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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568996719 639 LSPYQILHECLKRNHGMGDTSIKFEVVPGKNQKSEYVMACGKHTVRGWCKNKRVGKQLASQKILQLLHP 707
Cdd:cd19868    1 PSPYQILQECLKRNHGMGDTELKFEVINDKHQKHEYTMTVGKHTVTVICKNKKEGKQLAAQAILKKLHP 69

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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568996719 639 LSPYQILHECLKRNHGMGDTSIKFEVVPGKNQKSEYVMACGKHTVRGWCKNKRVGKQLASQKILQLLHP 707
Cdd:cd19868    1 PSPYQILQECLKRNHGMGDTELKFEVINDKHQKHEYTMTVGKHTVTVICKNKKEGKQLAAQAILKKLHP 69

Double-stranded RNA binding motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568996719   513 VCILHEYMQRvLKVRPVYNFFECENPSEP--FGASVTIDGVTYGSGTASSKKLAKNKAARATLEIL 576
Cdd:smart00358   2 KSLLQELAQK-RKLPPEYELVKEEGPDHAprFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRSL 66

dsRNA-specific ribonuclease [Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996719 496 DAPTKKEFVINPngKSEvciLHEYMQRVLKVRPVYNFFECENPS-EP-FGASVTIDGVTYGSGTASSKKLAKNKAARATL 573
Cdd:COG0571  148 EEIAPGGAGKDY--KTA---LQEWLQARGLPLPEYEVVEEEGPDhAKtFTVEVLVGGKVLGEGTGRSKKEAEQAAAKAAL 222

                 ...
gi 568996719 574 EIL 576
Cdd:COG0571  223 EKL 225

double-strand RNA-binding protein; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996719 498 PTKKefVINPNGKSEVCILHEYMQrvLKVRPVY-NFFECENPSEP-FGASVTIDGVTYGSGTASSKKLAKNKAARATLEI 575
Cdd:PHA03103  99 PYKK--IISWKDKNPCTVINEYCQ--ITSRDWSiNITSSGPSHSPtFTASVIISGIKFKPAIGSTKKEAKNNAAKLAMDK 174

                 ..
gi 568996719 576 LI 577
Cdd:PHA03103 175 IL 176

Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.

                         10        20
                 ....*....|....*....|....*....
gi 568996719 304 PDGWIMTFHNSGVPVYLHRESRVVTWSRP 332
Cdd:cd00201    1 PPGWEERWDPDGRVYYYNHNTKETQWEDP 29

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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568996719 639 LSPYQILHECLKRNHGMGDTSIKFEVVPGKNQKSEYVMACGKHTVRGWCKNKRVGKQLASQKILQLLHP 707
Cdd:cd19868    1 PSPYQILQECLKRNHGMGDTELKFEVINDKHQKHEYTMTVGKHTVTVICKNKKEGKQLAAQAILKKLHP 69

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 568996719 510 KSEVCILHEYMQRvLKVRPVYNFFECENPSEP-FGASVTIDGVTYGSGTASSKKLAKNKAARATLEIL 576
Cdd:cd19875    1 KNPVSALNEYCQK-RGLSLEFVDVSVGPDHCPgFTASATIDGIVFASATGTSKKEAKRAAAKLALKKL 67

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 568996719 517 HEYMQRVLKVRPVYNFFECENPSEP-FGASVTIDGVTYgSGTASSKKLAKNKAARATL 573
Cdd:cd00048    1 NELCQKNKWPPPEYETVEEGGPHNPrFTCTVTVNGQTF-EGEGKSKKEAKQAAAEKAL 57

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568996719 510 KSEVCILHEYMQRvLKVRPVYNFFECENPS-EP-FGASVTIDGVTyGSGTASSKKLAKNKAARATLEIL 576
Cdd:cd19862    1 KTPISVLQELCAK-RGITPKYELISSEGAVhEPtFTFRVTVGDIT-ATGSGTSKKKAKHAAAENALEQL 67

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as ribonuclease 3) digests double-stranded RNA formed within single-strand substrates, but not RNA-DNA hybrids. It is involved in the processing of rRNA precursors, viral transcripts, some mRNAs, and at least 1 tRNA (metY, a minor form of tRNA-init-Met). It cleaves the 30S primary rRNA transcript to yield the immediate precursors to the 16S and 23S rRNAs. The cleavage can occur in assembled 30S, 50S, and even 70S subunits and is influenced by the presence of ribosomal proteins. The RNase III family also includes the mitochondrion-specific ribosomal protein mL44 subfamily, which is composed of mitochondrial 54S ribosomal protein L3 (MRPL3) and mitochondrial 39S ribosomal protein L44 (MRPL44). Members of this family contain an RNase III domain and a C-terminal double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568996719 515 ILHEYMQRVLKVRPVYNFFECENPS-EP-FGASVTIDGVTYGSGTASSKKLAKNKAARATLEIL 576
Cdd:cd10845    6 ALQEYLQKRGLPLPEYELVEEEGPDhNKtFTVEVKVNGKVIGEGTGRSKKEAEQAAAKAALEKL 69

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        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568996719 505 INPngkseVCILHEYMQRVlkvRPVYNFFECEN----PSEPFGASVTIDGVTYGSGTASSKKLAKNKAARATLEILI 577
Cdd:cd19905    1 KNP-----VSALHEYAQMT---RLKLSFKETVTtgnvAGPYFAFCAVVDGIEYPTGVGKTKKEAKANAAKIALDELL 69

double-strand RNA-binding protein; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996719 498 PTKKefVINPNGKSEVCILHEYMQrvLKVRPVY-NFFECENPSEP-FGASVTIDGVTYGSGTASSKKLAKNKAARATLEI 575
Cdd:PHA03103  99 PYKK--IISWKDKNPCTVINEYCQ--ITSRDWSiNITSSGPSHSPtFTASVIISGIKFKPAIGSTKKEAKNNAAKLAMDK 174

                 ..
gi 568996719 576 LI 577
Cdd:PHA03103 175 IL 176

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 568996719 516 LHEYMQrvlKVRPVYNFFECENPSEP----FGASVTIDGVTYGSGTASSKKLAKNKAARATLEIL 576
Cdd:cd19903    7 LNEYCQ---KQKVVLDYVEVPTSGPShdprFTFQVVIDGKEYPEGEGKSKKEAKQAAAKLALEIL 68

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
                 ....*....|....*....|....*....|....*
gi 568996719 542 FGASVTIDGVTYgSGTASSKKLAKNKAARATLEIL 576
Cdd:cd19866   30 FVMSVTVDGQTF-EGTGRSKKLAKAAAAQAALAKL 63

first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; DHX9 (EC 3.6.4.13; also known as ATP-dependent RNA helicase A, DExH-box helicase 9 (DDX9), Leukophysin (LKP), nuclear DNA helicase II (NDH II), NDH2, or RNA helicase A) is a multifunctional ATP-dependent nucleic acid helicase that unwinds DNA and RNA in a 3' to 5' direction and plays important roles in many processes, such as DNA replication, transcriptional activation, post-transcriptional RNA regulation, mRNA translation, and RNA-mediated gene silencing. It contains two double-stranded RNA binding motifs (DSRMs) at the N-terminal region. This model corresponds to the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 568996719 525 KVRPVYNFFECENP-SEPFGASVTIDGVTY-GSGTASSKKLAKNKAARatleilipDFV 581
Cdd:cd19854   14 KLTPEYDIKEAGNKhRQRFKCEVRVEGFDYvGTGNATNKKDAQTNAAR--------DFL 64

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 568996719 510 KSEVCILHEYMQrVLKVRPVYNFFECENPS-EP-FGASVTIDGVTYGSGTASSKKLAKNKAARATLEILI 577
Cdd:cd19902    1 KNPVSALMEYAQ-SRGVTAEIEVLSQSGPPhNPrFKAAVFVGGRRFPSVEASSKKDAKQEAADLALRALI 69

double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) and similar proteins; DUS2L (also known as dihydrouridine synthase 2 (DUS2), up-regulated in lung cancer protein 8 (URLC8), or tRNA-dihydrouridine synthase 2-like) catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs. It negatively regulates the activation of EIF2AK2/PKR. DUS2L contains an N-terminal FMN-binding domain and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568996719 515 ILHEYMQRVLKVRPVYNFFECENpSEPFGASVTIDGVTYGSGT-ASSKKLAKNKAARATLEIL 576
Cdd:cd19871    5 ILNEWCRKNKLPQPVYETVQRPS-DRLFQSVVTVDGKKYTSSLwEKSKKLAEQAAAIVCLRAL 66

Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.

                         10        20
                 ....*....|....*....|....*....
gi 568996719 304 PDGWIMTFHNSGVPVYLHRESRVVTWSRP 332
Cdd:cd00201    1 PPGWEERWDPDGRVYYYNHNTKETQWEDP 29

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 568996719 510 KSEVCILHEYMQrvlkvrpvYNFFECE-------NPS-EP-FGASVTIDGVTYGSGTASSKKLAKNKAARATLEILI 577
Cdd:cd19913    1 KNPVSGLMEYAQ--------FLGQTCEfllleqsGPShDPrFKFQAVIDGRRFPPAEASSKKVAKKDAAAIALKILL 69