RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11) and similar proteins; This subgroup corresponds to the RRM of SRSF11, also termed arginine-rich 54 kDa nuclear protein (SRp54 or p54), which belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family). It is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SRSF11 has been identified as a tau exon 10 splicing repressor. It interacts with a purine-rich element in exon 10, and suppresses exon 10 inclusion by antagonizing Tra2beta, an SR-domain-containing protein that enhances exon 10 inclusion. SRSF11 is a unique SR family member and may regulate the alternative splicing in a tissue- and substrate-dependent manner. It can directly interact with the U2 auxiliary factor 65-kDa subunit (U2AF65), a protein associated with the 3' splice site. In addition, unlike the typical SR proteins, SRSF11 associates with other SR proteins but not with the U1 small nuclear ribonucleoprotein U1-70K or the U2 auxiliary factor 35-kDa subunit (U2AF35). SREK1 has unique properties in regulating alternative splicing of different pre-mRNAs; it promotes the use of the distal 5' splice site in E1A pre-mRNA alternative splicing. It also inhibits cryptic splice site selection on the beta-globin pre-mRNA containing competing 5' splice sites. SREK1 contains an RNA recognition motif (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and one serine-arginine (SR)-rich domains (SR domains).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2027535410  34 VIQVTNVSPSASSEQMRTLFGFLGKIDELRLFPPEklessknlllcDSPLPVSSRVCFVKFHDPDSAVVAQHLTNTVFVD 113
Cdd:cd12518     1 VIQVTNVSPSASSEQMRTLFGFLGKIDELRLFPPD-----------DSPLPVTSRVCFVKFHEPDSAVVAQHLTNTVFVD 69

                          90
                  ....*....|.
gi 2027535410 114 RALIVVPYAEG 124
Cdd:cd12518    70 RALIVVPYAEG 80

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11) and similar proteins; This subgroup corresponds to the RRM of SRSF11, also termed arginine-rich 54 kDa nuclear protein (SRp54 or p54), which belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family). It is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SRSF11 has been identified as a tau exon 10 splicing repressor. It interacts with a purine-rich element in exon 10, and suppresses exon 10 inclusion by antagonizing Tra2beta, an SR-domain-containing protein that enhances exon 10 inclusion. SRSF11 is a unique SR family member and may regulate the alternative splicing in a tissue- and substrate-dependent manner. It can directly interact with the U2 auxiliary factor 65-kDa subunit (U2AF65), a protein associated with the 3' splice site. In addition, unlike the typical SR proteins, SRSF11 associates with other SR proteins but not with the U1 small nuclear ribonucleoprotein U1-70K or the U2 auxiliary factor 35-kDa subunit (U2AF35). SREK1 has unique properties in regulating alternative splicing of different pre-mRNAs; it promotes the use of the distal 5' splice site in E1A pre-mRNA alternative splicing. It also inhibits cryptic splice site selection on the beta-globin pre-mRNA containing competing 5' splice sites. SREK1 contains an RNA recognition motif (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and one serine-arginine (SR)-rich domains (SR domains).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2027535410  34 VIQVTNVSPSASSEQMRTLFGFLGKIDELRLFPPEklessknlllcDSPLPVSSRVCFVKFHDPDSAVVAQHLTNTVFVD 113
Cdd:cd12518     1 VIQVTNVSPSASSEQMRTLFGFLGKIDELRLFPPD-----------DSPLPVTSRVCFVKFHEPDSAVVAQHLTNTVFVD 69

                          90
                  ....*....|.
gi 2027535410 114 RALIVVPYAEG 124
Cdd:cd12518    70 RALIVVPYAEG 80

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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2027535410  37 VTNVSPSASSEQMRTLFGFLGKIDELRLFPPEKLEssknlllcdsplpvSSRVCFVKFHDPDSAVVA-QHLTNTVFVDRA 115
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGR--------------SKGFAFVEFEDEEDAEKAiEALNGKELGGRE 68

                  .
gi 2027535410 116 L 116
Cdd:pfam00076  69 L 69

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11) and similar proteins; This subgroup corresponds to the RRM of SRSF11, also termed arginine-rich 54 kDa nuclear protein (SRp54 or p54), which belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family). It is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SRSF11 has been identified as a tau exon 10 splicing repressor. It interacts with a purine-rich element in exon 10, and suppresses exon 10 inclusion by antagonizing Tra2beta, an SR-domain-containing protein that enhances exon 10 inclusion. SRSF11 is a unique SR family member and may regulate the alternative splicing in a tissue- and substrate-dependent manner. It can directly interact with the U2 auxiliary factor 65-kDa subunit (U2AF65), a protein associated with the 3' splice site. In addition, unlike the typical SR proteins, SRSF11 associates with other SR proteins but not with the U1 small nuclear ribonucleoprotein U1-70K or the U2 auxiliary factor 35-kDa subunit (U2AF35). SREK1 has unique properties in regulating alternative splicing of different pre-mRNAs; it promotes the use of the distal 5' splice site in E1A pre-mRNA alternative splicing. It also inhibits cryptic splice site selection on the beta-globin pre-mRNA containing competing 5' splice sites. SREK1 contains an RNA recognition motif (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and one serine-arginine (SR)-rich domains (SR domains).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2027535410  34 VIQVTNVSPSASSEQMRTLFGFLGKIDELRLFPPEklessknlllcDSPLPVSSRVCFVKFHDPDSAVVAQHLTNTVFVD 113
Cdd:cd12518     1 VIQVTNVSPSASSEQMRTLFGFLGKIDELRLFPPD-----------DSPLPVTSRVCFVKFHEPDSAVVAQHLTNTVFVD 69

                          90
                  ....*....|.
gi 2027535410 114 RALIVVPYAEG 124
Cdd:cd12518    70 RALIVVPYAEG 80

RNA recognition motif 1 (RRM1) found in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subgroup corresponds to the RRM1 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), and is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 generally contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1; plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2027535410  34 VIQVTNVSPSASSEQMRTLFGFLGKIDELRLFPPEklessknlllcDSPLPVSSRVCFVKFHDPDSAVVAQHLTNTVFVD 113
Cdd:cd12519     1 VIQVTNLSAAVTSDQMRTLFSFLGDIEELRLYPPD-----------NAPLAFSSKVCYVKYREPSSVGVAQHLTNTVFID 69

                          90
                  ....*....|.
gi 2027535410 114 RALIVVPYAEG 124
Cdd:cd12519    70 RALIVVPCAEG 80

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 2027535410  35 IQVTNVSPSASSEQMRTLFGFLGKIDELRLFPpeklessknlllcdSPLPVSSRVCFVKFHDPDSAVVA-QHLTNTVFVD 113
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVR--------------DRDGKSKGFAFVEFESPEDAEKAlEALNGTELGG 66

                  ....*
gi 2027535410 114 RALIV 118
Cdd:cd00590    67 RPLKV 71

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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2027535410  37 VTNVSPSASSEQMRTLFGFLGKIDELRLFPPEKLEssknlllcdsplpvSSRVCFVKFHDPDSAVVA-QHLTNTVFVDRA 115
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGR--------------SKGFAFVEFEDEEDAEKAiEALNGKELGGRE 68

                  .
gi 2027535410 116 L 116
Cdd:pfam00076  69 L 69

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2027535410  35 IQVTNVSPSASSEQMRTLFGFLGKIDelRLFPPEKLESSKnlllcdsplpvsSR-VCFVKFHDPDSAVVA 103
Cdd:cd12408     2 IRVTNLSEDATEEDLRELFRPFGPIS--RVYLAKDKETGQ------------SKgFAFVTFETREDAERA 57

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2027535410  37 VTNVSPSASSEQMRTLFGFLGKIDELRLFPPEKLESSKNLllcdsplpvssrvCFVKFHDPDSAVVA-QHLTNTVFVDRA 115
Cdd:cd12316     4 VRNLPFTATEDELRELFEAFGKISEVHIPLDKQTKRSKGF-------------AFVLFVIPEDAVKAyQELDGSIFQGRL 70

                  .
gi 2027535410 116 L 116
Cdd:cd12316    71 L 71