RNA recognition motif (RRM) found in vertebrate methenyltetrahydrofolate synthetase domain-containing proteins; This subfamily corresponds to methenyltetrahydrofolate synthetase domain (MTHFSD), a putative RNA-binding protein found in various vertebrate species. It contains an N-terminal 5-formyltetrahydrofolate cyclo-ligase domain and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of MTHFSD remains unclear.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 795345956 307 DVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLRYPDSAAAQQAVSCLQGLRLGTDTLRVALAR 378
Cdd:cd12270    1 TVYVGNIPRSVRVSDLKSALRERGINPLRITWQGARGKAFLHYSDMADADSAVSSLQGLRIGGNTLTVELAK 72

RNA recognition motif (RRM) found in vertebrate methenyltetrahydrofolate synthetase domain-containing proteins; This subfamily corresponds to methenyltetrahydrofolate synthetase domain (MTHFSD), a putative RNA-binding protein found in various vertebrate species. It contains an N-terminal 5-formyltetrahydrofolate cyclo-ligase domain and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of MTHFSD remains unclear.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 795345956 307 DVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLRYPDSAAAQQAVSCLQGLRLGTDTLRVALAR 378
Cdd:cd12270    1 TVYVGNIPRSVRVSDLKSALRERGINPLRITWQGARGKAFLHYSDMADADSAVSSLQGLRIGGNTLTVELAK 72

5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 795345956 133 VDLVVVGSVAVSeKDGWRIGKGEGYAD--LEyammvsmgAVSNETPVVTIVHDCQVVD-IPeelLEEHDITVDYILTPTR 209
Cdd:COG0212  118 IDLVLVPLLAFD-RRGYRLGYGGGYYDrtLA--------RLRPRPLTIGLAFDCQLVDeLP---VEPHDVPLDAIVTEKG 185

                 .
gi 795345956 210 V 210
Cdd:COG0212  186 V 186

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 795345956  308 VYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQgPRRRAFLRYPDSAAAQQAVSCLQGLRLGTDTLR 373
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIksirlVRDETGR-SKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

5-formyltetrahydrofolate cyclo-ligase

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 795345956 133 VDLVVVGSVAVSEKdGWRIGKGEGYADLEYAMMVSMGAVSNETP--VVTIVHDCQVVDIPEELLEEHDITVDYILTPTRV 210
Cdd:PLN02812 132 LDLLLLPGLAFDRS-GRRLGRGGGYYDTFLSKYQELAKEKGWKQplLVALSYSPQILDEGSVPVDETDVLVDALVTPSGV 210

                 .
gi 795345956 211 I 211
Cdd:PLN02812 211 I 211

RNA recognition motif (RRM) found in vertebrate methenyltetrahydrofolate synthetase domain-containing proteins; This subfamily corresponds to methenyltetrahydrofolate synthetase domain (MTHFSD), a putative RNA-binding protein found in various vertebrate species. It contains an N-terminal 5-formyltetrahydrofolate cyclo-ligase domain and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of MTHFSD remains unclear.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 795345956 307 DVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLRYPDSAAAQQAVSCLQGLRLGTDTLRVALAR 378
Cdd:cd12270    1 TVYVGNIPRSVRVSDLKSALRERGINPLRITWQGARGKAFLHYSDMADADSAVSSLQGLRIGGNTLTVELAK 72

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        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 795345956 308 VYVGNLPRDARVSDLKRALRELGSV----PLRLTWQGPRRRAFLRYPDSAAAQQAVSCLQGLRLGTDTLRV 374
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGEVvsvrIVRDRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKV 71

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 795345956   308 VYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLRYPDSAAAQQAVSCLQGLRLGTDTLRV 374
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVesvrlVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 795345956 308 VYVGNLPRDARVSDLKRALRELGsvPLRLTW--QGPRRRAFLRYPDSAAAQQAVSCLQGLRLGTDTLRVALAR 378
Cdd:cd12373    2 VYVGNLGPRVTKRELEDAFEKYG--PLRNVWvaRNPPGFAFVEFEDPRDAEDAVRALDGRRICGSRVRVELSR 72

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 795345956 309 YVGNLPRDARVSDLKRALRELGSV------PLRLTwQGPRRRAFLRYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRD 382
Cdd:COG0724    5 YVGNLPYSVTEEDLRELFSEYGEVtsvkliTDRET-GRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPREE 83

                 .
gi 795345956 383 K 383
Cdd:COG0724   84 R 84

RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 795345956 308 VYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLRYPDSAAAQQAVSCLQGLRLGTDTLRV 374
Cdd:cd12399    1 LYVGNLPYSASEEQLKSLFGQFGAVfdvklPMDRETKRPRGFGFVELQEEESAEKAIAKLDGTDFMGRTIRV 72

RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 795345956 308 VYVGNLPRDARVSDLKRALRELGSV-PLRL---TWQGPRRRAFLRY-PDSAAAQQAVSCLQGLRLGTDTLRVALAR 378
Cdd:cd12226    2 LFVGGLSPSITEDDLERRFSRFGTVsDVEIirkKDAPDRGFAYIDLrTSEAALQKCLSTLNGVKWKGSRLKIQLAK 77

RNA recognition motif 2 (RRM2) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 795345956 306 ADVYVGNLPRDARVSDLKRALRELGSVP----LRLTWQG-PRRRAFLRYPDSAAAQQAVSCLQGLRL--GTDTLRVALA 377
Cdd:cd12651    3 TNLYVTNLPRTITEDELDTIFGAYGNIVqknlLRDKLTGrPRGVAFVRYDKREEAQAAISALNGTIPegGTQPLSVRLA 81

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 795345956 308 VYVGNLPRDARVSDLKRALRELG---SVPL---RLTwqGpRRR--AFLRYPDSAAAQQAVSCLQGLRLGTDTLRVALA 377
Cdd:cd21608    2 LYVGNLSWDTTEDDLRDLFSEFGeveSAKVitdRET--G-RSRgfGFVTFSTAEAAEAAIDALNGKELDGRSIVVNEA 76

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).

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 795345956 308 VYVGNLPRDARVSDLKRALRELGSVP-LRL-TWQG--PRRRAFLRYPDSAAAQQAVSCLQGLRLGTDTLRVALAR 378
Cdd:cd12392    5 LFVKGLPFSCTKEELEELFKQHGTVKdVRLvTYRNgkPKGLAYVEYENEADASQAVLKTDGTEIKDHTISVAISN 79

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 9 (SRSF9); This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 795345956 308 VYVGNLPRDARVSDLKR------ALREL------GSVPLrltwqgprrrAFLRYPDSAAAQQAVSCLQGLRLGTDTLRV 374
Cdd:cd12598    2 IYVGNLPSDVREKDLEDlfykygRIRDIelknrrGLVPF----------AFVRFEDPRDAEDAVFGRNGYDFGQCRLRV 70