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 1711132997   8 LQDTIGYKFHNPVFLEVALTHSSYANEVKHQLKYNERQEFLGDAVLSIIVSDYLFNNY-TVPEGELTKLRAAIVCEKSLD 86
Cdd:TIGR02191   1 LEKRLGYKFKNPELLEQALTHRSYANEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFpDASEGELSRLRAALVSEESLA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1711132997  87 VMANKIHLGEYLRLGRGEEMTGGRTRPSIIADAFEALIAAIYLDSGIESARAFVLPFVTEMLEHEDSLS-FKDYKTILQE 165
Cdd:TIGR02191  81 EVARELGLGDFLLLGKGEEKSGGRRRDSILADAFEALIGAIYLDSGLEAARKFILKLLIPRIDAIIKEEtLKDYKTALQE 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1711132997 166 IIQQNPEEKLVYKLVGEKGPDHDKRFVVDVMLNSNVIGKGEGRSKKNAEQMAAKEALELM 225
Cdd:TIGR02191 161 WAQARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGEPYGEGKGKSKKEAEQNAAKAALEKL 220

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 1711132997  25 ALTHSSYANEvkHQLKYNERQEFLGDAVLSIIVSDYLFNNY-TVPEGELTKLRAAIVCEKSLDVMANKIHLGEYLRLGRG 103
Cdd:cd00593     6 ALTHPSYANE--HGRFNNERLEFLGDAVLELVVTEYLFKKFpDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLGKG 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1711132997 104 EEMTGGRTRPSIIADAFEALIAAIYLDSGIESARAFVLPFVTEMLEHED 152
Cdd:cd00593    84 EEKSGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEEIS 132

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 1711132997   8 LQDTIGYKFHNPVFLEVALTHSSYANEVKHQLKYNERQEFLGDAVLSIIVSDYLFNNY-TVPEGELTKLRAAIVCEKSLD 86
Cdd:TIGR02191   1 LEKRLGYKFKNPELLEQALTHRSYANEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFpDASEGELSRLRAALVSEESLA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1711132997  87 VMANKIHLGEYLRLGRGEEMTGGRTRPSIIADAFEALIAAIYLDSGIESARAFVLPFVTEMLEHEDSLS-FKDYKTILQE 165
Cdd:TIGR02191  81 EVARELGLGDFLLLGKGEEKSGGRRRDSILADAFEALIGAIYLDSGLEAARKFILKLLIPRIDAIIKEEtLKDYKTALQE 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1711132997 166 IIQQNPEEKLVYKLVGEKGPDHDKRFVVDVMLNSNVIGKGEGRSKKNAEQMAAKEALELM 225
Cdd:TIGR02191 161 WAQARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGEPYGEGKGKSKKEAEQNAAKAALEKL 220

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 1711132997  25 ALTHSSYANEvkHQLKYNERQEFLGDAVLSIIVSDYLFNNY-TVPEGELTKLRAAIVCEKSLDVMANKIHLGEYLRLGRG 103
Cdd:cd00593     6 ALTHPSYANE--HGRFNNERLEFLGDAVLELVVTEYLFKKFpDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLGKG 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1711132997 104 EEMTGGRTRPSIIADAFEALIAAIYLDSGIESARAFVLPFVTEMLEHED 152
Cdd:cd00593    84 EEKSGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEEIS 132

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 1711132997 157 KDYKTILQEIIQQNPEEKLVYKLVGEKGPDHDKRFVVDVMLNSNVIGKGEGRSKKNAEQMAAKEALELM 225
Cdd:cd10845     1 KDYKTALQEYLQKRGLPLPEYELVEEEGPDHNKTFTVEVKVNGKVIGEGTGRSKKEAEQAAAKAALEKL 69

Double-stranded RNA binding motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1711132997  159 YKTILQEIIQQNPEEkLVYKLVGEKGPDHDKRFVVDVMLNSNVIGKGEGRSKKNAEQMAAKEALELMG 226
Cdd:smart00358   1 PKSLLQELAQKRKLP-PEYELVKEEGPDHAPRFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRSLK 67

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 1711132997 164 QEIIQQNPEEKLVYKLVGEkGPDHDKRFVVDVMLNsNVIGKGEGRSKKNAEQMAAKEAL 222
Cdd:cd00048     1 NELCQKNKWPPPEYETVEE-GGPHNPRFTCTVTVN-GQTFEGEGKSKKEAKQAAAEKAL 57

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1711132997 176 VYKLVGEKGPDHDKRFVVDVMLNSNVIGKGEGRSKKNAEQMAAKEALE 223
Cdd:cd19877    26 EYKVLQKSGPTNTRVYTVAVYFRGERIATGTGSSIQQAEMNAAEKALE 73

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
                  ....*....|....*....|....*....|....*....|....*....
gi 1711132997 174 KLVYKLVGEKGPDHDKRFVVDVMLNSNVIGKGEGRSKKNAEQMAAKEAL 222
Cdd:cd19857    16 RPQYTLVDEEGPAHKKTFTVKLTLGDEEEYEASGSSIKKAQHAAAEKAL 64

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1711132997 157 KDYKTILQEIIQQN---PEeklvYKLVGEKGPDHDKRFVVDVMLNsNVIGKGEGRSKKNAEQMAAKEALELM 225
Cdd:cd19862     1 KTPISVLQELCAKRgitPK----YELISSEGAVHEPTFTFRVTVG-DITATGSGTSKKKAKHAAAENALEQL 67

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1711132997 175 LVYKLVGEKGPDHDKRFVVDVMLNSNVIgKGEGRSKKNAEQMAAKEALE 223
Cdd:cd19866    14 LKYKCLSESGESHAKSFVMSVTVDGQTF-EGTGRSKKLAKAAAAQAALA 61

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
                  ....*....|....*....|....*....|....*....|....*....
gi 1711132997 175 LVYKLVGEKGPDHDKRFVVDVMLNSNVIgKGEGRSKKNAEQMAAKEALE 223
Cdd:cd19865    14 LQYKLTSQTGPVHAPVFTMSVEVNGQTF-EGTGRSKKKAKLEAAEKALR 61

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1711132997 158 DYKTILQEIIQQnpeEKLVYKLVGEK--GPDHDKRFVVDVMLNSNVIGKGEGRSKKNAEQMAAKEALE 223
Cdd:cd20314     2 NYVSLLNEYCQK---ERLTVKYEEEKrsGPTHKPRFFCKYIIDGKEYPEGEGKSKKEAKQAAARLAYE 66

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 1711132997 159 YKTILQEIIQQNPEEKLVYKLVGEkGPDHDKRFVVDVMLNSNVIGKGEGRS-KKNAEQMAAKEAL 222
Cdd:cd19907     2 YKSQLQEYAQKSCLNLPVYACIRE-GPDHAPRFRATVTFNGVIFESPPGFPtLKAAEHSAAEVAL 65

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1711132997 177 YKLVGEKGPDHDKRFVVDVMLNSNVIGKGEGRSKKNAEQMAAKEALELMGR 227
Cdd:cd19913    20 FLLLEQSGPSHDPRFKFQAVIDGRRFPPAEASSKKVAKKDAAAIALKILLR 70

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1711132997 163 LQEIIQQNPEEKLVYKLVGEKGPDHDKRFVVDVMLnSNVIGKGEGRSKKNAEQMAAKEALELMG 226
Cdd:cd19885    16 LAQIQQAKKEKEPEYTLITERGLPRRREFVMQVKV-GNQTAEGMGPNKKVAKRNAAEKMLELLG 78

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1711132997 175 LVYKLVGEKGPDHDKRFVVDVMLNSNVIgKGEGRSKKNAEQMAAKEALE 223
Cdd:cd19897    14 LKYELISETGGSHDKRFVMEVEVDGQKF-QGAGSNKKVAKANAALAALE 61

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1711132997 162 ILQEIIQQNPEEKLVYKLVGEKGPDHDKRFVVDVMLNsNVIGKGEGRSKKNAEQMAA 218
Cdd:cd19863     5 ILQELCVQRRWRLPEYEVEQESGPPHEKEFTIACRVE-NFSETGSGKSKKLAKRAAA 60

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
                  ....*....|....*....|....*....|....*....|....*..
gi 1711132997 177 YKLVGEKGPDHDKRFVVDVMLnSNVIGKGEGRSKKNAEQMAAKEALE 223
Cdd:cd19859    18 FEVLRESGPPHMKNFITRCTV-GSFVTEGEGNSKKVSKKRAAEKMLE 63

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1711132997 175 LVYKLVGEKGPDHDKRFVVDVMLNSNVIgKGEGRSKKNAEQMAAKEALE 223
Cdd:cd19911    14 LKYELISETGGSHDKRFVMEVEVDGQKF-RGAGPNKKVAKASAALAALE 61

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1711132997 177 YKLVGEKGPDHDKRFVVDVMLnSNVIGKGEGRSKKNAEQMAAKEALE 223
Cdd:cd19883    20 FEVTKETGPPHMKSFVTKVSV-GEFAGEGEGKSKKISKKNAAIAVLE 65

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
                  ....*....|....*....|....*....|....*....|....*.
gi 1711132997 177 YKLVGEKGPDHDKRFVVDVMLNSNVIGKGEGRSKKNAEQMAAKEAL 222
Cdd:cd19902    20 IEVLSQSGPPHNPRFKAAVFVGGRRFPSVEASSKKDAKQEAADLAL 65

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1711132997 175 LVYKLVGEKGPDHDKRFVVDVMLNSNVIgKGEGRSKKNAEQMAAKEAL 222
Cdd:cd19898    16 LKYEFVSESGESHAKNFVMSVTVDGQTF-EGSGRNKKLAKARAAQAAL 62

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1711132997 177 YKLVGEKGPDHDKRFVVDVMLNSNVIGKGEGRSKKNAEQMAAKEALELM 225
Cdd:cd19915    20 FKLVDQSGPPHEPKFVYQAKVGGRWFPAVCAHNKKQGKQEAADAALRVL 68