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Conserved domains on  [gi|62286941|sp|Q8WVV9|]
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RecName: Full=Heterogeneous nuclear ribonucleoprotein L-like; Short=hnRNPLL; AltName: Full=Stromal RNA-regulating factor

Protein Classification

hnRNP-L/PTB/hephaestus splicing factor family protein( domain architecture ID 11492984)

hnRNP-L/PTB/hephaestus splicing factor family protein similar to Homo sapiens heterogeneous nuclear ribonucleoprotein L (hnRNP-L), a splicing factor binding to exonic or intronic sites and acting as either an activator or repressor of exon inclusion

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
hnRNP-L_PTB TIGR01649
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
 74-541 0e+00

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).


:

Pssm-ID: 273733 [Multi-domain]  Cd Length: 481  Bit Score: 778.61  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941    74 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQQAFFNYSTSKRI 153
Cdd:TIGR01649   1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941   154 TRPGNTD-DPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNG-IQAMVEFESVLCAQKAKAALNGADIY 231
Cdd:TIGR01649  81 KRDGNSDfDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNvFQALVEFESVNSAQHAKAALNGADIY 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941   232 AGCCTLKIEYARPTRLNVIRNDNDSWDYTKPYL-GRRDRGKG---RQRQ-AILGEHPSSFRHDGYGSH-GPLLPLPSRYR 305
Cdd:TIGR01649 161 NGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLpGRRDPGLDqthRQRQpALLGQHPSSYGHDGYSSHgGPLAPLAGGDR 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941   306 MG------SRDTPELVAYPLPQASSSYMHGGNPSGSVVMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEM 379
Cdd:TIGR01649 241 MGpphgppSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEM 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941   380 GDEYAVERAVTHLNNVKLFGKRLNVCVSKQHSVVPSQIFELEDGTSSYKDFAMSKNNRFTSAGQASKNIIQPPSCVLHYY 459
Cdd:TIGR01649 321 ADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLS 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941   460 NVPLCVTEETFTKLCNDHEVLTFIKYKVFDAKpSAKTLSGLLEWECKTDAVEALTALNHYQIRVPNGSNPYTLKLCFSTS 539
Cdd:TIGR01649 401 NIPLSVSEEDLKELFAENGVHKVKKFKFFPKD-NERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTS 479


                  ..
gi 62286941   540 SH 541
Cdd:TIGR01649 480 RI 481
 
Name Accession Description Interval E-value
hnRNP-L_PTB TIGR01649
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
 74-541 0e+00

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).


Pssm-ID: 273733 [Multi-domain]  Cd Length: 481  Bit Score: 778.61  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941    74 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQQAFFNYSTSKRI 153
Cdd:TIGR01649   1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941   154 TRPGNTD-DPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNG-IQAMVEFESVLCAQKAKAALNGADIY 231
Cdd:TIGR01649  81 KRDGNSDfDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNvFQALVEFESVNSAQHAKAALNGADIY 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941   232 AGCCTLKIEYARPTRLNVIRNDNDSWDYTKPYL-GRRDRGKG---RQRQ-AILGEHPSSFRHDGYGSH-GPLLPLPSRYR 305
Cdd:TIGR01649 161 NGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLpGRRDPGLDqthRQRQpALLGQHPSSYGHDGYSSHgGPLAPLAGGDR 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941   306 MG------SRDTPELVAYPLPQASSSYMHGGNPSGSVVMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEM 379
Cdd:TIGR01649 241 MGpphgppSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEM 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941   380 GDEYAVERAVTHLNNVKLFGKRLNVCVSKQHSVVPSQIFELEDGTSSYKDFAMSKNNRFTSAGQASKNIIQPPSCVLHYY 459
Cdd:TIGR01649 321 ADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLS 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941   460 NVPLCVTEETFTKLCNDHEVLTFIKYKVFDAKpSAKTLSGLLEWECKTDAVEALTALNHYQIRVPNGSNPYTLKLCFSTS 539
Cdd:TIGR01649 401 NIPLSVSEEDLKELFAENGVHKVKKFKFFPKD-NERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTS 479


                  ..
gi 62286941   540 SH 541
Cdd:TIGR01649 480 RI 481
RRM2_hnRPLL cd12786
RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein ...
 165-260 7.00e-66

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).


Pssm-ID: 241230 [Multi-domain]  Cd Length: 96  Bit Score: 208.71  E-value: 7.00e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941 165 GNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARP 244
Cdd:cd12786   1 GNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVECAQKAKAALNGADIYAGCCTLKIEYARP 80

                        90
                ....*....|....*.
gi 62286941 245 TRLNVIRNDNDSWDYT 260
Cdd:cd12786  81 TRLNVIRNDNDSWDYT 96
RRM_5 pfam13893
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 316-433 1.99e-46

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.


Pssm-ID: 433561 [Multi-domain]  Cd Length: 125  Bit Score: 158.42  E-value: 1.99e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941   316 AYPLPQASSSYMHGGNPSGSVVMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNV 395
Cdd:pfam13893   8 YTGSVAATGWPGAAGVAGNSVLMVYGLNPDRVNCDKLFNLFCLYGNVARVKFMKNKKGTAMVQMGDASQVQRAIQHLNGH 87

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 62286941   396 KLFGKRLNVCVSKQHSVVPSQIFELEDGTSSYKDFAMS 433
Cdd:pfam13893  88 PLFGKRLQIILSKQQAVSYALPFELQDDSPSFKDYSNS 125
RRM smart00360
RNA recognition motif;
336-404 8.12e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 49.51  E-value: 8.12e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62286941    336 VVMVSGLHQlKMNCSRVFNLFCLYGNIEKVKFMKTIP-----GTALVEMGDEYAVERAVTHLNNVKLFGKRLNV 404
Cdd:smart00360   1 TLFVGNLPP-DTTEEELRELFSKFGKVESVRLVRDKEtgkskGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
 
Name Accession Description Interval E-value
hnRNP-L_PTB TIGR01649
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
 74-541 0e+00

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).


Pssm-ID: 273733 [Multi-domain]  Cd Length: 481  Bit Score: 778.61  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941    74 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQQAFFNYSTSKRI 153
Cdd:TIGR01649   1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941   154 TRPGNTD-DPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNG-IQAMVEFESVLCAQKAKAALNGADIY 231
Cdd:TIGR01649  81 KRDGNSDfDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNvFQALVEFESVNSAQHAKAALNGADIY 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941   232 AGCCTLKIEYARPTRLNVIRNDNDSWDYTKPYL-GRRDRGKG---RQRQ-AILGEHPSSFRHDGYGSH-GPLLPLPSRYR 305
Cdd:TIGR01649 161 NGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLpGRRDPGLDqthRQRQpALLGQHPSSYGHDGYSSHgGPLAPLAGGDR 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941   306 MG------SRDTPELVAYPLPQASSSYMHGGNPSGSVVMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEM 379
Cdd:TIGR01649 241 MGpphgppSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEM 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941   380 GDEYAVERAVTHLNNVKLFGKRLNVCVSKQHSVVPSQIFELEDGTSSYKDFAMSKNNRFTSAGQASKNIIQPPSCVLHYY 459
Cdd:TIGR01649 321 ADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLS 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941   460 NVPLCVTEETFTKLCNDHEVLTFIKYKVFDAKpSAKTLSGLLEWECKTDAVEALTALNHYQIRVPNGSNPYTLKLCFSTS 539
Cdd:TIGR01649 401 NIPLSVSEEDLKELFAENGVHKVKKFKFFPKD-NERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTS 479


                  ..
gi 62286941   540 SH 541
Cdd:TIGR01649 480 RI 481
RRM2_hnRPLL cd12786
RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein ...
 165-260 7.00e-66

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).


Pssm-ID: 241230 [Multi-domain]  Cd Length: 96  Bit Score: 208.71  E-value: 7.00e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941 165 GNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARP 244
Cdd:cd12786   1 GNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVECAQKAKAALNGADIYAGCCTLKIEYARP 80

                        90
                ....*....|....*.
gi 62286941 245 TRLNVIRNDNDSWDYT 260
Cdd:cd12786  81 TRLNVIRNDNDSWDYT 96
RRM4_hnRPLL cd12705
RNA recognition motif 4 (RRM4) found in vertebrate heterogeneous nuclear ribonucleoprotein ...
 452-536 2.86e-60

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).


Pssm-ID: 410104  Cd Length: 85  Bit Score: 193.65  E-value: 2.86e-60
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941 452 PSCVLHYYNVPLCVTEETFTKLCNDHEVLTFIKYKVFDAKPSAKTLSGLLEWECKTDAVEALTALNHYQIRVPNGSNPYT 531
Cdd:cd12705   1 PSCVLHYYNVPLCVTEETFQKLCEDHEVPTFIKYKVFDAKPSSKTLSGLLEWESKTEAVEALTVLNHYQIRVPNGSNPYT 80


                ....*
gi 62286941 532 LKLCF 536
Cdd:cd12705  81 LKLCF 85
RRM1_hnRPLL cd12781
RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein ...
 73-156 3.03e-59

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).


Pssm-ID: 410173 [Multi-domain]  Cd Length: 84  Bit Score: 191.02  E-value: 3.03e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941  73 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQQAFFNYSTSKR 152
Cdd:cd12781   1 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENVESAKKCVTFAADEPVYIAGQQAFFNYSTSKR 80


                ....
gi 62286941 153 ITRP 156
Cdd:cd12781  81 ITRP 84
RRM2_hnRNPL_like cd12694
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) ...
 166-251 2.31e-54

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).


Pssm-ID: 410094 [Multi-domain]  Cd Length: 86  Bit Score: 178.24  E-value: 2.31e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941 166 NKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPT 245
Cdd:cd12694   1 NHVLLFTILNPLYPITVDVIHTICSPYGKVLRIVIFRKNGVQAMVEFDSVESAQRAKAALNGADIYSGCCTLKIEYAKPT 80


                ....*.
gi 62286941 246 RLNVIR 251
Cdd:cd12694  81 RLNVYK 86
RRM2_hnRNPL cd12785
RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein L ...
 166-262 9.15e-50

RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein L (hnRNP-L); This subgroup corresponds to the RRM2 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).


Pssm-ID: 410177 [Multi-domain]  Cd Length: 100  Bit Score: 166.38  E-value: 9.15e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941 166 NKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPT 245
Cdd:cd12785   4 NNVLLFTILNPIYSITTDVLYTICNPCGPVQRIVIFRKNGVQAMVEFDSVQSAQRAKASLNGADIYSGCCTLKIEYAKPT 83

                        90
                ....*....|....*..
gi 62286941 246 RLNVIRNDNDSWDYTKP 262
Cdd:cd12785  84 RLNVFKNDQDTWDYTNP 100
RRM3_hnRPLL cd12700
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein ...
 336-409 9.98e-49

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).


Pssm-ID: 410100 [Multi-domain]  Cd Length: 74  Bit Score: 162.88  E-value: 9.98e-49
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62286941 336 VVMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNVCVSKQ 409
Cdd:cd12700   1 VAMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNVCVSKQ 74
RRM1_hnRNPL_like cd12689
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) ...
 75-153 2.78e-47

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).


Pssm-ID: 410090 [Multi-domain]  Cd Length: 80  Bit Score: 158.97  E-value: 2.78e-47
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62286941  75 SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQQAFFNYSTSKRI 153
Cdd:cd12689   2 SPVVHVRGLSEHVTEADLVEALQNFGPISYVTMMPKKRQALVEFEDIEGAKACVNYAQQNPIYVGGRPAYFNYSTSQKI 80
RRM_5 pfam13893
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 316-433 1.99e-46

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.


Pssm-ID: 433561 [Multi-domain]  Cd Length: 125  Bit Score: 158.42  E-value: 1.99e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941   316 AYPLPQASSSYMHGGNPSGSVVMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNV 395
Cdd:pfam13893   8 YTGSVAATGWPGAAGVAGNSVLMVYGLNPDRVNCDKLFNLFCLYGNVARVKFMKNKKGTAMVQMGDASQVQRAIQHLNGH 87

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 62286941   396 KLFGKRLNVCVSKQHSVVPSQIFELEDGTSSYKDFAMS 433
Cdd:pfam13893  88 PLFGKRLQIILSKQQAVSYALPFELQDDSPSFKDYSNS 125
RRM3_hnRNPL_like cd12424
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) ...
 336-409 1.44e-40

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.


Pssm-ID: 409858 [Multi-domain]  Cd Length: 74  Bit Score: 140.82  E-value: 1.44e-40
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62286941 336 VVMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNVCVSKQ 409
Cdd:cd12424   1 VLMVYGLDPDKMNCDRLFNLLCLYGNVLKIKFLKSKPGTAMVQMGDPVAADRAIQNLNNVVLFGQKLQLTYSKQ 74
RRM4_hnRNPL_like cd12427
RNA recognition motif 4 (RRM4) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) ...
 452-536 5.37e-39

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).


Pssm-ID: 409861 [Multi-domain]  Cd Length: 84  Bit Score: 136.99  E-value: 5.37e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941 452 PSCVLHYYNVPLCVTEETFTKLCNDHEVLTFIKYKVFDAKpSAKTLSGLLEWECKTDAVEALTALNHYQIRVPNGSNPYT 531
Cdd:cd12427   1 PSKVLHFFNAPPEITEETLKELFIEAGAPPPVKVKVFPSK-SERSSSGLLEFESVEDALEALALCNHTPIKNPNGKAPYT 79


                ....*
gi 62286941 532 LKLCF 536
Cdd:cd12427  80 LKLCF 84
RRM3_hnRNPL cd12699
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein L ...
 336-409 1.57e-36

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein L (hnRNP-L); This subgroup corresponds to the RRM3 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 with 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).


Pssm-ID: 410099 [Multi-domain]  Cd Length: 77  Bit Score: 130.05  E-value: 1.57e-36
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62286941 336 VVMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNVCVSKQ 409
Cdd:cd12699   4 VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKLNVCVSKQ 77
RRM1_hnRNPL cd12780
RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein L ...
 75-153 1.12e-34

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).


Pssm-ID: 410172 [Multi-domain]  Cd Length: 80  Bit Score: 125.36  E-value: 1.12e-34
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62286941  75 SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQQAFFNYSTSKRI 153
Cdd:cd12780   2 SPVVHIRGLIDGVVEADLVEALQEFGTISYVVVMPKKRQALVEFEDILGACNAVNYAADNQIYIAGHPAFVNYSTSQKI 80
RRM2_PTBP1_hnRNPL_like cd12422
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
 168-251 5.66e-34

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 RRM2 of 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, and RRM3 of PTBPH1 and PTBPH2. 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. This 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.


Pssm-ID: 409856 [Multi-domain]  Cd Length: 85  Bit Score: 123.45  E-value: 5.66e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941 168 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRN-GIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTR 246
Cdd:cd12422   1 VLLVTVTNLLYPVTVDVLHQVFSPYGAVEKIVIFEKGtGVQALVQFDSVESAEAAKKALNGRNIYDGCCTLDIQFSRLKE 80


                ....*
gi 62286941 247 LNVIR 251
Cdd:cd12422  81 LTVKY 85
RRM2_PTBP1_like cd12693
RNA recognition motif 2 (RRM2) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) ...
 166-260 9.86e-29

RNA recognition motif 2 (RRM2) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins; This subfamily corresponds to the RRM2 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).


Pssm-ID: 410093 [Multi-domain]  Cd Length: 96  Bit Score: 109.36  E-value: 9.86e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941 166 NKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNG-IQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARP 244
Cdd:cd12693   1 NPVLRVIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNqFQALIQFADAVSAQAAKLSLDGQNIYNGCCTLRIDFSKL 80

                        90
                ....*....|....*.
gi 62286941 245 TRLNVIRNDNDSWDYT 260
Cdd:cd12693  81 TSLNVKYNNDKSRDYT 96
RRM4_hnRNPL cd12704
RNA recognition motif 4 (RRM4) found in vertebrate heterogeneous nuclear ribonucleoprotein L ...
 452-536 4.89e-26

RNA recognition motif 4 (RRM4) found in vertebrate heterogeneous nuclear ribonucleoprotein L (hnRNP-L); This subgroup corresponds to the RRM4 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 with 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).


Pssm-ID: 410103  Cd Length: 84  Bit Score: 101.51  E-value: 4.89e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941 452 PSCVLHYYNVPLCVTEETFTKLCNDHEVLTFIKYKVFDAKpSAKTLSGLLEWECKTDAVEALTALNHYQIRVPNGSNPYT 531
Cdd:cd12704   1 PSNVLHFFNAPPEVTEENFFEICDELGVKRPTSVKVFSGK-SERSSSGLLEWDSKSDALETLGLLNHYQMKNPNGPYPYT 79


                ....*
gi 62286941 532 LKLCF 536
Cdd:cd12704  80 LKLCF 84
RRM1_PTBP1_hnRNPL_like cd12421
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
 77-150 5.12e-26

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.


Pssm-ID: 409855 [Multi-domain]  Cd Length: 74  Bit Score: 101.11  E-value: 5.12e-26
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62286941  77 VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQQAFFNYSTS 150
Cdd:cd12421   1 VVHIRNLPPDATEADLVALGLPFGKVTNVLLLKGKNQALVEMEDVESASSMVNYYTTVPPLIRGRPVYVQYSNH 74
RRM2_PTBPH3 cd12692
RNA recognition motif 2 (RRM2) found in plant polypyrimidine tract-binding protein homolog 3 ...
 166-249 6.35e-24

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).


Pssm-ID: 410092 [Multi-domain]  Cd Length: 88  Bit Score: 95.78  E-value: 6.35e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941 166 NKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRN-GIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARP 244
Cdd:cd12692   2 NRILLVTIHHPLYPITVDVLHQVFSPHGFVEKIVTFQKSaGLQALIQYQSQQSAVQARSALQGRNIYDGCCQLDIQFSNL 81


                ....*
gi 62286941 245 TRLNV 249
Cdd:cd12692  82 QELQV 86
RRM3_PTBPH1_PTBPH2 cd12690
RNA recognition motif 3 (RRM3) found in plant polypyrimidine tract-binding protein homolog 1 ...
 168-260 1.90e-22

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).


Pssm-ID: 410091 [Multi-domain]  Cd Length: 97  Bit Score: 91.85  E-value: 1.90e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941 168 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRN-GIQAMVEFESVLCAQKAKAALNGADIY-AGCCTLKIEYARPT 245
Cdd:cd12690   3 VLLASIENMQYAVTLDVLHTVFSAFGFVQKIAIFEKNgGFQALIQYPDVPTAVVAKEALEGHCIYdGGYCKLHLSYSRHT 82

                        90
                ....*....|....*
gi 62286941 246 RLNVIRNDNDSWDYT 260
Cdd:cd12690  83 DLNVKVNNDRSRDYT 97
RRM2_PTBP1 cd12782
RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein 1 (PTB) ...
 163-268 4.99e-22

RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein 1 (PTB); This subgroup corresponds to the RRM2 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.


Pssm-ID: 410174 [Multi-domain]  Cd Length: 108  Bit Score: 90.92  E-value: 4.99e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941 163 SGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIF-KRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEY 241
Cdd:cd12782   2 AGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFtKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF 81

                        90       100
                ....*....|....*....|....*..
gi 62286941 242 ARPTRLNVIRNDNDSWDYTKPYLGRRD 268
Cdd:cd12782  82 SKLTSLNVKYNNDKSRDYTRPDLPSGD 108
RRM2_PTBP2 cd12783
RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein 2 ...
 168-268 3.86e-21

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).


Pssm-ID: 410175 [Multi-domain]  Cd Length: 107  Bit Score: 88.53  E-value: 3.86e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941 168 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIF-KRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTR 246
Cdd:cd12783   3 VLRIIIDNMYYPVTLDVLHQIFSKFGTVLKIITFtKNNQFQALLQYGDPVNAQQAKLALDGQNIYNACCTLRIDFSKLVN 82

                        90       100
                ....*....|....*....|..
gi 62286941 247 LNVIRNDNDSWDYTKPYLGRRD 268
Cdd:cd12783  83 LNVKYNNDKSRDYTRPDLPSGD 104
RRM2_ROD1 cd12784
RNA recognition motif 2 (RRM2) found in vertebrate regulator of differentiation 1 (Rod1); This ...
 164-261 1.32e-18

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.


Pssm-ID: 410176 [Multi-domain]  Cd Length: 108  Bit Score: 81.20  E-value: 1.32e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941 164 GGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIF-KRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA 242
Cdd:cd12784   1 GQSPVLRIIVENLFYPVTLEVLHQIFSKFGTVLKIITFtKNNQFQALLQYADPMNAHHAKVALDGQNIYNACCTLRIEFS 80

                        90
                ....*....|....*....
gi 62286941 243 RPTRLNVIRNDNDSWDYTK 261
Cdd:cd12784  81 KLTSLNVKYNNDKSRDFTR 99
RRM3_PTBPH3 cd12698
RNA recognition motif 3 (RRM3) found in plant polypyrimidine tract-binding protein homolog 3 ...
 335-408 3.28e-18

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).


Pssm-ID: 410098 [Multi-domain]  Cd Length: 76  Bit Score: 78.94  E-value: 3.28e-18
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62286941 335 SVVMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNVCVSK 408
Cdd:cd12698   2 PVLLVSNLNPEKVDVDKLFNLFSLYGNIVRIKILRNKPDHALIQMSDPFQAELAVNYLKGAMLFGKSLEVNFSK 75
RRM3_PTBP1_like cd12423
RNA recognition motif 3 (RRM3) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) ...
 336-408 1.59e-14

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).


Pssm-ID: 409857 [Multi-domain]  Cd Length: 74  Bit Score: 68.41  E-value: 1.59e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62286941 336 VVMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNVCVSK 408
Cdd:cd12423   1 VLLVSNLNEEMVTPDALFTLFGVYGDVLRVKILFNKKDTALIQMADPQQAQTALQHLNGIKLFGKPIRVTLSK 73
RRM3_PTBP2 cd12696
RNA recognition motif 3 (RRM3) found in vertebrate polypyrimidine tract-binding protein 2 ...
 330-412 1.62e-11

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).


Pssm-ID: 410096 [Multi-domain]  Cd Length: 107  Bit Score: 61.16  E-value: 1.62e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941 330 GNPSGSVVMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNVCVSKQ 409
Cdd:cd12696   9 SAGGNTVLLVSNLNEEMVTPQSLFTLFGVYGDVQRVKILYNKKDSALIQMADGNQSQLAMSHLNGQKMYGKIIRVTLSKH 88


                ...
gi 62286941 410 HSV 412
Cdd:cd12696  89 QTV 91
RRM3_PTBP1 cd12695
RNA recognition motif 3 (RRM3) found in vertebrate polypyrimidine tract-binding protein 1 (PTB) ...
 336-427 4.96e-10

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.


Pssm-ID: 410095 [Multi-domain]  Cd Length: 93  Bit Score: 56.55  E-value: 4.96e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941 336 VVMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNVCVSKQHSV-VP 414
Cdd:cd12695   1 VLLVSNLNPERVTPQCLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGQKLHGKPIRITLSKHQTVqLP 80

                        90
                ....*....|...
gi 62286941 415 SQIFELEDGTSSY 427
Cdd:cd12695  81 REGQEDQGLTKDY 93
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 337-404 6.61e-10

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).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 55.37  E-value: 6.61e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 62286941 337 VMVSGLHQlKMNCSRVFNLFCLYGNIEKVKFMKTI----PGTALVEMGDEYAVERAVTHLNNVKLFGKRLNV 404
Cdd:cd00590   1 LFVGNLPP-DTTEEDLRELFSKFGEVVSVRIVRDRdgksKGFAFVEFESPEDAEKALEALNGTELGGRPLKV 71
RRM_8 pfam11835
RRM-like domain; This domain is related to the RRM domains suggesting it may have an ...
 168-244 6.77e-10

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


Pssm-ID: 432114  Cd Length: 89  Bit Score: 55.93  E-value: 6.77e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62286941   168 VLLLSIQNPLYPITVDVLYTVCNPVGKVQ-RIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARP 244
Cdd:pfam11835  12 VLRVTVSHILYPVTSEVLHQVYDTYGAVAvQVLAVSTWHVEALVSFMSSCDAERARSATHGRNIYDGGCLLDVQHAQP 89
RRM2_PTBPH1_PTBPH2 cd12691
RNA recognition motif 2 (RRM2) found in plant polypyrimidine tract-binding protein homolog 1 ...
 168-249 1.62e-09

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).


Pssm-ID: 241135 [Multi-domain]  Cd Length: 95  Bit Score: 54.85  E-value: 1.62e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941 168 VLLLSIQN-PLYPITVDVLYTVCNPVGKVQRIVIF-KRNGIQAMVEFESVLCAQKAKAALNGADI-------YAGCCTLK 238
Cdd:cd12691   3 VLLVTIEGvEAGDVSIDVLHLVFSAFGFVHKIATFeKTAGFQALVQFTDAETASAARSALDGRSIpryllpeHVGPCSLR 82

                        90
                ....*....|.
gi 62286941 239 IEYARPTRLNV 249
Cdd:cd12691  83 ISYSAHTDLNV 93
RRM3_ROD1 cd12697
RNA recognition motif 3 (RRM3) found in vertebrate regulator of differentiation 1 (Rod1); This ...
 335-410 6.82e-09

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.


Pssm-ID: 410097 [Multi-domain]  Cd Length: 76  Bit Score: 52.66  E-value: 6.82e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62286941 335 SVVMVSGLHQLKMNCSRVFNLFCLYGNIEKVKFMKTIPGTALVEMGDEYAVERAVTHLNNVKLFGKRLNVCVSKQH 410
Cdd:cd12697   1 SVLLVSNLNPDAITPHGLFILFGVYGDVLRVKIMFNKKENALVQMADATQAQIAMSHLNGQRLYGKVLRATLSKHQ 76
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 78-128 5.60e-08

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).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 49.97  E-value: 5.60e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 62286941  78 VHVRGLCESVVEADLVEALEKFGTICYVMMMP-----FKRQALVEFENIDSAKECV 128
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRdrdgkSKGFAFVEFESPEDAEKAL 56
RRM smart00360
RNA recognition motif;
336-404 8.12e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 49.51  E-value: 8.12e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62286941    336 VVMVSGLHQlKMNCSRVFNLFCLYGNIEKVKFMKTIP-----GTALVEMGDEYAVERAVTHLNNVKLFGKRLNV 404
Cdd:smart00360   1 TLFVGNLPP-DTTEEELRELFSKFGKVESVRLVRDKEtgkskGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM smart00360
RNA recognition motif;
77-128 5.81e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 47.20  E-value: 5.81e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 62286941     77 VVHVRGLCESVVEADLVEALEKFGTICYVMMMP------FKRQALVEFENIDSAKECV 128
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRdketgkSKGFAFVEFESEEDAEKAL 58
RRM1_PTBPH3 cd12687
RNA recognition motif 1 (RRM1) found in plant polypyrimidine tract-binding protein homolog 3 ...
 77-149 1.04e-06

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).


Pssm-ID: 410088 [Multi-domain]  Cd Length: 75  Bit Score: 46.40  E-value: 1.04e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62286941  77 VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQQAFFNYST 149
Cdd:cd12687   2 VLHVRNVGHEISENDLLQLAQPFGVVTKLVMLRAKNQALLQMQDVSAAISALQFYTSVQPSIRGRNVYIQFSS 74
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 171-240 1.30e-06

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).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 46.12  E-value: 1.30e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62286941 171 LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQ----AMVEFESVLCAQKAKAALNGADIyaGCCTLKIE 240
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKskgfAFVEFESPEDAEKALEALNGTEL--GGRPLKVS 72
RRM1_2_MATR3_like cd12436
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in the matrin 3 family of nuclear proteins; ...
 77-141 8.95e-06

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.


Pssm-ID: 409870 [Multi-domain]  Cd Length: 76  Bit Score: 43.87  E-value: 8.95e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62286941  77 VVHVRGLCES-VVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQ 141
Cdd:cd12436   2 VLYLTGLPVSkYSEEDVLKLAEPFGKVNNVLLIRSKREAFIEMETAEDAQAMLSYCKTKPITIKGK 67
RRM1_PTBP1 cd12777
RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 1 (PTB) ...
 77-153 9.16e-06

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.


Pssm-ID: 410169 [Multi-domain]  Cd Length: 81  Bit Score: 43.82  E-value: 9.16e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62286941  77 VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQQAFFNYSTSKRI 153
Cdd:cd12777   2 VIHVRKLPNDVTEAEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKEL 78
RRM1_PTBPH1_PTBPH2 cd12686
RNA recognition motif 1 (RRM1) found in plant polypyrimidine tract-binding protein homolog 1 ...
 75-149 1.09e-05

RNA recognition motif 1 (RRM1) found in plant polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2); This subfamily corresponds to the RRM1 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).


Pssm-ID: 410087 [Multi-domain]  Cd Length: 81  Bit Score: 43.64  E-value: 1.09e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62286941  75 SPVVHVRGLCESVVEADLVEALEKFGTICYVMMM--PFKRQALVEFENIDSAKECVTFAAD--EPVYIAGQQAFFNYST 149
Cdd:cd12686   2 SKVLHLRNLPWECTEEELIELCKPFGTVVNTKCNvgANKNQAFVEFADLNQAISMVSYYASssEPAQVRGKTVYLQYSN 80
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 80-128 1.33e-05

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.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 42.99  E-value: 1.33e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 62286941    80 VRGLCESVVEADLVEALEKFGTICYVMMMP-----FKRQALVEFENIDSAKECV 128
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGPIKSIRLVRdetgrSKGFAFVEFEDEEDAEKAI 56
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 178-231 3.16e-05

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.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 41.83  E-value: 3.16e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 62286941   178 YPITVDVLYTVCNPVGKVQRIVIFKRNGIQAM----VEFESVLCAQKAKAALNGADIY 231
Cdd:pfam00076   8 PDTTEEDLKDLFSKFGPIKSIRLVRDETGRSKgfafVEFEDEEDAEKAIEALNGKELG 65
RRM smart00360
RNA recognition motif;
178-231 4.78e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 41.43  E-value: 4.78e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 62286941    178 YPITVDVLYTVCNPVGKVQRIVIFK-----RNGIQAMVEFESVLCAQKAKAALNGADIY 231
Cdd:smart00360   9 PDTTEEELRELFSKFGKVESVRLVRdketgKSKGFAFVEFESEEDAEKALEALNGKELD 67
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 15-233 1.64e-04

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.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 44.14  E-value: 1.64e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941    15 DREYESQAKRLKTEEGEIDYSAEEGENRREatPRGGGDGGGGGRSFSQPEAGGSHHKVSVSP------VVHVRGLCESVV 88
Cdd:TIGR01622  50 DRDYYRGRERRSRSRRPNRRYRPREKRRRR--GDSYRRRRDDRRSRREKPRARDGTPEPLTEderdrrTVFVQQLAARAR 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941    89 EADLVEALEKFGTICYVMMMPFKRQ------ALVEFENIDSAKECVTFAA----DEPVYIAGQQAFFNYSTSKRITRPGN 158
Cdd:TIGR01622 128 ERDLYEFFSKVGKVRDVQIIKDRNSrrskgvGYVEFYDVDSVQAALALTGqkllGIPVIVQLSEAEKNRAARAATETSGH 207

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941   159 TDDPSGGNKvllLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-RNGIQA----MVEFESVLCAQKAKAALNGADIyAG 233
Cdd:TIGR01622 208 HPNSIPFHR---LYVGNLHFNITEQDLRQIFEPFGEIEFVQLQKdPETGRSkgygFIQFRDAEQAKEALEKMNGFEL-AG 283
RRM1_ROD1 cd12779
RNA recognition motif 1 (RRM1) found in vertebrate regulator of differentiation 1 (Rod1); This ...
 73-153 1.96e-04

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.


Pssm-ID: 410171 [Multi-domain]  Cd Length: 90  Bit Score: 40.39  E-value: 1.96e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62286941  73 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQQAFFNYSTSKR 152
Cdd:cd12779   3 SPSRVLHIRKIPNDVTEAEVISLGLPFGKVTNLLMLKGKNQAFLEMASEEAAVTMVNYYTTVTPHLRNQPVYIQYSNHRE 82


                .
gi 62286941 153 I 153
Cdd:cd12779  83 L 83
RRM4_PTBPH3 cd12426
RNA recognition motif 4 (RRM4) found in plant polypyrimidine tract-binding protein homolog 3 ...
 73-126 3.15e-04

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).


Pssm-ID: 409860 [Multi-domain]  Cd Length: 79  Bit Score: 39.49  E-value: 3.15e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 62286941  73 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMM--MPFKRQALVEFENIDSAKE 126
Cdd:cd12426   5 SPTKMIHVSSLPQDVTEEDVLNHLQEHGAIVNTKVfeSNGKKQALVLFENEEQATE 60
RRM1_PTBP2 cd12778
RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 2 ...
 75-153 4.37e-04

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).


Pssm-ID: 410170 [Multi-domain]  Cd Length: 82  Bit Score: 39.27  E-value: 4.37e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62286941  75 SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQQAFFNYSTSKRI 153
Cdd:cd12778   1 SRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYTAVTPHLRNQPIYIQYSNHKEL 79
RRM1_RBM26_like cd12257
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar ...
 97-136 5.66e-04

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.


Pssm-ID: 409702 [Multi-domain]  Cd Length: 72  Bit Score: 38.70  E-value: 5.66e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 62286941  97 EKFGTICYVMMMPFKRQALVEFENIDSAKECvtFAADEPV 136
Cdd:cd12257  24 SKFGTIVNIQVNYNPESALVQFSTSEEANKA--YRSPEAV 61
RRM1_PTBP1_like cd12688
RNA recognition motif 1 (RRM1) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) ...
 77-153 1.04e-03

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).


Pssm-ID: 410089 [Multi-domain]  Cd Length: 81  Bit Score: 38.06  E-value: 1.04e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62286941  77 VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYIAGQQAFFNYSTSKRI 153
Cdd:cd12688   2 VLHIRKLPCDVTEAEVISLGLPFGKVTNLLMLKGKNQAFLEMATEEAAVTMVNYYTPVTPHLRSQPIYIQYSNHKEL 78
RRM2_MRN1 cd12523
RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This ...
 78-145 1.31e-03

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).


Pssm-ID: 409943 [Multi-domain]  Cd Length: 78  Bit Score: 37.80  E-value: 1.31e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62286941  78 VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADEPVYiAGQQAFF 145
Cdd:cd12523   6 VYLGNLPESITEEELREDLEKFGPIDQIKIVKEKNIAFVHFLSIANAIKVVTTLPLNPKW-AKRRIYY 72
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
 185-243 1.80e-03

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.


Pssm-ID: 409692 [Multi-domain]  Cd Length: 78  Bit Score: 37.13  E-value: 1.80e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 62286941 185 LYTVCNPVGKVQRIVIFKRNGI--QAMVEFESVLCAQKAKAALNGADIYAGccTLKIEYAR 243
Cdd:cd12246  20 LYALFSQFGPVLDIVASKSLKMrgQAFVVFKDVESATNALRALQGFPFYGK--PMRIQYAK 78
RRM2_TatSF1_like cd12282
RNA recognition motif 2 (RRM2) found in HIV Tat-specific factor 1 (Tat-SF1) and similar ...
 177-241 4.78e-03

RNA recognition motif 2 (RRM2) found in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins; This subfamily corresponds to the RRM2 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well.


Pssm-ID: 409724 [Multi-domain]  Cd Length: 91  Bit Score: 36.45  E-value: 4.78e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62286941 177 LYPITVDVLYTVCNPVGKVQRIVIFKRN--GIqAMVEFESVLCAQKAKAALNGadIYAGCCTLKIEY 241
Cdd:cd12282  21 LINEIKEDLREECEKFGQVKKVVVFDRHpdGV-ASVKFKEPEEADKCIQALNG--RWFAGRKLEAET 84
RRM_ALKBH8 cd12431
RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and ...
 82-126 5.01e-03

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.


Pssm-ID: 409865 [Multi-domain]  Cd Length: 80  Bit Score: 36.02  E-value: 5.01e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 62286941  82 GLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKE 126
Cdd:cd12431  10 GLGNGVSREQLLEVFEKYGTVEDIVMLPGKPYSFVSFKSVEEAAK 54
RRM3_RBM39_like cd12285
RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar ...
 189-227 6.53e-03

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.


Pssm-ID: 409727 [Multi-domain]  Cd Length: 85  Bit Score: 35.99  E-value: 6.53e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 62286941 189 CNPVGKVQRIVIFKRN--GIqAMVEFESVLCAQKAKAALNG 227
Cdd:cd12285  32 CSKYGPVLHIYVDKNSpqGN-VYVKFKTIEAAQKCVQAMNG 71
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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