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 1720417259  676 SILLVSELPEDGFTEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSVKVCVPGK 751
Cdd:cd12716      1 CVVLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNFKEAVDSMVKYYETFPVLVGGKRLKISMAEK 76

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.

                            10        20        30
                    ....*....|....*....|....*....|...
gi 1720417259  1886 GFFCPICSLFYSGEKAMANHCKSTRHKQNTEKF 1918
Cdd:smart00451    3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKKR 35

MAEBL; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  740 KGKSVKVCVPGKKKPQNK----EMKKKPSDIKKSSASALKKETDASKTMETVSSSSSAKSGQIKSSTvkvNKCAAKSGKK 815
Cdd:PTZ00121  1297 KAEEKKKADEAKKKAEEAkkadEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAE---EKAEAAEKKK 1373

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720417259  816 SLEAKKSGNIKNKDSNKPvtvPANSEIKASSEDKatgKSAEESPSGTLEATEKEPVNKESEE 877
Cdd:PTZ00121  1374 EEAKKKADAAKKKAEEKK---KADEAKKKAEEDK---KKADELKKAAAAKKKADEAKKKAEE 1429

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); This subgroup corresponds to RRM1 and RRM2 of NP220, also termed zinc finger protein 638 (ZN638), or cutaneous T-cell lymphoma-associated antigen se33-1, or zinc finger matrin-like protein, a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). NP220 contains multiple domains, including MH1, MH2, and MH3, domains homologous to the acidic nuclear protein matrin 3; RS, an arginine/serine-rich domain commonly found in pre-mRNA splicing factors; PstI-HindIII, a domain essential for DNA binding; acidic repeat, a domain with nine repeats of the sequence LVTVDEVIEEEDL; and a Cys2-His2 zinc finger-like motif that is also present in matrin 3. It may be involved in packaging, transferring, or processing transcripts. This subgroup corresponds to the domain of MH2 that contains two tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720417259  676 SILLVSELPEDGFTEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSVKVCVPGK 751
Cdd:cd12716      1 CVVLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNFKEAVDSMVKYYETFPVLVGGKRLKISMAEK 76

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.

                            10        20        30
                    ....*....|....*....|....*....|...
gi 1720417259  1886 GFFCPICSLFYSGEKAMANHCKSTRHKQNTEKF 1918
Cdd:smart00451    3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKKR 35

hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720417259  983 RFVHLDNLPEDGLQC-VLCVGHQFGKVDRYMFMSNKNKVILQLESPESALSMYNFLKQNPQNIGEH 1047
Cdd:TIGR01649    3 PVVHVRNLPQDVVEAdLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQ 68

Zinc-finger double-stranded RNA-binding; This domain family is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localize in the nucleus, particularly the nucleolus. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localization.

                           10        20
                   ....*....|....*....|....*.
gi 1720417259 1887 FFCPICSLFYSGEKAMANHCKSTRHK 1912
Cdd:pfam12171    2 FYCVLCDKYFKSENALQNHLKSKKHK 27

MAEBL; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  740 KGKSVKVCVPGKKKPQNK----EMKKKPSDIKKSSASALKKETDASKTMETVSSSSSAKSGQIKSSTvkvNKCAAKSGKK 815
Cdd:PTZ00121  1297 KAEEKKKADEAKKKAEEAkkadEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAE---EKAEAAEKKK 1373

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720417259  816 SLEAKKSGNIKNKDSNKPvtvPANSEIKASSEDKatgKSAEESPSGTLEATEKEPVNKESEE 877
Cdd:PTZ00121  1374 EEAKKKADAAKKKAEEKK---KADEAKKKAEEDK---KKADELKKAAAAKKKADEAKKKAEE 1429

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); This subgroup corresponds to RRM1 and RRM2 of NP220, also termed zinc finger protein 638 (ZN638), or cutaneous T-cell lymphoma-associated antigen se33-1, or zinc finger matrin-like protein, a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). NP220 contains multiple domains, including MH1, MH2, and MH3, domains homologous to the acidic nuclear protein matrin 3; RS, an arginine/serine-rich domain commonly found in pre-mRNA splicing factors; PstI-HindIII, a domain essential for DNA binding; acidic repeat, a domain with nine repeats of the sequence LVTVDEVIEEEDL; and a Cys2-His2 zinc finger-like motif that is also present in matrin 3. It may be involved in packaging, transferring, or processing transcripts. This subgroup corresponds to the domain of MH2 that contains two tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720417259  676 SILLVSELPEDGFTEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSVKVCVPGK 751
Cdd:cd12716      1 CVVLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNFKEAVDSMVKYYETFPVLVGGKRLKISMAEK 76

RNA recognition motif 2 (RRM2) found in vertebrate matrin-3; This subgroup corresponds to the RRM2 of Matrin 3 (MATR3 or P130), a highly conserved inner nuclear matrix protein with a bipartite nuclear localization signal (NLS), two zinc finger domains predicted to bind DNA, and two RNA recognition motifs (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that are known to interact with RNA. MATR3 has been implicated in various biological processes. It is involved in RNA processing by interacting with other nuclear proteins to anchor hyperedited RNAs to the nuclear matrix. It plays a role in mRNA stabilization through maintaining the stability of certain mRNA species. Besides, it modulates the activity of proximal promoters by binding to highly repetitive sequences of matrix/scaffold attachment region (MAR/SAR). The phosphorylation of MATR3 is assumed to cause neuronal death. It is phosphorylated by the protein kinase ATM, which activates the cellular response to double strand breaks in the DNA. Its phosphorylation by protein kinase A (PKA) is responsible for the activation of the N-methyl-d-aspartic acid (NMDA) receptor. Furthermore, MATR3 has been identified as both a Ca2+-dependent CaM-binding protein and a downstream substrate of caspases. Additional research indicates that matrin 3 also binds Rev/Rev responsive element (RRE)-containing viral RNA and functions as a cofactor that mediates the post-transcriptional regulation of HIV-1.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720417259  677 ILLVSELPEDGFTEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSVKVCVPGKKK 753
Cdd:cd12715      2 VIHLSNLPHSGYSDAAVLKLAEPYGKVKNYILMRMKNQAFLEMESREDAMAMVDHCKKKPLWFQGRCVKVDLSQKYK 78

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
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720417259  683 LPEDGfTEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSV 744
Cdd:cd12421      7 LPPDA-TEADLVALGLPFGKVTNVLLLKGKNQALVEMEDVESASSMVNYYTTVPPLIRGRPV 67

RNA recognition motif 2 (RRM2) found in vertebrate matrin-3; This subgroup corresponds to the RRM2 of Matrin 3 (MATR3 or P130), a highly conserved inner nuclear matrix protein with a bipartite nuclear localization signal (NLS), two zinc finger domains predicted to bind DNA, and two RNA recognition motifs (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that are known to interact with RNA. MATR3 has been implicated in various biological processes. It is involved in RNA processing by interacting with other nuclear proteins to anchor hyperedited RNAs to the nuclear matrix. It plays a role in mRNA stabilization through maintaining the stability of certain mRNA species. Besides, it modulates the activity of proximal promoters by binding to highly repetitive sequences of matrix/scaffold attachment region (MAR/SAR). The phosphorylation of MATR3 is assumed to cause neuronal death. It is phosphorylated by the protein kinase ATM, which activates the cellular response to double strand breaks in the DNA. Its phosphorylation by protein kinase A (PKA) is responsible for the activation of the N-methyl-d-aspartic acid (NMDA) receptor. Furthermore, MATR3 has been identified as both a Ca2+-dependent CaM-binding protein and a downstream substrate of caspases. Additional research indicates that matrin 3 also binds Rev/Rev responsive element (RRE)-containing viral RNA and functions as a cofactor that mediates the post-transcriptional regulation of HIV-1.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1720417259  880 VVFISNLPNKGYSTEEIYNLAKPFGALKDILVLSSHKKAYIEI-NKKSADSMVKFYTCFPISMDGNQLSISMAPEHVDL 957
Cdd:cd12715      2 VIHLSNLPHSGYSDAAVLKLAEPYGKVKNYILMRMKNQAFLEMeSREDAMAMVDHCKKKPLWFQGRCVKVDLSQKYKTL 80

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 1720417259  677 ILLVSELPEDgFTEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSVKV 746
Cdd:cd12777      2 VIHVRKLPND-VTEAEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI 70

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 20 (RBM20); This subfamily corresponds to the RRM of RBM20, an alternative splicing regulator associated with dilated cardiomyopathy (DCM). It contains only one copy of RNA-recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1720417259  879 SVVFISNLPNKGYSTEEIYNLAKPFGALKDILVLSSHKKAYIEIN-KKSADSMVKFYTCFPISMDGNQLSISMA 951
Cdd:cd12685      1 RVVHICNLPEGSCTENDVINLGLPFGKVTNYILMRSTNQAFLEMAyTEAAQAMVQYYQEKPAMINEEKLLIRMS 74

RNA recognition motif;

                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1720417259   678 LLVSELPEDgFTEEDIRKAFLPFGKISDVLLVP------CRNEAYLEMELRKAVTSIMKYIETMplVIKGKSVKV 746
Cdd:smart00360    2 LFVGNLPPD-TTEEELRELFSKFGKVESVRLVRdketgkSKGFAFVEFESEEDAEKALEALNGK--ELDGRPLKV 73

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
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1720417259  880 VVFISNLPNKgySTE-EIYNLAKPFGALKDILVLSSHKKAYIEI-NKKSADSMVKFYTCFPISMDGNQL 946
Cdd:cd12421      1 VVHIRNLPPD--ATEaDLVALGLPFGKVTNVLLLKGKNQALVEMeDVESASSMVNYYTTVPPLIRGRPV 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        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  880 VVFISNLPNKgYSTEEIYNLAKPFGALKDILVLSSHKKAYIEIN-KKSADSMVKFYTCFPISMDGNQLSISMApEHVDLK 958
Cdd:cd12777      2 VIHVRKLPND-VTEAEVISLGLPFGKVTNLLMLKGKNQAFIEMNtEEAANTMVNYYTSVTPVLRGQPIYIQFS-NHKELK 79

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
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1720417259  680 VSELPEdGFTEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSV 744
Cdd:cd12689      7 VRGLSE-HVTEADLVEALQNFGPISYVTMMPKKRQALVEFEDIEGAKACVNYAQQNPIYVGGRPA 70

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
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1720417259  689 TEEDIRKAFLPFGKISDVLLVPCRNEAYLEMELRKAVTSIMKYIETMPLVIKGKSVKV 746
Cdd:cd12687     13 SENDLLQLAQPFGVVTKLVMLRAKNQALLQMQDVSAAISALQFYTSVQPSIRGRNVYI 70

hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1720417259  983 RFVHLDNLPEDGLQC-VLCVGHQFGKVDRYMFMSNKNKVILQLESPESALSMYNFLKQNPQNIGEH 1047
Cdd:TIGR01649    3 PVVHVRNLPQDVVEAdLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQ 68

RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 2 (PTBP2); This subgroup corresponds to the RRM1 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
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1720417259  880 VVFISNLPNKGYSTEEIyNLAKPFGALKDILVLSSHKKAYIEI-NKKSADSMVKFYT 935
Cdd:cd12778      3 VLHIRKLPGEVTETEVI-ALGLPFGKVTNILMLKGKNQAFLELaTEEAAITMVNYYT 58

RNA recognition motif 1 (RRM1) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins; This subfamily corresponds to the RRM1 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 functions at several 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 and 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        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  880 VVFISNLPnkGYSTE-EIYNLAKPFGALKDILVLSSHKKAYIEIN-KKSADSMVKFYTCFPISMDGNQLSISMApEHVDL 957
Cdd:cd12688      2 VLHIRKLP--CDVTEaEVISLGLPFGKVTNLLMLKGKNQAFLEMAtEEAAVTMVNYYTPVTPHLRSQPIYIQYS-NHKEL 78

                   .
gi 1720417259  958 K 958
Cdd:cd12688     79 K 79

RNA recognition motif 1 (RRM1) found in vertebrate regulator of differentiation 1 (Rod1); This subgroup corresponds to the RRM1 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 that 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
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1720417259  982 NRFVHLDNLPEDGLQC-VLCVGHQFGKVDRYMFMSNKNKVILQLESPESALSMYNF 1036
Cdd:cd12779      5 SRVLHIRKIPNDVTEAeVISLGLPFGKVTNLLMLKGKNQAFLEMASEEAAVTMVNY 60

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
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1720417259  983 RFVHLDNLPEDGLQC-VLCVGHQFGKVDRYMFMSNKNKVILQLESPESALSMYNF 1036
Cdd:cd12777      1 RVIHVRKLPNDVTEAeVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNY 55

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 1720417259  881 VFISNLPnKGYSTEEIYNLAKPFGALKDILVLSSHKK-----AYIE-INKKSADSMVKFYTCFPIsmDGNQLSIS 949
Cdd:cd00590      1 LFVGNLP-PDTTEEDLRELFSKFGEVVSVRIVRDRDGkskgfAFVEfESPEDAEKALEALNGTEL--GGRPLKVS 72

RNA recognition motif 1 (RRM1) found in vertebrate regulator of differentiation 1 (Rod1); This subgroup corresponds to the RRM1 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 that 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        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  880 VVFISNLPNKgYSTEEIYNLAKPFGALKDILVLSSHKKAYIEI-NKKSADSMVKFYTCFPISMDGNQLSISMApEHVDLK 958
Cdd:cd12779      7 VLHIRKIPND-VTEAEVISLGLPFGKVTNLLMLKGKNQAFLEMaSEEAAVTMVNYYTTVTPHLRNQPVYIQYS-NHRELK 84

                   ..
gi 1720417259  959 DE 960
Cdd:cd12779     85 TD 86

MAEBL; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720417259  740 KGKSVKVCVPGKKKPQnkEMKKKPSDIKKsSASALKKETDASKTMETVSSSSSAKsgqiksSTVKVNKCAAKSGKKSLEA 819
Cdd:PTZ00121  1386 KAEEKKKADEAKKKAE--EDKKKADELKK-AAAAKKKADEAKKKAEEKKKADEAK------KKAEEAKKADEAKKKAEEA 1456

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1720417259  820 KKSGNIKNKDSNKPVTVPANSEIKASSEDKATGKSAEESPSGTLEATEKEPVNKESEEM 878
Cdd:PTZ00121  1457 KKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEA 1515