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 2462518559 644 HVIEIYDFPQEFRTEDLLRVFCSYqkKGFDIKWVDDTHALGVFSSPITARDAL--GIKHTMVKIRPL 708
Cdd:cd12428     2 DHVFHLTFPKEWKTSDLYQLFSPF--GGIQVSWIDDTSAFVALSDPEQVNIALktITYHPSYRIRSY 66

RNA recognition motif (RRM) found in poly(A)-specific ribonuclease PARN and similar proteins; The subfamily corresponds to the RRM of PARN, also termed deadenylating nuclease, or deadenylation nuclease, or polyadenylate-specific ribonuclease, a processive poly(A)-specific 3'-exoribonuclease involved in the decay of eukaryotic mRNAs. It specifically binds both, the poly(A) tail at the 3' end and the 7-methylguanosine (m7G) cap located at the 5' end of eukaryotic mRNAs, and catalyzes the 3'- to 5'-end deadenylation of single-stranded mRNA with a free 3' hydroxyl group both in the nucleus and in the cytoplasm. PARN belongs to the DEDD superfamily of exonucleases. It contains a nuclease domain, an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an R3H domain. PARN exists as a homodimer. The nuclease domain is involved in the dimerization. RRM and R3H domains are essential for the RNA-binding.

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gi 2462518559 644 HVIEIYDFPQEFRTEDLLRVFCSYqkKGFDIKWVDDTHALGVFSSPITARDAL--GIKHTMVKIRPL 708
Cdd:cd12428     2 DHVFHLTFPKEWKTSDLYQLFSPF--GGIQVSWIDDTSAFVALSDPEQVNIALktITYHPSYRIRSY 66

RNA recognition motif (RRM) found in poly(A)-specific ribonuclease PARN and similar proteins; The subfamily corresponds to the RRM of PARN, also termed deadenylating nuclease, or deadenylation nuclease, or polyadenylate-specific ribonuclease, a processive poly(A)-specific 3'-exoribonuclease involved in the decay of eukaryotic mRNAs. It specifically binds both, the poly(A) tail at the 3' end and the 7-methylguanosine (m7G) cap located at the 5' end of eukaryotic mRNAs, and catalyzes the 3'- to 5'-end deadenylation of single-stranded mRNA with a free 3' hydroxyl group both in the nucleus and in the cytoplasm. PARN belongs to the DEDD superfamily of exonucleases. It contains a nuclease domain, an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an R3H domain. PARN exists as a homodimer. The nuclease domain is involved in the dimerization. RRM and R3H domains are essential for the RNA-binding.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462518559 644 HVIEIYDFPQEFRTEDLLRVFCSYqkKGFDIKWVDDTHALGVFSSPITARDAL--GIKHTMVKIRPL 708
Cdd:cd12428     2 DHVFHLTFPKEWKTSDLYQLFSPF--GGIQVSWIDDTSAFVALSDPEQVNIALktITYHPSYRIRSY 66