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 153945870 137 INPVSALHQFAQMQRVQLDLKETVTTGNVMGPYFAFCAVVDGIQYKTGLGQNKKESRSNAAKLALDELL 205
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 153945870  291 AIGTGEYNYSQ-CIKPNGRVLHDTHAVVTARRSLLRYFYRQLLLFYSKNPammEKSIFCTEPASNLLTLKQNINLYLYMN 369
Cdd:pfam02137   1 ALGTGTKCIGGsKLSPSGRVLNDSHAEVIARRSLLRYLYSQLLLALSGNP---SKSIFEPNPDSGKLRLKPGISFHLYIS 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 153945870  370 QLPKGSAQIKSQLRLNPHSISA---FEANEELSLHVAVEGKIYLTVYCSA---DGVN---RVNSMSSSDKLTRWEVLGVQ 440
Cdd:pfam02137  78 QTPCGDARIFSPLELEPESSPAhpvRRFRGQLRLKVETGAKTIPVESSEDqtwDGVKpgrRTLSMSCSDKLARWNVLGVQ 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 153945870  441 GALLSHFIQPVYISSILVGdGNCNDTRGLEIAINQRVDDALTSkLPMFYLVNRPHISLVPtayplqinldhkslslnwaq 520
Cdd:pfam02137 158 GALLSHFIEPIYLSSITVG-GSLYDTEHLERAIYQRLDGVLDS-LPPPYRVNKPLIGQVA-------------------- 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 153945870  521 gdnsleivdglngkitesspfksglsmaSRLCKAAMLSRFNLLAKEAKTDDLLEARTYHAAKCMSGPYQEAKALLKAYLQ 600
Cdd:pfam02137 216 ----------------------------SRLCKAALFSRFLKLLSELSREDLLAPLTYHEAKAAAKDYQEAKQQLKSLLR 267

                         330
                  ....*....|.
gi 153945870  601 QHGYGSWIVKS 611
Cdd:pfam02137 268 QQGLGSWIRKP 278

Double-stranded RNA binding motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 153945870   139 PVSALHQFAQMQRVQLDLKETVTTGNVMGPYFAFCAVVDGIQYKTGLGQNKKESRSNAAKLALDEL 204
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRSL 66

double-strand RNA-binding protein; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 153945870 124 LPKEFIMKYKrgEINPVSALHQFAQMQRVQLDLKETvTTGNVMGPYFAFCAVVDGIQYKTGLGQNKKESRSNAAKLALDE 203
Cdd:PHA03103  98 IPYKKIISWK--DKNPCTVINEYCQITSRDWSINIT-SSGPSHSPTFTASVIISGIKFKPAIGSTKKEAKNNAAKLAMDK 174

                 ..
gi 153945870 204 LL 205
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 153945870  291 AIGTGEYNYSQ-CIKPNGRVLHDTHAVVTARRSLLRYFYRQLLLFYSKNPammEKSIFCTEPASNLLTLKQNINLYLYMN 369
Cdd:pfam02137   1 ALGTGTKCIGGsKLSPSGRVLNDSHAEVIARRSLLRYLYSQLLLALSGNP---SKSIFEPNPDSGKLRLKPGISFHLYIS 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 153945870  370 QLPKGSAQIKSQLRLNPHSISA---FEANEELSLHVAVEGKIYLTVYCSA---DGVN---RVNSMSSSDKLTRWEVLGVQ 440
Cdd:pfam02137  78 QTPCGDARIFSPLELEPESSPAhpvRRFRGQLRLKVETGAKTIPVESSEDqtwDGVKpgrRTLSMSCSDKLARWNVLGVQ 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 153945870  441 GALLSHFIQPVYISSILVGdGNCNDTRGLEIAINQRVDDALTSkLPMFYLVNRPHISLVPtayplqinldhkslslnwaq 520
Cdd:pfam02137 158 GALLSHFIEPIYLSSITVG-GSLYDTEHLERAIYQRLDGVLDS-LPPPYRVNKPLIGQVA-------------------- 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 153945870  521 gdnsleivdglngkitesspfksglsmaSRLCKAAMLSRFNLLAKEAKTDDLLEARTYHAAKCMSGPYQEAKALLKAYLQ 600
Cdd:pfam02137 216 ----------------------------SRLCKAALFSRFLKLLSELSREDLLAPLTYHEAKAAAKDYQEAKQQLKSLLR 267

                         330
                  ....*....|.
gi 153945870  601 QHGYGSWIVKS 611
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 153945870 137 INPVSALHQFAQMQRVQLDLKEtVTTGNVMGPYFAFCAVVDGIQYKTGLGQNKKESRSNAAKLALDEL 204
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 153945870  139 PVSALHQFAQMQRVQLDLKETVTTGNVMGPYFAFCAVVDGIQYKTGLGQNKKESRSNAAKLALDEL 204
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 153945870 138 NPVSALHQFAQMQRVQLDLKETVTTGNVMGPYFAFCAVVDGIQYKTGLGQNKKESRSNAAKLALDELLQ 206
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 153945870 138 NPVSALHQFAQMQ-RVQLDLKETVTTGNVMGpyfaFCAVV--DGIQYKTGLGQNKKESRSNAAKLALDELL 205
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 153945870 138 NPVSALHQFAQMQRVQLDLKETVTTGNVMGPYFAFCAVVDGIQYKTGLGQNKKESRSNAAKLALDELLQ 206
Cdd:cd19913    2 NPVSGLMEYAQFLGQTCEFLLLEQSGPSHDPRFKFQAVIDGRRFPPAEASSKKVAKKDAAAIALKILLR 70

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 153945870 137 INPVSALHQFAQMqRVQLDLKETVTTGNVMGPYFAFCAVVDGIQYKtGLGQNKKESRSNAAKLALDELLQL 207
Cdd:cd19896    3 VTPKNALVQLNEL-KPGLQYRMVSQTGPVHAPVFAVAVEVNGLTFE-GTGPTKKKAKMRAAEMALKSFVQF 71

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 153945870 138 NPVSALHQFAQMQRVQLDLKETVTTGNVMGPYFAFCAVVDGIQYKTGLGQNKKESRSNAAKLALDELL 205
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 153945870 138 NPVSALHQFAQMQRVQLDLKETVTTGNVMGPYFAFCAVVDGIQyKTGLGQNKKESRSNAAKLALDELLQL 207
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 153945870 138 NPVSALHQFAQMQRVQLDLKETVT-TGNVMGPYFAFCAVVDGIQYKTGLGQ-NKKESRSNAAKLALDEL 204
Cdd:cd19870    3 HPVSALMELCNKRKWGPPEFRLVEeSGPPHRKHFLFKVVVNGVEYQPSVASgNKKDAKAQAATVALQAL 71