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Conserved domains on  [gi|67078460|ref|NP_001019951|]
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interferon-inducible double-stranded RNA-dependent protein kinase activator A [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DSRM_PRKRA_rpt3 cd19892
third double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 239-310 5.30e-46

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


:

Pssm-ID: 380721  Cd Length: 72  Bit Score: 150.04  E-value: 5.30e-46
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 67078460 239 TDYIQLLSEIAKEQGFSITYLDIEELSANGQYQCLAELSTSPITVCHGSGISCGNAQSDAAHNALQYLKIIA 310
Cdd:cd19892   1 TDYVQMLGEVAEEQGFNVTYLDIDELSVNGQYQCLAELSTSPVTVCHGTGISCGNAHNDAAHNALQYLKIMA 72
DSRM_PRKRA_rpt1 cd19889
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 32-102 3.26e-42

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: 140.43  E-value: 3.26e-42
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 67078460  32 GKTPIQVLHEYGTKTKNIPVYECERSDVQVHVPTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAINILKAN 102
Cdd:cd19889   1 GKTPIQLLHEYGTKTGNIPVYELEKSEGQAHLPSFTFRVTVGDITCTGEGTSKKLAKHRAAEAALNILKGN 71
DSRM_PRKRA_rpt2 cd19891
second double-stranded RNA binding motif of protein activator of the interferon-induced ...
 126-192 1.98e-41

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: 138.15  E-value: 1.98e-41
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 67078460 126 NPIGSLQELAIHHGWRLPEYTLSQEGGPAHKREYTTICRLESFMETGKGASKKQAKRNAAEKFLAKF 192
Cdd:cd19891   1 NPIGSLQELAVQKGWRLPEYTLAQESGPPHKREFTITCRVETFVETGTGTSKKVAKRNAAEKLLAKF 67
 
Name Accession Description Interval E-value
DSRM_PRKRA_rpt3 cd19892
third double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 239-310 5.30e-46

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


Pssm-ID: 380721  Cd Length: 72  Bit Score: 150.04  E-value: 5.30e-46
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 67078460 239 TDYIQLLSEIAKEQGFSITYLDIEELSANGQYQCLAELSTSPITVCHGSGISCGNAQSDAAHNALQYLKIIA 310
Cdd:cd19892   1 TDYVQMLGEVAEEQGFNVTYLDIDELSVNGQYQCLAELSTSPVTVCHGTGISCGNAHNDAAHNALQYLKIMA 72
DSRM_PRKRA_rpt1 cd19889
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 32-102 3.26e-42

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: 140.43  E-value: 3.26e-42
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 67078460  32 GKTPIQVLHEYGTKTKNIPVYECERSDVQVHVPTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAINILKAN 102
Cdd:cd19889   1 GKTPIQLLHEYGTKTGNIPVYELEKSEGQAHLPSFTFRVTVGDITCTGEGTSKKLAKHRAAEAALNILKGN 71
DSRM_PRKRA_rpt2 cd19891
second double-stranded RNA binding motif of protein activator of the interferon-induced ...
 126-192 1.98e-41

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: 138.15  E-value: 1.98e-41
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 67078460 126 NPIGSLQELAIHHGWRLPEYTLSQEGGPAHKREYTTICRLESFMETGKGASKKQAKRNAAEKFLAKF 192
Cdd:cd19891   1 NPIGSLQELAVQKGWRLPEYTLAQESGPPHKREFTITCRVETFVETGTGTSKKVAKRNAAEKLLAKF 67
DSRM smart00358
Double-stranded RNA binding motif;
35-100 2.92e-21

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 85.39  E-value: 2.92e-21
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 67078460     35 PIQVLHEYGTKTKNIPVYECERSDVQVHVPTFTFRVTVGD-ITCTGEGTSKKLAKHRAAEAAINILK 100
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGkRTGEGEGSSKKEAKQRAAEAALRSLK 67
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 35-99 4.51e-16

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: 71.49  E-value: 4.51e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 67078460    35 PIQVLHEYGTKTKNIPVYECERSDVQVHVPTFTFRVTVGD-ITCTGEGTSKKLAKHRAAEAAINIL 99
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGkLYGSGTGSSKKEAEQLAAEKALEKL 66
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
111-196 7.53e-14

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 69.36  E-value: 7.53e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67078460 111 DPLMPDPSKQPkNQLNPIGSLQELAIHHGWRLPEYTLSQEGGPAHKREYTTICRLE-SFMETGKGASKKQAKRNAAEKFL 189
Cdd:COG0571 144 EPRLEEIAPGG-AGKDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGgKVLGEGTGRSKKEAEQAAAKAAL 222


                ....*..
gi 67078460 190 AKFSNIS 196
Cdd:COG0571 223 EKLGKKE 229
DSRM smart00358
Double-stranded RNA binding motif;
127-191 3.25e-13

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 63.44  E-value: 3.25e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 67078460    127 PIGSLQELAIHHGWrLPEYTLSQEGGPAHKREYTTICRLESFME-TGKGASKKQAKRNAAEKFLAK 191
Cdd:smart00358   1 PKSLLQELAQKRKL-PPEYELVKEEGPDHAPRFTVTVKVGGKRTgEGEGSSKKEAKQRAAEAALRS 65
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 125-191 1.34e-11

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: 62.99  E-value: 1.34e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 67078460   125 LNPIGSLQELAIHHGWRLPEYTLSQEGGPAHKREYTTICRLE-SFMETGKGASKKQAKRNAAEKFLAK 191
Cdd:TIGR02191 152 KDYKTALQEWAQARGKPLPEYRLIKEEGPDHDKEFTVEVSVNgEPYGEGKGKSKKEAEQNAAKAALEK 219
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 127-191 1.56e-11

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: 58.78  E-value: 1.56e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 67078460   127 PIGSLQELAIHHGWRLPEYTLSQEGgPAHKREYTTICRLESF-METGKGASKKQAKRNAAEKFLAK 191
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEG-PPHSPKFTVTVKVDGKlYGSGTGSSKKEAEQLAAEKALEK 65
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
47-102 4.59e-07

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 49.71  E-value: 4.59e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 67078460  47 KNIPVYECERSDVQVHVPTFTFRVTVGD-ITCTGEGTSKKLAKHRAAEAAINILKAN 102
Cdd:COG0571 172 LPLPEYEVVEEEGPDHAKTFTVEVLVGGkVLGEGTGRSKKEAEQAAAKAALEKLGKK 228
PHA02701 PHA02701
ORF020 dsRNA-binding PKR inhibitor; Provisional
 35-107 5.16e-07

ORF020 dsRNA-binding PKR inhibitor; Provisional


Pssm-ID: 177482 [Multi-domain]  Cd Length: 183  Bit Score: 49.18  E-value: 5.16e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 67078460   35 PIQVLHEYGTKTKNIPVYECERSDVQVHVPTFTFRVTV-GDITCTGEGTSKKLAKHRAAEAAINILKANASICF 107
Cdd:PHA02701 110 PVSAVNEFCMRTHRPLEFCETRSGGHDHCPLFTCTIVVsGKVVATASGCSKKLARHAACADALTILINNCGISF 183
DSRM smart00358
Double-stranded RNA binding motif;
241-307 7.24e-06

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 43.02  E-value: 7.24e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 67078460    241 YIQLLSEIAKEQGFSITYLDIEE--LSANGQYQCLAELSTspITVCHGSGISCGNAQSDAAHNALQYLK 307
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELVKEegPDHAPRFTVTVKVGG--KRTGEGEGSSKKEAKQRAAEAALRSLK 67
seadorna_dsRNA TIGR04238
seadornavirus double-stranded RNA-binding protein; This protein family occurs in the ...
 35-102 2.00e-03

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: 38.77  E-value: 2.00e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 67078460    35 PIQVLHEYGTK-TKNIPVYE---CERSDvqvHVPTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAINILKAN 102
Cdd:TIGR04238   2 VVGMLQELAVKrGLELPVYEkvgKEGPD---HAPTFTIKLTANDIEVIEAASSKKQAEKLAAATIYEDMKEN 70
Staufen_C pfam16482
Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of ...
 243-312 2.59e-03

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: 36.81  E-value: 2.59e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 67078460   243 QLLSEIAKEQGFSITYLDIEELSANGQYQCLAeLSTSPITVCHGSGISCgnaqsDAAHN--ALQYLKIIAER 312
Cdd:pfam16482  44 QQLEYLARVQGFQVEYSDFPRQNKNEFLSLLT-LSSQPVQMTHGIGSSL-----EASHDqaALSALKQLSEQ 109
 
Name Accession Description Interval E-value
DSRM_PRKRA_rpt3 cd19892
third double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 239-310 5.30e-46

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


Pssm-ID: 380721  Cd Length: 72  Bit Score: 150.04  E-value: 5.30e-46
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 67078460 239 TDYIQLLSEIAKEQGFSITYLDIEELSANGQYQCLAELSTSPITVCHGSGISCGNAQSDAAHNALQYLKIIA 310
Cdd:cd19892   1 TDYVQMLGEVAEEQGFNVTYLDIDELSVNGQYQCLAELSTSPVTVCHGTGISCGNAHNDAAHNALQYLKIMA 72
DSRM_PRKRA_rpt1 cd19889
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 32-102 3.26e-42

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: 140.43  E-value: 3.26e-42
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 67078460  32 GKTPIQVLHEYGTKTKNIPVYECERSDVQVHVPTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAINILKAN 102
Cdd:cd19889   1 GKTPIQLLHEYGTKTGNIPVYELEKSEGQAHLPSFTFRVTVGDITCTGEGTSKKLAKHRAAEAALNILKGN 71
DSRM_PRKRA_rpt2 cd19891
second double-stranded RNA binding motif of protein activator of the interferon-induced ...
 126-192 1.98e-41

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: 138.15  E-value: 1.98e-41
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 67078460 126 NPIGSLQELAIHHGWRLPEYTLSQEGGPAHKREYTTICRLESFMETGKGASKKQAKRNAAEKFLAKF 192
Cdd:cd19891   1 NPIGSLQELAVQKGWRLPEYTLAQESGPPHKREFTITCRVETFVETGTGTSKKVAKRNAAEKLLAKF 67
DSRM_PRKRA-like_rpt3 cd19864
third double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family ...
 239-310 4.89e-37

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: 126.96  E-value: 4.89e-37
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 67078460 239 TDYIQLLSEIAKEQGFSITYLDIEELSANGQYQCLAELSTSPITVCHGSGISCGNAQSDAAHNALQYLKIIA 310
Cdd:cd19864   1 DDYCELLQELAEEQKFKVTYVDIEELSSSGKYQCLVQLSTLPPTVCHGSGASLEEAKEEAARNALEYLKIMT 72
DSRM_PRKRA-like_rpt1 cd19862
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 33-102 2.94e-33

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: 116.98  E-value: 2.94e-33
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67078460  33 KTPIQVLHEYGTKTKNIPVYECERSDVQVHVPTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAINILKAN 102
Cdd:cd19862   1 KTPISVLQELCAKRGITPKYELISSEGAVHEPTFTFRVTVGDITATGSGTSKKKAKHAAAENALEQLKGS 70
DSRM_PRKRA-like_rpt2 cd19863
second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family ...
 126-192 1.14e-31

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: 112.86  E-value: 1.14e-31
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 67078460 126 NPIGSLQELAIHHGWRLPEYTLSQEGGPAHKREYTTICRLESFMETGKGASKKQAKRNAAEKFLAKF 192
Cdd:cd19863   1 NPVGILQELCVQRRWRLPEYEVEQESGPPHEKEFTIACRVENFSETGSGKSKKLAKRAAAEKMLTRL 67
DSRM_TARBP2_rpt3 cd19893
third double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar ...
 243-310 5.99e-28

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


Pssm-ID: 380722  Cd Length: 72  Bit Score: 103.46  E-value: 5.99e-28
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 67078460 243 QLLSEIAKEQGFSITYLDIEELSANGQYQCLAELSTSPITVCHGSGISCGNAQSDAAHNALQYLKIIA 310
Cdd:cd19893   5 RLLRELSEEQAFHISYLDIEELSLSGLCQCLVELSTQPATVCHGSATTRDAARANAAHNALQYLKIMA 72
DSRM_TARBP2_rpt2 cd10844
second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and ...
 126-191 5.05e-26

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: 98.25  E-value: 5.05e-26
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 67078460 126 NPIGSLQELAIHHGWRLPEYTLSQEGGPAHKREYTTICRLESFMETGKGASKKQAKRNAAEKFLAK 191
Cdd:cd10844   1 NPVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFIEIGSGTSKKLAKRNAAAKMLLR 66
DSRM_TARBP2_rpt1 cd19890
first double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar ...
 31-100 9.98e-25

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: 94.81  E-value: 9.98e-25
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67078460  31 PGKTPIQVLHEYGTKTKNIPVYECERSDVQVHVPTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAINILK 100
Cdd:cd19890   1 PGKTPISLLQEYGTRIGKTPVYDLLKAEGQAHQPNFTFRVTVGDISCTGQGPSKKAAKHKAAEVALKLLK 70
DSRM smart00358
Double-stranded RNA binding motif;
35-100 2.92e-21

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 85.39  E-value: 2.92e-21
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 67078460     35 PIQVLHEYGTKTKNIPVYECERSDVQVHVPTFTFRVTVGD-ITCTGEGTSKKLAKHRAAEAAINILK 100
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGkRTGEGEGSSKKEAKQRAAEAALRSLK 67
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 35-99 4.51e-16

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: 71.49  E-value: 4.51e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 67078460    35 PIQVLHEYGTKTKNIPVYECERSDVQVHVPTFTFRVTVGD-ITCTGEGTSKKLAKHRAAEAAINIL 99
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGkLYGSGTGSSKKEAEQLAAEKALEKL 66
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 40-96 2.59e-14

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: 66.15  E-value: 2.59e-14
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 67078460  40 HEYGTKTKNI-PVYECERSDVQvHVPTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAI 96
Cdd:cd00048   1 NELCQKNKWPpPEYETVEEGGP-HNPRFTCTVTVNGQTFEGEGKSKKEAKQAAAEKAL 57
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 126-192 6.54e-14

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: 65.59  E-value: 6.54e-14
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 67078460 126 NPIGSLQELAIHHGWRLPEYTLSQEGGPAHKREYTTICRL-ESFMETGKGASKKQAKRNAAEKFLAKF 192
Cdd:cd10845   2 DYKTALQEYLQKRGLPLPEYELVEEEGPDHNKTFTVEVKVnGKVIGEGTGRSKKEAEQAAAKAALEKL 69
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
111-196 7.53e-14

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 69.36  E-value: 7.53e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67078460 111 DPLMPDPSKQPkNQLNPIGSLQELAIHHGWRLPEYTLSQEGGPAHKREYTTICRLE-SFMETGKGASKKQAKRNAAEKFL 189
Cdd:COG0571 144 EPRLEEIAPGG-AGKDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGgKVLGEGTGRSKKEAEQAAAKAAL 222


                ....*..
gi 67078460 190 AKFSNIS 196
Cdd:COG0571 223 EKLGKKE 229
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 33-99 3.21e-13

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: 63.44  E-value: 3.21e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 67078460  33 KTPIQVLHEYGTKTKnIPVYECERSDVQVHVPTFTFRVTVGDITC-TGEGTSKKLAKHRAAEAAINIL 99
Cdd:cd19875   1 KNPVSALNEYCQKRG-LSLEFVDVSVGPDHCPGFTASATIDGIVFaSATGTSKKEAKRAAAKLALKKL 67
DSRM smart00358
Double-stranded RNA binding motif;
127-191 3.25e-13

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 63.44  E-value: 3.25e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 67078460    127 PIGSLQELAIHHGWrLPEYTLSQEGGPAHKREYTTICRLESFME-TGKGASKKQAKRNAAEKFLAK 191
Cdd:smart00358   1 PKSLLQELAQKRKL-PPEYELVKEEGPDHAPRFTVTVKVGGKRTgEGEGSSKKEAKQRAAEAALRS 65
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 132-189 1.34e-12

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


Pssm-ID: 380679 [Multi-domain]  Cd Length: 57  Bit Score: 61.53  E-value: 1.34e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 67078460 132 QELAIHHGWRLPEYTLSQEGGPaHKREYTTICRLESFMETGKGASKKQAKRNAAEKFL 189
Cdd:cd00048   1 NELCQKNKWPPPEYETVEEGGP-HNPRFTCTVTVNGQTFEGEGKSKKEAKQAAAEKAL 57
DSRM_STAU_rpt5 cd19861
fifth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 243-307 8.64e-12

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: 59.54  E-value: 8.64e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 67078460 243 QLLSEIAKEQGFSITYLDIEELSaNGQYQCLAELSTSPITVCHGSGISCGNAQSDAAHNALQYLK 307
Cdd:cd19861   3 EQLEYLAKVLGFSVEFTDFPKGN-KSEYLSLVSLGTEPPQVCHGSGSSVEESRDAAALNALKLLK 66
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 125-191 1.34e-11

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: 62.99  E-value: 1.34e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 67078460   125 LNPIGSLQELAIHHGWRLPEYTLSQEGGPAHKREYTTICRLE-SFMETGKGASKKQAKRNAAEKFLAK 191
Cdd:TIGR02191 152 KDYKTALQEWAQARGKPLPEYRLIKEEGPDHDKEFTVEVSVNgEPYGEGKGKSKKEAEQNAAKAALEK 219
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 127-191 1.56e-11

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: 58.78  E-value: 1.56e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 67078460   127 PIGSLQELAIHHGWRLPEYTLSQEGgPAHKREYTTICRLESF-METGKGASKKQAKRNAAEKFLAK 191
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEG-PPHSPKFTVTVKVDGKlYGSGTGSSKKEAEQLAAEKALEK 65
DSRM_STAU_rpt3 cd19859
third double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 127-189 8.70e-10

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: 53.94  E-value: 8.70e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 67078460 127 PIGSLQELAIHHGWRLpEYTLSQEGGPAHKREYTTICRLESFMETGKGASKKQAKRNAAEKFL 189
Cdd:cd19859   1 EISLVHEIALKRNLTV-NFEVLRESGPPHMKNFITRCTVGSFVTEGEGNSKKVSKKRAAEKML 62
DSRM_STAU_rpt4 cd19860
fourth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 126-189 1.79e-09

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


Pssm-ID: 380689  Cd Length: 68  Bit Score: 53.10  E-value: 1.79e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 67078460 126 NPIGSLQELAIHHGWRLPEYTLSQEGGPAHKREYTTICRLESFMETGKGASKKQAKRNAAEKFL 189
Cdd:cd19860   1 NPISRLIQIQQARKEKEPVYSLVAERGTPRRREFVMQVTVGDKTATGTGPNKKLAKRNAAEAML 64
DSRM_DRADA_rpt2 cd19914
second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...
 33-99 2.59e-09

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: 52.93  E-value: 2.59e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 67078460  33 KTPIQVLHEYGTKTKNIPVYECERSDVQVHVPTFTFRVTVGDITC-TGEGTSKKLAKHRAAEAAINIL 99
Cdd:cd19914   1 KNPISVLMEHSQKSGNMCEFQLLSQEGPPHDPKFTYCVKVGEQTFpSVVANSKKVAKQMAAEEAVKEL 68
DSRM_STAU_rpt3 cd19859
third double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 35-96 5.58e-09

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: 51.63  E-value: 5.58e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 67078460  35 PIQVLHEYGTKtKNIPV-YECERSDVQVHVPTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAI 96
Cdd:cd19859   1 EISLVHEIALK-RNLTVnFEVLRESGPPHMKNFITRCTVGSFVTEGEGNSKKVSKKRAAEKML 62
DSRM_STAU2_rpt3 cd19884
third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 33-99 7.64e-09

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: 51.55  E-value: 7.64e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 67078460  33 KTPIQVLHEYGTKtKNIPV-YECERSDVQVHVPTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAINIL 99
Cdd:cd19884   1 KSEISLVFEIALK-RNMPVsFEVIKESGPPHMKSFVTRVTVGEFTAEGEGNSKKLSKKRAATSVLQEL 67
DSRM_STAU_rpt4 cd19860
fourth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 36-99 1.15e-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: 50.79  E-value: 1.15e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 67078460  36 IQVLHeygTKTKNIPVYE--CERSDVQVHvpTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAINIL 99
Cdd:cd19860   7 IQIQQ---ARKEKEPVYSlvAERGTPRRR--EFVMQVTVGDKTATGTGPNKKLAKRNAAEAMLELL 67
DSRM_STAU1_rpt4 cd19885
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 125-189 1.47e-08

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: 51.24  E-value: 1.47e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 67078460 125 LNPIGSLQELAIHHGWRLPEYTLSQEGGPAHKREYTTICRLESFMETGKGASKKQAKRNAAEKFL 189
Cdd:cd19885  10 MNPISRLAQIQQAKKEKEPEYTLITERGLPRRREFVMQVKVGNQTAEGMGPNKKVAKRNAAEKML 74
DSRM_DGCR8_rpt1 cd19867
first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and ...
 32-99 2.02e-08

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: 50.41  E-value: 2.02e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 67078460  32 GKTPIQVLHEYGTKT-KNIPVY---ECERSDVqvhvpTFTFRVTVGDIT-CTGEGTSKKLAKHRAAEAAINIL 99
Cdd:cd19867   5 GKSPVCILHEYCQRVlKVQPEYnftETENAAT-----PFSAEVFINGVEyGSGEASSKKLAKQKAARATLEIL 72
DSRM_STRBP_RED-like_rpt1 cd19865
first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 33-97 4.55e-08

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: 49.27  E-value: 4.55e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 67078460  33 KTPIQVLHEygtkTKNIPVYECERSDVQVHVPTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAIN 97
Cdd:cd19865   1 KNALMQLNE----LRPGLQYKLTSQTGPVHAPVFTMSVEVNGQTFEGTGRSKKKAKLEAAEKALR 61
DSRM_STAU2_rpt4 cd19886
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 125-189 8.09e-08

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: 49.18  E-value: 8.09e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 67078460 125 LNPIGSLQELAIHHGWRLPEYTLSQEGGPAHKREYTTICRLESFMETGKGASKKQAKRNAAEKFL 189
Cdd:cd19886   3 MNPISRLAQIQQAKKEKEPEYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKRNAAEAML 67
DSRM_DRADA cd19902
double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) ...
 33-101 9.40e-08

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: 48.44  E-value: 9.40e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67078460  33 KTPIQVLHEYGTKTKNIPVYECERSDVQVHVPTFTFRVTVGDIT-CTGEGTSKKLAKHRAAEAAINILKA 101
Cdd:cd19902   1 KNPVSALMEYAQSRGVTAEIEVLSQSGPPHNPRFKAAVFVGGRRfPSVEASSKKDAKQEAADLALRALIA 70
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 45-99 2.85e-07

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


Pssm-ID: 380682 [Multi-domain]  Cd Length: 69  Bit Score: 47.10  E-value: 2.85e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 67078460  45 KTKNIPVYECERSDVQVHVPTFTFRVTV-GDITCTGEGTSKKLAKHRAAEAAINIL 99
Cdd:cd10845  14 RGLPLPEYELVEEEGPDHNKTFTVEVKVnGKVIGEGTGRSKKEAEQAAAKAALEKL 69
DSRM_RED1_rpt2 cd19898
second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar ...
 32-96 3.28e-07

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


Pssm-ID: 380727  Cd Length: 70  Bit Score: 47.11  E-value: 3.28e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 67078460  32 GKTPIQVLHEYGTKTKnipvYECERSDVQVHVPTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAI 96
Cdd:cd19898   2 GKNPVMILNELRPGLK----YEFVSESGESHAKNFVMSVTVDGQTFEGSGRNKKLAKARAAQAAL 62
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
47-102 4.59e-07

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 49.71  E-value: 4.59e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 67078460  47 KNIPVYECERSDVQVHVPTFTFRVTVGD-ITCTGEGTSKKLAKHRAAEAAINILKAN 102
Cdd:COG0571 172 LPLPEYEVVEEEGPDHAKTFTVEVLVGGkVLGEGTGRSKKEAEQAAAKAALEKLGKK 228
PHA02701 PHA02701
ORF020 dsRNA-binding PKR inhibitor; Provisional
 35-107 5.16e-07

ORF020 dsRNA-binding PKR inhibitor; Provisional


Pssm-ID: 177482 [Multi-domain]  Cd Length: 183  Bit Score: 49.18  E-value: 5.16e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 67078460   35 PIQVLHEYGTKTKNIPVYECERSDVQVHVPTFTFRVTV-GDITCTGEGTSKKLAKHRAAEAAINILKANASICF 107
Cdd:PHA02701 110 PVSAVNEFCMRTHRPLEFCETRSGGHDHCPLFTCTIVVsGKVVATASGCSKKLARHAACADALTILINNCGISF 183
DSRM_DCL_plant cd19869
double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant ...
 132-191 8.85e-07

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


Pssm-ID: 380698  Cd Length: 70  Bit Score: 45.82  E-value: 8.85e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 67078460 132 QELAIHHGWRLPEYTLSQEGGPAHKREYTTICRLE----SFMETGKG---ASKKQAKRNAAEKFLAK 191
Cdd:cd19869   1 NEICLKRRWPMPVYRCVEEEGPAHAKRFTYMVRVKiperGWTIECEGepmRSKKRAKDSAALLLLEY 67
DSRM_STRBP_RED-like_rpt2 cd19866
second double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 33-99 9.36e-07

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: 45.62  E-value: 9.36e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 67078460  33 KTPIQVLHEYGTKTKnipvYECERSDVQVHVPTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAINIL 99
Cdd:cd19866   1 KNPVMLLNELRPGLK----YKCLSESGESHAKSFVMSVTVDGQTFEGTGRSKKLAKAAAAQAALAKL 63
seadorna_dsRNA TIGR04238
seadornavirus double-stranded RNA-binding protein; This protein family occurs in the ...
 126-200 2.10e-06

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: 47.63  E-value: 2.10e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 67078460   126 NPIGSLQELAIHHGWRLPEY-TLSQEgGPAHKREYTTICRLESFMETGKGASKKQAKRNAAEKFLAKFS-NISPENH 200
Cdd:TIGR04238   1 NVVGMLQELAVKRGLELPVYeKVGKE-GPDHAPTFTIKLTANDIEVIEAASSKKQAEKLAAATIYEDMKeNGLLEVH 76
DSRM_STAU1_rpt1 cd19879
first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 33-96 2.71e-06

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: 44.30  E-value: 2.71e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 67078460  33 KTPIQVLHEYGTKTKNIPVYECERSDVQVHVPTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAI 96
Cdd:cd19879   3 KTPMCLVNELARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTSIKKAQHAAAAKAL 66
DSRM_STRBP_RED-like_rpt1 cd19865
first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 126-192 6.09e-06

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: 43.10  E-value: 6.09e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 67078460 126 NPIGSLQELaiHHGWrlpEYTLSQEGGPAHKREYTTICRLESFMETGKGASKKQAKRNAAEKFLAKF 192
Cdd:cd19865   2 NALMQLNEL--RPGL---QYKLTSQTGPVHAPVFTMSVEVNGQTFEGTGRSKKKAKLEAAEKALRSF 63
DSRM_AtDRB-like_rpt2 cd19908
second double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 39-100 6.87e-06

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: 6.87e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 67078460  39 LHEYGTKTK-NIPVYECERSDVQvHVPTFTFRVTVGDITCTGEGT-SKKLAKHRAAEAAINILK 100
Cdd:cd19908   7 LQEYAQKAGlPLPLYTTVRSGPG-HVPTFTCTVEIAGITFTGEAAkTKKQAEKSAARTAWSSIK 69
DSRM smart00358
Double-stranded RNA binding motif;
241-307 7.24e-06

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 43.02  E-value: 7.24e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 67078460    241 YIQLLSEIAKEQGFSITYLDIEE--LSANGQYQCLAELSTspITVCHGSGISCGNAQSDAAHNALQYLK 307
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELVKEegPDHAPRFTVTVKVGG--KRTGEGEGSSKKEAKQRAAEAALRSLK 67
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 32-96 7.77e-06

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


Pssm-ID: 380699  Cd Length: 75  Bit Score: 43.04  E-value: 7.77e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 67078460  32 GKTPIQVLHEYGTKTK-NIPVYECERSDVQVHVPTFTFRVTVGDIT---CTGEGTsKKLAKHRAAEAAI 96
Cdd:cd19870   1 GKHPVSALMELCNKRKwGPPEFRLVEESGPPHRKHFLFKVVVNGVEyqpSVASGN-KKDAKAQAATVAL 68
PHA03103 PHA03103
double-strand RNA-binding protein; Provisional
 25-107 9.74e-06

double-strand RNA-binding protein; Provisional


Pssm-ID: 222987 [Multi-domain]  Cd Length: 183  Bit Score: 45.52  E-value: 9.74e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67078460   25 KMITAKPGKTPIQVLHEYGTKTKNIPVYECERSDvQVHVPTFTFRVTVGDITC-TGEGTSKKLAKHRAAEAAINILKANA 103
Cdd:PHA03103 101 KKIISWKDKNPCTVINEYCQITSRDWSINITSSG-PSHSPTFTASVIISGIKFkPAIGSTKKEAKNNAAKLAMDKILNYV 179


                 ....
gi 67078460  104 SICF 107
Cdd:PHA03103 180 IIKF 183
DSRM_STAU_rpt1 cd19857
first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 126-189 9.77e-06

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


Pssm-ID: 380686  Cd Length: 64  Bit Score: 42.64  E-value: 9.77e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 67078460 126 NPIGSLQELAIHHGWRlPEYTLSQEGGPAHKREYT---TICRLESFmeTGKGASKKQAKRNAAEKFL 189
Cdd:cd19857   1 TPMCLLNELARFNKIR-PQYTLVDEEGPAHKKTFTvklTLGDEEEY--EASGSSIKKAQHAAAEKAL 64
DSRM_DCL_plant cd19869
double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant ...
 50-100 3.62e-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: 41.20  E-value: 3.62e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 67078460  50 PVYECERSDVQVHVPTFTFRVTV------GDITCTGEGT-SKKLAKHRAAEAAINILK 100
Cdd:cd19869  12 PVYRCVEEEGPAHAKRFTYMVRVkipergWTIECEGEPMrSKKRAKDSAALLLLEYLK 69
DSRM_STAU1_rpt3 cd19883
third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 33-99 3.96e-05

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: 41.15  E-value: 3.96e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 67078460  33 KTPIQVLHEYGTKtKNIPV-YECERSDVQVHVPTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAINIL 99
Cdd:cd19883   1 KSEISQVFEIALK-RNMPVnFEVTKETGPPHMKSFVTKVSVGEFAGEGEGKSKKISKKNAAIAVLEEL 67
DSRM_RNT1p-like cd19876
double-stranded RNA binding motif of Saccharomyces cerevisiae ribonuclease 3 (RNT1p) and ...
 118-191 4.27e-05

double-stranded RNA binding motif of Saccharomyces cerevisiae ribonuclease 3 (RNT1p) and similar proteins; RNT1p (EC 3.1.26.3; also known as ribonuclease III (RNase III)) is a dsRNA-specific nuclease that cleaves eukaryotic pre-ribosomal RNA at the U3 snoRNP-dependent A0 site in the 5'-external transcribed spacer (ETS) and in the 3'-ETS. RNT1p contains a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380705  Cd Length: 69  Bit Score: 40.78  E-value: 4.27e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 67078460 118 SKQPKNQL-NPIGSLQelaiHHgwrlPEYTLSQEGGPaHKREYTTICR-LESFMETGKGASKKQAKRNAAEKFLAK 191
Cdd:cd19876   1 DKFAKQKLySLIGPAS----LK----PEYVVVKKEGG-NDPNYTVACRiNGEVLGTGVGRSIKKAGQRAAMSALSN 67
DSRM_ADAD2 cd19906
double-stranded RNA binding motif of adenosine deaminase domain-containing protein 2 (ADAD2) ...
 31-99 4.79e-05

double-stranded RNA binding motif of adenosine deaminase domain-containing protein 2 (ADAD2) and similar proteins; ADAD2 (also known as testis nuclear RNA-binding protein-like (TENRL)) is phylogenetically related to a family of adenosine deaminases involved in RNA editing. It is a double-stranded RNA binding protein with unclear biological function. ADAD2 contains a double-stranded RNA binding motif (DSRM) and a C-terminal adenosine-deaminase (editase) domain. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380735  Cd Length: 74  Bit Score: 40.98  E-value: 4.79e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 67078460  31 PGKTPIQVLHEYGTKTKnipvYECERSDVQVHVPTFTFRVTV-----GDITC----TGEGTSKKLAKHRAAEAAINIL 99
Cdd:cd19906   1 PPKTPLSLLHEYAAKLS----LEVEFRETQEEGPVGPFTVSArlrsrVQRTGvvcgAGTARAKKDAKQVAAAAALEKL 74
DSRM_AtDRB-like cd19878
double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins ...
 39-100 6.88e-05

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: 40.19  E-value: 6.88e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 67078460  39 LHEYGTKTK-NIPVYECERsDVQVHVPTFTFRVTVGDITCTGEG-TSKKLAKHRAAEAAINILK 100
Cdd:cd19878   5 LQEYAQKKKiPLPKYESAK-SGPSHQPTFVSTVIVLGVRFSSEGaKNKKQAEQSAAKVALKELG 67
DSRM_ADAD1 cd19905
double-stranded RNA binding motif of adenosine deaminase domain-containing protein 1 (ADAD1) ...
 33-99 1.11e-04

double-stranded RNA binding motif of adenosine deaminase domain-containing protein 1 (ADAD1) and similar proteins; ADAD1 (also known as testis nuclear RNA-binding protein (TENR)) is phylogenetically related to a family of adenosine deaminases involved in RNA editing. It 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. ADAD1 contains a double-stranded RNA binding motif (DSRM) and a C-terminal adenosine-deaminase (editase) domain. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380734  Cd Length: 69  Bit Score: 39.56  E-value: 1.11e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 67078460  33 KTPIQVLHEYGTKTKNIPVYECERSDVQVHVPTFTFRVTV-GDITCTGEGTSKKLAKHRAAEAAINIL 99
Cdd:cd19905   1 KNPVSALHEYAQMTRLKLSFKETVTTGNVAGPYFAFCAVVdGIEYPTGVGKTKKEAKANAAKIALDEL 68
DSRM_STAU_rpt1 cd19857
first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 34-96 1.19e-04

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


Pssm-ID: 380686  Cd Length: 64  Bit Score: 39.56  E-value: 1.19e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 67078460  34 TPIQVLHEYGTKTKNIPVYECERSDVQVHVPTFTFRVTVGD-ITCTGEGTSKKLAKHRAAEAAI 96
Cdd:cd19857   1 TPMCLLNELARFNKIRPQYTLVDEEGPAHKKTFTVKLTLGDeEEYEASGSSIKKAQHAAAEKAL 64
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 126-185 1.53e-04

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: 39.57  E-value: 1.53e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 67078460 126 NPIGSLQELAIHHGWRLPEYTLSQEGGPAHKRE--YTTICRLESFMETGKGASKKQAKRNAA 185
Cdd:cd19870   3 HPVSALMELCNKRKWGPPEFRLVEESGPPHRKHflFKVVVNGVEYQPSVASGNKKDAKAQAA 64
DSRM_STAU1_rpt4 cd19885
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 66-112 2.46e-04

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: 39.30  E-value: 2.46e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 67078460  66 FTFRVTVGDITCTGEGTSKKLAKHRAAEAAINILKanasicFAVPDP 112
Cdd:cd19885  44 FVMQVKVGNQTAEGMGPNKKVAKRNAAEKMLELLG------FKVPQP 84
DSRM_RED2_rpt1 cd19896
first double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar proteins; ...
 61-96 2.71e-04

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


Pssm-ID: 380725  Cd Length: 74  Bit Score: 38.92  E-value: 2.71e-04
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 67078460  61 VHVPTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAI 96
Cdd:cd19896  30 VHAPVFAVAVEVNGLTFEGTGPTKKKAKMRAAEMAL 65
DND1_DSRM pfam14709
double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead ...
 131-189 3.22e-04

double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead end protein 1 (DND1_HUMAN) homologous to double strand RNA binding domains (PF00035, PF00333)


Pssm-ID: 405408  Cd Length: 80  Bit Score: 38.86  E-value: 3.22e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67078460   131 LQELAIHHGWRLPEYTLSQEGGPAHKREYT---TICRLES--------FMETGKGASKKQAKRNAAEKFL 189
Cdd:pfam14709   7 LEELCQKNKWGSPVYELHSTAGPDGKQLFTykvVIPGIETpfpgviwiFMPGKLCSTKEEAKEAAAEQVL 76
DSRM_STAU_rpt2 cd19858
second double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 64-97 3.61e-04

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: 38.16  E-value: 3.61e-04
                        10        20        30
                ....*....|....*....|....*....|....
gi 67078460  64 PTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAIN 97
Cdd:cd19858  34 PPFYVTLTVGEREFIGEGRTRQAARHDAASKALK 67
DSRM_AtDRB-like_rpt1 cd19907
first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 39-99 4.10e-04

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


Pssm-ID: 380736 [Multi-domain]  Cd Length: 69  Bit Score: 38.23  E-value: 4.10e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 67078460  39 LHEYGTKTK-NIPVYECERSDVQvHVPTFTFRVTV-GDITCTGEGTS-KKLAKHRAAEAAINIL 99
Cdd:cd19907   6 LQEYAQKSClNLPVYACIREGPD-HAPRFRATVTFnGVIFESPPGFPtLKAAEHSAAEVALNSL 68
DSRM_AtDRB-like_rpt1 cd19907
first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 122-193 7.39e-04

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


Pssm-ID: 380736 [Multi-domain]  Cd Length: 69  Bit Score: 37.46  E-value: 7.39e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 67078460 122 KNQLnpigslQELAIHHGWRLPEYTLSQEgGPAHKREY--TTICRLESFMETGKGASKKQAKRNAAEKFLAKFS 193
Cdd:cd19907   3 KSQL------QEYAQKSCLNLPVYACIRE-GPDHAPRFraTVTFNGVIFESPPGFPTLKAAEHSAAEVALNSLA 69
DSRM_RED2_rpt2 cd19899
second double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar ...
 29-99 1.09e-03

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: 37.16  E-value: 1.09e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 67078460  29 AKPGKTPIQVLHEYGTKTKnipvYECERSDVQV-HVPTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAINIL 99
Cdd:cd19899   3 AESEKNPVVLLNELRPGLR----YVCLSETAEKqHIKSFVMAVRVDGRTFEGSGRSKKLAKAQAAQAALQAL 70
DSRM_DHX9_rpt1 cd19854
first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 39-100 1.49e-03

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


Pssm-ID: 380683  Cd Length: 69  Bit Score: 36.48  E-value: 1.49e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 67078460  39 LHEYGTKTKNIPVYECeRSDVQVHVPTFTFRVTVG--DITCTGEGTSKKLAKHRAAEAAINILK 100
Cdd:cd19854   6 LYAWCGKKKLTPEYDI-KEAGNKHRQRFKCEVRVEgfDYVGTGNATNKKDAQTNAARDFLNYLV 68
DSRM_RNAse_III_meta_like cd19877
double-stranded RNA binding motif of metazoan ribonuclease III (RNase III) and similar ...
 142-191 1.55e-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: 36.87  E-value: 1.55e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 67078460 142 LPEYTLSQEGGPAHKREYTTIC-----RLEsfmeTGKGASKKQAKRNAAEKFLAK 191
Cdd:cd19877  24 IPEYKVLQKSGPTNTRVYTVAVyfrgeRIA----TGTGSSIQQAEMNAAEKALEK 74
DSRM_STAU1_rpt3 cd19883
third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 145-185 1.69e-03

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: 36.53  E-value: 1.69e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 67078460 145 YTLSQEGGPAHKREYTTICRLESFMETGKGASKKQAKRNAA 185
Cdd:cd19883  20 FEVTKETGPPHMKSFVTKVSVGEFAGEGEGKSKKISKKNAA 60
seadorna_dsRNA TIGR04238
seadornavirus double-stranded RNA-binding protein; This protein family occurs in the ...
 35-102 2.00e-03

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: 38.77  E-value: 2.00e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 67078460    35 PIQVLHEYGTK-TKNIPVYE---CERSDvqvHVPTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAINILKAN 102
Cdd:TIGR04238   2 VVGMLQELAVKrGLELPVYEkvgKEGPD---HAPTFTIKLTANDIEVIEAASSKKQAEKLAAATIYEDMKEN 70
DSRM_DGCR8_rpt2 cd19868
second double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and ...
 33-100 2.01e-03

second double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and similar proteins; DGCR8 is a component of the microprocessor complex that acts as an RNA- and heme-binding protein that is involved in the initial step of microRNA (miRNA) biogenesis. Within the microprocessor complex, DGCR8 functions as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs DROSHA to cleave 11bp away from the junction to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. DGCR8 contains two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380697  Cd Length: 69  Bit Score: 36.11  E-value: 2.01e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 67078460  33 KTPIQVLHEYGTKTKNIPV----YECERSDVQVHvptfTFRVTVGDITCTGEGTSKKLAKHRAAEAainILK 100
Cdd:cd19868   1 PSPYQILQECLKRNHGMGDtelkFEVINDKHQKH----EYTMTVGKHTVTVICKNKKEGKQLAAQA---ILK 65
DSRM_EIF2AK2_rpt1 cd19903
first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha ...
 39-99 2.11e-03

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: 36.21  E-value: 2.11e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 67078460  39 LHEYGTKTKNIPVYECERSDVQVHVPTFTFRVTVGDITC-TGEGTSKKLAKHRAAEAAINIL 99
Cdd:cd19903   7 LNEYCQKQKVVLDYVEVPTSGPSHDPRFTFQVVIDGKEYpEGEGKSKKEAKQAAAKLALEIL 68
DSRM_EIF2AK2 cd20314
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 36-99 2.19e-03

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


Pssm-ID: 380746  Cd Length: 68  Bit Score: 36.22  E-value: 2.19e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 67078460  36 IQVLHEYGTKTKNIPVYECERSDVQVHVPTFTFRVTVGDITC-TGEGTSKKLAKHRAAEAAINIL 99
Cdd:cd20314   4 VSLLNEYCQKERLTVKYEEEKRSGPTHKPRFFCKYIIDGKEYpEGEGKSKKEAKQAAARLAYEEL 68
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 125-186 2.43e-03

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: 36.09  E-value: 2.43e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 67078460 125 LNPIGSLQELAIHHGWRLpEYTLSQEGgPAHKREYT---TICrlESFMETGKGASKKQAKRNAAE 186
Cdd:cd19875   1 KNPVSALNEYCQKRGLSL-EFVDVSVG-PDHCPGFTasaTID--GIVFASATGTSKKEAKRAAAK 61
Staufen_C pfam16482
Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of ...
 243-312 2.59e-03

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: 36.81  E-value: 2.59e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 67078460   243 QLLSEIAKEQGFSITYLDIEELSANGQYQCLAeLSTSPITVCHGSGISCgnaqsDAAHN--ALQYLKIIAER 312
Cdd:pfam16482  44 QQLEYLARVQGFQVEYSDFPRQNKNEFLSLLT-LSSQPVQMTHGIGSSL-----EASHDqaALSALKQLSEQ 109
DSRM_STAU2_rpt1 cd19880
first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 33-96 2.80e-03

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: 35.85  E-value: 2.80e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 67078460  33 KTPIQVLHEYGTKTKNIPVYECERSDVQVHVPTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAI 96
Cdd:cd19880   5 KTPMCLVNELARFNRIQPQYKLLNERGPAHAKIFTVQLTLGEQTWEAEGSSIKKAQHAAASKAL 68
DSRM_DHX9_rpt1 cd19854
first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 143-192 3.25e-03

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


Pssm-ID: 380683  Cd Length: 69  Bit Score: 35.71  E-value: 3.25e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 67078460 143 PEYTLSQEGGPaHKREYTTICRLESFMETGKG--ASKKQAKRNAAEKFLAKF 192
Cdd:cd19854  17 PEYDIKEAGNK-HRQRFKCEVRVEGFDYVGTGnaTNKKDAQTNAARDFLNYL 67
DSRM_PRKRA-like_rpt2 cd19863
second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family ...
 49-96 4.71e-03

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: 35.05  E-value: 4.71e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 67078460  49 IPVYECERSDVQVHVPTFTFRVTVGDITCTGEGTSKKLAKHRAAEAAI 96
Cdd:cd19863  17 LPEYEVEQESGPPHEKEFTIACRVENFSETGSGKSKKLAKRAAAEKML 64
 
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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