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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1386876242 284 VNNLHPRVTEEDIVELFCVCGALKRARLV------HPGVAEVVFVKKDDAITAYKKYNNRCLDG 341
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGPIKSIRLVrdetgrSKGFAFVEFEDEEDAEKAIEALNGKELGG 66

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

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1386876242 284 VNNLHPRVTEEDIVELFCVCGALKRARLVHP-------GVAEVVFVKKDDAITAYKKYNNRCLDG 341
Cdd:COG0724     6 VGNLPYSVTEEDLRELFSEYGEVTSVKLITDretgrsrGFGFVEMPDDEEAQAAIEALNGAELMG 70

RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1386876242 280 TKMTVNNLHPRVTEEDIVELFCVCGALKRARLVHP------GVAEVVFVKKDDAITAYKKYNNRCLDG 341
Cdd:cd12418     1 TRVRVSNLHPDVTEEDLRELFGRVGPVKSVKINYDrsgrstGTAYVVFERPEDAEKAIKQFDGVLLDG 68

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 1386876242 284 VNNLHPRVTEEDIVELFCVCGALKRARLVHP------GVAEVVFVKKDDAITAYKKYNNRCLDG 341
Cdd:cd00590     3 VGNLPPDTTEEDLRELFSKFGEVVSVRIVRDrdgkskGFAFVEFESPEDAEKALEALNGTELGG 66

RNA recognition motif;

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1386876242  284 VNNLHPRVTEEDIVELFCVCGALKRARLVHP-------GVAEVVFVKKDDAITAYKKYNNRCLDG 341
Cdd:smart00360   4 VGNLPPDTTEEELRELFSKFGKVESVRLVRDketgkskGFAFVEFESEEDAEKALEALNGKELDG 68

RNA recognition motif (RRM) found in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins; This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1386876242 280 TKMTVNNLHPRVTEEDIVELFCV-CGALKRARLVH------PGVAEVVFVKKDDAITAYKKYNNRCLDG 341
Cdd:cd12267     1 SKVIVSNLPKDVTEAQIREYFVSqIGPIKRVLLSYneggksTGIANITFKRAGDATKAYDKFNGRLDDG 69

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1386876242 278 EGTKMTVNNLHPRVTEEDIVELFCVCGALKRARLV-----HP-GVAEVVFVKKDDAITAYKKYNN 336
Cdd:cd12392     1 EKNKLFVKGLPFSCTKEELEELFKQHGTVKDVRLVtyrngKPkGLAYVEYENEADASQAVLKTDG 65

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1386876242 281 KMTVNNLHPRVTEEDIVELFCVCGALKRARLVHP-GVAEVVFVKKDDAITAYKKYNNRCLDGG 342
Cdd:cd12340     1 RLFVRPFPPDTSESAIREIFSPYGPVKEVKMLSDsNFAFVEFEELEDAIRAKDSVHGRVLNNE 63

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1386876242 284 VNNLHPRVTEEDIVELFCVCGALKRARLV------HP-GVAEVVFVKKDDAITAYKKYNNRCLDGG 342
Cdd:cd12415     5 IRNLSFDTTEEDLKEFFSKFGEVKYARIVldkdtgHSkGTAFVQFKTKESADKCIEAANDESEDGG 70