RNA recognition motif (RRM) found in Arabidopsis thaliana RNA-dependent RNA polymerase 1 (AtRDRP1) and similar proteins; AtRDRP1, also called RNA-directed RNA polymerase 1, is an RNA-dependent direct polymerase involved in antiviral silencing. It is required for the biogenesis of viral secondary siRNAs, process that follows the production of primary siRNAs derived from viral RNA replication. Members in this family contain an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19111994 489 TKLRVINVSpEKNEALLQYLFTVGGYEEITEPSTTERLISFQNRNSAEKFFGGVRNVEKLQELELAWV 556
Cdd:cd21612   1 KCVRHVPNS-EKQEELKKFLEQVGTYYAIAKKSTDDVIVSFSTRAAAEKLFYGVEDVPKVGKVEMNWV 67

phosphodiesterase; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111994  352 QNEEFHKLiEERQRQHEERL-KRINANKKALEELNQKKRELAQQqlkeQELLMQKIKETDRSGNKRLMLLETQHSLLKAE 430
Cdd:PRK12704  80 RRNELQKL-EKRLLQKEENLdRKLELLEKREEELEKKEKELEQK----QQELEKKEEELEELIEEQLQELERISGLTAEE 154

                 .
gi 19111994  431 A 431
Cdd:PRK12704 155 A 155

RNA recognition motif (RRM) found in Arabidopsis thaliana RNA-dependent RNA polymerase 1 (AtRDRP1) and similar proteins; AtRDRP1, also called RNA-directed RNA polymerase 1, is an RNA-dependent direct polymerase involved in antiviral silencing. It is required for the biogenesis of viral secondary siRNAs, process that follows the production of primary siRNAs derived from viral RNA replication. Members in this family contain an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19111994 489 TKLRVINVSpEKNEALLQYLFTVGGYEEITEPSTTERLISFQNRNSAEKFFGGVRNVEKLQELELAWV 556
Cdd:cd21612   1 KCVRHVPNS-EKQEELKKFLEQVGTYYAIAKKSTDDVIVSFSTRAAAEKLFYGVEDVPKVGKVEMNWV 67

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19111994   246 VRNIPEEhFNEENIRSFFSKFGVLEKVEL-----NPTHHSCVLEFTSHEAANNAWSS-PEPIFNNRFIK 308
Cdd:pfam00076   3 VGNLPPD-TTEEDLKDLFSKFGPIKSIRLvrdetGRSKGFAFVEFEDEEDAEKAIEAlNGKELGGRELK 70

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111994   230 RFSRNAGNDPTSTALEVRNIPEEhFNEENIRSFFSKFG-----VLEKVELNPTHHSCVLEFTSHEAANNA 294
Cdd:TIGR01628 167 KHEREAAPLKKFTNLYVKNLDPS-VNEDKLRELFAKFGeitsaAVMKDGSGRSRGFAFVNFEKHEDAAKA 235

Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111994 341 SSEDVDPASLLQNEEFHKLIEERQRQHEERLKRINANKKAL----EELNQKKRELAQQ--QLKEQ-ELLMQKIKEtdrSG 413
Cdd:COG1340   1 SKTDELSSSLEELEEKIEELREEIEELKEKRDELNEELKELaekrDELNAQVKELREEaqELREKrDELNEKVKE---LK 77

                ....*...
gi 19111994 414 NKRLMLLE 421
Cdd:COG1340  78 EERDELNE 85

Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19111994   348 ASLLQNEEFHKLIEERQRQHEERLKRINANKKALEELNQKKRELAQQQLKEQELLMQKIKE 408
Cdd:pfam20492  27 EELEESEETAEELEEERRQAEEEAERLEQKRQEAEEEKERLEESAEMEAEEKEQLEAELAE 87

RNA recognition motif (RRM) found in Arabidopsis thaliana RNA-dependent RNA polymerase 1 (AtRDRP1) and similar proteins; AtRDRP1, also called RNA-directed RNA polymerase 1, is an RNA-dependent direct polymerase involved in antiviral silencing. It is required for the biogenesis of viral secondary siRNAs, process that follows the production of primary siRNAs derived from viral RNA replication. Members in this family contain an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19111994 489 TKLRVINVSpEKNEALLQYLFTVGGYEEITEPSTTERLISFQNRNSAEKFFGGVRNVEKLQELELAWV 556
Cdd:cd21612   1 KCVRHVPNS-EKQEELKKFLEQVGTYYAIAKKSTDDVIVSFSTRAAAEKLFYGVEDVPKVGKVEMNWV 67

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 27 (RBM27); This subgroup corresponds to the RRM of RBM27 which contains a single RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although the specific function of the RRM in RBM27 remains unclear, it shows high sequence similarity with RRM1of RBM26, which functions as a cutaneous lymphoma (CL)-associated antigen.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19111994 241 STALEVRNIPEEHFNEENIRSFFSKFGVLEKVEL----NPthHSCVLEFTSHEAANNAWSSPEPIFNNRFIKIFWY 312
Cdd:cd12517   1 NTKLEVRKIPQELNNITQLNEHFSKFGTIVNIQVafggDP--EAALIQYTTNEEARRAISSTEAVLNNRFIRVLWH 74

RNA recognition motif (RRM) found in 80 kDa MCM3-associated protein (Map80) and similar proteins; This subfamily corresponds to the RRM of Map80, also termed germinal center-associated nuclear protein (GANP), involved in the nuclear localization pathway of MCM3, a protein necessary for the initiation of DNA replication and also involves in controls that ensure DNA replication is initiated once per cell cycle. Map80 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19111994 242 TALEVRNIPEEHFNEENIRSFFSKFGVLEKVELNPTHHSCVLEFTSHEAANNAWSSPEPIFNN-RFIKIFW 311
Cdd:cd12443   1 TAIVCKNIPEELNDKEILRRHFSKFGKVARVFCNPRKNLAIVHFKDHESAALAKKKGKLLSKGgKPIEIFW 71

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
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 19111994 244 LEVRNIPEEhFNEENIRSFFSKFGVLEKVELNPTHHS-----CVLEFTSHEAANNA 294
Cdd:cd00590   1 LFVGNLPPD-TTEEDLRELFSKFGEVVSVRIVRDRDGkskgfAFVEFESPEDAEKA 55

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19111994   246 VRNIPEEhFNEENIRSFFSKFGVLEKVEL-----NPTHHSCVLEFTSHEAANNAWSS-PEPIFNNRFIK 308
Cdd:pfam00076   3 VGNLPPD-TTEEDLKDLFSKFGPIKSIRLvrdetGRSKGFAFVEFEDEEDAEKAIEAlNGKELGGRELK 70

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111994   230 RFSRNAGNDPTSTALEVRNIPEEhFNEENIRSFFSKFG-----VLEKVELNPTHHSCVLEFTSHEAANNA 294
Cdd:TIGR01628 167 KHEREAAPLKKFTNLYVKNLDPS-VNEDKLRELFAKFGeitsaAVMKDGSGRSRGFAFVNFEKHEDAAKA 235

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 19111994 246 VRNIPEEHfNEENIRSFFSKFGVLEKVELNPTHHSCVLEFTSHEAANNA 294
Cdd:cd12354   5 VGNITKGL-TEALLQQTFSPFGQILEVRVFPDKGYAFIRFDSHEAATHA 52

Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111994 341 SSEDVDPASLLQNEEFHKLIEERQRQHEERLKRINANKKAL----EELNQKKRELAQQ--QLKEQ-ELLMQKIKEtdrSG 413
Cdd:COG1340   1 SKTDELSSSLEELEEKIEELREEIEELKEKRDELNEELKELaekrDELNAQVKELREEaqELREKrDELNEKVKE---LK 77

                ....*...
gi 19111994 414 NKRLMLLE 421
Cdd:COG1340  78 EERDELNE 85

RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM1 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19111994 244 LEVRNIPEeHFNEENIRSFFSKFGVLEKVELNPTHH-----SCVLEFTSHEAANNAWSSpEPIFNNRFIKIFWYNP 314
Cdd:cd12348   2 LWVGNLPE-NVREEKIIEHFKRFGRVESVKILPKRGseggvAAFVDFVDIKSAQKAHSA-VNKMGGRDLRTDYNEP 75

RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19111994 242 TALEVRNIPEeHFNEENIRSFFSKFGVLEKVELNPT-----HHSCVLEFTSHEAANNAWSSpepiFNNRFIK 308
Cdd:cd12564   1 SRLIVKNLPS-SITEDRLRKLFSAFGTITDVQLKYTkdgkfRRFGFVGFKSEEEAQKALKH----FNNSFID 67

Occluded RNA-recognition motif; This family is an unusual, usually C-terminal, RNA-recognition motif found in fungi. In yeast it is the fourth RRM domain on the essential splicing factor Prp24. Structurally, it has a non-canonical RRM fold with the expected beta-aloha-beta-beta-alpha-beta RRM-fold is flanked by N- and C-terminal alpha-helices. These two additional flanking alpha-helices occlude the beta-sheet face. The electropositive surface thereby presented is an alternative RNA-binding surface that allows both binding and unwinding of the U6 small nuclear RNA's internal stem loop, at least in vitro.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 19111994   255 NEENIRSFFSKF-GVLEKVELNPTHHSCVLEFTSHEAANNAWSSPEPI-FNNRFIKI 309
Cdd:pfam16842  14 NDARIRALVEEKeGPIVKIVLVPDHQGAIVEFKDVADAGKASLALDGSeFEGRKLRC 70

Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19111994   348 ASLLQNEEFHKLIEERQRQHEERLKRINANKKALEELNQKKRELAQQQLKEQELLMQKIKE 408
Cdd:pfam20492  27 EELEESEETAEELEEERRQAEEEAERLEQKRQEAEEEKERLEESAEMEAEEKEQLEAELAE 87

RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19111994 242 TALEVRNIPEEhFNEENIRSFFSKFGVLEKVEL-----NPTHHSCVLEFTSHEAANNA 294
Cdd:cd12297   1 CTLWVTNFPPS-YDERSIRDLFGDYGVILSVRLpslryNTSRRFCYIDFTSPESARAA 57