RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL); The subgroup corresponds to the RRM2 of hnRNP-LL which plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to heterogeneous nuclear ribonucleoprotein L (hnRNP-L), which is an abundant nuclear, multifunctional RNA-binding protein with three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767915408 165 GNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARP 244
Cdd:cd12786    1 GNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVECAQKAKAALNGADIYAGCCTLKIEYARP 80

                         90
                 ....*....|....*.
gi 767915408 245 TRLNVIRNDNDSWDYT 260
Cdd:cd12786   81 TRLNVIRNDNDSWDYT 96

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767915408   336 VVMVSGLHQlKMNCSRVFNLFCLYGNIEKVKFMKTIP-----GTALVEMGDEYAVERAVTHLNNVKLFGKRLNV 404
Cdd:smart00360   1 TLFVGNLPP-DTTEEELRELFSKFGKVESVRLVRDKEtgkskGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL); The subgroup corresponds to the RRM2 of hnRNP-LL which plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to heterogeneous nuclear ribonucleoprotein L (hnRNP-L), which is an abundant nuclear, multifunctional RNA-binding protein with three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767915408 165 GNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARP 244
Cdd:cd12786    1 GNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVECAQKAKAALNGADIYAGCCTLKIEYARP 80

                         90
                 ....*....|....*.
gi 767915408 245 TRLNVIRNDNDSWDYT 260
Cdd:cd12786   81 TRLNVIRNDNDSWDYT 96

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins; This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both nuclear and cytoplasmic roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767915408 166 NKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPT 245
Cdd:cd12694    1 NHVLLFTILNPLYPITVDVIHTICSPYGKVLRIVIFRKNGVQAMVEFDSVESAQRAKAALNGADIYSGCCTLKIEYAKPT 80

                 ....*.
gi 767915408 246 RLNVIR 251
Cdd:cd12694   81 RLNVYK 86

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL); The subgroup corresponds to the RRM3 of hnRNP-LL which plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to heterogeneous nuclear ribonucleoprotein L (hnRNP-L), which is an abundant nuclear, multifunctional RNA-binding protein with three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767915408 336 VVMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNVCVSKQ 409
Cdd:cd12700    1 VAMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNVCVSKQ 74

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins; This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767915408  75 SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQQAFFNYSTSKRI 153
Cdd:cd12689    2 SPVVHVRGLSEHVTEADLVEALQNFGPISYVTMMPKKRQALVEFEDIEGAKACVNYAQQNPIYVGGRPAYFNYSTSQKI 80

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins; This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RRMs.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767915408 336 VVMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNVCVSKQ 409
Cdd:cd12424    1 VLMVYGLDPDKMNCDRLFNLLCLYGNVLKIKFLKSKPGTAMVQMGDPVAADRAIQNLNNVVLFGQKLQLTYSKQ 74

RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein L (hnRNP-L); This subgroup corresponds to the RRM1 of hnRNP-L, a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-L shows significant sequence homology to polypyrimidine tract-binding protein (PTB or hnRNP I). Both, hnRNP-L and PTB, are localized in the nucleus but excluded from the nucleolus. hnRNP-L is an RNA-binding protein with three RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767915408  75 SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQQAFFNYSTSKRI 153
Cdd:cd12780    2 SPVVHIRGLIDGVVEADLVEALQEFGTISYVVVMPKKRQALVEFEDILGACNAVNYAADNQIYIAGHPAFVNYSTSQKI 80

RNA recognition motif 4 (RRM4) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins; This subfamily corresponds to the RRM4 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767915408 452 PSCVLHYYNVPLCVTEETFTKLCNDHEVLTFIKYKVFDAKpSAKTLSGLLEWECKTDAVEALTALNHYQIRVP 524
Cdd:cd12427    1 PSKVLHFFNAPPEITEETLKELFIEAGAPPPVKVKVFPSK-SERSSSGLLEFESVEDALEALALCNHTPIKNP 72

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins; This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767915408  77 VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQQAFFNYSTS 150
Cdd:cd12421    1 VVHIRNLPPDATEADLVALGLPFGKVTNVLLLKGKNQALVEMEDVESASSMVNYYTTVPPLIRGRPVYVQYSNH 74

RNA recognition motif 3 (RRM3) found in plant polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2); This subfamily corresponds to the RRM3 of PTBPH1 and PTBPH2. Although their biological roles remain unclear, PTBPH1 and PTBPH2 show significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Both, PTBPH1 and PTBPH2, contain three RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767915408 168 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRN-GIQAMVEFESVLCAQKAKAALNGADIY-AGCCTLKIEYARPT 245
Cdd:cd12690    3 VLLASIENMQYAVTLDVLHTVFSAFGFVQKIAIFEKNgGFQALIQYPDVPTAVVAKEALEGHCIYdGGYCKLHLSYSRHT 82

                         90
                 ....*....|....*
gi 767915408 246 RLNVIRNDNDSWDYT 260
Cdd:cd12690   83 DLNVKVNNDRSRDYT 97

RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein 2 (PTBP2); This subgroup corresponds to the RRM2 of PTBP2, also known as neural polypyrimidine tract-binding protein or neurally-enriched homolog of PTB (nPTB), highly homologous to polypyrimidine tract binding protein (PTB) and perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 contains four RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767915408 168 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIF-KRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTR 246
Cdd:cd12783    3 VLRIIIDNMYYPVTLDVLHQIFSKFGTVLKIITFtKNNQFQALLQYGDPVNAQQAKLALDGQNIYNACCTLRIDFSKLVN 82

                         90       100
                 ....*....|....*....|..
gi 767915408 247 LNVIRNDNDSWDYTKPYLGRRD 268
Cdd:cd12783   83 LNVKYNNDKSRDYTRPDLPSGD 104

RNA recognition motif 3 (RRM3) found in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3); This subgroup corresponds to the RRM3 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767915408 335 SVVMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNVCVSK 408
Cdd:cd12698    2 PVLLVSNLNPEKVDVDKLFNLFSLYGNIVRIKILRNKPDHALIQMSDPFQAELAVNYLKGAMLFGKSLEVNFSK 75

RNA recognition motif 3 (RRM3) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins; This subfamily corresponds to the RRM3 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767915408 336 VVMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNVCVSK 408
Cdd:cd12423    1 VLLVSNLNEEMVTPDALFTLFGVYGDVLRVKILFNKKDTALIQMADPQQAQTALQHLNGIKLFGKPIRVTLSK 73

RNA recognition motif 3 (RRM3) found in vertebrate polypyrimidine tract-binding protein 1 (PTB); This subgroup corresponds to the RRM3 of PTB, also known as 58 kDa RNA-binding protein PPTB-1 or heterogeneous nuclear ribonucleoprotein I (hnRNP I), an important negative regulator of alternative splicing in mammalian cells. PTB also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTB contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RRM1 and RRM2 are independent from each other and separated by flexible linkers. By contrast, there is an unusual and conserved interdomain interaction between RRM3 and RRM4. It is widely held that only RRMs 3 and 4 are involved in RNA binding and RRM2 mediates PTB homodimer formation. However, new evidence show that the RRMs 1 and 2 also contribute substantially to RNA binding. Moreover, PTB may not always dimerize to repress splicing. It is a monomer in solution.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767915408 336 VVMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNVCVSKQHSV-VP 414
Cdd:cd12695    1 VLLVSNLNPERVTPQCLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGQKLHGKPIRITLSKHQTVqLP 80

                         90
                 ....*....|...
gi 767915408 415 SQIFELEDGTSSY 427
Cdd:cd12695   81 REGQEDQGLTKDY 93

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 767915408 337 VMVSGLHQlKMNCSRVFNLFCLYGNIEKVKFMKTI----PGTALVEMGDEYAVERAVTHLNNVKLFGKRLNV 404
Cdd:cd00590    1 LFVGNLPP-DTTEEDLRELFSKFGEVVSVRIVRDRdgksKGFAFVEFESPEDAEKALEALNGTELGGRPLKV 71

RNA recognition motif 3 (RRM3) found in vertebrate regulator of differentiation 1 (Rod1); This subgroup corresponds to the RRM3 of ROD1 coding protein Rod1, a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. Rod1 contains four repeats of RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and does have RNA binding activities.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767915408 335 SVVMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNVCVSKQH 410
Cdd:cd12697    1 SVLLVSNLNPDAITPHGLFILFGVYGDVLRVKIMFNKKENALVQMADATQAQIAMSHLNGQRLYGKVLRATLSKHQ 76

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767915408   336 VVMVSGLHQlKMNCSRVFNLFCLYGNIEKVKFMKTIP-----GTALVEMGDEYAVERAVTHLNNVKLFGKRLNV 404
Cdd:smart00360   1 TLFVGNLPP-DTTEEELRELFSKFGKVESVRLVRDKEtgkskGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

RNA recognition motif 1 (RRM1) found in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3); This subfamily corresponds to the RRM1 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767915408  77 VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQQAFFNYST 149
Cdd:cd12687    2 VLHVRNVGHEISENDLLQLAQPFGVVTKLVMLRAKNQALLQMQDVSAAISALQFYTSVQPSIRGRNVYIQFSS 74

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in the matrin 3 family of nuclear proteins; This subfamily corresponds to the RRM of the matrin 3 family of nuclear proteins consisting of Matrin 3 (MATR3), nuclear protein 220 (NP220) and similar proteins. MATR3 is a highly conserved inner nuclear matrix protein that has been implicated in various biological processes. NP220 is a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). Both, Matrin 3 and NP220, contain two RNA recognition motif (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Cys2-His2 zinc finger-like motif at the C-terminal region.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767915408  77 VVHVRGLCES-VVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQ 141
Cdd:cd12436    2 VLYLTGLPVSkYSEEDVLKLAEPFGKVNNVLLIRSKREAFIEMETAEDAQAMLSYCKTKPITIKGK 67

RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 1 (PTB); This subgroup corresponds to the RRM1 of PTB, also known as 58 kDa RNA-binding protein PPTB-1 or heterogeneous nuclear ribonucleoprotein I (hnRNP I), an important negative regulator of alternative splicing in mammalian cells. PTB also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTB contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RRM1 and RRM2 are independent from each other and separated by flexible linkers. By contrast, there is an unusual and conserved interdomain interaction between RRM3 and RRM4. It is widely held that only RRMs 3 and 4 are involved in RNA binding and RRM2 mediates PTB homodimer formation. However, new evidence shows that the RRMs 1 and 2 also contribute substantially to RNA binding. Moreover, PTB may not always dimerize to repress splicing. It is a monomer in solution.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767915408  77 VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQQAFFNYSTSKRI 153
Cdd:cd12777    2 VIHVRKLPNDVTEAEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKEL 78

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
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 767915408  178 YPITVDVLYTVCNPVGKVQRIVIFKRNGIQAM----VEFESVLCAQKAKAALNGADIY 231
Cdd:pfam00076   8 PDTTEEDLKDLFSKFGPIKSIRLVRDETGRSKgfafVEFEDEEDAEKAIEALNGKELG 65

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767915408   15 DREYESQAKRLKTEEGEIDYSAEEGENRREatPRGGGDGGGGGRSFSQPEAGGSHHKVSVSP------VVHVRGLCESVV 88
Cdd:TIGR01622  50 DRDYYRGRERRSRSRRPNRRYRPREKRRRR--GDSYRRRRDDRRSRREKPRARDGTPEPLTEderdrrTVFVQQLAARAR 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767915408   89 EADLVEALEKFGTICYVMMMPFKRQ------ALVEFENIDSAKECVTFAA----DEPVYIAGQQAFFNYSTSKRITRPGN 158
Cdd:TIGR01622 128 ERDLYEFFSKVGKVRDVQIIKDRNSrrskgvGYVEFYDVDSVQAALALTGqkllGIPVIVQLSEAEKNRAARAATETSGH 207

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767915408  159 TDDPSGGNKvllLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-RNGIQA----MVEFESVLCAQKAKAALNGADIyAG 233
Cdd:TIGR01622 208 HPNSIPFHR---LYVGNLHFNITEQDLRQIFEPFGEIEFVQLQKdPETGRSkgygFIQFRDAEQAKEALEKMNGFEL-AG 283

RNA recognition motif 4 (RRM4) found in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3); This subfamily corresponds to the RRM4 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 767915408  73 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMM--MPFKRQALVEFENIDSAKE 126
Cdd:cd12426    5 SPTKMIHVSSLPQDVTEEDVLNHLQEHGAIVNTKVfeSNGKKQALVLFENEEQATE 60

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 767915408  97 EKFGTICYVMMMPFKRQALVEFENIDSAKECvtFAADEPV 136
Cdd:cd12257   24 SKFGTIVNIQVNYNPESALVQFSTSEEANKA--YRSPEAV 61

RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767915408  78 VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYiAGQQAFF 145
Cdd:cd12523    6 VYLGNLPESITEEELREDLEKFGPIDQIKIVKEKNIAFVHFLSIANAIKVVTTLPLNPKW-AKRRIYY 72

RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins; This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 767915408  82 GLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKE 126
Cdd:cd12431   10 GLGNGVSREQLLEVFEKYGTVEDIVMLPGKPYSFVSFKSVEEAAK 54

RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia 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. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 767915408 189 CNPVGKVQRIVIFKRN--GIqAMVEFESVLCAQKAKAALNG 227
Cdd:cd12285   32 CSKYGPVLHIYVDKNSpqGN-VYVKFKTIEAAQKCVQAMNG 71