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).

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193207639  13 TLMIGDVPMNFDFSHIDNLICNTYPTPIQLRKSPTRNETSIN--AFYQYSSFVDARNALRILNGAVVPGMENHYQLdmNF 90
Cdd:cd12344    1 TLWMGDLEPWMDEAYISSCFAKTGEEVVSVKIIRNKQTGKSAgyCFVEFATQEAAEQALEHLNGKPIPNTQQRFRL--NW 78

                 ...
gi 193207639  91 TKQ 93
Cdd:cd12344   79 ASF 81

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

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193207639  13 TLMIGDVPMNFDFSHIDNLICNTYPTPIQLRKSPTRNETSIN--AFYQYSSFVDARNALRILNGAVVPGMENHYQLdmNF 90
Cdd:cd12344    1 TLWMGDLEPWMDEAYISSCFAKTGEEVVSVKIIRNKQTGKSAgyCFVEFATQEAAEQALEHLNGKPIPNTQQRFRL--NW 78

                 ...
gi 193207639  91 TKQ 93
Cdd:cd12344   79 ASF 81

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

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193207639  13 TLMIGDVPMNFDFSHIDNLICNTYPTPIQLRKSPTRNETSIN--AFYQYSSFVDARNALRILNGAVVPGMENHYQLdmNF 90
Cdd:cd12344    1 TLWMGDLEPWMDEAYISSCFAKTGEEVVSVKIIRNKQTGKSAgyCFVEFATQEAAEQALEHLNGKPIPNTQQRFRL--NW 78

                 ...
gi 193207639  91 TKQ 93
Cdd:cd12344   79 ASF 81