RNA recognition motif (RRM) found in Arabidopsis thaliana nuclear speckle RNA-binding protein A (AtNSRA) and similar protein; AtNSRA is an alternative splicing (AS) regulator that binds to specific mRNAs and modulates auxin effects on the transcriptome. It can be displaced from its targets upon binding to AS competitor long non-coding RNA (ASCO-RNA). Members in this family contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 939204605 133 DASNTLYVEGLPSNCSRREVAHIFRPFVGYREVRLVTKDSKhrNGDPIVLCFVDFTNPACAATALSALQGYRMDENESDS 212
Cdd:cd21618    1 DASSTLYVEGLPLDATEREVAHIFRPFPGFKSVRLVPKEGK--RGRKLVLCFVDFADAQQAAAALETLQGYRLDEDDSDS 78

                 ....*....
gi 939204605 213 KFLRLQFSR 221
Cdd:cd21618   79 KGLRISFAR 87

RNA recognition motif (RRM) found in Arabidopsis thaliana nuclear speckle RNA-binding protein A (AtNSRA) and similar protein; AtNSRA is an alternative splicing (AS) regulator that binds to specific mRNAs and modulates auxin effects on the transcriptome. It can be displaced from its targets upon binding to AS competitor long non-coding RNA (ASCO-RNA). Members in this family contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 939204605 133 DASNTLYVEGLPSNCSRREVAHIFRPFVGYREVRLVTKDSKhrNGDPIVLCFVDFTNPACAATALSALQGYRMDENESDS 212
Cdd:cd21618    1 DASSTLYVEGLPLDATEREVAHIFRPFPGFKSVRLVPKEGK--RGRKLVLCFVDFADAQQAAAALETLQGYRLDEDDSDS 78

                 ....*....
gi 939204605 213 KFLRLQFSR 221
Cdd:cd21618   79 KGLRISFAR 87

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 939204605   137 TLYVEGLPSNCSRREVAHIFRPFVGYREVRLVT-KDSKHRNGdpivLCFVDFTNPACAATALSALQGYRMD 206
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRdKETGKSKG----FAFVEFESEEDAEKALEALNGKELD 67

RNA recognition motif (RRM) found in Arabidopsis thaliana nuclear speckle RNA-binding protein A (AtNSRA) and similar protein; AtNSRA is an alternative splicing (AS) regulator that binds to specific mRNAs and modulates auxin effects on the transcriptome. It can be displaced from its targets upon binding to AS competitor long non-coding RNA (ASCO-RNA). Members in this family contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 939204605 133 DASNTLYVEGLPSNCSRREVAHIFRPFVGYREVRLVTKDSKhrNGDPIVLCFVDFTNPACAATALSALQGYRMDENESDS 212
Cdd:cd21618    1 DASSTLYVEGLPLDATEREVAHIFRPFPGFKSVRLVPKEGK--RGRKLVLCFVDFADAQQAAAALETLQGYRLDEDDSDS 78

                 ....*....
gi 939204605 213 KFLRLQFSR 221
Cdd:cd21618   79 KGLRISFAR 87

RNA recognition motif 2 (RRM2) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 939204605 135 SNTLYVEGLPSNCSRREVAHIFRPFVGYREVRLVtkdsKHRNgdpivLCFVDFTNPACAATALSALQGYRMDENE 209
Cdd:cd12247    2 NKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLV----PRRG-----IAFVEFETEEQATVALQALQGFKITPGH 67

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 939204605 138 LYVEGLPSNCSRREVAHIFRPFVGYREVRLVTKDSKHRNGdpivLCFVDFTNPACAATALSALQGYRMD 206
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKSKG----FAFVEFESPEDAEKALEALNGTELG 65

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 939204605   137 TLYVEGLPSNCSRREVAHIFRPFVGYREVRLVT-KDSKHRNGdpivLCFVDFTNPACAATALSALQGYRMD 206
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRdKETGKSKG----FAFVEFESEEDAEKALEALNGKELD 67

RNA recognition motif (RRM) found in Drosophila couch potato (cpo) coding RNA-binding protein and similar proteins; This subfamily corresponds to the RRM of Cpo, an RNA-binding protein encoded by Drosophila couch potato (cpo) gene. Cpo contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It may control the processing of RNA molecules required for the proper functioning of the peripheral nervous system (PNS).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 939204605 137 TLYVEGLPSNCSRREVAHIFRPFVGYREVRLVTKDSKHRNGDPIvlCFVDFTNPACAATALSALQGYRMDENESDSkfLR 216
Cdd:cd12684    3 TLFVSGLPMDAKPRELYLLFRAYKGYEGSLLKVTSKNGKTTSPV--GFVTFLSRQAAEAAKQDLQGVRFDPDLPQT--LR 78

                 ....*
gi 939204605 217 LQFSR 221
Cdd:cd12684   79 LEFAK 83

RNA recognition motif 2 (RRM2) found in vertebrate U2 small nuclear ribonucleoprotein B" (U2B"); This subgroup corresponds to the RRM1 of U2B" (also termed U2 snRNP B"), a unique protein that comprises the U2 snRNP. It was initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 939204605 138 LYVEGLPSNCSRREVAHIFRPFVGYREVRLVTkdSKHRngdpivLCFVDFTNPACAATALSALQGYRMdeneSDSKFLRL 217
Cdd:cd12481    8 LFLNNLPEETNEMMLSMLFNQFPGFKEVRLVP--GRHD------IAFVEFENEAQAGAARDALQGFKI----TPSHAMKI 75

                 ....*
gi 939204605 218 QFSRK 222
Cdd:cd12481   76 TYAKK 80

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 (RRM5) found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 939204605 136 NTLYVEGLPSNCSRREVAHIFRPFVGYREVRLVTK-DSKHRNgdpivLCFVDFTNPACAATALSALQG 202
Cdd:cd12320    1 TKLIVKNVPFEATRKEIRELFSPFGQLKSVRLPKKfDGSHRG-----FAFVEFVTKQEAQNAMEALKS 63

RNA recognition motif 2 (RRM2) found in Drosophila melanogaster sex determination protein SNF and similar proteins; This subgroup corresponds to the RRM2 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 939204605 138 LYVEGLPSNCSRREVAHIFRPFVGYREVRLVTkdSKHRngdpivLCFVDFTNPACAATALSALQGYRMDENESdskfLRL 217
Cdd:cd12479    8 LFLTNLPEETNEMMLSMLFNQFPGFKEVRLVP--GRHD------IAFVEFENEVQSAAAKEALQGFKITPTHA----MKI 75

                 ....*
gi 939204605 218 QFSRK 222
Cdd:cd12479   76 TFAKK 80

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins; The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 939204605 137 TLYVEGLPSNCSRREVAHIFRPFVGYRE-VRLVTKDSKHRNGDpivlCFVDFTNPACAATALSALQGY 203
Cdd:cd12254    1 VVRLRGLPFSATEEDIRDFFSGLDIPPDgIHIVYDDDGRPTGE----AYVEFASEEDAQRALRRHKGK 64

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 939204605  132 SDASNTLYVEGLPSNCSRREVAHIFRPFVGYREVRLVtKDSKhrNGDPIVLCFVDFTNPACAATALSALQGYRMDEN 208
Cdd:TIGR01642 292 LDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLI-KDIA--TGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDN 365

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 939204605 138 LYVEGLPSNCSRREVAHIFRPFVGYREVRLVTK---DSKHRNgdpivLCFVDFTNPACAATALSALQ 201
Cdd:cd12571    3 ILVRNIPFQATVKEVRELFSTFGELKTVRLPKKmggTGQHRG-----FGFVDFITKQDAKRAFDALC 64

RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. 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 to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 939204605 138 LYVEGLPSNCSRREVAHIFRPFVGYREVRLVtKDSKhrNGDPIVLCFVDFTNPACAATALSALQGYR 204
Cdd:cd12375    2 LIVNYLPQSMTQEELRSLFGAIGPIESCKLV-RDKI--TGQSLGYGFVNYRDPNDARKAINTLNGLD 65