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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1954697392 372 YKNLLQELAQKECYGLPSYNTLKSGEPHVPIFVSTVEVEGELFTGREAKTKKQAEMSAARIAYKAIK 438
Cdd:cd19908     3 YKNLLQEYAQKAGLPLPLYTTVRSGPGHVPTFTCTVEIAGITFTGEAAKTKKQAEKSAARTAWSSIK 69

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1954697392   1 MYKTRLQEICQRKRWSLPKYSVEKTGLDHIPHFQATVTVNGLTFTSDDKCNSSKDAQNEAAMRAFNHLS 69
Cdd:cd19907     1 MYKSQLQEYAQKSCLNLPVYACIREGPDHAPRFRATVTFNGVIFESPPGFPTLKAAEHSAAEVALNSLA 69

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1954697392 372 YKNLLQELAQKECYGLPSYNTLKSGEPHVPIFVSTVEVEGELFTGREAKTKKQAEMSAARIAYKAIK 438
Cdd:cd19908     3 YKNLLQEYAQKAGLPLPLYTTVRSGPGHVPTFTCTVEIAGITFTGEAAKTKKQAEKSAARTAWSSIK 69

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1954697392   1 MYKTRLQEICQRKRWSLPKYSVEKTGLDHIPHFQATVTVNGLTFTSDDKCNSSKDAQNEAAMRAFNHLS 69
Cdd:cd19907     1 MYKSQLQEYAQKSCLNLPVYACIREGPDHAPRFRATVTFNGVIFESPPGFPTLKAAEHSAAEVALNSLA 69

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1954697392 144 IYKSKLNEFCQRNRWRPPDYMVKKKGPDHFPQFQATVTVNGVSFTTHDQCKSSKDAQNNAARIAFD 209
Cdd:cd19907     1 MYKSQLQEYAQKSCLNLPVYACIREGPDHAPRFRATVTFNGVIFESPPGFPTLKAAEHSAAEVALN 66

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]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954697392 345 MKEAEHVAAKVALMPLSKNEVQEDESRYKNLLQELAQKECYGLPSYNTLK-SGEPHVPIFVSTVEVEGELFTGREAKTKK 423
Cdd:TIGR02191 127 LEAARKFILKLLIPRIDAIIKEETLKDYKTALQEWAQARGKPLPEYRLIKeEGPDHDKEFTVEVSVNGEPYGEGKGKSKK 206

                          90
                  ....*....|....
gi 1954697392 424 QAEMSAARIAYKAI 437
Cdd:TIGR02191 207 EAEQNAAKAALEKL 220

Double-stranded RNA binding motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1954697392  372 YKNLLQELAQKECYgLPSYNTLK-SGEPHVPIFVSTVEVEGELFTGREAKTKKQAEMSAARIAYKAIK 438
Cdd:smart00358   1 PKSLLQELAQKRKL-PPEYELVKeEGPDHAPRFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRSLK 67

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1954697392   2 YKTRLQEICQRKRWSLPKYSVEKTGLDHIPHFQATVTVNGLTFTSdDKCNSSKDAQNEAAMRAFNHL 68
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYGS-GTGSSKKEAEQLAAEKALEKL 66

Double-stranded RNA binding motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1954697392    2 YKTRLQEICQRKRWsLPKY-SVEKTGLDHIPHFQATVTVNGLTFTSddkCNSS--KDAQNEAAMRA 64
Cdd:smart00358   1 PKSLLQELAQKRKL-PPEYeLVKEEGPDHAPRFTVTVKVGGKRTGE---GEGSskKEAKQRAAEAA 62

dsRNA-specific ribonuclease [Transcription];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954697392 120 GIATARLVIDN---DRCKDTDREAEANIYKSKLNEFCQRNRWRPPDY-MVKKKGPDHFPQFQATVTVNGVSFTThDQCKS 195
Cdd:COG0571   131 GLEAARKFVLRlfePRLEEIAPGGAGKDYKTALQEWLQARGLPLPEYeVVEEEGPDHAKTFTVEVLVGGKVLGE-GTGRS 209

                          90
                  ....*....|....
gi 1954697392 196 SKDAQNNAARIAFD 209
Cdd:COG0571   210 KKEAEQAAAKAALE 223

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1954697392 296 YKNQLQNYTQKSNVNLPAYYH--EGPPHTSHFKGVVGFGEKTYES-HElfPTMKEAEHVAAKVAL 357
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVseEGPPHSPKFTVTVKVDGKLYGSgTG--SSKKEAEQLAAEKAL 63

double-strand RNA-binding protein; Provisional

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1954697392   4 TRLQEICQ--RKRWSLpkySVEKTGLDHIPHFQATVTVNGLTFTSDDKcNSSKDAQNEAAMRAFNHL 68
Cdd:PHA03103  113 TVINEYCQitSRDWSI---NITSSGPSHSPTFTASVIISGIKFKPAIG-STKKEAKNNAAKLAMDKI 175

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1954697392 372 YKNLLQELAQKECYGLPSYNTLKSGEPHVPIFVSTVEVEGELFTGREAKTKKQAEMSAARIAYKAIK 438
Cdd:cd19908     3 YKNLLQEYAQKAGLPLPLYTTVRSGPGHVPTFTCTVEIAGITFTGEAAKTKKQAEKSAARTAWSSIK 69

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1954697392 296 YKNQLQNYTQKSNVNLPAYY--HEGPPHTSHFKGVVGFGEKTYESHELFPTMKEAEHVAAKVALMPLS 361
Cdd:cd19907     2 YKSQLQEYAQKSCLNLPVYAciREGPDHAPRFRATVTFNGVIFESPPGFPTLKAAEHSAAEVALNSLA 69

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1954697392 372 YKNLLQELAQKECYGLPSYNTLKSGEPHVPIFVSTVEVEGELFTGREA-KTKKQAEMSAARIAYKAI 437
Cdd:cd19907     2 YKSQLQEYAQKSCLNLPVYACIREGPDHAPRFRATVTFNGVIFESPPGfPTLKAAEHSAAEVALNSL 68

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1954697392 144 IYKSKLNEFCQRNRWRPPDYMVKKKGPDHFPQFQATVTVNGVSFTTHDQCKSSKDAQNNAARIAFD 209
Cdd:cd19907     1 MYKSQLQEYAQKSCLNLPVYACIREGPDHAPRFRATVTFNGVIFESPPGFPTLKAAEHSAAEVALN 66

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]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954697392 345 MKEAEHVAAKVALMPLSKNEVQEDESRYKNLLQELAQKECYGLPSYNTLK-SGEPHVPIFVSTVEVEGELFTGREAKTKK 423
Cdd:TIGR02191 127 LEAARKFILKLLIPRIDAIIKEETLKDYKTALQEWAQARGKPLPEYRLIKeEGPDHDKEFTVEVSVNGEPYGEGKGKSKK 206

                          90
                  ....*....|....
gi 1954697392 424 QAEMSAARIAYKAI 437
Cdd:TIGR02191 207 EAEQNAAKAALEKL 220

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1954697392 372 YKNLLQELAQKECYGLPSYNTLK-SGEPHVPIFVSTVEVEGELFTGREAKTKKQAEMSAARIAYKAI 437
Cdd:cd10845     3 YKTALQEYLQKRGLPLPEYELVEeEGPDHNKTFTVEVKVNGKVIGEGTGRSKKEAEQAAAKAALEKL 69

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1954697392 150 NEFCQRNRWRPPDYMVKKKGPDHFPQFQATVTVNGVSFTTHDqcKSSKDAQNNAARIA 207
Cdd:cd00048     1 NELCQKNKWPPPEYETVEEGGPHNPRFTCTVTVNGQTFEGEG--KSKKEAKQAAAEKA 56

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1954697392 377 QELAQKECYGLPSYNTLKSGEPHVPIFVSTVEVEGELFTGrEAKTKKQAEMSAARIAY 434
Cdd:cd00048     1 NELCQKNKWPPPEYETVEEGGPHNPRFTCTVTVNGQTFEG-EGKSKKEAKQAAAEKAL 57

Double-stranded RNA binding motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1954697392  145 YKSKLNEFCQRNRWrPPDY-MVKKKGPDHFPQFQATVTVNGVSFTThDQCKSSKDAQNNAARIA 207
Cdd:smart00358   1 PKSLLQELAQKRKL-PPEYeLVKEEGPDHAPRFTVTVKVGGKRTGE-GEGSSKKEAKQRAAEAA 62

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1954697392 145 YKSKLNEFCQRNRWRPPDYMVKKKGPDHFPQFQATVTVNGVSFTThDQCKSSKDAQNNAARIAF 208
Cdd:cd19878     1 YKNLLQEYAQKKKIPLPKYESAKSGPSHQPTFVSTVIVLGVRFSS-EGAKNKKQAEQSAAKVAL 63

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1954697392   2 YKTRLQEICQRKRWSLPKYSVEKTGLDHIPHFQATVTVNGLTFTSDDKCNsSKDAQNEAAMRAFNHL 68
Cdd:cd19878     1 YKNLLQEYAQKKKIPLPKYESAKSGPSHQPTFVSTVIVLGVRFSSEGAKN-KKQAEQSAAKVALKEL 66

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1954697392 296 YKNQLQNYTQKSNVNLPAYY--HEGPPHTSHFKGVVGFGEKTYESHElFPTMKEAEHVAAKVALMPL 360
Cdd:cd19878     1 YKNLLQEYAQKKKIPLPKYEsaKSGPSHQPTFVSTVIVLGVRFSSEG-AKNKKQAEQSAAKVALKEL 66

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1954697392   1 MYKTRLQEICQRKRWSLPKYSVEKTGLDHIPHFQATVTVNGLTFTSdDKCNSSKDAQNEAAMRAFNHL 68
Cdd:cd19908     2 LYKNLLQEYAQKAGLPLPLYTTVRSGPGHVPTFTCTVEIAGITFTG-EAAKTKKQAEKSAARTAWSSI 68

dsRNA-specific ribonuclease [Transcription];

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1954697392   2 YKTRLQEICQRKRWSLPKYSVEK-TGLDHIPHFQATVTVNGLTFTSdDKCNSSKDAQNEAAMRAFNHLSVPE 72
Cdd:COG0571   159 YKTALQEWLQARGLPLPEYEVVEeEGPDHAKTFTVEVLVGGKVLGE-GTGRSKKEAEQAAAKAALEKLGKKE 229

dsRNA-specific ribonuclease [Transcription];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954697392 120 GIATARLVIDN---DRCKDTDREAEANIYKSKLNEFCQRNRWRPPDY-MVKKKGPDHFPQFQATVTVNGVSFTThDQCKS 195
Cdd:COG0571   131 GLEAARKFVLRlfePRLEEIAPGGAGKDYKTALQEWLQARGLPLPEYeVVEEEGPDHAKTFTVEVLVGGKVLGE-GTGRS 209

                          90
                  ....*....|....
gi 1954697392 196 SKDAQNNAARIAFD 209
Cdd:COG0571   210 KKEAEQAAAKAALE 223

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1954697392   6 LQEICQRKRWSLPKYS-VEKTGLDHIPHFQATVTVNGLTFTSDDKCNSSKDAQNEAA 61
Cdd:cd19870     8 LMELCNKRKWGPPEFRlVEESGPPHRKHFLFKVVVNGVEYQPSVASGNKKDAKAQAA 64

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1954697392   6 LQEICQRKRWSLpKYSVEKTGLDHIPHFQATVTVNGLTFTSDDKcNSSKDAQNEAAMRAFNHL 68
Cdd:cd19875     7 LNEYCQKRGLSL-EFVDVSVGPDHCPGFTASATIDGIVFASATG-TSKKEAKRAAAKLALKKL 67

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1954697392 376 LQELAQkecyGLpSYNTL-KSGEPHVPIFVSTVEVEGELFTGReAKTKKQAEMSAARIAYKAI 437
Cdd:cd19865     7 LNELRP----GL-QYKLTsQTGPVHAPVFTMSVEVNGQTFEGT-GRSKKKAKLEAAEKALRSF 63

double-strand RNA-binding protein; Provisional

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1954697392 149 LNEFCQRNRwRPPDYMVKKKGPDHFPQFQATVTVNGVSFTTHDQcKSSKDAQNNAARIAFD 209
Cdd:PHA03103  115 INEYCQITS-RDWSINITSSGPSHSPTFTASVIISGIKFKPAIG-STKKEAKNNAAKLAMD 173

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)

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1954697392   6 LQEICQRKRWSLPKYSVEKT-GLDHIPHFQATVTVNGLT---------FTSDDKCNSSKDAQNEAAMRAFNHLS 69
Cdd:pfam14709   7 LEELCQKNKWGSPVYELHSTaGPDGKQLFTYKVVIPGIEtpfpgviwiFMPGKLCSTKEEAKEAAAEQVLEALG 80

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954697392   2 YKTRLQEICQRKRWSLPKYSVEKTGLDHIPhFQATVTVNGLTFTSDDKcNSSKDAQNEAA 61
Cdd:cd19867     8 PVCILHEYCQRVLKVQPEYNFTETENAATP-FSAEVFINGVEYGSGEA-SSKKLAKQKAA 65

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1954697392 375 LLQELAQKEcyGLP-SYNTLKSGEPHVPIFVSTVEVEGELFTGREAKTKKQAEMSAARIAYK 435
Cdd:cd19875     6 ALNEYCQKR--GLSlEFVDVSVGPDHCPGFTASATIDGIVFASATGTSKKEAKRAAAKLALK 65

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1954697392 296 YKNQLQNYTQKSNVNLPAYYH--EGPPHTSHFKGVVGFGEKTYES-HElfPTMKEAEHVAAKVAL 357
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVseEGPPHSPKFTVTVKVDGKLYGSgTG--SSKKEAEQLAAEKAL 63

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1954697392 301 QNYTQKSNVNLPAY--YHEGPPHTSHFKGVVGFGEKTYESHElfPTMKEAEHVAAKVAL 357
Cdd:cd00048     1 NELCQKNKWPPPEYetVEEGGPHNPRFTCTVTVNGQTFEGEG--KSKKEAKQAAAEKAL 57

double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) and similar proteins; DUS2L (also known as dihydrouridine synthase 2 (DUS2), up-regulated in lung cancer protein 8 (URLC8), or tRNA-dihydrouridine synthase 2-like) catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs. It negatively regulates the activation of EIF2AK2/PKR. DUS2L contains an N-terminal FMN-binding domain and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1954697392   3 KTRLQEICQRKRWSLPKYSVEKTGLDHipHFQATVTVNGLTFTSDDKCNSSKDAQNEAAMRAFNHL 68
Cdd:cd19871     3 KMILNEWCRKNKLPQPVYETVQRPSDR--LFQSVVTVDGKKYTSSLWEKSKKLAEQAAAIVCLRAL 66