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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004   97 ASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQKI 176
Cdd:TIGR01649   1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004  177 SRPGDSD-DSRSVNSVLLFTILNPIYSITTDVLYTICNPCGPVQRIVIFRKNG-VQAMVEFDSVQSAQRAKASLNGADIY 254
Cdd:TIGR01649  81 KRDGNSDfDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNvFQALVEFESVNSAQHAKAALNGADIY 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004  255 SGCCTLKIEYAKPTRLNVFKNDQDTWDYTNPNLSGQGDPGSNPNKRQRQPPLLGDHPAEYGgpHGGYHSHYhdegyGPPP 334
Cdd:TIGR01649 161 NGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYG--HDGYSSHG-----GPLA 233

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004  335 PHYEGRRMGPPVGGhrrgPSRYGPQYGHPPPPPPPPDYGPHADSP--VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFM 412
Cdd:TIGR01649 234 PLAGGDRMGPPHGP----PSRYRPAYEAAPLAPAISSYGPAGGGPgsVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFM 309

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004  413 KSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNR 492
Cdd:TIGR01649 310 KNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNN 389

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004  493 IQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP 572
Cdd:TIGR01649 390 IQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKDNERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAP 469

                         490
                  ....*....|..
gi 183980004  573 YTLKLCFSTAQH 584
Cdd:TIGR01649 470 YHLKVSFSTSRI 481

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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004   97 ASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQKI 176
Cdd:TIGR01649   1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004  177 SRPGDSD-DSRSVNSVLLFTILNPIYSITTDVLYTICNPCGPVQRIVIFRKNG-VQAMVEFDSVQSAQRAKASLNGADIY 254
Cdd:TIGR01649  81 KRDGNSDfDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNvFQALVEFESVNSAQHAKAALNGADIY 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004  255 SGCCTLKIEYAKPTRLNVFKNDQDTWDYTNPNLSGQGDPGSNPNKRQRQPPLLGDHPAEYGgpHGGYHSHYhdegyGPPP 334
Cdd:TIGR01649 161 NGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYG--HDGYSSHG-----GPLA 233

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004  335 PHYEGRRMGPPVGGhrrgPSRYGPQYGHPPPPPPPPDYGPHADSP--VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFM 412
Cdd:TIGR01649 234 PLAGGDRMGPPHGP----PSRYRPAYEAAPLAPAISSYGPAGGGPgsVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFM 309

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004  413 KSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNR 492
Cdd:TIGR01649 310 KNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNN 389

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004  493 IQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP 572
Cdd:TIGR01649 390 IQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKDNERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAP 469

                         490
                  ....*....|..
gi 183980004  573 YTLKLCFSTAQH 584
Cdd:TIGR01649 470 YHLKVSFSTSRI 481

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004  353 PSRYGPQYGHPPPPPPPPDYGPHADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRA 432
Cdd:pfam13893   1 PGRFGPSYTGSVAATGWPGAAGVAGNSVLMVYGLNPDRVNCDKLFNLFCLYGNVARVKFMKNKKGTAMVQMGDASQVQRA 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 183980004  433 ITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSES 477
Cdd:pfam13893  81 IQHLNGHPLFGKRLQIILSKQQAVSYALPFELQDDSPSFKDYSNS 125

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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004   97 ASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQKI 176
Cdd:TIGR01649   1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004  177 SRPGDSD-DSRSVNSVLLFTILNPIYSITTDVLYTICNPCGPVQRIVIFRKNG-VQAMVEFDSVQSAQRAKASLNGADIY 254
Cdd:TIGR01649  81 KRDGNSDfDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNvFQALVEFESVNSAQHAKAALNGADIY 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004  255 SGCCTLKIEYAKPTRLNVFKNDQDTWDYTNPNLSGQGDPGSNPNKRQRQPPLLGDHPAEYGgpHGGYHSHYhdegyGPPP 334
Cdd:TIGR01649 161 NGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYG--HDGYSSHG-----GPLA 233

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004  335 PHYEGRRMGPPVGGhrrgPSRYGPQYGHPPPPPPPPDYGPHADSP--VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFM 412
Cdd:TIGR01649 234 PLAGGDRMGPPHGP----PSRYRPAYEAAPLAPAISSYGPAGGGPgsVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFM 309

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004  413 KSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNR 492
Cdd:TIGR01649 310 KNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNN 389

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004  493 IQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP 572
Cdd:TIGR01649 390 IQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKDNERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAP 469

                         490
                  ....*....|..
gi 183980004  573 YTLKLCFSTAQH 584
Cdd:TIGR01649 470 YHLKVSFSTSRI 481

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 183980004 189 NSVLLFTILNPIYSITTDVLYTICNPCGPVQRIVIFRKNGVQAMVEFDSVQSAQRAKASLNGADIYSGCCTLKIEYAKPT 268
Cdd:cd12694    1 NHVLLFTILNPLYPITVDVIHTICSPYGKVLRIVIFRKNGVQAMVEFDSVESAQRAKAALNGADIYSGCCTLKIEYAKPT 80

                 ....*.
gi 183980004 269 RLNVFK 274
Cdd:cd12694   81 RLNVYK 86

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004  353 PSRYGPQYGHPPPPPPPPDYGPHADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRA 432
Cdd:pfam13893   1 PGRFGPSYTGSVAATGWPGAAGVAGNSVLMVYGLNPDRVNCDKLFNLFCLYGNVARVKFMKNKKGTAMVQMGDASQVQRA 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 183980004  433 ITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSES 477
Cdd:pfam13893  81 IQHLNGHPLFGKRLQIILSKQQAVSYALPFELQDDSPSFKDYSNS 125

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 183980004 189 NSVLLFTILNPIYSITTDVLYTICNPCGPVQRIVIFRKNGVQAMVEFDSVQSAQRAKASLNGADIYSGCCTLKIEYAKPT 268
Cdd:cd12786    2 NKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVECAQKAKAALNGADIYAGCCTLKIEYARPT 81

                         90
                 ....*....|....*
gi 183980004 269 RLNVFKNDQDTWDYT 283
Cdd:cd12786   82 RLNVIRNDNDSWDYT 96

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 183980004  98 SPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQKI 176
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 183980004 380 VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQ 453
Cdd:cd12424    1 VLMVYGLDPDKMNCDRLFNLLCLYGNVLKIKFLKSKPGTAMVQMGDPVAADRAIQNLNNVVLFGQKLQLTYSKQ 74

RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL); This subgroup corresponds to the RRM1 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 183980004  98 SPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQKIS 177
Cdd:cd12781    3 SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENVESAKKCVTFAADEPVYIAGQQAFFNYSTSKRIT 82

                 ..
gi 183980004 178 RP 179
Cdd:cd12781   83 RP 84

RNA recognition motif 4 (RRM4) found in vertebrate heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL); The subgroup corresponds to the RRM4 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 183980004 496 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK-SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYT 574
Cdd:cd12705    1 PSCVLHYYNVPLCVTEETFQKLCEDHEVPTFIKYKVFDAKpSSKTLSGLLEWESKTEAVEALTVLNHYQIRVPNGSNPYT 80

                 ....*
gi 183980004 575 LKLCF 579
Cdd:cd12705   81 LKLCF 85

RNA recognition motif 2 (RRM2) found in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3); This subfamily corresponds to the RRM2 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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004 189 NSVLLFTILNPIYSITTDVLYTICNPCGPVQRIVIFRKN-GVQAMVEFDSVQSAQRAKASLNGADIYSGCCTLKIEYAKP 267
Cdd:cd12692    2 NRILLVTIHHPLYPITVDVLHQVFSPHGFVEKIVTFQKSaGLQALIQYQSQQSAVQARSALQGRNIYDGCCQLDIQFSNL 81

                 ....*
gi 183980004 268 TRLNV 272
Cdd:cd12692   82 QELQV 86

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 183980004 191 VLLFTILNPIYSITTDVLYTICNPCGPVQRIVIFRKNG-VQAMVEFDSVQSAQRAKASLNGADIYSGCCTLKIEYAKPTR 269
Cdd:cd12783    3 VLRIIIDNMYYPVTLDVLHQIFSKFGTVLKIITFTKNNqFQALLQYGDPVNAQQAKLALDGQNIYNACCTLRIDFSKLVN 82

                         90       100
                 ....*....|....*....|....*
gi 183980004 270 LNVFKNDQDTWDYTNPNL-SGQGDP 293
Cdd:cd12783   83 LNVKYNNDKSRDYTRPDLpSGDGQP 107

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 183980004 190 SVLLFTILNPIYSITTDVLYTICNPCGPVQRIVIFRKN-GVQAMVEFDSVQSAQRAKASLNGADIYS-GCCTLKIEYAKP 267
Cdd:cd12690    2 NVLLASIENMQYAVTLDVLHTVFSAFGFVQKIAIFEKNgGFQALIQYPDVPTAVVAKEALEGHCIYDgGYCKLHLSYSRH 81

                         90
                 ....*....|....*.
gi 183980004 268 TRLNVFKNDQDTWDYT 283
Cdd:cd12690   82 TDLNVKVNNDRSRDYT 97

RNA recognition motif 2 (RRM2) found in vertebrate regulator of differentiation 1 (Rod1); This subgroup corresponds to the RRM2 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 and 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 183980004 191 VLLFTILNPIYSITTDVLYTICNPCGPVQRIVIFRKNG-VQAMVEFDSVQSAQRAKASLNGADIYSGCCTLKIEYAKPTR 269
Cdd:cd12784    5 VLRIIVENLFYPVTLEVLHQIFSKFGTVLKIITFTKNNqFQALLQYADPMNAHHAKVALDGQNIYNACCTLRIEFSKLTS 84

                         90       100
                 ....*....|....*....|...
gi 183980004 270 LNVFKNDQDTWDYTNPNL-SGQG 291
Cdd:cd12784   85 LNVKYNNDKSRDFTRLDLpSGDG 107

RNA recognition motif 3 (RRM3) found in vertebrate polypyrimidine tract-binding protein 2 (PTBP2); This subgroup corresponds to the RRM3 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 183980004 380 VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAI-MP 458
Cdd:cd12696   15 VLLVSNLNEEMVTPQSLFTLFGVYGDVQRVKILYNKKDSALIQMADGNQSQLAMSHLNGQKMYGKIIRVTLSKHQTVqLP 94

                         90
                 ....*....|....*.
gi 183980004 459 GQsyGLEDGSCSyKDF 474
Cdd:cd12696   95 RE--GLDDQGLT-KDF 107

RRM-like domain; This domain is related to the RRM domains suggesting it may have an RNA-binding function.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 183980004  190 SVLLFTILNPIYSITTDVLYTICNPCGPVQ-RIVIFRKNGVQAMVEFDSVQSAQRAKASLNGADIYSGCCTLKIEYAKP 267
Cdd:pfam11835  11 AVLRVTVSHILYPVTSEVLHQVYDTYGAVAvQVLAVSTWHVEALVSFMSSCDAERARSATHGRNIYDGGCLLDVQHAQP 89

RNA recognition motif 2 (RRM2) found in plant polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2); This subfamily corresponds to the RRM2 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 183980004 190 SVLLFTILN-PIYSITTDVLYTICNPCGPVQRIVIFRKN-GVQAMVEFDSVQSAQRAKASLNGADI-------YSGCCTL 260
Cdd:cd12691    2 NVLLVTIEGvEAGDVSIDVLHLVFSAFGFVHKIATFEKTaGFQALVQFTDAETASAARSALDGRSIpryllpeHVGPCSL 81

                         90
                 ....*....|..
gi 183980004 261 KIEYAKPTRLNV 272
Cdd:cd12691   82 RISYSAHTDLNV 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 183980004 381 LMVYGLDQSkMNCDRVFNVFCLYGNVEKVKFMKSK----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNV 448
Cdd:cd00590    1 LFVGNLPPD-TTEEDLRELFSKFGEVVSVRIVRDRdgksKGFAFVEFESPEDAEKALEALNGTELGGRPLKV 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 183980004 380 VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQ 453
Cdd:cd12697    2 VLLVSNLNPDAITPHGLFILFGVYGDVLRVKIMFNKKENALVQMADATQAQIAMSHLNGQRLYGKVLRATLSKH 75

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 183980004 100 VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQKI 176
Cdd:cd12777    2 VIHVRKLPNDVTEAEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKEL 78

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 183980004 101 VHIRGLIDGVVEADLVEALQEFGPISYVVVMPK-----KRQALVEFEDVLGACNAVNyaADNQIYIAGHPAFVN 169
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDrdgksKGFAFVEFESPEDAEKALE--ALNGTELGGRPLKVS 72

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        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 183980004 100 VVHIRGL-IDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPafVNYSTSQK 175
Cdd:cd12436    2 VLYLTGLpVSKYSEEDVLKLAEPFGKVNNVLLIRSKREAFIEMETAEDAQAMLSYCKTKPITIKGKK--VKVSVSQK 76

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains 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. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 183980004 208 LYTICNPCGPVQRIVIFRKNGV--QAMVEFDSVQSAQRAKASLNGADIYSGccTLKIEYAK 266
Cdd:cd12246   20 LYALFSQFGPVLDIVASKSLKMrgQAFVVFKDVESATNALRALQGFPFYGK--PMRIQYAK 78

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 183980004 100 VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQKI 176
Cdd:cd12688    2 VLHIRKLPCDVTEAEVISLGLPFGKVTNLLMLKGKNQAFLEMATEEAAVTMVNYYTPVTPHLRSQPIYIQYSNHKEL 78

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        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 183980004 105 GLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIA--GHPAFVNY 170
Cdd:cd12431   10 GLGNGVSREQLLEVFEKYGTVEDIVMLPGKPYSFVSFKSVEEAAKAYNALNGKELELPqqNVPLYLSF 77

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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183980004 191 VLLFTILNPiYSITTDVLYTICNPCGPVQRIVIFRKNGVQAMVEFDSVQSAQRAKASLNGADIYSgcctlkieyaKPTRL 270
Cdd:cd12423    1 VLLVSNLNE-EMVTPDALFTLFGVYGDVLRVKILFNKKDTALIQMADPQQAQTALQHLNGIKLFG----------KPIRV 69

                 ....*
gi 183980004 271 NVFKN 275
Cdd:cd12423   70 TLSKH 74

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 183980004 190 SVLLFTILNPiYSITTDVLYTICNPCGPVQRIVIFRKNGVQAMVEFDSVQSAQRAKASLNGADIY 254
Cdd:cd12697    1 SVLLVSNLNP-DAITPHGLFILFGVYGDVLRVKIMFNKKENALVQMADATQAQIAMSHLNGQRLY 64

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 183980004  96 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVV--MPKKRQALVEFEDVLGACNAV 151
Cdd:cd12426    5 SPTKMIHVSSLPQDVTEEDVLNHLQEHGAIVNTKVfeSNGKKQALVLFENEEQATEAL 62

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 183980004 212 CNPCGPVQRIVIFRKN--GVqAMVEFDSVQSAQRAKASLNG 250
Cdd:cd12285   32 CSKYGPVLHIYVDKNSpqGN-VYVKFKTIEAAQKCVQAMNG 71

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 183980004 204 TTDVLYTICNPCGPVQRIVIFRKNGVqAMVEFDSVQSAQRAKASLNGADIysGCCTLK 261
Cdd:cd12354   13 TEALLQQTFSPFGQILEVRVFPDKGY-AFIRFDSHEAATHAIVSVNGTII--NGQAVK 67

RNA recognition motif (RRM) found in the DnaJ homolog subfamily C member 17; The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 183980004 112 EADLVEALQEFGPISYVVVMPKKR-QALVEFEDVLGACNAV 151
Cdd:cd12429   18 EEELRKIFSKYGPVSDVVISSKKKgSAIVEFATVVAADAAV 58