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Conserved domains on  [gi|1934695737|ref|XP_037667016|]
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double-stranded RNA-binding protein Staufen homolog 1 isoform X12 [Choloepus didactylus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Staufen_C pfam16482
Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of ...
 449-558 1.90e-61

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: 198.20  E-value: 1.90e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934695737 449 KATVTAMIARELLYGGTSPTAETILKNSISSGHVPHGPlTRPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQP 528
Cdd:pfam16482   2 KATVTAAIARELLYGGTSPTAEAILKNNGKTGAVPCGL-VQPSQQLEYLARVQGFQVEYSDFPRQNKNEFLSLLTLSSQP 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 1934695737 529 PLISHGIGKDVESCHDMAALNILKLLSELD 558
Cdd:pfam16482  81 VQMTHGIGSSLEASHDQAALSALKQLSEQG 110
DSRM_STAU1_rpt4 cd19885
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 277-362 1.07e-53

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: 177.20  E-value: 1.07e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934695737 277 QTSPEYGQGMNPISRLAQIQQAKKEKEPEYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFK 356
Cdd:cd19885     1 QTSPEYGQGMNPISRLAQIQQAKKEKEPEYTLITERGLPRRREFVMQVKVGNQTAEGMGPNKKVAKRNAAEKMLELLGFK 80


                  ....*.
gi 1934695737 357 VPQAQP 362
Cdd:cd19885    81 VPQPQP 86
DSRM_STAU1_rpt3 cd19883
third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 183-249 7.19e-38

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: 133.98  E-value: 7.19e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1934695737 183 KSEISQVFEIALKRNLPVNFEVARESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:cd19883     1 KSEISQVFEIALKRNMPVNFEVTKETGPPHMKSFVTKVSVGEFAGEGEGKSKKISKKNAAIAVLEEL 67
DSRM_SF super family cl00054
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 82-146 8.59e-38

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.


The actual alignment was detected with superfamily member cd19881:

Pssm-ID: 444671  Cd Length: 79  Bit Score: 134.24  E-value: 8.59e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1934695737  82 VKLGRKPMYKPVDPYSRVQSTYNYNMRG-GAYPPRYFYPF-PVPPLLYQVELSVGGQQFNGKGRTRQ 146
Cdd:cd19881     1 MKLGKKPIYKPIDPYTGMRSAYNYNMRGnGAYPPRYFYPFpPVGPVLYQVELSIGGQQFHGKGRTRQ 67
 
Name Accession Description Interval E-value
Staufen_C pfam16482
Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of ...
 449-558 1.90e-61

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: 198.20  E-value: 1.90e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934695737 449 KATVTAMIARELLYGGTSPTAETILKNSISSGHVPHGPlTRPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQP 528
Cdd:pfam16482   2 KATVTAAIARELLYGGTSPTAEAILKNNGKTGAVPCGL-VQPSQQLEYLARVQGFQVEYSDFPRQNKNEFLSLLTLSSQP 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 1934695737 529 PLISHGIGKDVESCHDMAALNILKLLSELD 558
Cdd:pfam16482  81 VQMTHGIGSSLEASHDQAALSALKQLSEQG 110
DSRM_STAU1_rpt4 cd19885
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 277-362 1.07e-53

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: 177.20  E-value: 1.07e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934695737 277 QTSPEYGQGMNPISRLAQIQQAKKEKEPEYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFK 356
Cdd:cd19885     1 QTSPEYGQGMNPISRLAQIQQAKKEKEPEYTLITERGLPRRREFVMQVKVGNQTAEGMGPNKKVAKRNAAEKMLELLGFK 80


                  ....*.
gi 1934695737 357 VPQAQP 362
Cdd:cd19885    81 VPQPQP 86
DSRM_STAU1_rpt5 cd19887
fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 489-558 5.73e-41

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: 142.50  E-value: 5.73e-41
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934695737 489 RPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSELD 558
Cdd:cd19887     1 RPSEQLDYLSRVQGLQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSELD 70
DSRM_STAU1_rpt3 cd19883
third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 183-249 7.19e-38

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: 133.98  E-value: 7.19e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1934695737 183 KSEISQVFEIALKRNLPVNFEVARESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:cd19883     1 KSEISQVFEIALKRNMPVNFEVTKETGPPHMKSFVTKVSVGEFAGEGEGKSKKISKKNAAIAVLEEL 67
DSRM_STAU1_rpt2 cd19881
second double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 82-146 8.59e-38

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: 134.24  E-value: 8.59e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1934695737  82 VKLGRKPMYKPVDPYSRVQSTYNYNMRG-GAYPPRYFYPF-PVPPLLYQVELSVGGQQFNGKGRTRQ 146
Cdd:cd19881     1 MKLGKKPIYKPIDPYTGMRSAYNYNMRGnGAYPPRYFYPFpPVGPVLYQVELSIGGQQFHGKGRTRQ 67
DSRM smart00358
Double-stranded RNA binding motif;
186-250 3.98e-18

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 78.46  E-value: 3.98e-18
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1934695737  186 ISQVFEIALKRNLPVNFEVARESGPPHMKSFVTKVSVGGFI-GEGEGKSKKISKKNAAIAVLEELK 250
Cdd:smart00358   2 KSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGKRtGEGEGSSKKEAKQRAAEAALRSLK 67
DSRM smart00358
Double-stranded RNA binding motif;
288-354 6.81e-18

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 78.07  E-value: 6.81e-18
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1934695737  288 PISRLAQIQQAKKeKEPEYVLLTERGLPRRREFVMQVKV-GNHTAEGTGTNKKVAKRNAAENMLEILG 354
Cdd:smart00358   1 PKSLLQELAQKRK-LPPEYELVKEEGPDHAPRFTVTVKVgGKRTGEGEGSSKKEAKQRAAEAALRSLK 67
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 186-249 6.07e-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: 66.48  E-value: 6.07e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1934695737 186 ISQVFEIALKRNLPVNFEVARESGPPHMKSFVTKVSVGGF-IGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:pfam00035   2 KSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKlYGSGTGSSKKEAEQLAAEKALEKL 66
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
275-354 8.29e-14

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 70.90  E-value: 8.29e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934695737 275 KLQTSPEYGQGMNPISRLAQIQQAKKEKEPEYVLLTERGLPRRREFVMQVKVGNH-TAEGTGTNKKVAKRNAAENMLEIL 353
Cdd:COG0571   146 RLEEIAPGGAGKDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGGKvLGEGTGRSKKEAEQAAAKAALEKL 225


                  .
gi 1934695737 354 G 354
Cdd:COG0571   226 G 226
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 288-353 2.66e-12

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: 61.86  E-value: 2.66e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1934695737 288 PISRLAQIQQaKKEKEPEYVLLTERGLPRRREFVMQVKVGNHT-AEGTGTNKKVAKRNAAENMLEIL 353
Cdd:pfam00035   1 PKSLLQEYAQ-KNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLyGSGTGSSKKEAEQLAAEKALEKL 66
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
191-251 7.01e-11

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 62.42  E-value: 7.01e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1934695737 191 EIALKRNLPV-NFEVARESGPPHMKSFVTKVSVGG-FIGEGEGKSKKISKKNAAIAVLEELKK 251
Cdd:COG0571   165 EWLQARGLPLpEYEVVEEEGPDHAKTFTVEVLVGGkVLGEGTGRSKKEAEQAAAKAALEKLGK 227
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 191-249 1.53e-10

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 61.07  E-value: 1.53e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1934695737 191 EIALKRNLP-VNFEVARESGPPHMKSFVTKVSVGG-FIGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:TIGR02191 160 EWAQARGKPlPEYRLIKEEGPDHDKEFTVEVSVNGePYGEGKGKSKKEAEQNAAKAALEKL 220
 
Name Accession Description Interval E-value
Staufen_C pfam16482
Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of ...
 449-558 1.90e-61

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: 198.20  E-value: 1.90e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934695737 449 KATVTAMIARELLYGGTSPTAETILKNSISSGHVPHGPlTRPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQP 528
Cdd:pfam16482   2 KATVTAAIARELLYGGTSPTAEAILKNNGKTGAVPCGL-VQPSQQLEYLARVQGFQVEYSDFPRQNKNEFLSLLTLSSQP 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 1934695737 529 PLISHGIGKDVESCHDMAALNILKLLSELD 558
Cdd:pfam16482  81 VQMTHGIGSSLEASHDQAALSALKQLSEQG 110
DSRM_STAU1_rpt4 cd19885
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 277-362 1.07e-53

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: 177.20  E-value: 1.07e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934695737 277 QTSPEYGQGMNPISRLAQIQQAKKEKEPEYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFK 356
Cdd:cd19885     1 QTSPEYGQGMNPISRLAQIQQAKKEKEPEYTLITERGLPRRREFVMQVKVGNQTAEGMGPNKKVAKRNAAEKMLELLGFK 80


                  ....*.
gi 1934695737 357 VPQAQP 362
Cdd:cd19885    81 VPQPQP 86
DSRM_STAU1_rpt5 cd19887
fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 489-558 5.73e-41

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: 142.50  E-value: 5.73e-41
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934695737 489 RPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSELD 558
Cdd:cd19887     1 RPSEQLDYLSRVQGLQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSELD 70
DSRM_STAU2_rpt4 cd19886
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 284-364 5.16e-39

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: 137.78  E-value: 5.16e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934695737 284 QGMNPISRLAQIQQAKKEKEPEYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFKVP---QA 360
Cdd:cd19886     1 QGMNPISRLAQIQQAKKEKEPEYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKRNAAEAMLLQLGYKAStplQD 80


                  ....
gi 1934695737 361 QPTK 364
Cdd:cd19886    81 QTEK 84
DSRM_STAU_rpt4 cd19860
fourth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 287-354 7.13e-38

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: 134.00  E-value: 7.13e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1934695737 287 NPISRLAQIQQAKKEKEPEYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILG 354
Cdd:cd19860     1 NPISRLIQIQQARKEKEPVYSLVAERGTPRRREFVMQVTVGDKTATGTGPNKKLAKRNAAEAMLELLG 68
DSRM_STAU1_rpt3 cd19883
third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 183-249 7.19e-38

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: 133.98  E-value: 7.19e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1934695737 183 KSEISQVFEIALKRNLPVNFEVARESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:cd19883     1 KSEISQVFEIALKRNMPVNFEVTKETGPPHMKSFVTKVSVGEFAGEGEGKSKKISKKNAAIAVLEEL 67
DSRM_STAU1_rpt2 cd19881
second double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 82-146 8.59e-38

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: 134.24  E-value: 8.59e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1934695737  82 VKLGRKPMYKPVDPYSRVQSTYNYNMRG-GAYPPRYFYPF-PVPPLLYQVELSVGGQQFNGKGRTRQ 146
Cdd:cd19881     1 MKLGKKPIYKPIDPYTGMRSAYNYNMRGnGAYPPRYFYPFpPVGPVLYQVELSIGGQQFHGKGRTRQ 67
DSRM_STAU_rpt3 cd19859
third double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 185-249 1.45e-31

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: 116.34  E-value: 1.45e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1934695737 185 EISQVFEIALKRNLPVNFEVARESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:cd19859     1 EISLVHEIALKRNLTVNFEVLRESGPPHMKNFITRCTVGSFVTEGEGNSKKVSKKRAAEKMLEEL 65
DSRM_STAU2_rpt3 cd19884
third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 183-249 7.27e-30

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: 112.02  E-value: 7.27e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1934695737 183 KSEISQVFEIALKRNLPVNFEVARESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:cd19884     1 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVTVGEFTAEGEGNSKKLSKKRAATSVLQEL 67
DSRM_STAU_rpt5 cd19861
fifth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 490-557 6.97e-29

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: 109.23  E-value: 6.97e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1934695737 490 PSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSEL 557
Cdd:cd19861     1 PKEQLEYLAKVLGFSVEFTDFPKGNKSEYLSLVSLGTEPPQVCHGSGSSVEESRDAAALNALKLLKEL 68
DSRM smart00358
Double-stranded RNA binding motif;
186-250 3.98e-18

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 78.46  E-value: 3.98e-18
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1934695737  186 ISQVFEIALKRNLPVNFEVARESGPPHMKSFVTKVSVGGFI-GEGEGKSKKISKKNAAIAVLEELK 250
Cdd:smart00358   2 KSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGKRtGEGEGSSKKEAKQRAAEAALRSLK 67
DSRM smart00358
Double-stranded RNA binding motif;
288-354 6.81e-18

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 78.07  E-value: 6.81e-18
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1934695737  288 PISRLAQIQQAKKeKEPEYVLLTERGLPRRREFVMQVKV-GNHTAEGTGTNKKVAKRNAAENMLEILG 354
Cdd:smart00358   1 PKSLLQELAQKRK-LPPEYELVKEEGPDHAPRFTVTVKVgGKRTGEGEGSSKKEAKQRAAEAALRSLK 67
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 286-353 3.16e-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: 3.16e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1934695737 286 MNPISRLAQIQQAKKEKEPEYVLLTERGLPRRREFVMQVKVGNH-TAEGTGTNKKVAKRNAAENMLEIL 353
Cdd:cd10845     1 KDYKTALQEYLQKRGLPLPEYELVEEEGPDHNKTFTVEVKVNGKvIGEGTGRSKKEAEQAAAKAALEKL 69
DSRM_STAU2_rpt2 cd19882
second double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 75-160 9.12e-15

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: 69.74  E-value: 9.12e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934695737  75 VELNALCVKLGRKPMYKPVDPYSRVQSTYNYNMRGgAYPPRYFYPfpVPPLLYqVELSVGGQQFNGKGRTRQAAKHDAAA 154
Cdd:cd19882     1 VELNGLAMKRGEPAIYRPIDPKPPPNYRPNYNFRG-MYNQRYHYP--MPKTFY-VSLTVGNREFIGEGRTRQAARHNAAM 76


                  ....*.
gi 1934695737 155 KALRIL 160
Cdd:cd19882    77 KALQAL 82
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 186-249 6.07e-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: 66.48  E-value: 6.07e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1934695737 186 ISQVFEIALKRNLPVNFEVARESGPPHMKSFVTKVSVGGF-IGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:pfam00035   2 KSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKlYGSGTGSSKKEAEQLAAEKALEKL 66
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
275-354 8.29e-14

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 70.90  E-value: 8.29e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934695737 275 KLQTSPEYGQGMNPISRLAQIQQAKKEKEPEYVLLTERGLPRRREFVMQVKVGNH-TAEGTGTNKKVAKRNAAENMLEIL 353
Cdd:COG0571   146 RLEEIAPGGAGKDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGGKvLGEGTGRSKKEAEQAAAKAALEKL 225


                  .
gi 1934695737 354 G 354
Cdd:COG0571   226 G 226
DSRM_PRKRA-like_rpt2 cd19863
second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family ...
 287-350 1.71e-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: 65.48  E-value: 1.71e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1934695737 287 NPISRLAQIQQAKKEKEPEYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENML 350
Cdd:cd19863     1 NPVGILQELCVQRRWRLPEYEVEQESGPPHEKEFTIACRVENFSETGSGKSKKLAKRAAAEKML 64
DSRM_STAU2_rpt5 cd19888
fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 489-556 1.94e-13

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: 65.36  E-value: 1.94e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1934695737 489 RPSEQLDYLSRVQGFQVEYKDfpKNNKNEFVSLINCSSQpPLISHGIGKDVESCHDMAALNILKLLSE 556
Cdd:cd19888     2 QPSKQLEYLARIQGFQVQYSD--RQNGKECMTCLTLSPV-QMTFHGIGSSIEASHDQAALSALKQLSE 66
DSRM_PRKRA-like_rpt1 cd19862
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 183-250 1.95e-13

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: 65.36  E-value: 1.95e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1934695737 183 KSEISQVFEIALKRNLPVNFEVARESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEELK 250
Cdd:cd19862     1 KTPISVLQELCAKRGITPKYELISSEGAVHEPTFTFRVTVGDITATGSGTSKKKAKHAAAENALEQLK 68
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 294-350 7.49e-13

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: 63.46  E-value: 7.49e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1934695737 294 QIQQAKKEKEPEYVLLTERGlPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENML 350
Cdd:cd00048     2 ELCQKNKWPPPEYETVEEGG-PHNPRFTCTVTVNGQTFEGEGKSKKEAKQAAAEKAL 57
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 288-353 2.66e-12

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: 61.86  E-value: 2.66e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1934695737 288 PISRLAQIQQaKKEKEPEYVLLTERGLPRRREFVMQVKVGNHT-AEGTGTNKKVAKRNAAENMLEIL 353
Cdd:pfam00035   1 PKSLLQEYAQ-KNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLyGSGTGSSKKEAEQLAAEKALEKL 66
DSRM_PRKRA_rpt2 cd19891
second double-stranded RNA binding motif of protein activator of the interferon-induced ...
 287-350 1.62e-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: 1.62e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1934695737 287 NPISRLAQIQQAKKEKEPEYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENML 350
Cdd:cd19891     1 NPIGSLQELAVQKGWRLPEYTLAQESGPPHKREFTITCRVETFVETGTGTSKKVAKRNAAEKLL 64
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 187-249 1.76e-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: 59.81  E-value: 1.76e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1934695737 187 SQVFEIALKRNLP-VNFEVARESGPPHMKSFVTKVSVGG-FIGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:cd10845     5 TALQEYLQKRGLPlPEYELVEEEGPDHNKTFTVEVKVNGkVIGEGTGRSKKEAEQAAAKAALEKL 69
DSRM_STAU_rpt2 cd19858
second double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 100-147 1.80e-11

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: 59.73  E-value: 1.80e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1934695737 100 QSTYNYNMRGGA-----YPPRYFYPF--PVPPLLYQVELSVGGQQFNGKGRTRQA 147
Cdd:cd19858     2 QEHPNYNNYGMPqrrgdYRFRYPYPNnpSGPPPPFYVTLTVGEREFIGEGRTRQA 56
DSRM_PRKRA-like_rpt1 cd19862
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 287-353 3.23e-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: 59.20  E-value: 3.23e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1934695737 287 NPISRLAQIQqAKKEKEPEYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEIL 353
Cdd:cd19862     2 TPISVLQELC-AKRGITPKYELISSEGAVHEPTFTFRVTVGDITATGSGTSKKKAKHAAAENALEQL 67
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
191-251 7.01e-11

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 62.42  E-value: 7.01e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1934695737 191 EIALKRNLPV-NFEVARESGPPHMKSFVTKVSVGG-FIGEGEGKSKKISKKNAAIAVLEELKK 251
Cdd:COG0571   165 EWLQARGLPLpEYEVVEEEGPDHAKTFTVEVLVGGkVLGEGTGRSKKEAEQAAAKAALEKLGK 227
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 190-246 8.23e-11

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: 57.68  E-value: 8.23e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1934695737 190 FEIALKRNLP-VNFEVArESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVL 246
Cdd:cd00048     1 NELCQKNKWPpPEYETV-EEGGPHNPRFTCTVTVNGQTFEGEGKSKKEAKQAAAEKAL 57
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 191-249 1.53e-10

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 61.07  E-value: 1.53e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1934695737 191 EIALKRNLP-VNFEVARESGPPHMKSFVTKVSVGG-FIGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:TIGR02191 160 EWAQARGKPlPEYRLIKEEGPDHDKEFTVEVSVNGePYGEGKGKSKKEAEQNAAKAALEKL 220
DSRM_PRKRA-like_rpt3 cd19864
third double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family ...
 490-554 2.03e-09

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


Pssm-ID: 380693  Cd Length: 72  Bit Score: 54.15  E-value: 2.03e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1934695737 490 PSEQLDYLSRVQGFQVEYKDFPKNNKN-EFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLL 554
Cdd:cd19864     3 YCELLQELAEEQKFKVTYVDIEELSSSgKYQCLVQLSTLPPTVCHGSGASLEEAKEEAARNALEYL 68
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 182-253 3.55e-09

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


Pssm-ID: 380699  Cd Length: 75  Bit Score: 53.44  E-value: 3.55e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1934695737 182 NKSEISQVFEIALKRNL-PVNFEVARESGPPHMKSFVTKVSVGG--FIGEGEGKSKKISKKNAAIAVLEELKKLP 253
Cdd:cd19870     1 GKHPVSALMELCNKRKWgPPEFRLVEESGPPHRKHFLFKVVVNGveYQPSVASGNKKDAKAQAATVALQALGLVP 75
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 183-249 4.48e-09

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: 53.04  E-value: 4.48e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1934695737 183 KSEISQVFEIALKRNLPVNFEVAReSGPPHMKSFVTKVSVGG-FIGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:cd19875     1 KNPVSALNEYCQKRGLSLEFVDVS-VGPDHCPGFTASATIDGiVFASATGTSKKEAKRAAAKLALKKL 67
DSRM_PRKRA-like_rpt2 cd19863
second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family ...
 191-249 4.66e-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: 4.66e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1934695737 191 EIALKRN--LPVnFEVARESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:cd19863     8 ELCVQRRwrLPE-YEVEQESGPPHEKEFTIACRVENFSETGSGKSKKLAKRAAAEKMLTRL 67
DSRM_STRBP_RED-like_rpt2 cd19866
second double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 287-353 5.40e-09

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: 52.55  E-value: 5.40e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1934695737 287 NPISRLAQIQQAKKekepeYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEIL 353
Cdd:cd19866     2 NPVMLLNELRPGLK-----YKCLSESGESHAKSFVMSVTVDGQTFEGTGRSKKLAKAAAAQAALAKL 63
DSRM_TARBP2_rpt2 cd10844
second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and ...
 287-350 1.93e-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: 51.26  E-value: 1.93e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1934695737 287 NPISRLAQIQQAKKEKEPEYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENML 350
Cdd:cd10844     1 NPVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFIEIGSGTSKKLAKRNAAAKML 64
DSRM_STAU_rpt4 cd19860
fourth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 186-249 4.38e-08

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: 50.02  E-value: 4.38e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1934695737 186 ISQVFEI--ALKRNLPVnFEVARESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:cd19860     3 ISRLIQIqqARKEKEPV-YSLVAERGTPRRREFVMQVTVGDKTATGTGPNKKLAKRNAAEAMLELL 67
DSRM_STRBP_RED-like_rpt2 cd19866
second double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 200-249 9.43e-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: 49.09  E-value: 9.43e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1934695737 200 VNFEVARESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:cd19866    14 LKYKCLSESGESHAKSFVMSVTVDGQTFEGTGRSKKLAKAAAAQAALAKL 63
DSRM_EIF2AK2 cd20314
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 186-249 1.06e-07

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: 48.93  E-value: 1.06e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1934695737 186 ISQVFEIALKRNLPVNFEVARESGPPHMKSFVTKVSVGGF-IGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:cd20314     4 VSLLNEYCQKERLTVKYEEEKRSGPTHKPRFFCKYIIDGKeYPEGEGKSKKEAKQAAARLAYEEL 68
DSRM_EIF2AK2_rpt1 cd19903
first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha ...
 287-353 1.34e-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: 1.34e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1934695737 287 NPISRLAQIQQAKKEKEpEYVLLTERGLPRRREFVMQVKV-GNHTAEGTGTNKKVAKRNAAENMLEIL 353
Cdd:cd19903     2 NYMGKLNEYCQKQKVVL-DYVEVPTSGPSHDPRFTFQVVIdGKEYPEGEGKSKKEAKQAAAKLALEIL 68
DSRM_DHX9_rpt1 cd19854
first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 299-353 1.42e-07

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: 48.81  E-value: 1.42e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1934695737 299 KKEKEPEYVLlTERGLPRRREFVMQVKVGNHT--AEGTGTNKKVAKRNAAENMLEIL 353
Cdd:cd19854    12 KKKLTPEYDI-KEAGNKHRQRFKCEVRVEGFDyvGTGNATNKKDAQTNAARDFLNYL 67
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 285-355 2.48e-07

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: 48.05  E-value: 2.48e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1934695737 285 GMNPISRLAQIQQAKKEKEPEYVLLTERGLPRRREFVMQVKVGN--HTAEGTGTNKKVAKRNAAENMLEILGF 355
Cdd:cd19870     1 GKHPVSALMELCNKRKWGPPEFRLVEESGPPHRKHFLFKVVVNGveYQPSVASGNKKDAKAQAATVALQALGL 73
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 287-353 3.67e-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: 3.67e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1934695737 287 NPISRLAQIQQaKKEKEPEYVLlTERGLPRRREFVMQVKVGNHT-AEGTGTNKKVAKRNAAENMLEIL 353
Cdd:cd19875     2 NPVSALNEYCQ-KRGLSLEFVD-VSVGPDHCPGFTASATIDGIVfASATGTSKKEAKRAAAKLALKKL 67
DSRM_STRBP_RED-like_rpt1 cd19865
first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 286-351 4.73e-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: 46.96  E-value: 4.73e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1934695737 286 MNPISRLAQIQQAKKekepeYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLE 351
Cdd:cd19865     1 KNALMQLNELRPGLQ-----YKLTSQTGPVHAPVFTMSVEVNGQTFEGTGRSKKKAKLEAAEKALR 61
DSRM_DHX9_rpt1 cd19854
first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 195-251 5.06e-07

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: 47.27  E-value: 5.06e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1934695737 195 KRNLPVNFEVaRESGPPHMKSFVTKVSVGGF--IGEGEGKSKKISKKNAAIAVLEELKK 251
Cdd:cd19854    12 KKKLTPEYDI-KEAGNKHRQRFKCEVRVEGFdyVGTGNATNKKDAQTNAARDFLNYLVR 69
DSRM_EIF2AK2_rpt1 cd19903
first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha ...
 195-249 9.12e-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: 46.23  E-value: 9.12e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1934695737 195 KRNLPVNFEVARESGPPHMKSFVTKVSVGGF-IGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:cd19903    13 KQKVVLDYVEVPTSGPSHDPRFTFQVVIDGKeYPEGEGKSKKEAKQAAAKLALEIL 68
DSRM_PRKRA_rpt2 cd19891
second double-stranded RNA binding motif of protein activator of the interferon-induced ...
 186-249 1.06e-06

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: 46.09  E-value: 1.06e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1934695737 186 ISQVFEIALKRN--LPvNFEVARESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:cd19891     3 IGSLQELAVQKGwrLP-EYTLAQESGPPHKREFTITCRVETFVETGTGTSKKVAKRNAAEKLLAKF 67
DSRM_STRBP-like_rpt2 cd19897
second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family ...
 287-353 1.78e-06

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: 45.43  E-value: 1.78e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1934695737 287 NPISRLAQiqqakKEKEPEYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEIL 353
Cdd:cd19897     2 NPVMELNE-----KRRGLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKANAALAALEKL 63
DSRM_STRBP-like_rpt2 cd19897
second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family ...
 189-249 2.44e-06

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: 45.04  E-value: 2.44e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1934695737 189 VFEIALKRNlPVNFEVARESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:cd19897     4 VMELNEKRR-GLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKANAALAALEKL 63
DSRM_ILF3_rpt2 cd19912
second double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and ...
 284-353 3.61e-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: 45.03  E-value: 3.61e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934695737 284 QGMNPISRLAQiqqakKEKEPEYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEIL 353
Cdd:cd19912     5 HGKNPVMELNE-----KRRGLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKAYAALAALEKL 69
DSRM_DRADA cd19902
double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) ...
 287-353 4.82e-06

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: 44.59  E-value: 4.82e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1934695737 287 NPISRLAQIQQAKKEkEPEYVLLTERGLPRRREFVMQVKVGNHT-AEGTGTNKKVAKRNAAENMLEIL 353
Cdd:cd19902     2 NPVSALMEYAQSRGV-TAEIEVLSQSGPPHNPRFKAAVFVGGRRfPSVEASSKKDAKQEAADLALRAL 68
DSRM_RED2_rpt2 cd19899
second double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar ...
 212-249 9.31e-06

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: 43.71  E-value: 9.31e-06
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1934695737 212 HMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:cd19899    33 HIKSFVMAVRVDGRTFEGSGRSKKLAKAQAAQAALQAL 70
DSRM_DCL_plant cd19869
double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant ...
 191-251 1.02e-05

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: 43.51  E-value: 1.02e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1934695737 191 EIALKRNLPV-NFEVARESGPPHMKSFVTKVSV----GGFIGEGEG---KSKKISKKNAAIAVLEELKK 251
Cdd:cd19869     2 EICLKRRWPMpVYRCVEEEGPAHAKRFTYMVRVkipeRGWTIECEGepmRSKKRAKDSAALLLLEYLKK 70
DSRM_RED1_rpt2 cd19898
second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar ...
 284-353 1.07e-05

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: 43.64  E-value: 1.07e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934695737 284 QGMNPISRLAQIQQAKKekepeYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEIL 353
Cdd:cd19898     1 SGKNPVMILNELRPGLK-----YEFVSESGESHAKNFVMSVTVDGQTFEGSGRNKKLAKARAAQAALAKL 65
DSRM_RED2_rpt2 cd19899
second double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar ...
 306-353 1.07e-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: 43.71  E-value: 1.07e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1934695737 306 YVLLTERGLPRR-REFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEIL 353
Cdd:cd19899    22 YVCLSETAEKQHiKSFVMAVRVDGRTFEGSGRSKKLAKAQAAQAALQAL 70
DSRM_STAU1_rpt4 cd19885
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 207-256 1.07e-05

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: 43.92  E-value: 1.07e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1934695737 207 ESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEEL--KKLPPLP 256
Cdd:cd19885    35 ERGLPRRREFVMQVKVGNQTAEGMGPNKKVAKRNAAEKMLELLgfKVPQPQP 86
DSRM_AtDRB-like_rpt2 cd19908
second double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 191-250 1.16e-05

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: 43.24  E-value: 1.16e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1934695737 191 EIALKRNLPVNFEVARESGPPHMKSFVTKVSVGG--FIGEgEGKSKKISKKNAAIAVLEELK 250
Cdd:cd19908     9 EYAQKAGLPLPLYTTVRSGPGHVPTFTCTVEIAGitFTGE-AAKTKKQAEKSAARTAWSSIK 69
DSRM_TARBP2_rpt2 cd10844
second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and ...
 202-246 1.33e-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: 43.17  E-value: 1.33e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1934695737 202 FEVARESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVL 246
Cdd:cd10844    20 YTVTQESGPAHRKEFTMTCRVERFIEIGSGTSKKLAKRNAAAKML 64
DSRM_RED1_rpt2 cd19898
second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar ...
 202-254 1.98e-05

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: 42.87  E-value: 1.98e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1934695737 202 FEVARESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEELKKLPP 254
Cdd:cd19898    18 YEFVSESGESHAKNFVMSVTVDGQTFEGSGRNKKLAKARAAQAALAKLFNLQL 70
DSRM_STAU_rpt1 cd19857
first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 287-350 2.89e-05

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: 41.87  E-value: 2.89e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1934695737 287 NPISRLAQIqqAKKEK-EPEYVLLTERGLPRRREFVMQVKVGNHTA-EGTGTNKKVAKRNAAENML 350
Cdd:cd19857     1 TPMCLLNEL--ARFNKiRPQYTLVDEEGPAHKKTFTVKLTLGDEEEyEASGSSIKKAQHAAAEKAL 64
DSRM_PRKRA_rpt1 cd19889
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 183-250 3.77e-05

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: 41.82  E-value: 3.77e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1934695737 183 KSEISQVFEIALK-RNLPVnFEVARESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEELK 250
Cdd:cd19889     2 KTPIQLLHEYGTKtGNIPV-YELEKSEGQAHLPSFTFRVTVGDITCTGEGTSKKLAKHRAAEAALNILK 69
DSRM_STAU_rpt1 cd19857
first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 186-246 4.54e-05

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: 41.48  E-value: 4.54e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1934695737 186 ISQVFEIALKRNLPVNFEVARESGPPHMKSFVTKVSVG-GFIGEGEGKSKKISKKNAAIAVL 246
Cdd:cd19857     3 MCLLNELARFNKIRPQYTLVDEEGPAHKKTFTVKLTLGdEEEYEASGSSIKKAQHAAAEKAL 64
DSRM_DGCR8_rpt1 cd19867
first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and ...
 282-354 4.68e-05

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: 41.93  E-value: 4.68e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1934695737 282 YGQGMNPISRLAQIQQAKKEKEPEY--VLLTERGLPrrreFVMQVKVGNHT-AEGTGTNKKVAKRNAAENMLEILG 354
Cdd:cd19867     2 NPDGKSPVCILHEYCQRVLKVQPEYnfTETENAATP----FSAEVFINGVEyGSGEASSKKLAKQKAARATLEILI 73
DSRM_ILF3_rpt2 cd19912
second double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and ...
 181-249 5.57e-05

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: 41.56  E-value: 5.57e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1934695737 181 LNKSEISQVFEIALKRNlPVNFEVARESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:cd19912     2 LTKHGKNPVMELNEKRR-GLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKAYAALAALEKL 69
DSRM_STRBP_rpt1 cd19909
first double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...
 284-355 6.35e-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: 41.55  E-value: 6.35e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1934695737 284 QGMNPISRLAQIQQAKkekepEYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGF 355
Cdd:cd19909     4 QPMNALMRLNQIRPGL-----QYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGY 70
seadorna_dsRNA TIGR04238
seadornavirus double-stranded RNA-binding protein; This protein family occurs in the ...
 186-263 8.56e-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: 43.78  E-value: 8.56e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1934695737 186 ISQVFEIALKRNLPV-NFEVARESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEELKKLPPLPAVERVKP 263
Cdd:TIGR04238   3 VGMLQELAVKRGLELpVYEKVGKEGPDHAPTFTIKLTANDIEVIEAASSKKQAEKLAAATIYEDMKENGLLEVHDTRKS 81
DSRM_DRADA_rpt2 cd19914
second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...
 287-353 9.17e-05

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: 40.99  E-value: 9.17e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1934695737 287 NPISRLAQIQQaKKEKEPEYVLLTERGLPRRREFVMQVKVGNHT-AEGTGTNKKVAKRNAAENMLEIL 353
Cdd:cd19914     2 NPISVLMEHSQ-KSGNMCEFQLLSQEGPPHDPKFTYCVKVGEQTfPSVVANSKKVAKQMAAEEAVKEL 68
DSRM_DRADA cd19902
double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) ...
 183-249 1.04e-04

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


Pssm-ID: 380731  Cd Length: 71  Bit Score: 40.74  E-value: 1.04e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1934695737 183 KSEISQVFEIALKRNLPVNFEVARESGPPHMKSFVTKVSVGG-FIGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:cd19902     1 KNPVSALMEYAQSRGVTAEIEVLSQSGPPHNPRFKAAVFVGGrRFPSVEASSKKDAKQEAADLALRAL 68
DSRM_STRBP_RED-like_rpt1 cd19865
first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 202-247 2.61e-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: 39.25  E-value: 2.61e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1934695737 202 FEVARESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLE 247
Cdd:cd19865    16 YKLTSQTGPVHAPVFTMSVEVNGQTFEGTGRSKKKAKLEAAEKALR 61
DSRM_STAU2_rpt4 cd19886
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 207-249 2.77e-04

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: 39.94  E-value: 2.77e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1934695737 207 ESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:cd19886    28 ERGMPRRREFVMQVKVGNEVATGTGPNKKIAKRNAAEAMLLQL 70
DSRM_MRPL3_like cd19873
double-stranded RNA binding motif of Saccharomyces cerevisiae mitochondrial 54S ribosomal ...
 287-350 2.92e-04

double-stranded RNA binding motif of Saccharomyces cerevisiae mitochondrial 54S ribosomal protein L3 (MRPL3) and similar proteins; MRPL3 (also called mitochondrial large ribosomal subunit protein mL44) is a component of the mitochondrial ribosome (mitoribosome), a dedicated translation machinery responsible for the synthesis of mitochondrial genome-encoded proteins, including at least some of the essential transmembrane subunits of the mitochondrial respiratory chain. MRPL3 contains a RNase III-like domain and a double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380702  Cd Length: 84  Bit Score: 39.89  E-value: 2.92e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1934695737 287 NPISRLAQIQQAKKEKEPEYVLLTERG-LPRRREFVMQVKVGNHT-AEGTGTNKKVAKRNAAENML 350
Cdd:cd19873    13 NPKRTLSALLKREGLEPPVSRLLKESGrASHTPTFVVGVYSGSQKlGEGAGSSIKMAEIRAARDAL 78
DSRM_DGCR8_rpt2 cd19868
second double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and ...
 311-354 3.32e-04

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: 39.19  E-value: 3.32e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1934695737 311 ERGLPRRREFVMqvKVGNHTAEGTGTNKKVAKRNAAENMLEILG 354
Cdd:cd19868    27 INDKHQKHEYTM--TVGKHTVTVICKNKKEGKQLAAQAILKKLH 68
DSRM_EIF2AK2_rpt2 cd19904
second double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha ...
 186-242 3.52e-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: 39.03  E-value: 3.52e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1934695737 186 ISQVFEIALKRNLPVNFEVARESGPPHMKSFVTKVSVGG-FIGEGEGKSKKISKKNAA 242
Cdd:cd19904     4 ISLLNQYAQKKRLTVNYEQCASTGVPGPPRFSCKCKIGQkEYGIGTGSTKQEAKQAAA 61
DSRM_STRBP_rpt2 cd19911
second double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...
 287-353 3.63e-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: 38.96  E-value: 3.63e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1934695737 287 NPISRLAQiqqakKEKEPEYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEIL 353
Cdd:cd19911     2 NPVMELNE-----KRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEKL 63
DSRM_STRBP_rpt2 cd19911
second double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...
 189-249 4.79e-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: 38.58  E-value: 4.79e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1934695737 189 VFEIALKRNlPVNFEVARESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:cd19911     4 VMELNEKRR-GLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEKL 63
DSRM_STAU2_rpt1 cd19880
first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 286-350 4.85e-04

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: 38.93  E-value: 4.85e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1934695737 286 MNPISRLAQIQqakkekePEYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENML 350
Cdd:cd19880    11 VNELARFNRIQ-------PQYKLLNERGPAHAKIFTVQLTLGEQTWEAEGSSIKKAQHAAASKAL 68
DSRM_DRADA_rpt1 cd19913
first double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...
 287-353 8.38e-04

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: 38.31  E-value: 8.38e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1934695737 287 NPISRLAQIQQAKKEkEPEYVLLTERGLPRRREFVMQVKV-GNHTAEGTGTNKKVAKRNAAENMLEIL 353
Cdd:cd19913     2 NPVSGLMEYAQFLGQ-TCEFLLLEQSGPSHDPRFKFQAVIdGRRFPPAEASSKKVAKKDAAAIALKIL 68
DSRM_TARBP2_rpt1 cd19890
first double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar ...
 285-353 9.82e-04

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: 38.19  E-value: 9.82e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1934695737 285 GMNPISrLAQIQQAKKEKEPEYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEIL 353
Cdd:cd19890     2 GKTPIS-LLQEYGTRIGKTPVYDLLKAEGQAHQPNFTFRVTVGDISCTGQGPSKKAAKHKAAEVALKLL 69
DSRM_PRKRA_rpt1 cd19889
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 285-353 1.12e-03

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: 37.97  E-value: 1.12e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1934695737 285 GMNPISRLAQIQqAKKEKEPEYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEIL 353
Cdd:cd19889     1 GKTPIQLLHEYG-TKTGNIPVYELEKSEGQAHLPSFTFRVTVGDITCTGEGTSKKLAKHRAAEAALNIL 68
DSRM_STAU1_rpt1 cd19879
first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 286-350 1.16e-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: 37.75  E-value: 1.16e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1934695737 286 MNPISRLAQIQqakkekePEYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENML 350
Cdd:cd19879     9 VNELARFNKIQ-------PEYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTSIKKAQHAAAAKAL 66
DSRM_RNAse_III_meta_like cd19877
double-stranded RNA binding motif of metazoan ribonuclease III (RNase III) and similar ...
 294-353 1.77e-03

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: 37.25  E-value: 1.77e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934695737 294 QIQQA-----KKEKE----PEYVLLTERGLPRRREFVMQVKV-GNHTAEGTGTNKKVAKRNAAENMLEIL 353
Cdd:cd19877     6 QLQQCcltlrTEGKKepdiPEYKVLQKSGPTNTRVYTVAVYFrGERIATGTGSSIQQAEMNAAEKALEKL 75
DSRM_AtDRB-like cd19878
double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins ...
 191-250 2.69e-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: 36.73  E-value: 2.69e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1934695737 191 EIALKRNLPVNFEVARESGPPHMKSFVTKVSVGGFIGEGEG-KSKKISKKNAAIAVLEELK 250
Cdd:cd19878     7 EYAQKKKIPLPKYESAKSGPSHQPTFVSTVIVLGVRFSSEGaKNKKQAEQSAAKVALKELG 67
DSRM_STRBP_rpt1 cd19909
first double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...
 200-249 2.76e-03

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: 36.93  E-value: 2.76e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1934695737 200 VNFEVARESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:cd19909    19 LQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAM 68
DSRM_STRBP-like_rpt1 cd19894
first double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family ...
 202-249 3.12e-03

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


Pssm-ID: 380723  Cd Length: 63  Bit Score: 36.21  E-value: 3.12e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1934695737 202 FEVARESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEEL 249
Cdd:cd19894    16 YKLASQTGPVHAPQFTMSVEVDGVTYEASGPSKKTAKLHVAVKVLQAM 63
DSRM_STRBP-like_rpt1 cd19894
first double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family ...
 286-353 3.69e-03

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


Pssm-ID: 380723  Cd Length: 63  Bit Score: 36.21  E-value: 3.69e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1934695737 286 MNPISRLAQIQQAKkekepEYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEIL 353
Cdd:cd19894     1 MNALMRLNQLRPGL-----QYKLASQTGPVHAPQFTMSVEVDGVTYEASGPSKKTAKLHVAVKVLQAM 63
DSRM_RED1_rpt1 cd19895
first double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins; ...
 305-350 5.16e-03

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: 35.83  E-value: 5.16e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1934695737 305 EYVLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENML 350
Cdd:cd19895    20 QYKLLSQTGPVHAPVFVMSVEVNGQVFEGSGPTKKKAKLHAAEKAL 65
DSRM_RED1_rpt1 cd19895
first double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins; ...
 200-253 7.28e-03

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: 35.44  E-value: 7.28e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1934695737 200 VNFEVARESGPPHMKSFVTKVSVGGFIGEGEGKSKKISKKNAAIAVLEELKKLP 253
Cdd:cd19895    19 LQYKLLSQTGPVHAPVFVMSVEVNGQVFEGSGPTKKKAKLHAAEKALRSFVQFP 72
 
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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