domain in DSRM or ZnF_C2H2 domain containing proteins;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907137116   81 TLCGVMRIGLVAKGLLIKDDMDLELVLMCKDKPTETLLNTVKDNLPIQIQKLTEEkyqveqcinEASIIIRNTKEPTLTL 160
Cdd:smart00572   1 TLKGVMRVGSFAKGTLLKGDNVAELVLLCKEKPTSELVARLARKLPEQLKAVTED---------EALIIVTSTKEPTMEV 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907137116  161 KVILTSPLIRDELEKK-DGENVMMKDPPDLLDRQKCLNALASLRHAKWFQARANGLKSCVIVLRILRDLCNRVPTWAPLK 239
Cdd:smart00572  72 GILITSPLARVELLITtVPENLRKLDPEDHLDRKKCLSALASLRHAKWFQARASGLQSCVIVIRVLRDLCNRVPTWQPLS 151

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907137116  240 GWPLELICEKSIGTCNRPLGAGEALRRVMECLASGILLPGGPGLHDPCERDPTDALSYMTTQQKEDITHSAQHALRLSAF 319
Cdd:smart00572 152 GWPLELLVEKAIGSARQPLGLGDAFRRVFECLASGILLPGSPGLTDPCEKDNTDALTALTLQQREDVTASAQTALRLLAF 231

                          250
                   ....*....|....*
gi 1907137116  320 GQIYKVLEMDPLPSS 334
Cdd:smart00572 232 GQIHKILGMDPLPSM 246

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 1907137116 512 KNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEKLF 575
Cdd:cd19911     1 KNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEKLF 64

domain in DSRM or ZnF_C2H2 domain containing proteins;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907137116   81 TLCGVMRIGLVAKGLLIKDDMDLELVLMCKDKPTETLLNTVKDNLPIQIQKLTEEkyqveqcinEASIIIRNTKEPTLTL 160
Cdd:smart00572   1 TLKGVMRVGSFAKGTLLKGDNVAELVLLCKEKPTSELVARLARKLPEQLKAVTED---------EALIIVTSTKEPTMEV 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907137116  161 KVILTSPLIRDELEKK-DGENVMMKDPPDLLDRQKCLNALASLRHAKWFQARANGLKSCVIVLRILRDLCNRVPTWAPLK 239
Cdd:smart00572  72 GILITSPLARVELLITtVPENLRKLDPEDHLDRKKCLSALASLRHAKWFQARASGLQSCVIVIRVLRDLCNRVPTWQPLS 151

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907137116  240 GWPLELICEKSIGTCNRPLGAGEALRRVMECLASGILLPGGPGLHDPCERDPTDALSYMTTQQKEDITHSAQHALRLSAF 319
Cdd:smart00572 152 GWPLELLVEKAIGSARQPLGLGDAFRRVFECLASGILLPGSPGLTDPCEKDNTDALTALTLQQREDVTASAQTALRLLAF 231

                          250
                   ....*....|....*
gi 1907137116  320 GQIYKVLEMDPLPSS 334
Cdd:smart00572 232 GQIHKILGMDPLPSM 246

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 1907137116 384 KAIDLMNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGYPTGFDADIEC 463
Cdd:cd19909     1 DANQPMNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGYPTGFDTDLEC 80

                  ....
gi 1907137116 464 ISSD 467
Cdd:cd19909    81 MSSD 84

Double-stranded RNA binding motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907137116  389 MNALMRLNQIRP-GLQYKLLSQSGPVHAPVFTMSVDVDGT-TYEASGPSKKTAKLHVAVKVLQAMG 452
Cdd:smart00358   2 KSLLQELAQKRKlPPEYELVKEEGPDHAPRFTVTVKVGGKrTGEGEGSSKKEAKQRAAEAALRSLK 67

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907137116 389 MNALMRLNQ-IRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTY-EASGPSKKTAKLHVAVKVLQ 449
Cdd:pfam00035   2 KSLLQEYAQkNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYgSGTGSSKKEAEQLAAEKALE 64

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
                  ....*....|....*....|....*....|....*....|....*....|
gi 1907137116 514 PVMELNE----KRRGLKYELISETGGSHDKRFVMEVEVDGQKF-RGAGPN 558
Cdd:pfam00035   1 PKSLLQEyaqkNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYgSGTGSS 50

Sulphur globule protein; Sulphur globules are membrane-bounded intracellular globules, used by purple sulphur bacteria to transiently store sulphur during the oxidization of reduced sulphur compounds. This proteobacterial family contains structural proteins of these sulphur globules, and includes sulphur globule protein CV1 (SgpA) and sulphur globule protein CV2 (SgpB).

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907137116 608 RGRGRGTLTRGAFVGATAAPGYIAP-GYGTPYGYSTAAPAYGgffidSPYCQPLSVAP 664
Cdd:pfam17228  38 RGRGRGYGRGYGDYGYGNPYGYGYPyGYGAPYGAPYGYGPYG-----APYGAPVAPAP 90

domain in DSRM or ZnF_C2H2 domain containing proteins;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907137116   81 TLCGVMRIGLVAKGLLIKDDMDLELVLMCKDKPTETLLNTVKDNLPIQIQKLTEEkyqveqcinEASIIIRNTKEPTLTL 160
Cdd:smart00572   1 TLKGVMRVGSFAKGTLLKGDNVAELVLLCKEKPTSELVARLARKLPEQLKAVTED---------EALIIVTSTKEPTMEV 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907137116  161 KVILTSPLIRDELEKK-DGENVMMKDPPDLLDRQKCLNALASLRHAKWFQARANGLKSCVIVLRILRDLCNRVPTWAPLK 239
Cdd:smart00572  72 GILITSPLARVELLITtVPENLRKLDPEDHLDRKKCLSALASLRHAKWFQARASGLQSCVIVIRVLRDLCNRVPTWQPLS 151

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907137116  240 GWPLELICEKSIGTCNRPLGAGEALRRVMECLASGILLPGGPGLHDPCERDPTDALSYMTTQQKEDITHSAQHALRLSAF 319
Cdd:smart00572 152 GWPLELLVEKAIGSARQPLGLGDAFRRVFECLASGILLPGSPGLTDPCEKDNTDALTALTLQQREDVTASAQTALRLLAF 231

                          250
                   ....*....|....*
gi 1907137116  320 GQIYKVLEMDPLPSS 334
Cdd:smart00572 232 GQIHKILGMDPLPSM 246

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 1907137116 384 KAIDLMNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGYPTGFDADIEC 463
Cdd:cd19909     1 DANQPMNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGYPTGFDTDLEC 80

                  ....
gi 1907137116 464 ISSD 467
Cdd:cd19909    81 MSSD 84

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907137116 389 MNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGYPTG 456
Cdd:cd19910     6 MNALMRLNQLKPGLQYKLISQTGPVHAPVFTMSVEVDGKTFEASGPSKKTAKLHVAVKVLQDMGLPTG 73

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 1907137116 389 MNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAM 451
Cdd:cd19865     1 KNALMQLNELRPGLQYKLTSQTGPVHAPVFTMSVEVNGQTFEGTGRSKKKAKLEAAEKALRSF 63

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907137116 390 NALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQA 450
Cdd:cd19895     7 NALMQLNEIKPGLQYKLLSQTGPVHAPVFVMSVEVNGQVFEGSGPTKKKAKLHAAEKALRS 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 1907137116 512 KNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPN 558
Cdd:cd19866     1 KNPVMLLNELRPGLKYKCLSESGESHAKSFVMSVTVDGQTFEGTGRS 47

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 1907137116 510 SGKNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPN 558
Cdd:cd19898     1 SGKNPVMILNELRPGLKYEFVSESGESHAKNFVMSVTVDGQTFEGSGRN 49

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 1907137116 512 KNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGP 557
Cdd:cd19865     1 KNALMQLNELRPGLQYKLTSQTGPVHAPVFTMSVEVNGQTFEGTGR 46

Double-stranded RNA binding motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907137116  389 MNALMRLNQIRP-GLQYKLLSQSGPVHAPVFTMSVDVDGT-TYEASGPSKKTAKLHVAVKVLQAMG 452
Cdd:smart00358   2 KSLLQELAQKRKlPPEYELVKEEGPDHAPRFTVTVKVGGKrTGEGEGSSKKEAKQRAAEAALRSLK 67

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907137116 390 NALMRLNQIRPGLQYKLLSQSGPV-HAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAM 451
Cdd:cd19899     8 NPVVLLNELRPGLRYVCLSETAEKqHIKSFVMAVRVDGRTFEGSGRSKKLAKAQAAQAALQAL 70

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907137116 390 NALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAM 451
Cdd:cd19912     8 NPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKAYAALAALEKL 69

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 1907137116 513 NPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPN 558
Cdd:cd19894     2 NALMRLNQLRPGLQYKLASQTGPVHAPQFTMSVEVDGVTYEASGPS 47

Double-stranded RNA binding motif;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1907137116  512 KNPVMELNEKRR-GLKYELISETGGSHDKRFVMEVEVDG-QKFRGAGPN 558
Cdd:smart00358   2 KSLLQELAQKRKlPPEYELVKEEGPDHAPRFTVTVKVGGkRTGEGEGSS 50

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 1907137116 388 LMNALMRLNQIRPglQYKLLSQSGPVHAPVFTMSVDV-DGTTYEASGPSKKTAKLHVAVKVL 448
Cdd:cd19857     5 LLNELARFNKIRP--QYTLVDEEGPAHKKTFTVKLTLgDEEEYEASGSSIKKAQHAAAEKAL 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
                  ....*....|....*....|....*....|....*....|....*.
gi 1907137116 403 QYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKlHVAVKVL 448
Cdd:cd19862    19 KYELISSEGAVHEPTFTFRVTVGDITATGSGTSKKKAK-HAAAENA 63

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 1907137116 389 MNALMRLNQ-IRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTY-EASGPSKKTAKLHVAVKVLQ 449
Cdd:pfam00035   2 KSLLQEYAQkNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYgSGTGSSKKEAEQLAAEKALE 64

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907137116 512 KNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEKLFSGPNA 580
Cdd:cd19896     6 KNALVQLNELKPGLQYRMVSQTGPVHAPVFAVAVEVNGLTFEGTGPTKKKAKMRAAEMALKSFVQFPNA 74

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907137116 390 NALMRLNQIRP----GLQYKLLSQSGPVHAPVFTMSVDVDGTTY-EASGPSKKTAKLHVAVKVLQAM 451
Cdd:cd19903     2 NYMGKLNEYCQkqkvVLDYVEVPTSGPSHDPRFTFQVVIDGKEYpEGEGKSKKEAKQAAAKLALEIL 68

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 1907137116 391 ALMRLNQIRP-GLQYKLLSQSGPVHAPVFTMSVDVDGTTY-EASGPSKKTAKLHVAVKVLQAM 451
Cdd:cd19902     6 ALMEYAQSRGvTAEIEVLSQSGPPHNPRFKAAVFVGGRRFpSVEASSKKDAKQEAADLALRAL 68

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
                  ....*....|....*....|....*....|....*....|....*....|
gi 1907137116 403 QYKLLSQSGPVHAPVFTMSVDVDGTTY-EASGPSKKTAKLHVAVKVLQAM 451
Cdd:cd10845    20 EYELVEEEGPDHNKTFTVEVKVNGKVIgEGTGRSKKEAEQAAAKAALEKL 69

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 1907137116 403 QYKLLSQSGPVHAPVFTMSVDVDGTTY-EASGPSKKTAK---LHVAVKVL 448
Cdd:cd19914    19 EFQLLSQEGPPHDPKFTYCVKVGEQTFpSVVANSKKVAKqmaAEEAVKEL 68

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
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907137116 512 KNPVMELNE--KRRGL---KYELISETGGSHDKRFVMEVEVDGQKF-RGAGPN 558
Cdd:cd10845     1 KDYKTALQEylQKRGLplpEYELVEEEGPDHNKTFTVEVKVNGKVIgEGTGRS 53

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
                  ....*....|....*....|....*....|....*....|....*....|
gi 1907137116 514 PVMELNE----KRRGLKYELISETGGSHDKRFVMEVEVDGQKF-RGAGPN 558
Cdd:pfam00035   1 PKSLLQEyaqkNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYgSGTGSS 50

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
                  ....*....|....*....|....*....|....*....|....*...
gi 1907137116 403 QYKLLSQSGPVHAPVFTMSVDVDGTTYE-ASGPSKKTAKLHVAVKVLQ 449
Cdd:cd19913    19 EFLLLEQSGPSHDPRFKFQAVIDGRRFPpAEASSKKVAKKDAAAIALK 66

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
                  ....*....|....*....|....*....|....*....|....*....|
gi 1907137116 402 LQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAM 451
Cdd:cd19859    16 VNFEVLRESGPPHMKNFITRCTVGSFVTEGEGNSKKVSKKRAAEKMLEEL 65

fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 2 (Staufen 2) and similar proteins; Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen 2 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907137116 389 MNALMRLNQIRPGLQ-----YKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGY 453
Cdd:cd19886     3 MNPISRLAQIQQAKKekepeYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKRNAAEAMLLQLGY 72

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907137116 403 QYKLLSQSGPVHAPVFTMSVDV----DGTTYEASG---PSKKTAKLHVAVKVLQ 449
Cdd:cd19869    13 VYRCVEEEGPAHAKRFTYMVRVkipeRGWTIECEGepmRSKKRAKDSAALLLLE 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
                  ....*....|....*....|....*....|....*....|.
gi 1907137116 409 QSGPVHAPVFTMSVDVDGTTYEASG--PSKKTAKlHVAVKV 447
Cdd:cd19907    24 REGPDHAPRFRATVTFNGVIFESPPgfPTLKAAE-HSAAEV 63

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
                  ....*....|....*....|....*....|..
gi 1907137116 527 YELISETGGSHDKRFVMEVEVDGQKFRGAGPN 558
Cdd:cd19860    20 YSLVAERGTPRRREFVMQVTVGDKTATGTGPN 51

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1907137116 403 QYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVL 448
Cdd:cd10844    19 EYTVTQESGPAHRKEFTMTCRVERFIEIGSGTSKKLAKRNAAAKML 64

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 1907137116 404 YKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAK---LHVAVKVLQ 449
Cdd:cd19890    22 YDLLKAEGQAHQPNFTFRVTVGDISCTGQGPSKKAAKhkaAEVALKLLK 70