double-stranded RNA binding motif of adenosine deaminase domain-containing protein 1 (ADAD1) and similar proteins; ADAD1 (also known as testis nuclear RNA-binding protein (TENR)) is phylogenetically related to a family of adenosine deaminases involved in RNA editing. It 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. ADAD1 contains a double-stranded RNA binding motif (DSRM) and a C-terminal adenosine-deaminase (editase) domain. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 530377173  95 INPVSALHQFAQMQRVQLDLKETVTTGNVMGPYFAFCAVVDGIQYKTGLGQNKKESRSNAAKLALDELL 163
Cdd:cd19905    1 KNPVSALHEYAQMTRLKLSFKETVTTGNVAGPYFAFCAVVDGIEYPTGVGKTKKEAKANAAKIALDELL 69

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 530377173  249 AIGTGEYNYSQD-IKPDGRVLHDTHAVVTARRSLLRYFYRQLLLFYSKNPammEKSIFCTEPTSNLLTLKQNINICLYMN 327
Cdd:pfam02137   1 ALGTGTKCIGGSkLSPSGRVLNDSHAEVIARRSLLRYLYSQLLLALSGNP---SKSIFEPNPDSGKLRLKPGISFHLYIS 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530377173  328 QLPKGSAQIKSQLRLNPHSISA---FEANEELCLHVAVEGKIYLTVYCP---KDGVN---RISSMSSSDKLTRWEVLGVQ 398
Cdd:pfam02137  78 QTPCGDARIFSPLELEPESSPAhpvRRFRGQLRLKVETGAKTIPVESSEdqtWDGVKpgrRTLSMSCSDKLARWNVLGVQ 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530377173  399 GALLSHFIQPVYISSILIGdGNCSDTRGLEIAIKQRVDDALTSkLPMFYLVNRPHISLVPsayplqmnleykflslnwaq 478
Cdd:pfam02137 158 GALLSHFIEPIYLSSITVG-GSLYDTEHLERAIYQRLDGVLDS-LPPPYRVNKPLIGQVA-------------------- 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530377173  479 gdvsleivdglsgkitesspfksgmsmaSRLCKAAMLSRFNLLAKEAKKELLEAG-TYHAAKCMSASYQEAKCKLKSYLQ 557
Cdd:pfam02137 216 ----------------------------SRLCKAALFSRFLKLLSELSREDLLAPlTYHEAKAAAKDYQEAKQQLKSLLR 267

                         330
                  ....*....|.
gi 530377173  558 QHGYGSWIVKS 568
Cdd:pfam02137 268 QQGLGSWIRKP 278

Double-stranded RNA binding motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 530377173    97 PVSALHQFAQMQRVQLDLKETVTTGNVMGPYFAFCAVVDGIQYKTGLGQNKKESRSNAAKLALDEL 162
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRSL 66

double-strand RNA-binding protein; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530377173  82 IPKEFIMKYKrgEINPVSALHQFAQMQRVQLDLKETvTTGNVMGPYFAFCAVVDGIQYKTGLGQNKKESRSNAAKLALDE 161
Cdd:PHA03103  98 IPYKKIISWK--DKNPCTVINEYCQITSRDWSINIT-SSGPSHSPTFTASVIISGIKFKPAIGSTKKEAKNNAAKLAMDK 174

                 ..
gi 530377173 162 LL 163
Cdd:PHA03103 175 IL 176

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 530377173  249 AIGTGEYNYSQD-IKPDGRVLHDTHAVVTARRSLLRYFYRQLLLFYSKNPammEKSIFCTEPTSNLLTLKQNINICLYMN 327
Cdd:pfam02137   1 ALGTGTKCIGGSkLSPSGRVLNDSHAEVIARRSLLRYLYSQLLLALSGNP---SKSIFEPNPDSGKLRLKPGISFHLYIS 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530377173  328 QLPKGSAQIKSQLRLNPHSISA---FEANEELCLHVAVEGKIYLTVYCP---KDGVN---RISSMSSSDKLTRWEVLGVQ 398
Cdd:pfam02137  78 QTPCGDARIFSPLELEPESSPAhpvRRFRGQLRLKVETGAKTIPVESSEdqtWDGVKpgrRTLSMSCSDKLARWNVLGVQ 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530377173  399 GALLSHFIQPVYISSILIGdGNCSDTRGLEIAIKQRVDDALTSkLPMFYLVNRPHISLVPsayplqmnleykflslnwaq 478
Cdd:pfam02137 158 GALLSHFIEPIYLSSITVG-GSLYDTEHLERAIYQRLDGVLDS-LPPPYRVNKPLIGQVA-------------------- 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530377173  479 gdvsleivdglsgkitesspfksgmsmaSRLCKAAMLSRFNLLAKEAKKELLEAG-TYHAAKCMSASYQEAKCKLKSYLQ 557
Cdd:pfam02137 216 ----------------------------SRLCKAALFSRFLKLLSELSREDLLAPlTYHEAKAAAKDYQEAKQQLKSLLR 267

                         330
                  ....*....|.
gi 530377173  558 QHGYGSWIVKS 568
Cdd:pfam02137 268 QQGLGSWIRKP 278

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; The family includes EIF2AK2 and adenosine deaminase domain-containing proteins, ADAD1 and ADAD2. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. ADAD1 (also called testis nuclear RNA-binding protein (TENR)) and ADAD2 (also called testis nuclear RNA-binding protein-like (TENRL)) are phylogenetically related to a family of adenosine deaminases involved in RNA editing. ADAD1 plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs. ADAD2 is a double-stranded RNA binding protein with unclear biological function. Members of this group contains varying numbers of double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 530377173  95 INPVSALHQFAQMQRVQLDLKEtVTTGNVMGPYFAFCAVVDGIQYKTGLGQNKKESRSNAAKLALDEL 162
Cdd:cd19875    1 KNPVSALNEYCQKRGLSLEFVD-VSVGPDHCPGFTASATIDGIVFASATGTSKKEAKRAAAKLALKKL 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 530377173   97 PVSALHQFAQMQRVQLDLKETVTTGNVMGPYFAFCAVVDGIQYKTGLGQNKKESRSNAAKLALDEL 162
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKALEKL 66

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 530377173  96 NPVSALHQFAQMQRVQLDLKETVTTGNVMGPYFAFCAVVDGIQYKTGLGQNKKESRSNAAKLALDELLQ 164
Cdd:cd19902    2 NPVSALMEYAQSRGVTAEIEVLSQSGPPHNPRFKAAVFVGGRRFPSVEASSKKDAKQEAADLALRALIA 70

first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and similar proteins; DGCR8 is a component of the microprocessor complex that acts as an RNA- and heme-binding protein that is involved in the initial step of microRNA (miRNA) biogenesis. Within the microprocessor complex, DGCR8 functions as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs DROSHA to cleave 11bp away from the junction to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. DGCR8 contains two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 530377173  96 NPVSALHQFAQMQ-RVQLDLKETVTTGNVMGpyfaFCAVV--DGIQYKTGLGQNKKESRSNAAKLALDELL 163
Cdd:cd19867    7 SPVCILHEYCQRVlKVQPEYNFTETENAATP----FSAEVfiNGVEYGSGEASSKKLAKQKAARATLEILI 73

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        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 530377173  96 NPVSALHQFAQMQRVQLDLKETVTTGNVMGPYFAFCAVVDGIQYKTGLGQNKKESRSNAAKLALDELLQ 164
Cdd:cd19913    2 NPVSGLMEYAQFLGQTCEFLLLEQSGPSHDPRFKFQAVIDGRRFPPAEASSKKVAKKDAAAIALKILLR 70

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 530377173  99 SALHQFAQMQRVQLDLKETVTTGNVMGPYFAFCAVVDGIQYKTGLGQNKKESRSNAAKLALDEL 162
Cdd:cd19878    3 NLLQEYAQKKKIPLPKYESAKSGPSHQPTFVSTVIVLGVRFSSEGAKNKKQAEQSAAKVALKEL 66

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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 530377173  96 NPVSALHQFAQMQRVQLDLKETVTTGNVMGPYFAFCAVVDGIQYKTGLGQNKKESRSNAAKLALDELL 163
Cdd:cd19904    2 NYISLLNQYAQKKRLTVNYEQCASTGVPGPPRFSCKCKIGQKEYGIGTGSTKQEAKQAAAKEAYEQLL 69

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 530377173  96 NPVSALHQFAQMQRVQLDLKETVTTGNVMGPYFAFCAVVDGIQyKTGLGQNKKESRSNAAKLALDELLQL 165
Cdd:cd19862    2 TPISVLQELCAKRGITPKYELISSEGAVHEPTFTFRVTVGDIT-ATGSGTSKKKAKHAAAENALEQLKGS 70

double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known as Bax antagonist selected in saccharomyces 1 (BASS1), negative regulatory element-binding protein (NRE-binding protein), or protein DBP-5, or SON3) is an RNA-binding protein which acts as an mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. It specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Members of this group contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 530377173  96 NPVSALHQFAQMQRVQLDLKETVT-TGNVMGPYFAFCAVVDGIQYKTGLGQ-NKKESRSNAAKLALDEL 162
Cdd:cd19870    3 HPVSALMELCNKRKWGPPEFRLVEeSGPPHRKHFLFKVVVNGVEYQPSVASgNKKDAKAQAATVALQAL 71