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        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18959240 123 WSMTPKNALVQLHELKPGLQYRMVSQTGPVHAPVFAVAVEVNGLTFEGTGPTKKKAKMRAAEMALKSFVQFPNA 196
Cdd:cd19896   1 WSVTPKNALVQLNELKPGLQYRMVSQTGPVHAPVFAVAVEVNGLTFEGTGPTKKKAKMRAAEMALKSFVQFPNA 74

Adenosine-deaminase (editase) domain; Adenosine deaminases acting on RNA (ADARs) can deaminate adenosine to form inosine. In long double-stranded RNA, this process is non-specific; it occurs site-specifically in RNA transcripts. The former is important in defence against viruses, whereas the latter may affect splicing or untranslated regions. They are primarily nuclear proteins, but a longer isoform of ADAR1 is found predominantly in the cytoplasm. ADARs are derived from the Tad1-like tRNA deaminases that are present across eukaryotes. These in turn belong to the nucleotide/nucleic acid deaminase superfamily and are characterized by a distinct insert between the two conserved cysteines that are involved in binding zinc.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18959240   416 LSSGTKCISGEHISDQGLVVNDCHAEIVARRAFLHFLYTQLELHLSKHqedPERSIFIRVKEGG-YRLRENILFHLYVST 494
Cdd:pfam02137   2 LGTGTKCIGGSKLSPSGRVLNDSHAEVIARRSLLRYLYSQLLLALSGN---PSKSIFEPNPDSGkLRLKPGISFHLYISQ 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18959240   495 SPCGDARLNSPYEITIDlNSSKHIVRKFRGHLRTKIESGEGTVPVrGPSAVQTWDGILLGEQLVTMSCTDKIASWNVLGL 574
Cdd:pfam02137  79 TPCGDARIFSPLELEPE-SSPAHPVRRFRGQLRLKVETGAKTIPV-ESSEDQTWDGVKPGRRTLSMSCSDKLARWNVLGV 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18959240   575 QGALLCHFIEPVYLHSIIV-GSLHHTGHLARVMSHRMEGI-GQLPASYRQNRPLLSGVsnaearqpgksphfsanwvvgs 652
Cdd:pfam02137 157 QGALLSHFIEPIYLSSITVgGSLYDTEHLERAIYQRLDGVlDSLPPPYRVNKPLIGQV---------------------- 214

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18959240   653 adleiinattgkrscggSSRLCKHVFSARWARLHGRLStriPGHGDTPSMYCEAKRGAHTYQSVKQQLFKAFQKAGLGTW 732
Cdd:pfam02137 215 -----------------ASRLCKAALFSRFLKLLSELS---REDLLAPLTYHEAKAAAKDYQEAKQQLKSLLRQQGLGSW 274

                  ....
gi 18959240   733 VRKP 736
Cdd:pfam02137 275 IRKP 278

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

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18959240 277 PGALGERNPVVVLNELRSGLRYVCLSETAEKPRVKSFVMAVCVDGRTFEGSGRSKKLAKGQAAQAALQALFDIR 350
Cdd:cd19899   1 SPAESEKNPVVLLNELRPGLRYVCLSETAEKQHIKSFVMAVRVDGRTFEGSGRSKKLAKAQAAQAALQALFNIR 74

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 18959240   127 PKNALVQL-HELKPGLQYRMVSQTGPVHAPVFAVAVEVNGLTF-EGTGPTKKKAKMRAAEMALK 188
Cdd:pfam00035   1 PKSLLQEYaQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYgSGTGSSKKEAEQLAAEKALE 64

double-strand RNA-binding protein; Provisional

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 18959240  146 VSQTGPVHAPVFAVAVEVNGLTFE-GTGPTKKKAKMRAAEMAL 187
Cdd:PHA03103 130 ITSSGPSHSPTFTASVIISGIKFKpAIGSTKKEAKNNAAKLAM 172

seadornavirus double-stranded RNA-binding protein; This protein family occurs in the seadornavirus virus group, with an N-terminal domain for binding double-stranded RNA, is designated VP12 in Banna virus, VP8 in Kadipiro virus, and VP11 in Liao ning virus.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 18959240   129 NALVQLHEL--KPGLQ---YRMVSQTGPVHAPVFAVAVEVNGLTFEGTGPTKKKAKMRAA 183
Cdd:TIGR04238   1 NVVGMLQELavKRGLElpvYEKVGKEGPDHAPTFTIKLTANDIEVIEAASSKKQAEKLAA 60

Adenosine-deaminase (editase) domain; Adenosine deaminases acting on RNA (ADARs) can deaminate adenosine to form inosine. In long double-stranded RNA, this process is non-specific; it occurs site-specifically in RNA transcripts. The former is important in defence against viruses, whereas the latter may affect splicing or untranslated regions. They are primarily nuclear proteins, but a longer isoform of ADAR1 is found predominantly in the cytoplasm. ADARs are derived from the Tad1-like tRNA deaminases that are present across eukaryotes. These in turn belong to the nucleotide/nucleic acid deaminase superfamily and are characterized by a distinct insert between the two conserved cysteines that are involved in binding zinc.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18959240   416 LSSGTKCISGEHISDQGLVVNDCHAEIVARRAFLHFLYTQLELHLSKHqedPERSIFIRVKEGG-YRLRENILFHLYVST 494
Cdd:pfam02137   2 LGTGTKCIGGSKLSPSGRVLNDSHAEVIARRSLLRYLYSQLLLALSGN---PSKSIFEPNPDSGkLRLKPGISFHLYISQ 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18959240   495 SPCGDARLNSPYEITIDlNSSKHIVRKFRGHLRTKIESGEGTVPVrGPSAVQTWDGILLGEQLVTMSCTDKIASWNVLGL 574
Cdd:pfam02137  79 TPCGDARIFSPLELEPE-SSPAHPVRRFRGQLRLKVETGAKTIPV-ESSEDQTWDGVKPGRRTLSMSCSDKLARWNVLGV 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18959240   575 QGALLCHFIEPVYLHSIIV-GSLHHTGHLARVMSHRMEGI-GQLPASYRQNRPLLSGVsnaearqpgksphfsanwvvgs 652
Cdd:pfam02137 157 QGALLSHFIEPIYLSSITVgGSLYDTEHLERAIYQRLDGVlDSLPPPYRVNKPLIGQV---------------------- 214

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18959240   653 adleiinattgkrscggSSRLCKHVFSARWARLHGRLStriPGHGDTPSMYCEAKRGAHTYQSVKQQLFKAFQKAGLGTW 732
Cdd:pfam02137 215 -----------------ASRLCKAALFSRFLKLLSELS---REDLLAPLTYHEAKAAAKDYQEAKQQLKSLLRQQGLGSW 274

                  ....
gi 18959240   733 VRKP 736
Cdd:pfam02137 275 IRKP 278

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 18959240 128 KNALVQLHELKPGLQYRMVSQTGPVHAPVFAVAVEVNGLTFEGTGPTKKKAKMRAAEMALKSF 190
Cdd:cd19865   1 KNALMQLNELRPGLQYKLTSQTGPVHAPVFTMSVEVNGQTFEGTGRSKKKAKLEAAEKALRSF 63

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

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18959240 277 PGALGERNPVVVLNELRSGLRYVCLSETAEKPRVKSFVMAVCVDGRTFEGSGRSKKLAKGQAAQAALQALFDIR 350
Cdd:cd19899   1 SPAESEKNPVVLLNELRPGLRYVCLSETAEKQHIKSFVMAVRVDGRTFEGSGRSKKLAKAQAAQAALQALFNIR 74

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18959240 127 PKNALVQLHELKPGLQYRMVSQTGPVHAPVFAVAVEVNGLTFEGTGPTKKKAKMRAAEMALKSfVQFPNAFQAHLAMGSS 206
Cdd:cd19909   5 PMNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQA-MGYPTGFDTDLECMSS 83

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        50
                ....*....|....*....|....*....|....*....|....*....|
gi 18959240 283 RNPVVVLNELRSGLRYVCLSETAEkPRVKSFVMAVCVDGRTFEGSGRSKK 332
Cdd:cd19866   1 KNPVMLLNELRPGLKYKCLSESGE-SHAKSFVMSVTVDGQTFEGTGRSKK 49

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        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 18959240 128 KNALVQLHELKPGLQYRMVSQTGPVHAPVFAVAVEVNGLTFEGTGPTKKKAKMRAAEMAL 187
Cdd:cd19866   1 KNPVMLLNELRPGLKYKCLSESGESHAKSFVMSVTVDGQTFEGTGRSKKLAKAAAAQAAL 60

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        50
                ....*....|....*....|....*....|....*....|....*....|
gi 18959240 283 RNPVVVLNELRSGLRYVCLSETAEKpRVKSFVMAVCVDGRTFEGSGRSKK 332
Cdd:cd19898   3 KNPVMILNELRPGLKYEFVSESGES-HAKNFVMSVTVDGQTFEGSGRNKK 51

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 18959240 127 PKNALVQ-LHELKPGL-QYRMVSQTGPVHAPVFAVAVEVNG-LTFEGTGPTKKKAKMRAAEMALKSF 190
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
                ....*....|....*....|....*....|....*....|....*....
gi 18959240 139 PGLQYRMVSQTGPvHAPVFAVAVEVNGLTFEGTGPTKKKAKMRAAEMAL 187
Cdd:cd00048  10 PPPEYETVEEGGP-HNPRFTCTVTVNGQTFEGEGKSKKEAKQAAAEKAL 57

dsRNA-specific ribonuclease [Transcription];

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18959240 127 PKNAL---VQLHELKPgLQYRMVSQTGPVHAPVFAVAVEVNG-LTFEGTGPTKKKAKMRAAEMALK 188
Cdd:COG0571 159 YKTALqewLQARGLPL-PEYEVVEEEGPDHAKTFTVEVLVGGkVLGEGTGRSKKEAEQAAAKAALE 223

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        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18959240 128 KNALVQLHELKPGLQYRMVSQTGPVHAPVFAVAVEVNGLTFEGTGPTKKKAKMRAAEMALK 188
Cdd:cd19897   1 KNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKANAALAALE 61

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        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18959240 128 KNALVQLHELKPGLQYRMVSQTGPVHAPVFAVAVEVNGLTFEGTGPTKKKAKMRAAEMALKSF 190
Cdd:cd19911   1 KNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEKL 63

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        50
                ....*....|....*....|....*....|....*....|....*....|
gi 18959240 283 RNPVVVLNELRSGLRYVCLSETAeKPRVKSFVMAVCVDGRTFEGSGRSKK 332
Cdd:cd19897   1 KNPVMELNEKRRGLKYELISETG-GSHDKRFVMEVEVDGQKFQGAGSNKK 49

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 18959240 283 RNPVVVLNELRSGLRYVCLSETAEKpRVKSFVMAVCVDGRTFEGSGRSKK 332
Cdd:cd19912   7 KNPVMELNEKRRGLKYELISETGGS-HDKRFVMEVEVDGQKFQGAGSNKK 55

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 18959240 128 KNALvQLHELKPGL---QYRMVsQTGPVHAPVFAVAVEVNGLTFEGTG-PTKKKAKMRAAEMALKS 189
Cdd:cd19878   2 KNLL-QEYAQKKKIplpKYESA-KSGPSHQPTFVSTVIVLGVRFSSEGaKNKKQAEQSAAKVALKE 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
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 18959240 133 QLHELKpgLQYRMVSQtGPVHAPVFAVAVEVNGLTF-EGTGPTKKKAKMRAAEMALKSF 190
Cdd:cd19875  12 QKRGLS--LEFVDVSV-GPDHCPGFTASATIDGIVFaSATGTSKKEAKRAAAKLALKKL 67

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

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 18959240 284 NPVVVLNELRSGLRYVCLSETAEKpRVKSFVMAVCVDGRTFEGSGRSKK 332
Cdd:cd19894   2 NALMRLNQLRPGLQYKLASQTGPV-HAPQFTMSVEVDGVTYEASGPSKK 49

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        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18959240 129 NALVQLHEL----KPGLQYRMVSQTGPVHAPVFAVAVEVN-GLTFEGTGPTKKKAKMRAAEMAL 187
Cdd:cd19857   1 TPMCLLNELarfnKIRPQYTLVDEEGPAHKKTFTVKLTLGdEEEYEASGSSIKKAQHAAAEKAL 64

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        50
                ....*....|....*....|....*....|....*....|....*....|
gi 18959240 283 RNPVVVLNELRSGLRYVCLSETAEKpRVKSFVMAVCVDGRTFEGSGRSKK 332
Cdd:cd19911   1 KNPVMELNEKRRGLKYELISETGGS-HDKRFVMEVEVDGQKFRGAGPNKK 49

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 18959240 142 QYRMVSQTGPVHAPVFAVAVEVNGLTF-EGTGPTKKKAKMRAAEMALKS 189
Cdd:cd19877  26 EYKVLQKSGPTNTRVYTVAVYFRGERIaTGTGSSIQQAEMNAAEKALEK 74

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

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 18959240 284 NPVVVLNELRSGLRYVCLSETAEKpRVKSFVMAVCVDGRTFEGSGRSKK 332
Cdd:cd19909   7 NALMRLNQIRPGLQYKLLSQSGPV-HAPVFTMSVDVDGTTYEASGPSKK 54

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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18959240 127 PKNALVQL----HELKPglQYRMVSQTGPVHAPVFAVAVEVNGLTFEGTGPTKKKAKMRAAEMAL 187
Cdd:cd19860   2 PISRLIQIqqarKEKEP--VYSLVAERGTPRRREFVMQVTVGDKTATGTGPNKKLAKRNAAEAML 64

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        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18959240 128 KNALVQLHELKP----GLQYRMVSQTGPVHAPVFAVAVEVNGLTFEG-TGPTKKKAKMRAAEMALKSFV 191
Cdd:cd19915   1 TNPVSGLLEYARskgfAAEFKLVDQSGPPHEPKFVYQAKVGGRWFPAvCAHNKKQGKQEAADAALRVLI 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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 18959240 134 LHE--LKPGL--QYRMVSQTGPVHAPVFAVAVEVNGLTFEGTGPTKKKAKMRAAEMAL 187
Cdd:cd19889   8 LHEygTKTGNipVYELEKSEGQAHLPSFTFRVTVGDITCTGEGTSKKLAKHRAAEAAL 65

first double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar proteins; TARBP2 (also known as TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)), participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. TARBP2 contains three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 18959240 143 YRMVSQTGPVHAPVFAVAVEVNGLTFEGTGPTKKKAKMRAAEMALK 188
Cdd:cd19890  22 YDLLKAEGQAHQPNFTFRVTVGDISCTGQGPSKKAAKHKAAEVALK 67

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

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18959240 124 SMTPKNALVQL---HELKPglQYRMVSQTGPvHAPVFAVAVEVNG-LTFEGTGPTKKKAKMRAAEMALKS 189
Cdd:cd19876   1 DKFAKQKLYSLigpASLKP--EYVVVKKEGG-NDPNYTVACRINGeVLGTGVGRSIKKAGQRAAMSALSN 67

double-strand RNA-binding protein; Provisional

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 18959240  146 VSQTGPVHAPVFAVAVEVNGLTFE-GTGPTKKKAKMRAAEMAL 187
Cdd:PHA03103 130 ITSSGPSHSPTFTASVIISGIKFKpAIGSTKKEAKNNAAKLAM 172