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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1126180457 310 KNPISALMEYAQSRHVKASIEVIAETGPPHNPRFTMAAVVGGRQFPAVIAKAKKDGKREAADVALRTLISE 380
Cdd:cd19902     1 KNPVSALMEYAQSRGVTAEIEVLSQSGPPHNPRFKAAVFVGGRRFPSVEASSKKDAKQEAADLALRALIAE 71

Adenosine deaminase z-alpha domain; This family consists of the N-terminus and thus the z-alpha domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA- editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of this region to B-DNA has been shown to be disfavoured by steric hindrance.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1126180457   40 SLEDRLLAALSRADSP-INSNDLAKMVGFrTKKEINPTLFAMQRKGLVKKVNDVPPLWQVVEAA 102
Cdd:smart00550   6 SLEEKILEFLENSGDEtSTALQLAKNLGL-PKKEVNRVLYSLEKKGKVCKQGGTPPLWKLTDKA 68

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 1126180457 453 SIGTGNRCIAGDQLSRQGLAINDSHAEIMCRRAFLRYLYQQLLSYYD-DPENSIFQECDEDSKqhFKLKPDVTFHLYIST 531
Cdd:pfam02137   1 ALGTGTKCIGGSKLSPSGRVLNDSHAEVIARRSLLRYLYSQLLLALSgNPSKSIFEPNPDSGK--LRLKPGISFHLYISQ 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1126180457 532 APCGDGALFSLHDTEQvseveeplemsDNIQHTPIFSDPGKqglLRTKMEQGEGTIPIDPDTPiQTWDGVLRGERLRTMS 611
Cdd:pfam02137  79 TPCGDARIFSPLELEP-----------ESSPAHPVRRFRGQ---LRLKVETGAKTIPVESSED-QTWDGVKPGRRTLSMS 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1126180457 612 CSDKIARWNIVGLQGALLSHFLEPVYLSSVTLGAisCPgknrrqrriylsrrqsmmYIHGHLTRAVCCRWARgdveLQSL 691
Cdd:pfam02137 144 CSDKLARWNVLGVQGALLSHFIEPIYLSSITVGG--SL------------------YDTEHLERAIYQRLDG----VLDS 199

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1126180457 692 LPPNYKLNHPQVGRVmtfrppretektkplsinwclgqdiaevidstkgkcverygchpVSKVSKSSLYVLFRTLCSKMN 771
Cdd:pfam02137 200 LPPPYRVNKPLIGQV--------------------------------------------ASRLCKAALFSRFLKLLSELS 235

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|...
gi 1126180457 772 RDDLLAAKTYHQAKLMAKEFQTAKAALFEICEKNGYGKWMQKP 814
Cdd:pfam02137 236 REDLLAPLTYHEAKAAAKDYQEAKQQLKSLLRQQGLGSWIRKP 278

Double-stranded RNA binding motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1126180457  312 PISALMEYAQSRHVKASIEVIAETGPPHNPRFTMAAVVGGRQFPAVIAKAKKDGKREAADVALRTL 377
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRSL 66

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 1126180457 312 PISALMEYAQSRHVKASIEVIAETGPPHNPRFTMAAVVGGRQFPAVIAKAKKDGKREAADVALRTL 377
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKALEKL 66

Z-DNA-binding domain in adenosine deaminases; Helix-turn-helix-containing domain. Also known as Zab.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1126180457  169 LAKRENQKTTSLDLAKALGFqTKKDINPTLYALQNKGFVAKINDCPPCWTI 219
Cdd:smart00550  15 LENSGDETSTALQLAKNLGL-PKKEVNRVLYSLEKKGKVCKQGGTPPLWKL 64

Adenosine deaminase z-alpha domain; This family consists of the N-terminus and thus the z-alpha domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA- editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of this region to B-DNA has been shown to be disfavoured by steric hindrance.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1126180457  40 SLEDRLLAALSRADSPINSNDLAKMVGFRT-KKEINPTLFAMQRKGLVKKVNDVPPLWQVVEA 101
Cdd:pfam02295   4 ECAEKILELLENLGEGKAATAIALERGLSTpKREINRVLYDLERKGDVYREDGTPPRWFLTCA 66

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1126180457 311 NPISALMEYAQSRHVKA-SIEVIAETGPPHNPRFTMAAVVGGRQFPAvIAKAKKDGKREAADVALRTLISEGHLQLP 386
Cdd:TIGR04238   1 NVVGMLQELAVKRGLELpVYEKVGKEGPDHAPTFTIKLTANDIEVIE-AASSKKQAEKLAAATIYEDMKENGLLEVH 76

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 1126180457 453 SIGTGNRCIAGDQLSRQGLAINDSHAEIMCRRAFLRYLYQQLLSYYD-DPENSIFQECDEDSKqhFKLKPDVTFHLYIST 531
Cdd:pfam02137   1 ALGTGTKCIGGSKLSPSGRVLNDSHAEVIARRSLLRYLYSQLLLALSgNPSKSIFEPNPDSGK--LRLKPGISFHLYISQ 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1126180457 532 APCGDGALFSLHDTEQvseveeplemsDNIQHTPIFSDPGKqglLRTKMEQGEGTIPIDPDTPiQTWDGVLRGERLRTMS 611
Cdd:pfam02137  79 TPCGDARIFSPLELEP-----------ESSPAHPVRRFRGQ---LRLKVETGAKTIPVESSED-QTWDGVKPGRRTLSMS 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1126180457 612 CSDKIARWNIVGLQGALLSHFLEPVYLSSVTLGAisCPgknrrqrriylsrrqsmmYIHGHLTRAVCCRWARgdveLQSL 691
Cdd:pfam02137 144 CSDKLARWNVLGVQGALLSHFIEPIYLSSITVGG--SL------------------YDTEHLERAIYQRLDG----VLDS 199

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1126180457 692 LPPNYKLNHPQVGRVmtfrppretektkplsinwclgqdiaevidstkgkcverygchpVSKVSKSSLYVLFRTLCSKMN 771
Cdd:pfam02137 200 LPPPYRVNKPLIGQV--------------------------------------------ASRLCKAALFSRFLKLLSELS 235

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|...
gi 1126180457 772 RDDLLAAKTYHQAKLMAKEFQTAKAALFEICEKNGYGKWMQKP 814
Cdd:pfam02137 236 REDLLAPLTYHEAKAAAKDYQEAKQQLKSLLRQQGLGSWIRKP 278

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1126180457 310 KNPISALMEYAQSRHVKASIEVIAETGPPHNPRFTMAAVVGGRQFPAVIAKAKKDGKREAADVALRTLISE 380
Cdd:cd19915     1 TNPVSGLLEYARSKGFAAEFKLVDQSGPPHEPKFVYQAKVGGRWFPAVCAHNKKQGKQEAADAALRVLIGE 71

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1126180457 310 KNPISALMEYAQSRHVKASIEVIAETGPPHNPRFTMAAVVGGRQFPAVIAKAKKDGKREAADVALRTLISE 380
Cdd:cd19913     1 KNPVSGLMEYAQFLGQTCEFLLLEQSGPSHDPRFKFQAVIDGRRFPPAEASSKKVAKKDAAAIALKILLRE 71

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        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1126180457 310 KNPISALMEYAQSRHVKASIEVIAETGPPHNPRFTMAAVVGGRQFPAVIAKAKKDGKREAADVALRTLISE 380
Cdd:cd19914     1 KNPISVLMEHSQKSGNMCEFQLLSQEGPPHDPKFTYCVKVGEQTFPSVVANSKKVAKQMAAEEAVKELMGE 71

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 1126180457 310 KNPISALMEYAQSRHVKASIEVIAETGPPHNPRFTMAAVVGGRQFPAVIAKAKKDGKREAADVALRTLI 378
Cdd:cd19905     1 KNPVSALHEYAQMTRLKLSFKETVTTGNVAGPYFAFCAVVDGIEYPTGVGKTKKEAKANAAKIALDELL 69

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 1126180457 312 PISALMEYAQSRHVKASIEVIAETGPPHNPRFTMAAVVGGRQFPAVIAKAKKDGKREAADVALRTL 377
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKALEKL 66

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1126180457 309 NKNPISALMEYAQSRHVKA-SIEVIAETGPPHNPRFTMAAVVGGRQF-PAVIAKAKKDGKREAADVALRTL 377
Cdd:cd19870     1 GKHPVSALMELCNKRKWGPpEFRLVEESGPPHRKHFLFKVVVNGVEYqPSVASGNKKDAKAQAATVALQAL 71

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 1126180457 310 KNPISALMEYAQSRHVKASIEVIAETGPPHNPRFTMAAVVGGrqfpaVIAKA----KKDGKREAADVALRTLIS 379
Cdd:cd19862     1 KTPISVLQELCAKRGITPKYELISSEGAVHEPTFTFRVTVGD-----ITATGsgtsKKKAKHAAAENALEQLKG 69

Z-DNA-binding domain in adenosine deaminases; Helix-turn-helix-containing domain. Also known as Zab.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1126180457   40 SLEDRLLAALSRADSP-INSNDLAKMVGFrTKKEINPTLFAMQRKGLVKKVNDVPPLWQVVEAA 102
Cdd:smart00550   6 SLEEKILEFLENSGDEtSTALQLAKNLGL-PKKEVNRVLYSLEKKGKVCKQGGTPPLWKLTDKA 68

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 1126180457 310 KNPISALMEYAQSRHVKasieVIAETGPPHNPRFTMAAVVGGRQFPAvIAKAKKDGKREAADVALRTL 377
Cdd:cd19865     1 KNALMQLNELRPGLQYK----LTSQTGPVHAPVFTMSVEVNGQTFEG-TGRSKKKAKLEAAEKALRSF 63

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1126180457 311 NPISALMEYAQSRHVKASIEVIAETGPPHNPRFTMAAVVGGRQFPAVIAKAKKDGKREAADVALRTL 377
Cdd:cd20314     2 NYVSLLNEYCQKERLTVKYEEEKRSGPTHKPRFFCKYIIDGKEYPEGEGKSKKEAKQAAARLAYEEL 68

Adenosine deaminase z-alpha domain; This family consists of the N-terminus and thus the z-alpha domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA- editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of this region to B-DNA has been shown to be disfavoured by steric hindrance.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1126180457  40 SLEDRLLAALSRADSPINSNDLAKMVGFRT-KKEINPTLFAMQRKGLVKKVNDVPPLWQVVEA 101
Cdd:pfam02295   4 ECAEKILELLENLGEGKAATAIALERGLSTpKREINRVLYDLERKGDVYREDGTPPRWFLTCA 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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1126180457 312 PISALMEYAQSRHVKASIEVIAETGPPHNPRFTMAAVVGgrQFPAV-IAKAKKDGKREAADVALRTL 377
Cdd:cd19859     1 EISLVHEIALKRNLTVNFEVLRESGPPHMKNFITRCTVG--SFVTEgEGNSKKVSKKRAAEKMLEEL 65

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1126180457 310 KNPISALMEYAQSRHVKASIEVIAETGPPHNPRFTMAAVVGgrQFPAV-IAKAKKDGKREAADVALRTL 377
Cdd:cd19884     1 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVTVG--EFTAEgEGNSKKLSKKRAATSVLQEL 67

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 1126180457 311 NPISALMEYAQSRHVKASIEVIAETGPPHNPRFTMAAVVGGRQFPAVIAKAKKDGKREAADVALRTLI 378
Cdd:cd19904     2 NYISLLNQYAQKKRLTVNYEQCASTGVPGPPRFSCKCKIGQKEYGIGTGSTKQEAKQAAAKEAYEQLL 69

Adenosine deaminase z-alpha domain; This family consists of the N-terminus and thus the z-alpha domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA- editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of this region to B-DNA has been shown to be disfavoured by steric hindrance.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1126180457 164 ETLIELAKRENQKTTSLDLAKALGFQT-KKDINPTLYALQNKGFVAKINDCPPCWTI 219
Cdd:pfam02295   7 EKILELLENLGEGKAATAIALERGLSTpKREINRVLYDLERKGDVYREDGTPPRWFL 63

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1126180457 316 LMEYAQSRHVKASIEVIAETGPPHNPRFTMAAVVGGRQFPAVIAKAKKDGKREAADVALRTL 377
Cdd:cd19908     7 LQEYAQKAGLPLPLYTTVRSGPGHVPTFTCTVEIAGITFTGEAAKTKKQAEKSAARTAWSSI 68

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1126180457 310 KNPISALMEYAQSrhvkASIEVIAETGPPHNPRFTMAAVVGGRQFPAViAKAKKDGKREAADVALRTL 377
Cdd:cd19898     3 KNPVMILNELRPG----LKYEFVSESGESHAKNFVMSVTVDGQTFEGS-GRNKKLAKARAAQAALAKL 65

first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRBs)and similar proteins; This family includes a group of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRB1-5). They bind double-stranded RNA (dsRNA) and may be involved in RNA-mediated silencing. Members of this family contain two to three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1126180457 314 SALMEYAQSRHVKASIEVIAETGPPHNPRFTMAAVVGGRQFPAV-IAKAKKDGKREAADVALRTL 377
Cdd:cd19907     4 SQLQEYAQKSCLNLPVYACIREGPDHAPRFRATVTFNGVIFESPpGFPTLKAAEHSAAEVALNSL 68

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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1126180457 291 PVERQAAPV-LNNETFAALNknpISALMEYAQSRHVKasieviaetgpphnpRFTMAAVVGGRQFPAViAKAKKDGKREA 369
Cdd:cd19899     2 PAESEKNPVvLLNELRPGLR---YVCLSETAEKQHIK---------------SFVMAVRVDGRTFEGS-GRSKKLAKAQA 62

                  ....*...
gi 1126180457 370 ADVALRTL 377
Cdd:cd19899    63 AQAALQAL 70