RNA recognition motif (RRM) found in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins; This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19113914 364 RLFLGHLNTKSLSKRNLWKVFKIYGPLAQIVLKANYGFVQFFTNEDCARALNAEQGNFVRGQKLHLEISKI 434
Cdd:cd12342   1 RLFIGNLPTKRVSKEDLFRIFSPYGHLMQIVIKNAFGFVQFDSPQSCRNAIECEQGEMNRGKKLHLEVSKS 71

RNA recognition motif (RRM) found in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins; This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19113914 364 RLFLGHLNTKSLSKRNLWKVFKIYGPLAQIVLKANYGFVQFFTNEDCARALNAEQGNFVRGQKLHLEISKI 434
Cdd:cd12342   1 RLFIGNLPTKRVSKEDLFRIFSPYGHLMQIVIKNAFGFVQFDSPQSCRNAIECEQGEMNRGKKLHLEVSKS 71

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 19113914   365 LFLGHLnTKSLSKRNLWKVFKIYGPL--AQIVLKAN-----YGFVQFFTNEDCARALNAEQGNFVRGQKLH 428
Cdd:pfam00076   1 LFVGNL-PPDTTEEDLKDLFSKFGPIksIRLVRDETgrskgFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

RNA recognition motif (RRM) found in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins; This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19113914 364 RLFLGHLNTKSLSKRNLWKVFKIYGPLAQIVLKANYGFVQFFTNEDCARALNAEQGNFVRGQKLHLEISKI 434
Cdd:cd12342   1 RLFIGNLPTKRVSKEDLFRIFSPYGHLMQIVIKNAFGFVQFDSPQSCRNAIECEQGEMNRGKKLHLEVSKS 71

RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins; This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19113914 365 LFLGHLNTKSLSKRNLWKVFKIYGPLAQIVLKANYGFVQFFTNEDCARALNAEQGNFVRGQKLHLE 430
Cdd:cd12233   2 LFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRKTFAFVEFEDSEDATKALEALHGSRIDGSVLTVE 67

RNA recognition motif (RRM) found in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2); This subgroup corresponds to the RRM of heterogeneous nuclear ribonucleoprotein C (hnRNP) proteins C1 and C2, produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex. They are involved in the packaging of hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. hnRNP C proteins contain two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes the variable region, the basic region and the KSG box rich in repeated Lys-Ser-Gly sequences, the leucine zipper, and the acidic region. The RRM is capable of binding poly(U). The KSG box may bind to RNA. The leucine zipper may be involved in dimer formation. The acidic and hydrophilic C-teminus harbors a putative nucleoside triphosphate (NTP)-binding fold and a protein kinase phosphorylation site.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19113914 363 SRLFLGHLNTKSLSKRNLWKVFKIYGPLAQIVLKANYGFVQfFTNEDCAR-ALNAEQGNFVRGQKLHLEIS 432
Cdd:cd12603   7 SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQ-YVNERNARaAVAGEDGRMIAGQVLDINLA 76

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 19113914 365 LFLGHLNtKSLSKRNLWKVFKIYGPLAQIVLK-------ANYGFVQFFTNEDCARALNAEQGNFVRGQKLHLE 430
Cdd:cd00590   1 LFVGNLP-PDTTEEDLRELFSKFGEVVSVRIVrdrdgksKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72

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 19113914   365 LFLGHLnTKSLSKRNLWKVFKIYGPL--AQIVLKAN-----YGFVQFFTNEDCARALNAEQGNFVRGQKLH 428
Cdd:pfam00076   1 LFVGNL-PPDTTEEDLKDLFSKFGPIksIRLVRDETgrskgFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain).

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113914 365 LFLGHLNTKSlSKRNLWKVFKIYGPLAQIVL-----------KANYGFVQFFTNEDCARALNAEQGNFVRGQKLHLEISK 433
Cdd:cd12223   4 LYVGNLPPSV-TEEVLLREFGRFGPLASVKImwprteeerrrNRNCGFVAFMSRADAERAMRELNGKDVMGYELKLGWGK 82

RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants; This subgroup corresponds to the RRM2 in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 19113914 365 LFLGHLNTKSLSKRNLWKVFKIYGPLAQIVLKANYGFVQFFTNEDCARALNAEQ 418
Cdd:cd12466   2 LFVINFDPIRTKERDLERHFEPYGKVVNVRIRRNFAFVQYETQEDATKALDATQ 55

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19113914 364 RLFLGHLNTKsLSKRNLWKVFKIYGPL-----------AQIVLKANYGFVQFFTNEDCARALNAEQGNFVRGQKL 427
Cdd:cd12355   1 RLWIGNLDPR-LTEYHLLKLLSKYGKIkkfdflfhktgPLKGQPRGYCFVTFETKEEAEKAIECLNGKLALGKKL 74

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 19113914 364 RLFLGHLnTKSLSKRNLWKVFKIYGPLAQIVLKAN---YGFVQFFTNEDCARALNAEQGNFVRGQKLHLEISK 433
Cdd:cd12373   1 KVYVGNL-GPRVTKRELEDAFEKYGPLRNVWVARNppgFAFVEFEDPRDAEDAVRALDGRRICGSRVRVELSR 72

RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar proteins; This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19113914 364 RLFLGHLnTKSLSKRNLWKVFKIYGPLAQIVLKA-----NYGFVQFFTNEDCARALNAEQGNFVRGQKLHLEI 431
Cdd:cd12599   1 RVYVGNL-PMDIREREVEDLFSKYGPVVSIDLKIpprppAYAFVEFEDARDAEDAIRGRDGYDFDGHRLRVEL 72

amidase domain-containing protein;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113914   55 QTQDDTLFNNVDERTLENKDGNKSDDANFDQVSgipsgsleipilnSATSNIRLTPSDTYNNIPVSDTNNEEI---SKNI 131
Cdd:PRK08581  50 ETSKDTSSKDTDKADNNNTSNQDNNDKKFSTID-------------SSTSDSNNIIDFIYKNLPQTNINQLLTknkYDDN 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113914  132 YGAPILESTSSDFQSK-DSLSTTQPSVSGGNGSTSQSPPSLDVEQNkPFSISNEPVEQETENSSTKDLQVYDFQTASEhl 210
Cdd:PRK08581 117 YSLTTLIQNLFNLNSDiSDYEQPRNSEKSTNDSNKNSDSSIKNDTD-TQSSKQDKADNQKAPSSNNTKPSTSNKQPNS-- 193

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113914  211 PEQSLQNTTYYDPsktYSSVNFEEIEYGKSHEKLDLPYRTTDFIPYSKDLSTSPEAHRTSiysysanlpNYYNEHNELHE 290
Cdd:PRK08581 194 PKPTQPNQSNSQP---ASDDTANQKSSSKDNQSMSDSALDSILDQYSEDAKKTQKDYASQ---------SKKDKTETSNT 261

                        250
                 ....*....|....
gi 19113914  291 hHNPQTPSSPESAY 304
Cdd:PRK08581 262 -KNPQLPTQDELKH 274

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 5 (SRSF5); This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19113914 364 RLFLGHLNtKSLSKRNLWKVFKIYGPLAQIVLKANYGFVQFFTNEDCARALNAEQGNFVRGQKLHLEISKI 434
Cdd:cd12595   1 RVFIGRLN-PAAREKDVERFFKGYGRIRDIDLKRGFGFVEFEDPRDADDAVYELDGKELCNERVTIEHARV 70