and an OCtamer REpeat (OCRE) domain that is usually related to RNA processing.

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 954443199 477 VSQFQYDQTSGYYYDPTTGLYYDSNSQYFYNNTTQQ 512
Cdd:cd16165    5 AGDWVLDSKSGYYYNAATRYYYDPKTGMYYSDETGK 40

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).

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 954443199 256 LLFRNLPYSVDEVKLTDHLNRTCamTIQQVLIARNvENGFSRGYAYVQMTNVNDAAQLLTTLTavsKLIIDGREILVS 333
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFG--EVVSVRIVRD-RDGKSKGFAFVEFESPEDAEKALEALN---GTELGGRPLKVS 72

RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins; This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954443199 111 NSTLVVKGIPLSYNEELVRNAVVEMGvtPID-VRILRKRESGESRGFGFIEFMSIEEATKYMERSQGfLEVNGRRMaELQ 189
Cdd:cd12363    1 SRCLGVFGLSLYTTERDLREVFSRYG--PIEkVQVVYDQQTGRSRGFGFVYFESVEDAKEAKERLNG-QEIDGRRI-RVD 76

                 ...
gi 954443199 190 YSI 192
Cdd:cd12363   77 YSI 79

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 954443199 114 LVVKGIPLSYNEELVRNAVVEMGvTPIDVRILRKRESGESRGFGFIEFMSIEEATKYMERSQGFlEVNGRRM 185
Cdd:cd21609    2 LYVGNIPRNVTSEELAKIFEEAG-TVEIAEVMYDRYTGRSRGFGFVTMGSVEDAKAAIEKLNGT-EVGGREI 71

RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subfamily corresponds to the RRM1 of RBM19 and 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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 954443199 112 STLVVKGIPLSYNEELVRNAVVE----MGVTPIDVRILRKREsGESRGFGFIEFMSIEEATKYME 172
Cdd:cd12315    1 SRLIVKNLPLSLDEDQFRRLFSQkckdIGLTITDCKLLTKSG-GVSRRFGFVGFKDEEDAQKAKE 64

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).

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954443199 252 PCDTLLFRNLPYSVDEVKLTDHLNRTCamTIQQVLIARNVENGFSRGYAYVQMTNVNDAAQLLTTLTAVSKLIIDGREIL 331
Cdd:cd21615   17 PYKTLFVGRLDYSLTELELQKKFSKFG--EIEKIRIVRDKETGKSRGYAFIVFKSESDAKNAFKEGNGLRGLKINDRTCI 94

                 ...
gi 954443199 332 VSY 334
Cdd:cd21615   95 VDI 97

RNA recognition motif (RRM) found in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins; This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954443199 109 EPNSTLVVKGIPLSYNEELVRNAVVEMGvtPID-VRILRKRESGESRGFGFIEFMSIEEATKYMERSQGfLEVNGRRMaE 187
Cdd:cd12642    2 DPNTCLGVFGLSLYTTERDLREVFSRYG--PLAgVNVVYDQRTGRSRGFAFVYFERIDDSKEAMERANG-MELDGRRI-R 77

                 ....*..
gi 954443199 188 LQYSINK 194
Cdd:cd12642   78 VDYSITK 84

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.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 954443199 113 TLVVKGIPLSYNEELVRNaVVEMGVtpiDVRILRKREsGESRGFGFIEFMSIEEATKYMERSQGfLEVNGRRM 185
Cdd:cd12404    5 TLFVKNLPYSTTQDELKE-VFEDAV---DIRIPMGRD-GRSKGIAYIEFKSEAEAEKALEEKQG-TEVDGRSI 71

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

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 954443199 113 TLVVKGIPLSYNEELVRNAVVEMG-VTpiDVRILRKRESGESRGFGFIEFMSIEEATKYMERSQGFlEVNGRRM 185
Cdd:COG0724    3 KIYVGNLPYSVTEEDLRELFSEYGeVT--SVKLITDRETGRSRGFGFVEMPDDEEAQAAIEALNGA-ELMGRTL 73

RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43); This subgroup corresponds to the RRM1 of SECp43, 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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 954443199 124 NEELVRNAVVEMGVTPIDVRILRKRESGESRGFGFIEFMSIEEATKYMersqgfLEVNGR 183
Cdd:cd12610   12 DENFIKRAFATMGETVLSVKIIRNRVTGGPAGYCFVEFADEATAERCL------HKLNGK 65

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 954443199  114 LVVKGIPLSYNEELVRNAVVEMGvtPI-DVRILRKrESGESRGFGFIEFMSIEEATKYMERSQGFlEVNGRRM 185
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFG--PIkSIRLVRD-ETGRSKGFAFVEFEDEEDAEKAIEALNGK-ELGGREL 69

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.

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                 ....*....|....*....|....*....|....*....|....*
gi 954443199 141 DVRILRKRESGESRGFGFIEFMSIEEATKYMERSQGFlEVNGRRM 185
Cdd:cd12284   27 FVQLQKDPETGRSKGYGFIQFRDAEDAKKALEQLNGF-ELAGRPM 70

RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 954443199 116 VKGIPLSYNEELVRNAVVEMGvTPIDVRILRKRESGESRGFGFIEFMSIEEATKYMerSQGFLEVNGR 183
Cdd:cd12330    4 VGGLAPDVTEEEFKEYFEQFG-TVVDAVVMLDHDTGRSRGFGFVTFDSESAVEKVL--SKGFHELGGK 68

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).

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954443199 255 TLLFRNLPYSVDEVKLTDHLNRtcAMTIQQVLIARNVENGFSRGYAYVQMTNVNDAAQLLttltAVSKLIIDGREILVSY 334
Cdd:cd12450    1 TLFVGNLSWSATQDDLENFFSD--CGEVVDVRIAMDRDDGRSKGFGHVEFASAESAQKAL----EKSGQDLGGREIRLDL 74

                 ..
gi 954443199 335 SK 336
Cdd:cd12450   75 AN 76

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.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954443199 116 VKGIPLSYNEELVRNAVVEMGVTpIDVRILRKRESGESRGFGFIEFMSIEEATKYMERSQGFlEVNGRRM 185
Cdd:cd12671   11 VGNIPYEATEEQLKDIFSEVGPV-VSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGY-ELNGRAL 78

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 954443199 112 STLVVKGIPLSYNEELVRNAVVEMGvTPIDVRILRKREsGESRGFGFIEFMSIEEATKYMERSQG 176
Cdd:cd12320    1 TKLIVKNVPFEATRKEIRELFSPFG-QLKSVRLPKKFD-GSHRGFAFVEFVTKQEAQNAMEALKS 63

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins; This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 954443199 141 DVRILRKRESGESRGFGFIEFMSIEEATKYMERSQGFlEVNGRRM 185
Cdd:cd12311   27 DVYIPRDRYTRESRGFAFVRFYDKRDAEDAIDAMDGA-ELDGREL 70