dsRNA-specific ribonuclease [Transcription];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1251105452   2 NQWEELQESVGFDFKNVELLKQAFTHSSYVNEHRreNVKDNERLEFLGDAVLELTVSDYLFNKYPDMAEGHMTKMRAAIV 81
Cdd:COG0571     2 EDLEELEERLGYRFKDPELLEQALTHRSYANEHG--GLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1251105452  82 CEPSLVEFAEAVHFSKYVRLGKGEEKAGGRTRPALLADVFESFIGALYLDNGIDKVVTFLERVIFPKIDAGAYLQTV-DY 160
Cdd:COG0571    80 SEETLAEIARELGLGDYLRLGKGEEKSGGRRRPSILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGAGkDY 159

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1251105452 161 KTQLQEIVQRDRDVLIEYDILGETGPAHNKAFDAQVIVNGQVLGKGSGRTKKQAEQSAAQFAINKL 226
Cdd:COG0571   160 KTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGGKVLGEGTGRSKKEAEQAAAKAALEKL 225

dsRNA-specific ribonuclease [Transcription];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1251105452   2 NQWEELQESVGFDFKNVELLKQAFTHSSYVNEHRreNVKDNERLEFLGDAVLELTVSDYLFNKYPDMAEGHMTKMRAAIV 81
Cdd:COG0571     2 EDLEELEERLGYRFKDPELLEQALTHRSYANEHG--GLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1251105452  82 CEPSLVEFAEAVHFSKYVRLGKGEEKAGGRTRPALLADVFESFIGALYLDNGIDKVVTFLERVIFPKIDAGAYLQTV-DY 160
Cdd:COG0571    80 SEETLAEIARELGLGDYLRLGKGEEKSGGRRRPSILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGAGkDY 159

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1251105452 161 KTQLQEIVQRDRDVLIEYDILGETGPAHNKAFDAQVIVNGQVLGKGSGRTKKQAEQSAAQFAINKL 226
Cdd:COG0571   160 KTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGGKVLGEGTGRSKKEAEQAAAKAALEKL 225

RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1251105452  19 ELLKQAFTHSSYVNEHRRENvkdNERLEFLGDAVLELTVSDYLFNKYPDMAEGHMTKMRAAIVCEPSLVEFAEAVHFSKY 98
Cdd:cd00593     1 SLLLEALTHPSYANEHGRFN---NERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKY 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1251105452  99 VRLGKGEEKAGGRTRPALLADVFESFIGALYLDNGIDKVVTFLERVIFPKID 150
Cdd:cd00593    78 LRLGKGEEKSGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIE 129

Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA processing. They probably also cleave a stem-loop structure at the 3' end of U2 snRNA to ensure formation of the correct U2 3' end; they are involved in polyadenylation-independent transcription termination. Some members may be mitochondrial ribosomal protein subunit L15, others may be 60S ribosomal protein L3.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1251105452  19 ELLKQAFTHSSYVNEHRRenvkDNERLEFLGDAVLELTVSDYLFnKYPDMAEGHMTKMRAAIVCEPSLVEFAEAVHFSKY 98
Cdd:pfam14622   2 ELLLQALTHKSYANGRKP----YNERLEFLGDAVLELSVSEYLF-KKPDLDEGGLTKLRASIVSEESLAEIAREIGLGKY 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1251105452  99 VRLGKGEEKAGGRTRPALLADVFESFIGALYLDNGIDKVVTFLERVIFPKI 149
Cdd:pfam14622  77 LRLGKGEEETGGSGRESILADALEALIGAIYLDGGFEVAKEFILKKILPDL 127

dsRNA-specific ribonuclease [Transcription];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1251105452   2 NQWEELQESVGFDFKNVELLKQAFTHSSYVNEHRreNVKDNERLEFLGDAVLELTVSDYLFNKYPDMAEGHMTKMRAAIV 81
Cdd:COG0571     2 EDLEELEERLGYRFKDPELLEQALTHRSYANEHG--GLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1251105452  82 CEPSLVEFAEAVHFSKYVRLGKGEEKAGGRTRPALLADVFESFIGALYLDNGIDKVVTFLERVIFPKIDAGAYLQTV-DY 160
Cdd:COG0571    80 SEETLAEIARELGLGDYLRLGKGEEKSGGRRRPSILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGAGkDY 159

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1251105452 161 KTQLQEIVQRDRDVLIEYDILGETGPAHNKAFDAQVIVNGQVLGKGSGRTKKQAEQSAAQFAINKL 226
Cdd:COG0571   160 KTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGGKVLGEGTGRSKKEAEQAAAKAALEKL 225

RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1251105452  19 ELLKQAFTHSSYVNEHRRENvkdNERLEFLGDAVLELTVSDYLFNKYPDMAEGHMTKMRAAIVCEPSLVEFAEAVHFSKY 98
Cdd:cd00593     1 SLLLEALTHPSYANEHGRFN---NERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKY 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1251105452  99 VRLGKGEEKAGGRTRPALLADVFESFIGALYLDNGIDKVVTFLERVIFPKID 150
Cdd:cd00593    78 LRLGKGEEKSGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIE 129

Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA processing. They probably also cleave a stem-loop structure at the 3' end of U2 snRNA to ensure formation of the correct U2 3' end; they are involved in polyadenylation-independent transcription termination. Some members may be mitochondrial ribosomal protein subunit L15, others may be 60S ribosomal protein L3.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1251105452  19 ELLKQAFTHSSYVNEHRRenvkDNERLEFLGDAVLELTVSDYLFnKYPDMAEGHMTKMRAAIVCEPSLVEFAEAVHFSKY 98
Cdd:pfam14622   2 ELLLQALTHKSYANGRKP----YNERLEFLGDAVLELSVSEYLF-KKPDLDEGGLTKLRASIVSEESLAEIAREIGLGKY 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1251105452  99 VRLGKGEEKAGGRTRPALLADVFESFIGALYLDNGIDKVVTFLERVIFPKI 149
Cdd:pfam14622  77 LRLGKGEEETGGSGRESILADALEALIGAIYLDGGFEVAKEFILKKILPDL 127

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 1251105452 159 DYKTQLQEIVQRDRDVLIEYDILGETGPAHNKAFDAQVIVNGQVLGKGSGRTKKQAEQSAAQFAINKL 226
Cdd:cd10845     2 DYKTALQEYLQKRGLPLPEYELVEEEGPDHNKTFTVEVKVNGKVIGEGTGRSKKEAEQAAAKAALEKL 69

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 1251105452 160 YKTQLQEIVQRDRdVLIEYDILGETGPAHNKAFDAQVIVNGQVLGKGSGRTKKQAEQSAAQFAINKL 226
Cdd:pfam00035   1 PKSLLQEYAQKNG-KPPPYEYVSEEGPPHSPKFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKALEKL 66

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 1251105452 165 QEIVQRDRDVLIEYDILgETGPAHNKAFDAQVIVNGQVlGKGSGRTKKQAEQSAAQFAI 223
Cdd:cd00048     1 NELCQKNKWPPPEYETV-EEGGPHNPRFTCTVTVNGQT-FEGEGKSKKEAKQAAAEKAL 57

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 1251105452 162 TQLQEIVQRdrdvlIEYDILGETGPAHNKAFDAQVIVNGQVLgKGSGRTKKQAEQSAAQFAIN 224
Cdd:cd19865     5 MQLNELRPG-----LQYKLTSQTGPVHAPVFTMSVEVNGQTF-EGTGRSKKKAKLEAAEKALR 61

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1251105452 164 LQEIVQRdRDVLIEYDILGETGPAHNKAFDAQVIVNGQVLGKGSGRTKKQAEQSAAQFAINKLI 227
Cdd:cd19902     7 LMEYAQS-RGVTAEIEVLSQSGPPHNPRFKAAVFVGGRRFPSVEASSKKDAKQEAADLALRALI 69

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1251105452 154 YLQTVDYKTQLQEIVQRDRDVLIEYdILGETGPAhNKAFDAQVIVNGQVLGKGSGRTKKQAEQSAAQFAINKLI 227
Cdd:cd19867     2 NPDGKSPVCILHEYCQRVLKVQPEY-NFTETENA-ATPFSAEVFINGVEYGSGEASSKKLAKQKAARATLEILI 73

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1251105452 164 LQEIVQRdRDVLIEYDILGETGPAHNKAFDAQVIVnGQVLGKGSGRTKKQAEQSAAQFAINKL 226
Cdd:cd19862     7 LQELCAK-RGITPKYELISSEGAVHEPTFTFRVTV-GDITATGSGTSKKKAKHAAAENALEQL 67

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1251105452 176 IEYDILGETGPAHNKAFDAQVIVNGQVLgKGSGRTKKQAEQSAAQFAINKLIH 228
Cdd:cd19895    19 LQYKLLSQTGPVHAPVFVMSVEVNGQVF-EGSGPTKKKAKLHAAEKALRSFVQ 70

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1251105452 174 VLIEYDILGETGPAHNKAFDAQVIVNGQVLGKGSGRTKKQAEQSAAQFAI 223
Cdd:cd19857    15 IRPQYTLVDEEGPAHKKTFTVKLTLGDEEEYEASGSSIKKAQHAAAEKAL 64

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1251105452 162 TQLQEIVQRdRDVLIEYDILGETGPAHNKAFDAQVIVnGQVLGKGSGRTKKQAEQSAAQFAINKL 226
Cdd:cd19859     3 SLVHEIALK-RNLTVNFEVLRESGPPHMKNFITRCTV-GSFVTEGEGNSKKVSKKRAAEKMLEEL 65

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1251105452 176 IEYDILGETGPAHNKAFDAQVIVNGQVLgKGSGRTKKQAEQSAAQFAINKLIH 228
Cdd:cd19896    19 LQYRMVSQTGPVHAPVFAVAVEVNGLTF-EGTGPTKKKAKMRAAEMALKSFVQ 70

double-strand RNA-binding protein; Provisional

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1251105452 166 EIVQRDRDVLIEydilgETGPAHNKAFDAQVIVNGQVLGKGSGRTKKQAEQSAAQFAINKLI 227
Cdd:PHA03103  120 QITSRDWSINIT-----SSGPSHSPTFTASVIISGIKFKPAIGSTKKEAKNNAAKLAMDKIL 176

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 1251105452 177 EYDILGETGPAHNKAFDAQVIVNGQVLG-KGSGRTKKQAEQSAAQFAINKL 226
Cdd:cd19870    21 EFRLVEESGPPHRKHFLFKVVVNGVEYQpSVASGNKKDAKAQAATVALQAL 71

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1251105452 172 RDVLIEYDILgETGPAHNKAFDAQVIVNG-QVLGKGSGRTKKQAEQSAAQFAINKLI 227
Cdd:cd19854    13 KKLTPEYDIK-EAGNKHRQRFKCEVRVEGfDYVGTGNATNKKDAQTNAARDFLNYLV 68

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1251105452 176 IEYDILGETGPAHNKAFDAQVIVNGQVLGKGSGRTKKQAEQSAAQFAINKL 226
Cdd:cd19914    18 CEFQLLSQEGPPHDPKFTYCVKVGEQTFPSVVANSKKVAKQMAAEEAVKEL 68

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

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                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1251105452 170 RDRDVLIEYDILGETGPAHNKAFDAQVIVNGQVLGKGSGRTKKQAEQSAAQFAINKLI 227
Cdd:cd19915    12 RSKGFAAEFKLVDQSGPPHEPKFVYQAKVGGRWFPAVCAHNKKQGKQEAADAALRVLI 69

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

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1251105452 161 KTQLQEIVQRDRDvlIEYDILGETGPAHNKAFDAQVIVNGQVLgKGSGRTKKQAEQSAAQFAINKL 226
Cdd:cd19912     7 KNPVMELNEKRRG--LKYELISETGGSHDKRFVMEVEVDGQKF-QGAGSNKKVAKAYAALAALEKL 69

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.

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                  ....*....|....*....|....*....|....*....|....*....|
gi 1251105452 177 EYDILGETGPAHNKAFDAQVIVnGQVLGKGSGRTKKQAEQSAAQFAINKL 226
Cdd:cd19889    20 VYELEKSEGQAHLPSFTFRVTV-GDITCTGEGTSKKLAKHRAAEAALNIL 68

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

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1251105452 161 KTQLQEIVQRDRDvlIEYDILGETGPAHNKAFDAQVIVNGQVLgKGSGRTKKQAEQSAAQFAINKL 226
Cdd:cd19911     1 KNPVMELNEKRRG--LKYELISETGGSHDKRFVMEVEVDGQKF-RGAGPNKKVAKASAALAALEKL 63

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1251105452 164 LQEIVQRDRDVLIEYDILGETGPAHNKAFDAQVIVNgQVLGKGSGRTKKQAEQSAA 219
Cdd:cd10844     6 LQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVE-RFIEIGSGTSKKLAKRNAA 60

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1251105452 164 LQEIVQRDRDVLIEYDILGETGPAHNKAFDAQVIVNgQVLGKGSGRTKKQAEQSAAQFAINKL 226
Cdd:cd19891     6 LQELAVQKGWRLPEYTLAQESGPPHKREFTITCRVE-TFVETGTGTSKKVAKRNAAEKLLAKF 67

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1251105452 177 EYDILGETGPAHNKAFDAQVIVN-----------GQVLgkgsgRTKKQAEQSAAQFAINKLIH 228
Cdd:cd19869    13 VYRCVEEEGPAHAKRFTYMVRVKipergwtieceGEPM-----RSKKRAKDSAALLLLEYLKK 70