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Conserved domains on  [gi|149047906|gb|EDM00522|]
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spermatid perinuclear RNA binding protein, isoform CRA_b [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DZF smart00572
domain in DSRM or ZnF_C2H2 domain containing proteins;
81-334 7.42e-144

domain in DSRM or ZnF_C2H2 domain containing proteins;


:

Pssm-ID: 128842  Cd Length: 246  Bit Score: 417.93  E-value: 7.42e-144
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149047906    81 TLCGVMRIGLVAKGLLIKDDMDLELVLMCKDKPTETLLNTVKDNLPIQIQKLTEEkyqveqcinEASIIIRNTKEPTLTL 160
Cdd:smart00572   1 TLKGVMRVGSFAKGTLLKGDNVAELVLLCKEKPTSELVARLARKLPEQLKAVTED---------EALIIVTSTKEPTMEV 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149047906   161 KVILTSPLIRDELEKK-DGENVMMKDPPDLLDRQKCLNALASLRHAKWFQARANGLKSCVIVLRILRDLCNRVPTWAPLK 239
Cdd:smart00572  72 GILITSPLARVELLITtVPENLRKLDPEDHLDRKKCLSALASLRHAKWFQARASGLQSCVIVIRVLRDLCNRVPTWQPLS 151

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149047906   240 GWPLELICEKSIGTCNRPLGAGEALRRVMECLASGILLPGGPGLHDPCERDPTDALSYMTTQQKEDITHSAQHALRLSAF 319
Cdd:smart00572 152 GWPLELLVEKAIGSARQPLGLGDAFRRVFECLASGILLPGSPGLTDPCEKDNTDALTALTLQQREDVTASAQTALRLLAF 231

                          250
                   ....*....|....*
gi 149047906   320 GQIYKVLEMDPLPSS 334
Cdd:smart00572 232 GQIHKILGMDPLPSM 246
DSRM_STRBP_rpt1 cd19909
first double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...
 384-467 1.07e-56

first double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) and similar proteins; STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. STRBP contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


:

Pssm-ID: 380738  Cd Length: 84  Bit Score: 186.39  E-value: 1.07e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149047906 384 KAIDLMNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGYPTGFDADIEC 463
Cdd:cd19909    1 DANQPMNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGYPTGFDTDLEC 80


                 ....
gi 149047906 464 MSSD 467
Cdd:cd19909   81 MSSD 84
DSRM_STRBP_rpt2 cd19911
second double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...
 512-575 3.59e-34

second double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) and similar proteins; STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. STRBP contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


:

Pssm-ID: 380740  Cd Length: 64  Bit Score: 124.09  E-value: 3.59e-34
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 149047906 512 KNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEKLF 575
Cdd:cd19911    1 KNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEKLF 64
 
Name Accession Description Interval E-value
DZF smart00572
domain in DSRM or ZnF_C2H2 domain containing proteins;
81-334 7.42e-144

domain in DSRM or ZnF_C2H2 domain containing proteins;


Pssm-ID: 128842  Cd Length: 246  Bit Score: 417.93  E-value: 7.42e-144
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149047906    81 TLCGVMRIGLVAKGLLIKDDMDLELVLMCKDKPTETLLNTVKDNLPIQIQKLTEEkyqveqcinEASIIIRNTKEPTLTL 160
Cdd:smart00572   1 TLKGVMRVGSFAKGTLLKGDNVAELVLLCKEKPTSELVARLARKLPEQLKAVTED---------EALIIVTSTKEPTMEV 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149047906   161 KVILTSPLIRDELEKK-DGENVMMKDPPDLLDRQKCLNALASLRHAKWFQARANGLKSCVIVLRILRDLCNRVPTWAPLK 239
Cdd:smart00572  72 GILITSPLARVELLITtVPENLRKLDPEDHLDRKKCLSALASLRHAKWFQARASGLQSCVIVIRVLRDLCNRVPTWQPLS 151

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149047906   240 GWPLELICEKSIGTCNRPLGAGEALRRVMECLASGILLPGGPGLHDPCERDPTDALSYMTTQQKEDITHSAQHALRLSAF 319
Cdd:smart00572 152 GWPLELLVEKAIGSARQPLGLGDAFRRVFECLASGILLPGSPGLTDPCEKDNTDALTALTLQQREDVTASAQTALRLLAF 231

                          250
                   ....*....|....*
gi 149047906   320 GQIYKVLEMDPLPSS 334
Cdd:smart00572 232 GQIHKILGMDPLPSM 246
DZF pfam07528
DZF domain; The function of this domain is unknown. It is often found associated with ...
 87-333 1.86e-91

DZF domain; The function of this domain is unknown. It is often found associated with pfam00098 or pfam00035. This domain has been predicted to belong to the nucleotidyltransferase superfamily.


Pssm-ID: 284860  Cd Length: 248  Bit Score: 283.31  E-value: 1.86e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149047906   87 RIGLVAKGLLIKDDMDLELVLMCKDKPTETLLNTVKDNLPIQIQKLTEEKYQVEQcinEASIIIRNTKEPTLTLKVILTS 166
Cdd:pfam07528   1 QVGSFKKGTLLKGSNVADVVVILKTLPTTELVDALAKKVEEDLKTSMKTEILQSV---EALIVIKNTKEPPLELGFHITS 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149047906  167 PLIRDELEKKD-GENVMMKDPPDLLDRQKCLNALASLRHAKWFQARANGLKSCVIVLRILRDLCNRVPTWAPLKGWPLEL 245
Cdd:pfam07528  78 PVAKVRMLIATlPENLRKLEPEDHLDRKKMQSHLASIRHTRWFEENAHHLKSIKVLIRVLKDLCRRFDTFGPLSGWPLDL 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149047906  246 ICEKSIG--TCNRPLGAGEALRRVMECLASGILLPGGPGLHDPCERDPTDALSYMTTQQKEDITHSAQHALRLSAFGQIY 323
Cdd:pfam07528 158 LAHKAIMnnPSRQALPAGEAFRRVFELLASGIFLPGSAGITDPCEKGHTRVHTHLTLQQQDDCCMTAQTLLRVLAHGGYK 237

                         250
                  ....*....|
gi 149047906  324 KVLEMDPLPS 333
Cdd:pfam07528 238 HILGMDGNTS 247
DSRM_STRBP_rpt1 cd19909
first double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...
 384-467 1.07e-56

first double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) and similar proteins; STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. STRBP contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380738  Cd Length: 84  Bit Score: 186.39  E-value: 1.07e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149047906 384 KAIDLMNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGYPTGFDADIEC 463
Cdd:cd19909    1 DANQPMNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGYPTGFDTDLEC 80


                 ....
gi 149047906 464 MSSD 467
Cdd:cd19909   81 MSSD 84
DSRM_STRBP_rpt2 cd19911
second double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...
 512-575 3.59e-34

second double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) and similar proteins; STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. STRBP contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380740  Cd Length: 64  Bit Score: 124.09  E-value: 3.59e-34
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 149047906 512 KNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEKLF 575
Cdd:cd19911    1 KNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEKLF 64
DSRM smart00358
Double-stranded RNA binding motif;
389-452 8.50e-14

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 66.52  E-value: 8.50e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 149047906   389 MNALMRLNQIRP-GLQYKLLSQSGPVHAPVFTMSVDVDGT-TYEASGPSKKTAKLHVAVKVLQAMG 452
Cdd:smart00358   2 KSLLQELAQKRKlPPEYELVKEEGPDHAPRFTVTVKVGGKrTGEGEGSSKKEAKQRAAEAALRSLK 67
DSRM smart00358
Double-stranded RNA binding motif;
512-558 3.60e-10

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 56.12  E-value: 3.60e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 149047906   512 KNPVMELNEKRR-GLKYELISETGGSHDKRFVMEVEVDG-QKFRGAGPN 558
Cdd:smart00358   2 KSLLQELAQKRKlPPEYELVKEEGPDHAPRFTVTVKVGGkRTGEGEGSS 50
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 389-449 3.98e-09

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 53.00  E-value: 3.98e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 149047906  389 MNALMRLNQ-IRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTY-EASGPSKKTAKLHVAVKVLQ 449
Cdd:pfam00035   2 KSLLQEYAQkNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYgSGTGSSKKEAEQLAAEKALE 64
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
403-452 6.17e-07

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 50.87  E-value: 6.17e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 149047906 403 QYKLLSQSGPVHAPVFTMSVDVDGTTY-EASGPSKKTAKLHVAVKVLQAMG 452
Cdd:COG0571  176 EYEVVEEEGPDHAKTFTVEVLVGGKVLgEGTGRSKKEAEQAAAKAALEKLG 226
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 514-558 1.71e-05

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 42.99  E-value: 1.71e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 149047906  514 PVMELNE----KRRGLKYELISETGGSHDKRFVMEVEVDGQKF-RGAGPN 558
Cdd:pfam00035   1 PKSLLQEyaqkNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYgSGTGSS 50
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
522-558 7.03e-05

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 44.70  E-value: 7.03e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 149047906 522 RRGL---KYELISETGGSHDKRFVMEVEVDGQKF-RGAGPN 558
Cdd:COG0571  169 ARGLplpEYEVVEEEGPDHAKTFTVEVLVGGKVLgEGTGRS 209
PHA03103 PHA03103
double-strand RNA-binding protein; Provisional
 407-440 9.99e-03

double-strand RNA-binding protein; Provisional


Pssm-ID: 222987 [Multi-domain]  Cd Length: 183  Bit Score: 37.82  E-value: 9.99e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 149047906 407 LSQSGPVHAPVFTMSVDVDGTTYE-ASGPSKKTAK 440
Cdd:PHA03103 130 ITSSGPSHSPTFTASVIISGIKFKpAIGSTKKEAK 164
 
Name Accession Description Interval E-value
DZF smart00572
domain in DSRM or ZnF_C2H2 domain containing proteins;
81-334 7.42e-144

domain in DSRM or ZnF_C2H2 domain containing proteins;


Pssm-ID: 128842  Cd Length: 246  Bit Score: 417.93  E-value: 7.42e-144
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149047906    81 TLCGVMRIGLVAKGLLIKDDMDLELVLMCKDKPTETLLNTVKDNLPIQIQKLTEEkyqveqcinEASIIIRNTKEPTLTL 160
Cdd:smart00572   1 TLKGVMRVGSFAKGTLLKGDNVAELVLLCKEKPTSELVARLARKLPEQLKAVTED---------EALIIVTSTKEPTMEV 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149047906   161 KVILTSPLIRDELEKK-DGENVMMKDPPDLLDRQKCLNALASLRHAKWFQARANGLKSCVIVLRILRDLCNRVPTWAPLK 239
Cdd:smart00572  72 GILITSPLARVELLITtVPENLRKLDPEDHLDRKKCLSALASLRHAKWFQARASGLQSCVIVIRVLRDLCNRVPTWQPLS 151

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149047906   240 GWPLELICEKSIGTCNRPLGAGEALRRVMECLASGILLPGGPGLHDPCERDPTDALSYMTTQQKEDITHSAQHALRLSAF 319
Cdd:smart00572 152 GWPLELLVEKAIGSARQPLGLGDAFRRVFECLASGILLPGSPGLTDPCEKDNTDALTALTLQQREDVTASAQTALRLLAF 231

                          250
                   ....*....|....*
gi 149047906   320 GQIYKVLEMDPLPSS 334
Cdd:smart00572 232 GQIHKILGMDPLPSM 246
DZF pfam07528
DZF domain; The function of this domain is unknown. It is often found associated with ...
 87-333 1.86e-91

DZF domain; The function of this domain is unknown. It is often found associated with pfam00098 or pfam00035. This domain has been predicted to belong to the nucleotidyltransferase superfamily.


Pssm-ID: 284860  Cd Length: 248  Bit Score: 283.31  E-value: 1.86e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149047906   87 RIGLVAKGLLIKDDMDLELVLMCKDKPTETLLNTVKDNLPIQIQKLTEEKYQVEQcinEASIIIRNTKEPTLTLKVILTS 166
Cdd:pfam07528   1 QVGSFKKGTLLKGSNVADVVVILKTLPTTELVDALAKKVEEDLKTSMKTEILQSV---EALIVIKNTKEPPLELGFHITS 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149047906  167 PLIRDELEKKD-GENVMMKDPPDLLDRQKCLNALASLRHAKWFQARANGLKSCVIVLRILRDLCNRVPTWAPLKGWPLEL 245
Cdd:pfam07528  78 PVAKVRMLIATlPENLRKLEPEDHLDRKKMQSHLASIRHTRWFEENAHHLKSIKVLIRVLKDLCRRFDTFGPLSGWPLDL 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149047906  246 ICEKSIG--TCNRPLGAGEALRRVMECLASGILLPGGPGLHDPCERDPTDALSYMTTQQKEDITHSAQHALRLSAFGQIY 323
Cdd:pfam07528 158 LAHKAIMnnPSRQALPAGEAFRRVFELLASGIFLPGSAGITDPCEKGHTRVHTHLTLQQQDDCCMTAQTLLRVLAHGGYK 237

                         250
                  ....*....|
gi 149047906  324 KVLEMDPLPS 333
Cdd:pfam07528 238 HILGMDGNTS 247
DSRM_STRBP_rpt1 cd19909
first double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...
 384-467 1.07e-56

first double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) and similar proteins; STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. STRBP contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380738  Cd Length: 84  Bit Score: 186.39  E-value: 1.07e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149047906 384 KAIDLMNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGYPTGFDADIEC 463
Cdd:cd19909    1 DANQPMNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGYPTGFDTDLEC 80


                 ....
gi 149047906 464 MSSD 467
Cdd:cd19909   81 MSSD 84
DSRM_STRBP-like_rpt1 cd19894
first double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family ...
 389-451 4.80e-41

first double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3). STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. Members of this STRBP/ILF3 group contain an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380723  Cd Length: 63  Bit Score: 143.29  E-value: 4.80e-41
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 149047906 389 MNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAM 451
Cdd:cd19894    1 MNALMRLNQLRPGLQYKLASQTGPVHAPQFTMSVEVDGVTYEASGPSKKTAKLHVAVKVLQAM 63
DSRM_ILF3_rpt1 cd19910
first double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and ...
 389-456 1.56e-38

first double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and similar proteins; ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. ILF3 contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380739  Cd Length: 73  Bit Score: 136.81  E-value: 1.56e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 149047906 389 MNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGYPTG 456
Cdd:cd19910    6 MNALMRLNQLKPGLQYKLISQTGPVHAPVFTMSVEVDGKTFEASGPSKKTAKLHVAVKVLQDMGLPTG 73
DSRM_STRBP_rpt2 cd19911
second double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...
 512-575 3.59e-34

second double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) and similar proteins; STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. STRBP contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380740  Cd Length: 64  Bit Score: 124.09  E-value: 3.59e-34
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 149047906 512 KNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEKLF 575
Cdd:cd19911    1 KNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEKLF 64
DSRM_STRBP_RED-like_rpt1 cd19865
first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 389-451 1.38e-33

first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3), as well as two RNA-editing deaminases, RED1 and RED2. STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. RED1 (EC 3.5.4.37; also called double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. RED2 (also called double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA, but also to ssRNA. RED2 lacks editing activity for currently known substrate RNAs. Members of this group contain two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380694  Cd Length: 63  Bit Score: 122.46  E-value: 1.38e-33
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 149047906 389 MNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAM 451
Cdd:cd19865    1 KNALMQLNELRPGLQYKLTSQTGPVHAPVFTMSVEVNGQTFEGTGRSKKKAKLEAAEKALRSF 63
DSRM_RED1_rpt1 cd19895
first double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins; ...
 390-450 3.14e-27

first double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins; RED1 (EC 3.5.4.37; also known as double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. It contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the first DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380724  Cd Length: 72  Bit Score: 104.78  E-value: 3.14e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 149047906 390 NALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQA 450
Cdd:cd19895    7 NALMQLNEIKPGLQYKLLSQTGPVHAPVFVMSVEVNGQVFEGSGPTKKKAKLHAAEKALRS 67
DSRM_ILF3_rpt2 cd19912
second double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and ...
 506-558 4.43e-27

second double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and similar proteins; ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. ILF3 contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380741  Cd Length: 72  Bit Score: 104.35  E-value: 4.43e-27
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 149047906 506 ILTASGKNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPN 558
Cdd:cd19912    1 ILTKHGKNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSN 53
DSRM_STRBP-like_rpt2 cd19897
second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family ...
 512-558 1.61e-25

second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3). STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. Members of this STRBP/ILF3 group contain an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380726  Cd Length: 64  Bit Score: 99.74  E-value: 1.61e-25
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 149047906 512 KNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPN 558
Cdd:cd19897    1 KNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSN 47
DSRM_STRBP_RED-like_rpt2 cd19866
second double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 512-558 2.46e-23

second double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3), as well as two RNA-editing deaminases, RED1 and RED2. STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. RED1 (EC 3.5.4.37; also called double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. RED2 (also called double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA but also to ssRNA. RED2 lacks editing activity for currently known substrate RNAs. Members of this group contain two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380695  Cd Length: 63  Bit Score: 93.39  E-value: 2.46e-23
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 149047906 512 KNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPN 558
Cdd:cd19866    1 KNPVMLLNELRPGLKYKCLSESGESHAKSFVMSVTVDGQTFEGTGRS 47
DSRM_RED2_rpt1 cd19896
first double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar proteins; ...
 390-450 4.49e-22

first double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar proteins; RED2 (also known as double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA but also to ssRNA. RED2 contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the first DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. RED2 lacks editing activity for currently known substrate RNAs, and may have an inactive editase domain.


Pssm-ID: 380725  Cd Length: 74  Bit Score: 90.15  E-value: 4.49e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 149047906 390 NALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQA 450
Cdd:cd19896    7 NALVQLNELKPGLQYRMVSQTGPVHAPVFAVAVEVNGLTFEGTGPTKKKAKMRAAEMALKS 67
DSRM_RED1_rpt2 cd19898
second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar ...
 510-558 8.25e-20

second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins; RED1 (EC 3.5.4.37; also known as double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. It contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the second DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380727  Cd Length: 70  Bit Score: 83.70  E-value: 8.25e-20
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 149047906 510 SGKNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPN 558
Cdd:cd19898    1 SGKNPVMILNELRPGLKYEFVSESGESHAKNFVMSVTVDGQTFEGSGRN 49
DSRM_STRBP_RED-like_rpt2 cd19866
second double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 390-449 4.72e-17

second double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3), as well as two RNA-editing deaminases, RED1 and RED2. STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. RED1 (EC 3.5.4.37; also called double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. RED2 (also called double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA but also to ssRNA. RED2 lacks editing activity for currently known substrate RNAs. Members of this group contain two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380695  Cd Length: 63  Bit Score: 75.67  E-value: 4.72e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 149047906 390 NALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQ 449
Cdd:cd19866    2 NPVMLLNELRPGLKYKCLSESGESHAKSFVMSVTVDGQTFEGTGRSKKLAKAAAAQAALA 61
DSRM_STRBP_RED-like_rpt1 cd19865
first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 512-557 9.58e-16

first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3), as well as two RNA-editing deaminases, RED1 and RED2. STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. RED1 (EC 3.5.4.37; also called double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. RED2 (also called double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA, but also to ssRNA. RED2 lacks editing activity for currently known substrate RNAs. Members of this group contain two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380694  Cd Length: 63  Bit Score: 71.99  E-value: 9.58e-16
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 149047906 512 KNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGP 557
Cdd:cd19865    1 KNALMQLNELRPGLQYKLTSQTGPVHAPVFTMSVEVNGQTFEGTGR 46
DSRM_RED1_rpt2 cd19898
second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar ...
 390-451 1.21e-15

second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins; RED1 (EC 3.5.4.37; also known as double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. It contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the second DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380727  Cd Length: 70  Bit Score: 71.76  E-value: 1.21e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 149047906 390 NALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAM 451
Cdd:cd19898    4 NPVMILNELRPGLKYEFVSESGESHAKNFVMSVTVDGQTFEGSGRNKKLAKARAAQAALAKL 65
DSRM smart00358
Double-stranded RNA binding motif;
389-452 8.50e-14

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 66.52  E-value: 8.50e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 149047906   389 MNALMRLNQIRP-GLQYKLLSQSGPVHAPVFTMSVDVDGT-TYEASGPSKKTAKLHVAVKVLQAMG 452
Cdd:smart00358   2 KSLLQELAQKRKlPPEYELVKEEGPDHAPRFTVTVKVGGKrTGEGEGSSKKEAKQRAAEAALRSLK 67
DSRM_RED1_rpt1 cd19895
first double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins; ...
 504-557 7.46e-13

first double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins; RED1 (EC 3.5.4.37; also known as double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. It contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the first DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380724  Cd Length: 72  Bit Score: 63.95  E-value: 7.46e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 149047906 504 GPILTasgKNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGP 557
Cdd:cd19895    1 GPVLP---KNALMQLNEIKPGLQYKLLSQTGPVHAPVFVMSVEVNGQVFEGSGP 51
DSRM_RED2_rpt2 cd19899
second double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar ...
 390-451 2.56e-12

second double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar proteins; RED2 (also known as double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA but also to ssRNA. RED2 contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the second DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. RED2 lacks editing activity for currently known substrate RNAs, and may have an inactive editase domain.


Pssm-ID: 380728  Cd Length: 74  Bit Score: 62.58  E-value: 2.56e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 149047906 390 NALMRLNQIRPGLQYKLLSQSGPV-HAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAM 451
Cdd:cd19899    8 NPVVLLNELRPGLRYVCLSETAEKqHIKSFVMAVRVDGRTFEGSGRSKKLAKAQAAQAALQAL 70
DSRM_STRBP-like_rpt2 cd19897
second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family ...
 390-451 5.75e-12

second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3). STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. Members of this STRBP/ILF3 group contain an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380726  Cd Length: 64  Bit Score: 61.22  E-value: 5.75e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 149047906 390 NALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAM 451
Cdd:cd19897    2 NPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKANAALAALEKL 63
DSRM_ILF3_rpt2 cd19912
second double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and ...
 390-451 1.16e-10

second double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and similar proteins; ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. ILF3 contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380741  Cd Length: 72  Bit Score: 57.74  E-value: 1.16e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 149047906 390 NALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAM 451
Cdd:cd19912    8 NPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKAYAALAALEKL 69
DSRM_STAU2_rpt1 cd19880
first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 388-448 1.24e-10

first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 2 (Staufen 2) and similar proteins; Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen 2 contains five double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380709  Cd Length: 68  Bit Score: 57.42  E-value: 1.24e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 149047906 388 LMNALMRLNQIRPglQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVL 448
Cdd:cd19880   10 LVNELARFNRIQP--QYKLLNERGPAHAKIFTVQLTLGEQTWEAEGSSIKKAQHAAASKAL 68
DSRM_STRBP-like_rpt1 cd19894
first double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family ...
 513-558 1.30e-10

first double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3). STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. Members of this STRBP/ILF3 group contain an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380723  Cd Length: 63  Bit Score: 57.39  E-value: 1.30e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 149047906 513 NPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPN 558
Cdd:cd19894    2 NALMRLNQLRPGLQYKLASQTGPVHAPQFTMSVEVDGVTYEASGPS 47
DSRM smart00358
Double-stranded RNA binding motif;
512-558 3.60e-10

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 56.12  E-value: 3.60e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 149047906   512 KNPVMELNEKRR-GLKYELISETGGSHDKRFVMEVEVDG-QKFRGAGPN 558
Cdd:smart00358   2 KSLLQELAQKRKlPPEYELVKEEGPDHAPRFTVTVKVGGkRTGEGEGSS 50
DSRM_RED2_rpt2 cd19899
second double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar ...
 508-556 4.19e-10

second double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar proteins; RED2 (also known as double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA but also to ssRNA. RED2 contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the second DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. RED2 lacks editing activity for currently known substrate RNAs, and may have an inactive editase domain.


Pssm-ID: 380728  Cd Length: 74  Bit Score: 56.42  E-value: 4.19e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 149047906 508 TASGKNPVMELNEKRRGLKYELISETGGS-HDKRFVMEVEVDGQKFRGAG 556
Cdd:cd19899    3 AESEKNPVVLLNELRPGLRYVCLSETAEKqHIKSFVMAVRVDGRTFEGSG 52
DSRM_STRBP_rpt2 cd19911
second double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...
 390-451 4.30e-10

second double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) and similar proteins; STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. STRBP contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380740  Cd Length: 64  Bit Score: 55.91  E-value: 4.30e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 149047906 390 NALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAM 451
Cdd:cd19911    2 NPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEKL 63
DSRM_STAU1_rpt1 cd19879
first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 388-448 5.84e-10

first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380708  Cd Length: 66  Bit Score: 55.47  E-value: 5.84e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 149047906 388 LMNALMRLNQIRPglQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVL 448
Cdd:cd19879    8 LVNELARFNKIQP--EYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTSIKKAQHAAAAKAL 66
DSRM_STAU_rpt1 cd19857
first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 388-448 6.98e-10

first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins; Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380686  Cd Length: 64  Bit Score: 55.35  E-value: 6.98e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 149047906 388 LMNALMRLNQIRPglQYKLLSQSGPVHAPVFTMSVDV-DGTTYEASGPSKKTAKLHVAVKVL 448
Cdd:cd19857    5 LLNELARFNKIRP--QYTLVDEEGPAHKKTFTVKLTLgDEEEYEASGSSIKKAQHAAAEKAL 64
DSRM_PRKRA-like_rpt1 cd19862
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 403-448 9.98e-10

first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; This family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)), participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. This family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380691 [Multi-domain]  Cd Length: 70  Bit Score: 54.96  E-value: 9.98e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 149047906 403 QYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKlHVAVKVL 448
Cdd:cd19862   19 KYELISSEGAVHEPTFTFRVTVGDITATGSGTSKKKAK-HAAAENA 63
DSRM_ILF3_rpt1 cd19910
first double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and ...
 513-558 1.36e-09

first double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and similar proteins; ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. ILF3 contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380739  Cd Length: 73  Bit Score: 54.76  E-value: 1.36e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 149047906 513 NPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPN 558
Cdd:cd19910    7 NALMRLNQLKPGLQYKLISQTGPVHAPVFTMSVEVDGKTFEASGPS 52
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 391-452 3.59e-09

double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known as Bax antagonist selected in saccharomyces 1 (BASS1), negative regulatory element-binding protein (NRE-binding protein), or protein DBP-5, or SON3) is an RNA-binding protein which acts as an mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. It specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Members of this group contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380699  Cd Length: 75  Bit Score: 53.44  E-value: 3.59e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 149047906 391 ALMRLNQIR--PGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPS--KKTAKLHVAVKVLQAMG 452
Cdd:cd19870    7 ALMELCNKRkwGPPEFRLVEESGPPHRKHFLFKVVVNGVEYQPSVASgnKKDAKAQAATVALQALG 72
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 389-449 3.98e-09

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 53.00  E-value: 3.98e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 149047906  389 MNALMRLNQ-IRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTY-EASGPSKKTAKLHVAVKVLQ 449
Cdd:pfam00035   2 KSLLQEYAQkNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYgSGTGSSKKEAEQLAAEKALE 64
DSRM_RED2_rpt1 cd19896
first double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar proteins; ...
 512-580 4.14e-09

first double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar proteins; RED2 (also known as double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA but also to ssRNA. RED2 contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the first DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. RED2 lacks editing activity for currently known substrate RNAs, and may have an inactive editase domain.


Pssm-ID: 380725  Cd Length: 74  Bit Score: 53.56  E-value: 4.14e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 149047906 512 KNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEKLFSGPNA 580
Cdd:cd19896    6 KNALVQLNELKPGLQYRMVSQTGPVHAPVFAVAVEVNGLTFEGTGPTKKKAKMRAAEMALKSFVQFPNA 74
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 400-448 4.86e-09

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis.


Pssm-ID: 380679 [Multi-domain]  Cd Length: 57  Bit Score: 52.67  E-value: 4.86e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 149047906 400 PGLQYKLLSQSGPvHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVL 448
Cdd:cd00048   10 PPPEYETVEEGGP-HNPRFTCTVTVNGQTFEGEGKSKKEAKQAAAEKAL 57
DSRM_EIF2AK2_rpt1 cd19903
first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha ...
 390-451 3.05e-08

first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. EIF2AK2 proteins contain two to three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380732  Cd Length: 68  Bit Score: 50.85  E-value: 3.05e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 149047906 390 NALMRLNQIRP----GLQYKLLSQSGPVHAPVFTMSVDVDGTTY-EASGPSKKTAKLHVAVKVLQAM 451
Cdd:cd19903    2 NYMGKLNEYCQkqkvVLDYVEVPTSGPSHDPRFTFQVVIDGKEYpEGEGKSKKEAKQAAAKLALEIL 68
DSRM_STRBP_rpt1 cd19909
first double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...
 513-558 3.81e-08

first double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) and similar proteins; STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. STRBP contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380738  Cd Length: 84  Bit Score: 51.18  E-value: 3.81e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 149047906 513 NPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPN 558
Cdd:cd19909    7 NALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPS 52
DSRM_DRADA cd19902
double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) ...
 391-451 1.05e-07

double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins; DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. DRADA family members contain at least one double-stranded RNA binding motifs (DSRM); vertebrate proteins contain three. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380731  Cd Length: 71  Bit Score: 49.21  E-value: 1.05e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 149047906 391 ALMRLNQIRP-GLQYKLLSQSGPVHAPVFTMSVDVDGTTY-EASGPSKKTAKLHVAVKVLQAM 451
Cdd:cd19902    6 ALMEYAQSRGvTAEIEVLSQSGPPHNPRFKAAVFVGGRRFpSVEASSKKDAKQEAADLALRAL 68
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
403-452 6.17e-07

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 50.87  E-value: 6.17e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 149047906 403 QYKLLSQSGPVHAPVFTMSVDVDGTTY-EASGPSKKTAKLHVAVKVLQAMG 452
Cdd:COG0571  176 EYEVVEEEGPDHAKTFTVEVLVGGKVLgEGTGRSKKEAEQAAAKAALEKLG 226
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 403-451 7.11e-07

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as ribonuclease 3) digests double-stranded RNA formed within single-strand substrates, but not RNA-DNA hybrids. It is involved in the processing of rRNA precursors, viral transcripts, some mRNAs, and at least 1 tRNA (metY, a minor form of tRNA-init-Met). It cleaves the 30S primary rRNA transcript to yield the immediate precursors to the 16S and 23S rRNAs. The cleavage can occur in assembled 30S, 50S, and even 70S subunits and is influenced by the presence of ribosomal proteins. The RNase III family also includes the mitochondrion-specific ribosomal protein mL44 subfamily, which is composed of mitochondrial 54S ribosomal protein L3 (MRPL3) and mitochondrial 39S ribosomal protein L44 (MRPL44). Members of this family contain an RNase III domain and a C-terminal double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380682 [Multi-domain]  Cd Length: 69  Bit Score: 46.72  E-value: 7.11e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 149047906 403 QYKLLSQSGPVHAPVFTMSVDVDGTTY-EASGPSKKTAKLHVAVKVLQAM 451
Cdd:cd10845   20 EYELVEEEGPDHNKTFTVEVKVNGKVIgEGTGRSKKEAEQAAAKAALEKL 69
DSRM_STAU1_rpt4 cd19885
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 389-453 1.06e-06

fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380714  Cd Length: 86  Bit Score: 47.00  E-value: 1.06e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149047906 389 MNALMRLNQIRPGL-----QYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGY 453
Cdd:cd19885   10 MNPISRLAQIQQAKkekepEYTLITERGLPRRREFVMQVKVGNQTAEGMGPNKKVAKRNAAEKMLELLGF 79
DSRM_DRADA_rpt2 cd19914
second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...
 403-448 1.80e-06

second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins; DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. Vertebrate DRADA contains three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380743  Cd Length: 71  Bit Score: 45.99  E-value: 1.80e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 149047906 403 QYKLLSQSGPVHAPVFTMSVDVDGTTY-EASGPSKKTAK---LHVAVKVL 448
Cdd:cd19914   19 EFQLLSQEGPPHDPKFTYCVKVGEQTFpSVVANSKKVAKqmaAEEAVKEL 68
DSRM_STAU_rpt4 cd19860
fourth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 390-452 4.05e-06

fourth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins; Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380689  Cd Length: 68  Bit Score: 44.63  E-value: 4.05e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 149047906 390 NALMRLNQIRPGLQ-----YKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMG 452
Cdd:cd19860    1 NPISRLIQIQQARKekepvYSLVAERGTPRRREFVMQVTVGDKTATGTGPNKKLAKRNAAEAMLELLG 68
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 511-557 7.88e-06

double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known as Bax antagonist selected in saccharomyces 1 (BASS1), negative regulatory element-binding protein (NRE-binding protein), or protein DBP-5, or SON3) is an RNA-binding protein which acts as an mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. It specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Members of this group contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380699  Cd Length: 75  Bit Score: 44.19  E-value: 7.88e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 149047906 511 GKNPV---MELNEKRR--GLKYELISETGGSHDKRFVMEVEVDGQKFRGAGP 557
Cdd:cd19870    1 GKHPVsalMELCNKRKwgPPEFRLVEESGPPHRKHFLFKVVVNGVEYQPSVA 52
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 512-558 8.84e-06

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as ribonuclease 3) digests double-stranded RNA formed within single-strand substrates, but not RNA-DNA hybrids. It is involved in the processing of rRNA precursors, viral transcripts, some mRNAs, and at least 1 tRNA (metY, a minor form of tRNA-init-Met). It cleaves the 30S primary rRNA transcript to yield the immediate precursors to the 16S and 23S rRNAs. The cleavage can occur in assembled 30S, 50S, and even 70S subunits and is influenced by the presence of ribosomal proteins. The RNase III family also includes the mitochondrion-specific ribosomal protein mL44 subfamily, which is composed of mitochondrial 54S ribosomal protein L3 (MRPL3) and mitochondrial 39S ribosomal protein L44 (MRPL44). Members of this family contain an RNase III domain and a C-terminal double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380682 [Multi-domain]  Cd Length: 69  Bit Score: 43.64  E-value: 8.84e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 149047906 512 KNPVMELNE--KRRGL---KYELISETGGSHDKRFVMEVEVDGQKF-RGAGPN 558
Cdd:cd10845    1 KDYKTALQEylQKRGLplpEYELVEEEGPDHNKTFTVEVKVNGKVIgEGTGRS 53
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 514-558 1.71e-05

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 42.99  E-value: 1.71e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 149047906  514 PVMELNE----KRRGLKYELISETGGSHDKRFVMEVEVDGQKF-RGAGPN 558
Cdd:pfam00035   1 PKSLLQEyaqkNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYgSGTGSS 50
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 408-448 2.11e-05

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; The family includes EIF2AK2 and adenosine deaminase domain-containing proteins, ADAD1 and ADAD2. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. ADAD1 (also called testis nuclear RNA-binding protein (TENR)) and ADAD2 (also called testis nuclear RNA-binding protein-like (TENRL)) are phylogenetically related to a family of adenosine deaminases involved in RNA editing. ADAD1 plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs. ADAD2 is a double-stranded RNA binding protein with unclear biological function. Members of this group contains varying numbers of double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380704  Cd Length: 67  Bit Score: 42.64  E-value: 2.11e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 149047906 408 SQSGPVHAPVFTMSVDVDGTTY-EASGPSKKTAKLH---VAVKVL 448
Cdd:cd19875   23 VSVGPDHCPGFTASATIDGIVFaSATGTSKKEAKRAaakLALKKL 67
DSRM_DRADA_rpt1 cd19913
first double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...
 403-449 2.89e-05

first double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA); DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. Vertebrate DRADA contains three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380742  Cd Length: 71  Bit Score: 42.55  E-value: 2.89e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 149047906 403 QYKLLSQSGPVHAPVFTMSVDVDGTTYE-ASGPSKKTAKLHVAVKVLQ 449
Cdd:cd19913   19 EFLLLEQSGPSHDPRFKFQAVIDGRRFPpAEASSKKVAKKDAAAIALK 66
DSRM_EIF2AK2_rpt1 cd19903
first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha ...
 513-552 6.02e-05

first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. EIF2AK2 proteins contain two to three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380732  Cd Length: 68  Bit Score: 41.61  E-value: 6.02e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 149047906 513 NPVMELNE----KRRGLKYELISETGGSHDKRFVMEVEVDGQKF 552
Cdd:cd19903    2 NYMGKLNEycqkQKVVLDYVEVPTSGPSHDPRFTFQVVIDGKEY 45
DSRM_STAU_rpt3 cd19859
third double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 402-451 6.42e-05

third double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins; Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380688  Cd Length: 65  Bit Score: 41.23  E-value: 6.42e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 149047906 402 LQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAM 451
Cdd:cd19859   16 VNFEVLRESGPPHMKNFITRCTVGSFVTEGEGNSKKVSKKRAAEKMLEEL 65
DSRM_PRKRA-like_rpt1 cd19862
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 512-557 6.99e-05

first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; This family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)), participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. This family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380691 [Multi-domain]  Cd Length: 70  Bit Score: 41.09  E-value: 6.99e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 149047906 512 KNPVMELNEK--RRGL--KYELISETGGSHDKRFVMEVEVDGQKFRGAGP 557
Cdd:cd19862    1 KTPISVLQELcaKRGItpKYELISSEGAVHEPTFTFRVTVGDITATGSGT 50
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
522-558 7.03e-05

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 44.70  E-value: 7.03e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 149047906 522 RRGL---KYELISETGGSHDKRFVMEVEVDGQKF-RGAGPN 558
Cdd:COG0571  169 ARGLplpEYEVVEEEGPDHAKTFTVEVLVGGKVLgEGTGRS 209
DSRM_STAU2_rpt4 cd19886
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 389-453 8.58e-05

fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 2 (Staufen 2) and similar proteins; Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen 2 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380715  Cd Length: 86  Bit Score: 41.48  E-value: 8.58e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149047906 389 MNALMRLNQIRPGLQ-----YKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGY 453
Cdd:cd19886    3 MNPISRLAQIQQAKKekepeYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKRNAAEAMLLQLGY 72
DSRM_DCL_plant cd19869
double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant ...
 403-449 1.04e-04

double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant Dicer-like (DCL) proteins and other ribonuclease (RNase) III-like (RTL) proteins. DCLs are endoribonucleases involved in RNA-mediated post-transcriptional gene silencing (PTGS). They function in the microRNA (miRNA) biogenesis pathway by cleaving primary miRNAs (pri-miRNAs) and precursor miRNAs (pre-miRNAs). Family members contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380698  Cd Length: 70  Bit Score: 40.81  E-value: 1.04e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 149047906 403 QYKLLSQSGPVHAPVFTMSVDV----DGTTYEASG---PSKKTAKLHVAVKVLQ 449
Cdd:cd19869   13 VYRCVEEEGPAHAKRFTYMVRVkipeRGWTIECEGepmRSKKRAKDSAALLLLE 66
DSRM_DRADA cd19902
double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) ...
 512-552 2.67e-04

double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins; DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. DRADA family members contain at least one double-stranded RNA binding motifs (DSRM); vertebrate proteins contain three. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380731  Cd Length: 71  Bit Score: 39.58  E-value: 2.67e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 149047906 512 KNPV---MELNEKRR-GLKYELISETGGSHDKRFVMEVEVDGQKF 552
Cdd:cd19902    1 KNPVsalMEYAQSRGvTAEIEVLSQSGPPHNPRFKAAVFVGGRRF 45
DSRM_AtDRB-like_rpt1 cd19907
first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 409-447 7.62e-04

first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRBs)and similar proteins; This family includes a group of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRB1-5). They bind double-stranded RNA (dsRNA) and may be involved in RNA-mediated silencing. Members of this family contain two to three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380736 [Multi-domain]  Cd Length: 69  Bit Score: 38.23  E-value: 7.62e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 149047906 409 QSGPVHAPVFTMSVDVDGTTYEASG--PSKKTAKlHVAVKV 447
Cdd:cd19907   24 REGPDHAPRFRATVTFNGVIFESPPgfPTLKAAE-HSAAEV 63
DSRM_STAU_rpt4 cd19860
fourth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 527-558 1.32e-03

fourth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins; Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380689  Cd Length: 68  Bit Score: 37.70  E-value: 1.32e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 149047906 527 YELISETGGSHDKRFVMEVEVDGQKFRGAGPN 558
Cdd:cd19860   20 YSLVAERGTPRRREFVMQVTVGDKTATGTGPN 51
DSRM_STAU1_rpt4 cd19885
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 511-558 1.38e-03

fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380714  Cd Length: 86  Bit Score: 38.14  E-value: 1.38e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 149047906 511 GKNPVMELNE-----KRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPN 558
Cdd:cd19885    9 GMNPISRLAQiqqakKEKEPEYTLITERGLPRRREFVMQVKVGNQTAEGMGPN 61
DSRM_TARBP2_rpt2 cd10844
second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and ...
 403-448 1.81e-03

second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar proteins; TARBP2 (also known as TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)) participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. TARBP2 contains three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380681  Cd Length: 67  Bit Score: 37.39  E-value: 1.81e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 149047906 403 QYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVL 448
Cdd:cd10844   19 EYTVTQESGPAHRKEFTMTCRVERFIEIGSGTSKKLAKRNAAAKML 64
DSRM_STAU2_rpt3 cd19884
third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 402-451 2.06e-03

third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 2 (Staufen 2) and similar proteins; Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen 2 contains five double-stranded RNA binding motifs (DSRMs). This model describes the third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380713  Cd Length: 67  Bit Score: 37.29  E-value: 2.06e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 149047906 402 LQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAM 451
Cdd:cd19884   18 VSFEVIKESGPPHMKSFVTRVTVGEFTAEGEGNSKKLSKKRAATSVLQEL 67
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 525-562 6.60e-03

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis.


Pssm-ID: 380679 [Multi-domain]  Cd Length: 57  Bit Score: 35.34  E-value: 6.60e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 149047906 525 LKYELISEtGGSHDKRFVMEVEVDGQKFRGAGPNKKVA 562
Cdd:cd00048   12 PEYETVEE-GGPHNPRFTCTVTVNGQTFEGEGKSKKEA 48
DSRM_TARBP2_rpt1 cd19890
first double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar ...
 404-449 6.95e-03

first double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar proteins; TARBP2 (also known as TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)), participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. TARBP2 contains three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380719  Cd Length: 72  Bit Score: 35.88  E-value: 6.95e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 149047906 404 YKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAK---LHVAVKVLQ 449
Cdd:cd19890   22 YDLLKAEGQAHQPNFTFRVTVGDISCTGQGPSKKAAKhkaAEVALKLLK 70
DSRM_DRADA_rpt1 cd19913
first double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...
 512-555 7.98e-03

first double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA); DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. Vertebrate DRADA contains three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380742  Cd Length: 71  Bit Score: 35.62  E-value: 7.98e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 149047906 512 KNPVMELNEKRRGLKYE----LISETGGSHDKRFVMEVEVDGQKFRGA 555
Cdd:cd19913    1 KNPVSGLMEYAQFLGQTceflLLEQSGPSHDPRFKFQAVIDGRRFPPA 48
PHA03103 PHA03103
double-strand RNA-binding protein; Provisional
 407-440 9.99e-03

double-strand RNA-binding protein; Provisional


Pssm-ID: 222987 [Multi-domain]  Cd Length: 183  Bit Score: 37.82  E-value: 9.99e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 149047906 407 LSQSGPVHAPVFTMSVDVDGTTYE-ASGPSKKTAK 440
Cdd:PHA03103 130 ITSSGPSHSPTFTASVIISGIKFKpAIGSTKKEAK 164
 
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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