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 2020930311 287 RLSEEEIRKIpmFSSYnpgEPNKEKKGPPIQFRMMT-GRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEFG 361
Cdd:cd12239    12 RVSEKDLKYI--FGRF---VDSSSEEKNMFDIRLMTeGRMKGQAFITFPSEELAEKALNLTNGYVLHGKPMVVQFA 82

RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear.

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gi 2020930311 287 RLSEEEIRKIpmFSSYnpgEPNKEKKGPPIQFRMMT-GRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEFG 361
Cdd:cd12239    12 RVSEKDLKYI--FGRF---VDSSSEEKNMFDIRLMTeGRMKGQAFITFPSEELAEKALNLTNGYVLHGKPMVVQFA 82

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 2020930311 288 LSEEEIRKIpmFSSYnpgepnkekkGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKIL 356
Cdd:pfam00076  10 TTEEDLKDL--FSKF----------GPIKSIRLVrdeTGRSKGFAFVEFEDEEDAEKAIEALNGKELGGREL 69

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

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2020930311 287 RLSEEEIRKipMFSSYnpgepnkekkGPPIQFRMM----TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEFGK 362
Cdd:COG0724    12 SVTEEDLRE--LFSEY----------GEVTSVKLItdreTGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEAR 79

                  ....*.
gi 2020930311 363 NKKQRS 368
Cdd:COG0724    80 PREERP 85

RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear.

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gi 2020930311 287 RLSEEEIRKIpmFSSYnpgEPNKEKKGPPIQFRMMT-GRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEFG 361
Cdd:cd12239    12 RVSEKDLKYI--FGRF---VDSSSEEKNMFDIRLMTeGRMKGQAFITFPSEELAEKALNLTNGYVLHGKPMVVQFA 82

RNA recognition motif;

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gi 2020930311  289 SEEEIRKIpmFSSYnpgepnkekkGPPIQFRMM----TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVI 358
Cdd:smart00360  12 TEEELREL--FSKF----------GKVESVRLVrdkeTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily 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. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.

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gi 2020930311 288 LSEEEIRKIpmFSsynpgepnkeKKGPPIQFRMM----TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEF 360
Cdd:cd12398    12 ATEEQLKEI--FS----------EVGPVVSFRLVtdreTGKPKGYGFCEFRDAETALSAVRNLNGYELNGRPLRVDF 76

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 2020930311 288 LSEEEIRKIpmFSSYnpgepnkekkGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKIL 356
Cdd:pfam00076  10 TTEEDLKDL--FSKF----------GPIKSIRLVrdeTGRSKGFAFVEFEDEEDAEKAIEALNGKELGGREL 69

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 2020930311 289 SEEEIRKIpmFSSYnpgepnkekkGPPIQFRMM----TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIE 359
Cdd:cd12671    19 TEEQLKDI--FSEV----------GPVVSFRLVydreTGKPKGYGFCEYQDQETALSAMRNLNGYELNGRALRVD 81

RNA recognition motif 1 (RRM1) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM1 of RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein), It serves as a bridging factor between the U11 and U12 snRNPs. It contains two repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions.

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gi 2020930311 323 GRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEF 360
Cdd:cd12238    35 GKLKHTAFATFDNEQAASKALSRLHQLKILGKRLVVEY 72

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs.

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gi 2020930311 283 IQRNrLSEEEIrkIPMFssynpgepnkEKKGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYKL 351
Cdd:cd12249     9 IPRD-VFEDEL--VPLF----------EKCGKIYELRLMmdfSGLNRGYAFVTYTNKEAAQRAVKTLNNYEI 67

RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 47 (RBM47); This subgroup corresponds to the RRM3 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

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gi 2020930311 289 SEEEIRKIpmFSSYNPGEPNKEKKgppiqfrmmtgrMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEFGK 362
Cdd:cd12497    14 TEDTIKKI--FGQFNPGCVERVKK------------IRDYAFVHFASRDDAVVAMNNLNGTELEGSCIEVTLAK 73

RNA recognition motif 1 (RRM1) found in vertebrate APOBEC-1 complementation factor (ACF); This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1.

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gi 2020930311 307 PNKEKKGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYKL-HGKIL 356
Cdd:cd12486    20 PLCEKIGKIYEMRMMmdfNGNNRGYAFVTFSNKQEARNAIKQLNNYEIrNGRLL 73

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM1 of Nop4p (also known as 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 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

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gi 2020930311 322 TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEFGK 362
Cdd:cd12674    38 TKKSRGYGFVSFSTHDDAEEALAKLKNRKLSGHILKLDFAK 78

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 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 2020930311 322 TGRMRGQAFITFPNKEIAWQALHLVNGYKLHGKILVIEFGKNK 364
Cdd:cd12413    37 KDKCRGFGYVTFALAEDAQRALEEVKGKKFGGRKIKVELAKKK 79

RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA.

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gi 2020930311 313 GPPIQFRMMT----GRMRGQAFITFPNKEIAWQALHLvNGYKLHGKILVIE 359
Cdd:cd12271    23 GEVRSVDLMRfpdsGNFRGIAFITFKTEEAAKRALAL-DGEMLGNRFLKVE 72

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 2020930311 288 LSEEEIRKIpmFSSYNPGEPNKEKKGPPiqfrmmTGRMRGQAFITFPNKEIAWQALHLVNGYKLHGK 354
Cdd:cd12284    10 ITEDMLRGI--FEPFGKIEFVQLQKDPE------TGRSKGYGFIQFRDAEDAKKALEQLNGFELAGR 68