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Conserved domains on  [gi|1938847083|ref|XP_037856321|]
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double-stranded RNA-binding protein Staufen homolog 2 isoform X6 [Chlorocebus sabaeus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DSRM_STAU2_rpt4 cd19886
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 200-285 8.09e-59

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: 191.71  E-value: 8.09e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938847083 200 QGMNPISRLAQIQQAKKEKEPDYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQLGYKASTNLQD 279
Cdd:cd19886     1 QGMNPISRLAQIQQAKKEKEPEYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKRNAAEAMLLQLGYKASTPLQD 80


                  ....*.
gi 1938847083 280 QLEKTG 285
Cdd:cd19886    81 QTEKSG 86
DSRM_STAU2_rpt2 cd19882
second double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 1-75 5.07e-53

second 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 second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


:

Pssm-ID: 380711  Cd Length: 82  Bit Score: 176.06  E-value: 5.07e-53
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1938847083   1 MKRGEPAIYRPLDPKPFPNYRANYNFRGMYNQRYHCPVPKIFYVQLTVGNNEFFGEGKTRQAARHNAAMKALQAL 75
Cdd:cd19882     8 MKRGEPAIYRPIDPKPPPNYRPNYNFRGMYNQRYHYPMPKTFYVSLTVGNREFIGEGRTRQAARHNAAMKALQAL 82
DSRM_STAU2_rpt3 cd19884
third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 102-168 2.07e-39

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: 138.60  E-value: 2.07e-39
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1938847083 102 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd19884     1 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVTVGEFTAEGEGNSKKLSKKRAATSVLQEL 67
Staufen_C super family cl24900
Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of ...
 357-444 7.83e-38

Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of an N-terminal Staufen-swapping motif (SSM) comprising two alpha helices, connected by a linker region to a dsRNA-binding-like domain ('RBD'). The 'RBD' has the fold of a functional dsRNA-binding domain, but lacks the residues required to bind RNA. This domain is responsible for dimerization, the SSM from one molecule interacts with the 'RBD' of another.


The actual alignment was detected with superfamily member pfam16482:

Pssm-ID: 465131  Cd Length: 110  Bit Score: 135.80  E-value: 7.83e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938847083 357 SATIARELLMNGTSSTAEAI-GLKGSSPTPPCSPVQPSKQLEYLARIQGFQVHYCD--RQSGKECVTCLTLA--PVQMTf 431
Cdd:pfam16482   6 TAAIARELLYGGTSPTAEAIlKNNGKTGAVPCGLVQPSQQLEYLARVQGFQVEYSDfpRQNKNEFLSLLTLSsqPVQMT- 84

                          90
                  ....*....|...
gi 1938847083 432 HAIGSSIEASHDQ 444
Cdd:pfam16482  85 HGIGSSLEASHDQ 97
 
Name Accession Description Interval E-value
DSRM_STAU2_rpt4 cd19886
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 200-285 8.09e-59

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: 191.71  E-value: 8.09e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938847083 200 QGMNPISRLAQIQQAKKEKEPDYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQLGYKASTNLQD 279
Cdd:cd19886     1 QGMNPISRLAQIQQAKKEKEPEYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKRNAAEAMLLQLGYKASTPLQD 80


                  ....*.
gi 1938847083 280 QLEKTG 285
Cdd:cd19886    81 QTEKSG 86
DSRM_STAU2_rpt2 cd19882
second double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 1-75 5.07e-53

second 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 second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380711  Cd Length: 82  Bit Score: 176.06  E-value: 5.07e-53
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1938847083   1 MKRGEPAIYRPLDPKPFPNYRANYNFRGMYNQRYHCPVPKIFYVQLTVGNNEFFGEGKTRQAARHNAAMKALQAL 75
Cdd:cd19882     8 MKRGEPAIYRPIDPKPPPNYRPNYNFRGMYNQRYHYPMPKTFYVSLTVGNREFIGEGRTRQAARHNAAMKALQAL 82
DSRM_STAU2_rpt3 cd19884
third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 102-168 2.07e-39

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: 138.60  E-value: 2.07e-39
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1938847083 102 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd19884     1 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVTVGEFTAEGEGNSKKLSKKRAATSVLQEL 67
Staufen_C pfam16482
Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of ...
 357-444 7.83e-38

Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of an N-terminal Staufen-swapping motif (SSM) comprising two alpha helices, connected by a linker region to a dsRNA-binding-like domain ('RBD'). The 'RBD' has the fold of a functional dsRNA-binding domain, but lacks the residues required to bind RNA. This domain is responsible for dimerization, the SSM from one molecule interacts with the 'RBD' of another.


Pssm-ID: 465131  Cd Length: 110  Bit Score: 135.80  E-value: 7.83e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938847083 357 SATIARELLMNGTSSTAEAI-GLKGSSPTPPCSPVQPSKQLEYLARIQGFQVHYCD--RQSGKECVTCLTLA--PVQMTf 431
Cdd:pfam16482   6 TAAIARELLYGGTSPTAEAIlKNNGKTGAVPCGLVQPSQQLEYLARVQGFQVEYSDfpRQNKNEFLSLLTLSsqPVQMT- 84

                          90
                  ....*....|...
gi 1938847083 432 HAIGSSIEASHDQ 444
Cdd:pfam16482  85 HGIGSSLEASHDQ 97
DSRM_STAU2_rpt5 cd19888
fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 390-444 4.11e-35

fifth 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 fifth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380717  Cd Length: 68  Bit Score: 126.99  E-value: 4.11e-35
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1938847083 390 VQPSKQLEYLARIQGFQVHYCDRQSGKECVTCLTLAPVQMTFHAIGSSIEASHDQ 444
Cdd:cd19888     1 VQPSKQLEYLARIQGFQVQYSDRQNGKECMTCLTLSPVQMTFHGIGSSIEASHDQ 55
DSRM smart00358
Double-stranded RNA binding motif;
204-270 2.07e-18

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 79.61  E-value: 2.07e-18
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1938847083  204 PISRLAQIQQAKKeKEPDYVLLSERGMPRRREFVMQVKV-GNEVATGTGPNKKIAKKNAAEAMLLQLG 270
Cdd:smart00358   1 PKSLLQELAQKRK-LPPEYELVKEEGPDHAPRFTVTVKVgGKRTGEGEGSSKKEAKQRAAEAALRSLK 67
DSRM smart00358
Double-stranded RNA binding motif;
105-169 3.46e-17

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 76.15  E-value: 3.46e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1938847083  105 ISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFS-AEGEGNSKKLSKKRAATTVLQELK 169
Cdd:smart00358   2 KSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGKRtGEGEGSSKKEAKQRAAEAALRSLK 67
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 204-269 2.75e-14

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: 67.64  E-value: 2.75e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1938847083 204 PISRLAQIQQaKKEKEPDYVLLSERGMPRRREFVMQVKV-GNEVATGTGPNKKIAKKNAAEAMLLQL 269
Cdd:pfam00035   1 PKSLLQEYAQ-KNGKPPPYEYVSEEGPPHSPKFTVTVKVdGKLYGSGTGSSKKEAEQLAAEKALEKL 66
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
189-270 4.11e-14

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 72.05  E-value: 4.11e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938847083 189 KTIVKAGPEYGQGMNPISRLAQIQQAKKEKEPDYVLLSERGMPRRREFVMQVKVGNEV-ATGTGPNKKIAKKNAAEAMLL 267
Cdd:COG0571   144 EPRLEEIAPGGAGKDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGGKVlGEGTGRSKKEAEQAAAKAALE 223


                  ...
gi 1938847083 268 QLG 270
Cdd:COG0571   224 KLG 226
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 105-168 4.40e-13

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: 64.17  E-value: 4.40e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1938847083 105 ISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFS-AEGEGNSKKLSKKRAATTVLQEL 168
Cdd:pfam00035   2 KSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLyGSGTGSSKKEAEQLAAEKALEKL 66
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
110-170 1.39e-10

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 61.65  E-value: 1.39e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1938847083 110 EIALKRNMPV-SFEVIKESGPPHMKSFVTRVSV-GEFSAEGEGNSKKLSKKRAATTVLQELKK 170
Cdd:COG0571   165 EWLQARGLPLpEYEVVEEEGPDHAKTFTVEVLVgGKVLGEGTGRSKKEAEQAAAKAALEKLGK 227
DSRM smart00358
Double-stranded RNA binding motif;
35-76 3.57e-06

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 44.95  E-value: 3.57e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1938847083   35 HCPVpkiFYVQLTVGNNEFF-GEGKTRQAARHNAAMKALQALQ 76
Cdd:smart00358  28 HAPR---FTVTVKVGGKRTGeGEGSSKKEAKQRAAEAALRSLK 67
seadorna_dsRNA TIGR04238
seadornavirus double-stranded RNA-binding protein; This protein family occurs in the ...
 105-185 2.47e-05

seadornavirus double-stranded RNA-binding protein; This protein family occurs in the seadornavirus virus group, with an N-terminal domain for binding double-stranded RNA, is designated VP12 in Banna virus, VP8 in Kadipiro virus, and VP11 in Liao ning virus.


Pssm-ID: 275074 [Multi-domain]  Cd Length: 201  Bit Score: 45.71  E-value: 2.47e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938847083 105 ISLVFEIALKRNMPV-SFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQELKKLPPLPVVEKPKLF 183
Cdd:TIGR04238   3 VGMLQELAVKRGLELpVYEKVGKEGPDHAPTFTIKLTANDIEVIEAASSKKQAEKLAAATIYEDMKENGLLEVHDTRKSV 82


                  ..
gi 1938847083 184 FK 185
Cdd:TIGR04238  83 SI 84
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 37-75 3.19e-04

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: 39.14  E-value: 3.19e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1938847083  37 PVPKIFYVQLTVGNNEFF-GEGKTRQAARHNAAMKALQAL 75
Cdd:pfam00035  27 PHSPKFTVTVKVDGKLYGsGTGSSKKEAEQLAAEKALEKL 66
 
Name Accession Description Interval E-value
DSRM_STAU2_rpt4 cd19886
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 200-285 8.09e-59

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: 191.71  E-value: 8.09e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938847083 200 QGMNPISRLAQIQQAKKEKEPDYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQLGYKASTNLQD 279
Cdd:cd19886     1 QGMNPISRLAQIQQAKKEKEPEYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKRNAAEAMLLQLGYKASTPLQD 80


                  ....*.
gi 1938847083 280 QLEKTG 285
Cdd:cd19886    81 QTEKSG 86
DSRM_STAU2_rpt2 cd19882
second double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 1-75 5.07e-53

second 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 second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380711  Cd Length: 82  Bit Score: 176.06  E-value: 5.07e-53
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1938847083   1 MKRGEPAIYRPLDPKPFPNYRANYNFRGMYNQRYHCPVPKIFYVQLTVGNNEFFGEGKTRQAARHNAAMKALQAL 75
Cdd:cd19882     8 MKRGEPAIYRPIDPKPPPNYRPNYNFRGMYNQRYHYPMPKTFYVSLTVGNREFIGEGRTRQAARHNAAMKALQAL 82
DSRM_STAU1_rpt4 cd19885
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 196-272 8.22e-44

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: 151.39  E-value: 8.22e-44
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1938847083 196 PEYGQGMNPISRLAQIQQAKKEKEPDYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQLGYK 272
Cdd:cd19885     4 PEYGQGMNPISRLAQIQQAKKEKEPEYTLITERGLPRRREFVMQVKVGNQTAEGMGPNKKVAKRNAAEKMLELLGFK 80
DSRM_STAU_rpt4 cd19860
fourth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 203-270 3.83e-40

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: 140.55  E-value: 3.83e-40
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1938847083 203 NPISRLAQIQQAKKEKEPDYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQLG 270
Cdd:cd19860     1 NPISRLIQIQQARKEKEPVYSLVAERGTPRRREFVMQVTVGDKTATGTGPNKKLAKRNAAEAMLELLG 68
DSRM_STAU2_rpt3 cd19884
third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 102-168 2.07e-39

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: 138.60  E-value: 2.07e-39
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1938847083 102 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd19884     1 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVTVGEFTAEGEGNSKKLSKKRAATSVLQEL 67
Staufen_C pfam16482
Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of ...
 357-444 7.83e-38

Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of an N-terminal Staufen-swapping motif (SSM) comprising two alpha helices, connected by a linker region to a dsRNA-binding-like domain ('RBD'). The 'RBD' has the fold of a functional dsRNA-binding domain, but lacks the residues required to bind RNA. This domain is responsible for dimerization, the SSM from one molecule interacts with the 'RBD' of another.


Pssm-ID: 465131  Cd Length: 110  Bit Score: 135.80  E-value: 7.83e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938847083 357 SATIARELLMNGTSSTAEAI-GLKGSSPTPPCSPVQPSKQLEYLARIQGFQVHYCD--RQSGKECVTCLTLA--PVQMTf 431
Cdd:pfam16482   6 TAAIARELLYGGTSPTAEAIlKNNGKTGAVPCGLVQPSQQLEYLARVQGFQVEYSDfpRQNKNEFLSLLTLSsqPVQMT- 84

                          90
                  ....*....|...
gi 1938847083 432 HAIGSSIEASHDQ 444
Cdd:pfam16482  85 HGIGSSLEASHDQ 97
DSRM_STAU_rpt3 cd19859
third double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 104-168 4.97e-36

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: 129.06  E-value: 4.97e-36
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1938847083 104 EISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd19859     1 EISLVHEIALKRNLTVNFEVLRESGPPHMKNFITRCTVGSFVTEGEGNSKKVSKKRAAEKMLEEL 65
DSRM_STAU2_rpt5 cd19888
fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 390-444 4.11e-35

fifth 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 fifth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380717  Cd Length: 68  Bit Score: 126.99  E-value: 4.11e-35
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1938847083 390 VQPSKQLEYLARIQGFQVHYCDRQSGKECVTCLTLAPVQMTFHAIGSSIEASHDQ 444
Cdd:cd19888     1 VQPSKQLEYLARIQGFQVQYSDRQNGKECMTCLTLSPVQMTFHGIGSSIEASHDQ 55
DSRM_STAU1_rpt3 cd19883
third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 102-168 4.60e-35

third 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 third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380712  Cd Length: 67  Bit Score: 126.67  E-value: 4.60e-35
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1938847083 102 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd19883     1 KSEISQVFEIALKRNMPVNFEVTKETGPPHMKSFVTKVSVGEFAGEGEGKSKKISKKNAAIAVLEEL 67
DSRM_STAU_rpt2 cd19858
second double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 18-73 4.93e-22

second 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 second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380687  Cd Length: 67  Bit Score: 89.77  E-value: 4.93e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1938847083  18 PNYRANYNF--RGMYNQRYHCP-----VPKIFYVQLTVGNNEFFGEGKTRQAARHNAAMKALQ 73
Cdd:cd19858     5 PNYNNYGMPqrRGDYRFRYPYPnnpsgPPPPFYVTLTVGEREFIGEGRTRQAARHDAASKALK 67
DSRM_STAU1_rpt2 cd19881
second double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 1-73 1.72e-19

second 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 second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380710  Cd Length: 79  Bit Score: 83.01  E-value: 1.72e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1938847083   1 MKRGEPAIYRPLDPKPFPNYRANYNFRGM--YNQRYH---CPVPKIFY-VQLTVGNNEFFGEGKTRQAARHNAAMKALQ 73
Cdd:cd19881     1 MKLGKKPIYKPIDPYTGMRSAYNYNMRGNgaYPPRYFypfPPVGPVLYqVELSIGGQQFHGKGRTRQAAKHDAAAKALK 79
DSRM smart00358
Double-stranded RNA binding motif;
204-270 2.07e-18

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 79.61  E-value: 2.07e-18
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1938847083  204 PISRLAQIQQAKKeKEPDYVLLSERGMPRRREFVMQVKV-GNEVATGTGPNKKIAKKNAAEAMLLQLG 270
Cdd:smart00358   1 PKSLLQELAQKRK-LPPEYELVKEEGPDHAPRFTVTVKVgGKRTGEGEGSSKKEAKQRAAEAALRSLK 67
DSRM smart00358
Double-stranded RNA binding motif;
105-169 3.46e-17

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 76.15  E-value: 3.46e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1938847083  105 ISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFS-AEGEGNSKKLSKKRAATTVLQELK 169
Cdd:smart00358   2 KSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGKRtGEGEGSSKKEAKQRAAEAALRSLK 67
DSRM_PRKRA-like_rpt1 cd19862
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 102-169 3.06e-15

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: 70.75  E-value: 3.06e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1938847083 102 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQELK 169
Cdd:cd19862     1 KTPISVLQELCAKRGITPKYELISSEGAVHEPTFTFRVTVGDITATGSGTSKKKAKHAAAENALEQLK 68
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 202-269 3.54e-15

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: 70.21  E-value: 3.54e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1938847083 202 MNPISRLAQIQQAKKEKEPDYVLLSERGMPRRREFVMQVKVGNEV-ATGTGPNKKIAKKNAAEAMLLQL 269
Cdd:cd10845     1 KDYKTALQEYLQKRGLPLPEYELVEEEGPDHNKTFTVEVKVNGKViGEGTGRSKKEAEQAAAKAALEKL 69
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 204-269 2.75e-14

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: 67.64  E-value: 2.75e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1938847083 204 PISRLAQIQQaKKEKEPDYVLLSERGMPRRREFVMQVKV-GNEVATGTGPNKKIAKKNAAEAMLLQL 269
Cdd:pfam00035   1 PKSLLQEYAQ-KNGKPPPYEYVSEEGPPHSPKFTVTVKVdGKLYGSGTGSSKKEAEQLAAEKALEKL 66
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
189-270 4.11e-14

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 72.05  E-value: 4.11e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938847083 189 KTIVKAGPEYGQGMNPISRLAQIQQAKKEKEPDYVLLSERGMPRRREFVMQVKVGNEV-ATGTGPNKKIAKKNAAEAMLL 267
Cdd:COG0571   144 EPRLEEIAPGGAGKDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGGKVlGEGTGRSKKEAEQAAAKAALE 223


                  ...
gi 1938847083 268 QLG 270
Cdd:COG0571   224 KLG 226
DSRM_PRKRA-like_rpt2 cd19863
second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family ...
 203-269 4.20e-13

second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The 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. The 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 second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380692  Cd Length: 67  Bit Score: 64.32  E-value: 4.20e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1938847083 203 NPISRLAQIQQAKKEKEPDYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 269
Cdd:cd19863     1 NPVGILQELCVQRRWRLPEYEVEQESGPPHEKEFTIACRVENFSETGSGKSKKLAKRAAAEKMLTRL 67
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 105-168 4.40e-13

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: 64.17  E-value: 4.40e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1938847083 105 ISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFS-AEGEGNSKKLSKKRAATTVLQEL 168
Cdd:pfam00035   2 KSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLyGSGTGSSKKEAEQLAAEKALEKL 66
DSRM_STAU_rpt5 cd19861
fifth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 392-444 4.95e-13

fifth 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 fifth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380690  Cd Length: 68  Bit Score: 64.16  E-value: 4.95e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1938847083 392 PSKQLEYLARIQGFQVHYCDRQSGK--ECVTCLTLAPV-QMTFHAIGSSIEASHDQ 444
Cdd:cd19861     1 PKEQLEYLAKVLGFSVEFTDFPKGNksEYLSLVSLGTEpPQVCHGSGSSVEESRDA 56
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 210-266 1.65e-12

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: 62.30  E-value: 1.65e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1938847083 210 QIQQAKKEKEPDYVLLSERGmPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAML 266
Cdd:cd00048     2 ELCQKNKWPPPEYETVEEGG-PHNPRFTCTVTVNGQTFEGEGKSKKEAKQAAAEKAL 57
DSRM_PRKRA_rpt2 cd19891
second double-stranded RNA binding motif of protein activator of the interferon-induced ...
 203-269 1.65e-11

second double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; 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. PRKRA 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: 380720  Cd Length: 67  Bit Score: 59.95  E-value: 1.65e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1938847083 203 NPISRLAQIQQAKKEKEPDYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 269
Cdd:cd19891     1 NPIGSLQELAVQKGWRLPEYTLAQESGPPHKREFTITCRVETFVETGTGTSKKVAKRNAAEKLLAKF 67
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 101-172 2.87e-11

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: 59.60  E-value: 2.87e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1938847083 101 NKSEISLVFEIALKRN-MPVSFEVIKESGPPHMKSFVTRVSVG--EFSAEGEGNSKKLSKKRAATTVLQELKKLP 172
Cdd:cd19870     1 GKHPVSALMELCNKRKwGPPEFRLVEESGPPHRKHFLFKVVVNgvEYQPSVASGNKKDAKAQAATVALQALGLVP 75
DSRM_PRKRA-like_rpt1 cd19862
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 203-269 5.62e-11

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: 58.43  E-value: 5.62e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1938847083 203 NPISRLAQIQqAKKEKEPDYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 269
Cdd:cd19862     2 TPISVLQELC-AKRGITPKYELISSEGAVHEPTFTFRVTVGDITATGSGTSKKKAKHAAAENALEQL 67
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 106-168 5.91e-11

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: 58.27  E-value: 5.91e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1938847083 106 SLVFEIALKRNMP-VSFEVIKESGPPHMKSFVTRVSV-GEFSAEGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd10845     5 TALQEYLQKRGLPlPEYELVEEEGPDHNKTFTVEVKVnGKVIGEGTGRSKKEAEQAAAKAALEKL 69
DSRM_STRBP_RED-like_rpt2 cd19866
second double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 203-269 9.03e-11

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: 57.56  E-value: 9.03e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1938847083 203 NPISRLAQIQQAKKekepdYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 269
Cdd:cd19866     2 NPVMLLNELRPGLK-----YKCLSESGESHAKSFVMSVTVDGQTFEGTGRSKKLAKAAAAQAALAKL 63
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
110-170 1.39e-10

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 61.65  E-value: 1.39e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1938847083 110 EIALKRNMPV-SFEVIKESGPPHMKSFVTRVSV-GEFSAEGEGNSKKLSKKRAATTVLQELKK 170
Cdd:COG0571   165 EWLQARGLPLpEYEVVEEEGPDHAKTFTVEVLVgGKVLGEGTGRSKKEAEQAAAKAALEKLGK 227
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 109-165 7.26e-10

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: 54.98  E-value: 7.26e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1938847083 109 FEIALKRNMP-VSFEVIkESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVL 165
Cdd:cd00048     1 NELCQKNKWPpPEYETV-EEGGPHNPRFTCTVTVNGQTFEGEGKSKKEAKQAAAEKAL 57
DSRM_STAU_rpt4 cd19860
fourth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 105-168 1.30e-09

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: 54.65  E-value: 1.30e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1938847083 105 ISLVFEI--ALKRNMPVsFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd19860     3 ISRLIQIqqARKEKEPV-YSLVAERGTPRRREFVMQVTVGDKTATGTGPNKKLAKRNAAEAMLELL 67
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 201-270 2.89e-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: 53.82  E-value: 2.89e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1938847083 201 GMNPISRLAQIQQAKKEKEPDYVLLSERGMPRRREFVMQVKVGNEV--ATGTGPNKKIAKKNAAEAMLLQLG 270
Cdd:cd19870     1 GKHPVSALMELCNKRKWGPPEFRLVEESGPPHRKHFLFKVVVNGVEyqPSVASGNKKDAKAQAATVALQALG 72
DSRM_PRKRA-like_rpt2 cd19863
second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family ...
 110-168 5.44e-09

second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The 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. The 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 second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380692  Cd Length: 67  Bit Score: 52.76  E-value: 5.44e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938847083 110 EIALKRN-MPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd19863     8 ELCVQRRwRLPEYEVEQESGPPHEKEFTIACRVENFSETGSGKSKKLAKRAAAEKMLTRL 67
DSRM_STRBP_RED-like_rpt2 cd19866
second double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 119-168 1.07e-08

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: 51.78  E-value: 1.07e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1938847083 119 VSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd19866    14 LKYKCLSESGESHAKSFVMSVTVDGQTFEGTGRSKKLAKAAAAQAALAKL 63
DSRM_PRKRA_rpt1 cd19889
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 102-169 1.15e-08

first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; 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. PRKRA 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: 380718 [Multi-domain]  Cd Length: 71  Bit Score: 51.84  E-value: 1.15e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1938847083 102 KSEISLVFEIALK-RNMPVsFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQELK 169
Cdd:cd19889     2 KTPIQLLHEYGTKtGNIPV-YELEKSEGQAHLPSFTFRVTVGDITCTGEGTSKKLAKHRAAEAALNILK 69
DSRM_TARBP2_rpt2 cd10844
second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and ...
 203-269 2.44e-08

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: 50.88  E-value: 2.44e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1938847083 203 NPISRLAQIQQAKKEKEPDYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 269
Cdd:cd10844     1 NPVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFIEIGSGTSKKLAKRNAAAKMLLRI 67
DSRM_EIF2AK2_rpt1 cd19903
first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha ...
 203-269 1.30e-07

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: 48.92  E-value: 1.30e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1938847083 203 NPISRLAQIQQAKKEKEpDYVLLSERGMPRRREFVMQVKV-GNEVATGTGPNKKIAKKNAAEAMLLQL 269
Cdd:cd19903     2 NYMGKLNEYCQKQKVVL-DYVEVPTSGPSHDPRFTFQVVIdGKEYPEGEGKSKKEAKQAAAKLALEIL 68
DSRM_RED1_rpt2 cd19898
second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar ...
 121-173 1.89e-07

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: 48.65  E-value: 1.89e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1938847083 121 FEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQELKKLPP 173
Cdd:cd19898    18 YEFVSESGESHAKNFVMSVTVDGQTFEGSGRNKKLAKARAAQAALAKLFNLQL 70
DSRM_STRBP-like_rpt2 cd19897
second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family ...
 203-269 2.20e-07

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: 48.13  E-value: 2.20e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1938847083 203 NPISRLAQIQQAKKekepdYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 269
Cdd:cd19897     2 NPVMELNEKRRGLK-----YELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKANAALAALEKL 63
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 37-72 2.51e-07

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: 47.66  E-value: 2.51e-07
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1938847083  37 PVPKIFYVQLTVGNNEFFGEGKTRQAARHNAAMKAL 72
Cdd:cd00048    22 PHNPRFTCTVTVNGQTFEGEGKSKKEAKQAAAEKAL 57
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 102-168 3.59e-07

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: 47.65  E-value: 3.59e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1938847083 102 KSEISLVFEIALKRNMPVSFEVIkESGPPHMKSFVTRVSVGEFS-AEGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd19875     1 KNPVSALNEYCQKRGLSLEFVDV-SVGPDHCPGFTASATIDGIVfASATGTSKKEAKRAAAKLALKKL 67
DSRM_RED1_rpt2 cd19898
second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar ...
 200-269 4.02e-07

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: 47.49  E-value: 4.02e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938847083 200 QGMNPISRLAQIQQAKKekepdYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 269
Cdd:cd19898     1 SGKNPVMILNELRPGLK-----YEFVSESGESHAKNFVMSVTVDGQTFEGSGRNKKLAKARAAQAALAKL 65
DSRM_DRADA cd19902
double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) ...
 102-168 6.58e-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: 46.90  E-value: 6.58e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1938847083 102 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGE--FsAEGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd19902     1 KNPVSALMEYAQSRGVTAEIEVLSQSGPPHNPRFKAAVFVGGrrF-PSVEASSKKDAKQEAADLALRAL 68
DSRM_STAU1_rpt4 cd19885
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 114-175 7.14e-07

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: 47.39  E-value: 7.14e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1938847083 114 KRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL--KKLPPLP 175
Cdd:cd19885    23 KKEKEPEYTLITERGLPRRREFVMQVKVGNQTAEGMGPNKKVAKRNAAEKMLELLgfKVPQPQP 86
DSRM_STRBP_RED-like_rpt1 cd19865
first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 202-266 8.41e-07

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: 46.57  E-value: 8.41e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1938847083 202 MNPISRLAQIQQAKKekepdYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAML 266
Cdd:cd19865     1 KNALMQLNELRPGLQ-----YKLTSQTGPVHAPVFTMSVEVNGQTFEGTGRSKKKAKLEAAEKAL 60
DSRM_DRADA cd19902
double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) ...
 203-269 9.01e-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: 46.51  E-value: 9.01e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1938847083 203 NPISRLAQIQQAKKEkEPDYVLLSERGMPRRREFVMQVKVG-NEVATGTGPNKKIAKKNAAEAMLLQL 269
Cdd:cd19902     2 NPVSALMEYAQSRGV-TAEIEVLSQSGPPHNPRFKAAVFVGgRRFPSVEASSKKDAKQEAADLALRAL 68
DSRM_DCL_plant cd19869
double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant ...
 110-170 9.09e-07

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: 46.59  E-value: 9.09e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938847083 110 EIALKRN--MPVsFEVIKESGPPHMKSFVTRVSV------GEFSAEGEG-NSKKLSKKRAATTVLQELKK 170
Cdd:cd19869     2 EICLKRRwpMPV-YRCVEEEGPAHAKRFTYMVRVkipergWTIECEGEPmRSKKRAKDSAALLLLEYLKK 70
DSRM_ILF3_rpt2 cd19912
second double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and ...
 200-269 1.17e-06

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: 46.57  E-value: 1.17e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938847083 200 QGMNPISRLAQIQQAKKekepdYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 269
Cdd:cd19912     5 HGKNPVMELNEKRRGLK-----YELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKAYAALAALEKL 69
DSRM_TARBP2_rpt1 cd19890
first double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar ...
 102-169 1.17e-06

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: 46.28  E-value: 1.17e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1938847083 102 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQELK 169
Cdd:cd19890     3 KTPISLLQEYGTRIGKTPVYDLLKAEGQAHQPNFTFRVTVGDISCTGQGPSKKAAKHKAAEVALKLLK 70
DSRM_DRADA_rpt2 cd19914
second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...
 102-168 1.66e-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: 1.66e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1938847083 102 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGE-FSAEGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd19914     1 KNPISVLMEHSQKSGNMCEFQLLSQEGPPHDPKFTYCVKVGEqTFPSVVANSKKVAKQMAAEEAVKEL 68
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 203-269 1.84e-06

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: 45.72  E-value: 1.84e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1938847083 203 NPISRLAQIQQaKKEKEPDYVLLSeRGMPRRREFVMQVKVGNEV-ATGTGPNKKIAKKNAAEAMLLQL 269
Cdd:cd19875     2 NPVSALNEYCQ-KRGLSLEFVDVS-VGPDHCPGFTASATIDGIVfASATGTSKKEAKRAAAKLALKKL 67
DSRM_STRBP_rpt2 cd19911
second double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...
 203-269 1.87e-06

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: 45.51  E-value: 1.87e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1938847083 203 NPISRLAQIQQAKKekepdYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 269
Cdd:cd19911     2 NPVMELNEKRRGLK-----YELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEKL 63
DSRM_STAU_rpt1 cd19857
first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 105-165 3.39e-06

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: 44.95  E-value: 3.39e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1938847083 105 ISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSA-EGEGNSKKLSKKRAATTVL 165
Cdd:cd19857     3 MCLLNELARFNKIRPQYTLVDEEGPAHKKTFTVKLTLGDEEEyEASGSSIKKAQHAAAEKAL 64
DSRM smart00358
Double-stranded RNA binding motif;
35-76 3.57e-06

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 44.95  E-value: 3.57e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1938847083   35 HCPVpkiFYVQLTVGNNEFF-GEGKTRQAARHNAAMKALQALQ 76
Cdd:smart00358  28 HAPR---FTVTVKVGGKRTGeGEGSSKKEAKQRAAEAALRSLK 67
DSRM_TARBP2_rpt1 cd19890
first double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar ...
 201-269 4.52e-06

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: 44.74  E-value: 4.52e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1938847083 201 GMNPISrLAQIQQAKKEKEPDYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 269
Cdd:cd19890     2 GKTPIS-LLQEYGTRIGKTPVYDLLKAEGQAHQPNFTFRVTVGDISCTGQGPSKKAAKHKAAEVALKLL 69
DSRM_EIF2AK2 cd20314
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 105-168 5.84e-06

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). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380746  Cd Length: 68  Bit Score: 44.31  E-value: 5.84e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1938847083 105 ISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVG--EFSaEGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd20314     4 VSLLNEYCQKERLTVKYEEEKRSGPTHKPRFFCKYIIDgkEYP-EGEGKSKKEAKQAAARLAYEEL 68
DSRM_DHX9_rpt1 cd19854
first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 215-262 7.48e-06

first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; DHX9 (EC 3.6.4.13; also known as ATP-dependent RNA helicase A, DExH-box helicase 9 (DDX9), Leukophysin (LKP), nuclear DNA helicase II (NDH II), NDH2, or RNA helicase A) is a multifunctional ATP-dependent nucleic acid helicase that unwinds DNA and RNA in a 3' to 5' direction and plays important roles in many processes, such as DNA replication, transcriptional activation, post-transcriptional RNA regulation, mRNA translation, and RNA-mediated gene silencing. It contains two double-stranded RNA binding motifs (DSRMs) at the N-terminal region. This model corresponds to the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380683  Cd Length: 69  Bit Score: 43.80  E-value: 7.48e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1938847083 215 KKEKEPDYVLLsERGMPRRREFVMQVKVGN--EVATGTGPNKKIAKKNAA 262
Cdd:cd19854    12 KKKLTPEYDIK-EAGNKHRQRFKCEVRVEGfdYVGTGNATNKKDAQTNAA 60
DSRM_STRBP_rpt1 cd19909
first double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...
 200-271 1.65e-05

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: 43.48  E-value: 1.65e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1938847083 200 QGMNPISRLAQIQQAKKekepdYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQLGY 271
Cdd:cd19909     4 QPMNALMRLNQIRPGLQ-----YKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGY 70
DSRM_PRKRA_rpt2 cd19891
second double-stranded RNA binding motif of protein activator of the interferon-induced ...
 110-168 1.70e-05

second double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; 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. PRKRA 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: 380720  Cd Length: 67  Bit Score: 43.00  E-value: 1.70e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1938847083 110 EIALKRN--MPvSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd19891     8 ELAVQKGwrLP-EYTLAQESGPPHKREFTITCRVETFVETGTGTSKKVAKRNAAEKLLAKF 67
DSRM_STRBP_RED-like_rpt1 cd19865
first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 119-166 2.27e-05

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: 42.33  E-value: 2.27e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1938847083 119 VSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQ 166
Cdd:cd19865    14 LQYKLTSQTGPVHAPVFTMSVEVNGQTFEGTGRSKKKAKLEAAEKALR 61
seadorna_dsRNA TIGR04238
seadornavirus double-stranded RNA-binding protein; This protein family occurs in the ...
 105-185 2.47e-05

seadornavirus double-stranded RNA-binding protein; This protein family occurs in the seadornavirus virus group, with an N-terminal domain for binding double-stranded RNA, is designated VP12 in Banna virus, VP8 in Kadipiro virus, and VP11 in Liao ning virus.


Pssm-ID: 275074 [Multi-domain]  Cd Length: 201  Bit Score: 45.71  E-value: 2.47e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938847083 105 ISLVFEIALKRNMPV-SFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQELKKLPPLPVVEKPKLF 183
Cdd:TIGR04238   3 VGMLQELAVKRGLELpVYEKVGKEGPDHAPTFTIKLTANDIEVIEAASSKKQAEKLAAATIYEDMKENGLLEVHDTRKSV 82


                  ..
gi 1938847083 184 FK 185
Cdd:TIGR04238  83 SI 84
DSRM_TARBP2_rpt2 cd10844
second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and ...
 99-165 2.83e-05

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: 42.40  E-value: 2.83e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1938847083  99 DANKSEISLVFEIALKrnMPvSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVL 165
Cdd:cd10844     1 NPVGALQELVVQKGWR--LP-EYTVTQESGPAHRKEFTMTCRVERFIEIGSGTSKKLAKRNAAAKML 64
DSRM_RED2_rpt2 cd19899
second double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar ...
 131-168 4.21e-05

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: 42.17  E-value: 4.21e-05
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1938847083 131 HMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd19899    33 HIKSFVMAVRVDGRTFEGSGRSKKLAKAQAAQAALQAL 70
DSRM_STAU2_rpt1 cd19880
first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 102-165 4.27e-05

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: 42.01  E-value: 4.27e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1938847083 102 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVL 165
Cdd:cd19880     5 KTPMCLVNELARFNRIQPQYKLLNERGPAHAKIFTVQLTLGEQTWEAEGSSIKKAQHAAASKAL 68
DSRM_EIF2AK2_rpt1 cd19903
first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha ...
 119-168 5.71e-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: 5.71e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1938847083 119 VSFEVIKESGPPHMKSFVTRVSVGEFS-AEGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd19903    18 LDYVEVPTSGPSHDPRFTFQVVIDGKEyPEGEGKSKKEAKQAAAKLALEIL 68
DSRM_STAU1_rpt1 cd19879
first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 102-165 6.18e-05

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: 41.22  E-value: 6.18e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1938847083 102 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVL 165
Cdd:cd19879     3 KTPMCLVNELARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTSIKKAQHAAAAKAL 66
DSRM_DHX9_rpt2 cd19855
second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 114-168 6.50e-05

second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; DHX9 (EC 3.6.4.13; also known as ATP-dependent RNA helicase A, DExH-box helicase 9 (DDX9), Leukophysin (LKP), nuclear DNA helicase II (NDH II), NDH2, or RNA helicase A) is a multifunctional ATP-dependent nucleic acid helicase that unwinds DNA and RNA in a 3' to 5' direction and plays important roles in many processes, such as DNA replication, transcriptional activation, post-transcriptional RNA regulation, mRNA translation and RNA-mediated gene silencing. It contains two double-stranded RNA binding motifs (DSRMs) at the N-terminal region. This model corresponds to the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380684  Cd Length: 75  Bit Score: 41.43  E-value: 6.50e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1938847083 114 KRNMPVSFEvIKESGPPHMKSFVTRVSV------GEFSAEGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd19855    14 KNKIPAEYK-YTSVGPDHNRSFIAELSIfvkqlgKTIYARETGSNKKLASQSCALSLVRQL 73
DSRM_STAU1_rpt5 cd19887
fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 391-443 7.58e-05

fifth 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 fifth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380716  Cd Length: 70  Bit Score: 41.19  E-value: 7.58e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1938847083 391 QPSKQLEYLARIQGFQVHYCD--RQSGKECVT---CLTLAPvqMTFHAIGSSIEASHD 443
Cdd:cd19887     1 RPSEQLDYLSRVQGLQVEYKDfpKNNKNEFVSlinCSSQPP--LISHGIGKDVESCHD 56
DSRM_DGCR8_rpt1 cd19867
first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and ...
 198-270 1.03e-04

first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and similar proteins; DGCR8 is a component of the microprocessor complex that acts as an RNA- and heme-binding protein that is involved in the initial step of microRNA (miRNA) biogenesis. Within the microprocessor complex, DGCR8 functions as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs DROSHA to cleave 11bp away from the junction to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. DGCR8 contains 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: 380696  Cd Length: 74  Bit Score: 40.78  E-value: 1.03e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1938847083 198 YGQGMNPISRLAQIQQAKKEKEPDY--VLLSERGMPrrreFVMQVKV-GNEVATGTGPNKKIAKKNAAEAMLLQLG 270
Cdd:cd19867     2 NPDGKSPVCILHEYCQRVLKVQPEYnfTETENAATP----FSAEVFInGVEYGSGEASSKKLAKQKAARATLEILI 73
DSRM_STRBP-like_rpt2 cd19897
second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family ...
 108-168 1.20e-04

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: 40.42  E-value: 1.20e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1938847083 108 VFEIALKRNmPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd19897     4 VMELNEKRR-GLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKANAALAALEKL 63
DSRM_STRBP_RED-like_rpt1 cd19865
first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 35-75 1.22e-04

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: 40.41  E-value: 1.22e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1938847083  35 HCPVpkiFYVQLTVGNNEFFGEGKTRQAARHNAAMKALQAL 75
Cdd:cd19865    26 HAPV---FTMSVEVNGQTFEGTGRSKKKAKLEAAEKALRSF 63
DSRM_RED2_rpt2 cd19899
second double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar ...
 222-269 1.38e-04

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: 40.63  E-value: 1.38e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1938847083 222 YVLLSERGMPRR-REFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 269
Cdd:cd19899    22 YVCLSETAEKQHiKSFVMAVRVDGRTFEGSGRSKKLAKAQAAQAALQAL 70
DSRM_STAU_rpt1 cd19857
first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 40-72 1.64e-04

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: 39.94  E-value: 1.64e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1938847083  40 KIFYVQLTVGNNE-FFGEGKTRQAARHNAAMKAL 72
Cdd:cd19857    31 KTFTVKLTLGDEEeYEASGSSIKKAQHAAAEKAL 64
DSRM_DRADA_rpt2 cd19914
second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...
 203-269 1.73e-04

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: 40.22  E-value: 1.73e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1938847083 203 NPISRLAQIQQaKKEKEPDYVLLSERGMPRRREFVMQVKVGNEV-ATGTGPNKKIAKKNAAEAMLLQL 269
Cdd:cd19914     2 NPISVLMEHSQ-KSGNMCEFQLLSQEGPPHDPKFTYCVKVGEQTfPSVVANSKKVAKQMAAEEAVKEL 68
DSRM_RED1_rpt1 cd19895
first double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins; ...
 204-266 1.91e-04

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: 40.06  E-value: 1.91e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1938847083 204 PISRLAQIQQAKKEKEpdYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAML 266
Cdd:cd19895     5 PKNALMQLNEIKPGLQ--YKLLSQTGPVHAPVFVMSVEVNGQVFEGSGPTKKKAKLHAAEKAL 65
DSRM_EIF2AK2_rpt2 cd19904
second double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha ...
 105-168 2.72e-04

second 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 second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380733  Cd Length: 69  Bit Score: 39.42  E-value: 2.72e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1938847083 105 ISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGE-FSAEGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd19904     4 ISLLNQYAQKKRLTVNYEQCASTGVPGPPRFSCKCKIGQkEYGIGTGSTKQEAKQAAAKEAYEQL 68
DSRM_RED2_rpt1 cd19896
first double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar proteins; ...
 119-172 3.07e-04

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: 39.69  E-value: 3.07e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1938847083 119 VSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQELKKLP 172
Cdd:cd19896    19 LQYRMVSQTGPVHAPVFAVAVEVNGLTFEGTGPTKKKAKMRAAEMALKSFVQFP 72
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 37-75 3.19e-04

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: 39.14  E-value: 3.19e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1938847083  37 PVPKIFYVQLTVGNNEFF-GEGKTRQAARHNAAMKALQAL 75
Cdd:pfam00035  27 PHSPKFTVTVKVDGKLYGsGTGSSKKEAEQLAAEKALEKL 66
DSRM_PRKRA_rpt1 cd19889
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 201-266 4.69e-04

first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; 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. PRKRA 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: 380718 [Multi-domain]  Cd Length: 71  Bit Score: 39.13  E-value: 4.69e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1938847083 201 GMNPISRLAQIQqAKKEKEPDYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAML 266
Cdd:cd19889     1 GKTPIQLLHEYG-TKTGNIPVYELEKSEGQAHLPSFTFRVTVGDITCTGEGTSKKLAKHRAAEAAL 65
DSRM_RNAse_III_meta_like cd19877
double-stranded RNA binding motif of metazoan ribonuclease III (RNase III) and similar ...
 204-266 5.04e-04

double-stranded RNA binding motif of metazoan ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as Drosha, or ribonuclease 3) is a double-stranded RNA (dsRNA)-specific endoribonuclease that is involved in the initial step of microRNA (miRNA) biogenesis. It is a component of the microprocessor complex that is required to process primary miRNA transcripts (pri-miRNAs) to release precursor miRNA (pre-miRNA) in the nucleus. Within the microprocessor complex, RNase III cleaves the 3' and 5' strands of a stem-loop in pri-miRNAs (processing center 11 bp from the dsRNA-ssRNA junction) to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. It is also involved in pre-rRNA processing. Metazoan RNase III is a larger protein than bacterial RNase III. It contains two RNase III domains in the C-terminal half of the protein followed by a double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380706  Cd Length: 75  Bit Score: 38.80  E-value: 5.04e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1938847083 204 PISRLaqiQQA------KKEKEPD---YVLLSERGMPRRREFVMQVKV-GNEVATGTGPNKKIAKKNAAEAML 266
Cdd:cd19877     3 PKSQL---QQCcltlrtEGKKEPDipeYKVLQKSGPTNTRVYTVAVYFrGERIATGTGSSIQQAEMNAAEKAL 72
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 40-75 7.67e-04

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: 38.24  E-value: 7.67e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1938847083  40 KIFYVQLTVGNNEFF-GEGKTRQAARHNAAMKALQAL 75
Cdd:cd10845    33 KTFTVEVKVNGKVIGeGTGRSKKEAEQAAAKAALEKL 69
DSRM_STRBP_rpt2 cd19911
second double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...
 108-168 8.20e-04

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: 38.19  E-value: 8.20e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1938847083 108 VFEIALKRNmPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd19911     4 VMELNEKRR-GLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEKL 63
DSRM_ILF3_rpt2 cd19912
second double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and ...
 108-168 1.06e-03

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: 38.09  E-value: 1.06e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1938847083 108 VFEIALKRNmPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd19912    10 VMELNEKRR-GLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKAYAALAALEKL 69
DSRM_DHX9_rpt1 cd19854
first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 114-170 1.18e-03

first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; DHX9 (EC 3.6.4.13; also known as ATP-dependent RNA helicase A, DExH-box helicase 9 (DDX9), Leukophysin (LKP), nuclear DNA helicase II (NDH II), NDH2, or RNA helicase A) is a multifunctional ATP-dependent nucleic acid helicase that unwinds DNA and RNA in a 3' to 5' direction and plays important roles in many processes, such as DNA replication, transcriptional activation, post-transcriptional RNA regulation, mRNA translation, and RNA-mediated gene silencing. It contains two double-stranded RNA binding motifs (DSRMs) at the N-terminal region. This model corresponds to the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380683  Cd Length: 69  Bit Score: 37.64  E-value: 1.18e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1938847083 114 KRNMPVSFEvIKESGPPHMKSFVTRVSVGEFS--AEGEGNSKKLSKKRAATTVLQELKK 170
Cdd:cd19854    12 KKKLTPEYD-IKEAGNKHRQRFKCEVRVEGFDyvGTGNATNKKDAQTNAARDFLNYLVR 69
DSRM_RNT1p-like cd19876
double-stranded RNA binding motif of Saccharomyces cerevisiae ribonuclease 3 (RNT1p) and ...
 220-266 1.49e-03

double-stranded RNA binding motif of Saccharomyces cerevisiae ribonuclease 3 (RNT1p) and similar proteins; RNT1p (EC 3.1.26.3; also known as ribonuclease III (RNase III)) is a dsRNA-specific nuclease that cleaves eukaryotic pre-ribosomal RNA at the U3 snoRNP-dependent A0 site in the 5'-external transcribed spacer (ETS) and in the 3'-ETS. RNT1p contains 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: 380705  Cd Length: 69  Bit Score: 37.32  E-value: 1.49e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1938847083 220 PDYVLLsERGMPRRREFVMQVKVGNE-VATGTGPNKKIAKKNAAEAML 266
Cdd:cd19876    19 PEYVVV-KKEGGNDPNYTVACRINGEvLGTGVGRSIKKAGQRAAMSAL 65
DSRM_STAU1_rpt1 cd19879
first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 35-72 2.26e-03

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: 36.98  E-value: 2.26e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1938847083  35 HCpvpKIFYVQLTVGNNEFFGEGKTRQAARHNAAMKAL 72
Cdd:cd19879    32 HS---KVFTVQLTLGDQHWEAEGTSIKKAQHAAAAKAL 66
DSRM_DGCR8_rpt2 cd19868
second double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and ...
 231-270 2.28e-03

second double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and similar proteins; DGCR8 is a component of the microprocessor complex that acts as an RNA- and heme-binding protein that is involved in the initial step of microRNA (miRNA) biogenesis. Within the microprocessor complex, DGCR8 functions as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs DROSHA to cleave 11bp away from the junction to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. DGCR8 contains 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: 380697  Cd Length: 69  Bit Score: 36.88  E-value: 2.28e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1938847083 231 PRRREFVMqvKVGNEVATGTGPNKKIAKKNAAEAMLLQLG 270
Cdd:cd19868    31 HQKHEYTM--TVGKHTVTVICKNKKEGKQLAAQAILKKLH 68
DSRM_DRADA_rpt1 cd19913
first double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...
 102-168 2.72e-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: 36.77  E-value: 2.72e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1938847083 102 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVG--EFSAeGEGNSKKLSKKRAATTVLQEL 168
Cdd:cd19913     1 KNPVSGLMEYAQFLGQTCEFLLLEQSGPSHDPRFKFQAVIDgrRFPP-AEASSKKVAKKDAAAIALKIL 68
DSRM_EIF2AK2 cd20314
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 203-269 3.05e-03

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). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380746  Cd Length: 68  Bit Score: 36.60  E-value: 3.05e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1938847083 203 NPISRLAQIQQakKEKEP-DYVLLSERGMPRRREFVMQVKV-GNEVATGTGPNKKIAKKNAAEAMLLQL 269
Cdd:cd20314     2 NYVSLLNEYCQ--KERLTvKYEEEKRSGPTHKPRFFCKYIIdGKEYPEGEGKSKKEAKQAAARLAYEEL 68
DSRM_AtDRB-like cd19878
double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins ...
 206-270 3.43e-03

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). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380707 [Multi-domain]  Cd Length: 67  Bit Score: 36.34  E-value: 3.43e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1938847083 206 SRLAQIQQAKKEKEPDYVLlSERGMPRRREFVMQVKVGNEVATGTG-PNKKIAKKNAAEAMLLQLG 270
Cdd:cd19878     3 NLLQEYAQKKKIPLPKYES-AKSGPSHQPTFVSTVIVLGVRFSSEGaKNKKQAEQSAAKVALKELG 67
DSRM_DCL_plant cd19869
double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant ...
 213-270 4.65e-03

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: 36.19  E-value: 4.65e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1938847083 213 QAKKEKEPDYVLLSERGMPRRREFVMQVKVGNEVATGT----G---PNKKIAKKNAAEAMLLQLG 270
Cdd:cd19869     5 LKRRWPMPVYRCVEEEGPAHAKRFTYMVRVKIPERGWTieceGepmRSKKRAKDSAALLLLEYLK 69
DSRM_DRADA_rpt3 cd19915
third double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...
 102-168 4.72e-03

third 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 third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380744  Cd Length: 71  Bit Score: 36.07  E-value: 4.72e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1938847083 102 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGE--FSAEGeGNSKKLSKKRAATTVLQEL 168
Cdd:cd19915     1 TNPVSGLLEYARSKGFAAEFKLVDQSGPPHEPKFVYQAKVGGrwFPAVC-AHNKKQGKQEAADAALRVL 68
DSRM_AtDRB-like_rpt2 cd19908
second double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 107-169 5.92e-03

second 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 second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380737 [Multi-domain]  Cd Length: 69  Bit Score: 35.92  E-value: 5.92e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1938847083 107 LVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGE-GNSKKLSKKRAATTVLQELK 169
Cdd:cd19908     6 LLQEYAQKAGLPLPLYTTVRSGPGHVPTFTCTVEIAGITFTGEaAKTKKQAEKSAARTAWSSIK 69
DSRM_ILF3_rpt1 cd19910
first double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and ...
 200-270 6.34e-03

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: 35.89  E-value: 6.34e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1938847083 200 QGMNPISRLAQIQQAKKekepdYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQLG 270
Cdd:cd19910     4 QAMNALMRLNQLKPGLQ-----YKLISQTGPVHAPVFTMSVEVDGKTFEASGPSKKTAKLHVAVKVLQDMG 69
 
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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