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
                  ....*....|....*....|....*....|....*
gi 568957773  239 ALGTGSSSCAG-WLEFSGRRLHDCHGLVIARRALL 272
Cdd:pfam02137   1 ALGTGTKCIGGsKLSPSGRVLNDSHAEVIARRSLL 35

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
                  ....*....|....*....|....*....|....*
gi 568957773  239 ALGTGSSSCAG-WLEFSGRRLHDCHGLVIARRALL 272
Cdd:pfam02137   1 ALGTGTKCIGGsKLSPSGRVLNDSHAEVIARRSLL 35

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 568957773   94 AVALLTQCMANLGVSLTFLEDQTAGPGSS--FSVCADLDGLVCPAGTGSSKLEAKQQAALSALQYI 157
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSpkFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKALEKL 66

double-strand RNA-binding protein; Provisional

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 568957773 116 TAGPGSS--FSVCADLDGLVCPAGTGSSKLEAKQQAALSALQYI 157
Cdd:PHA03103 132 SSGPSHSptFTASVIISGIKFKPAIGSTKKEAKNNAAKLAMDKI 175

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
                  ....*....|....*....|....*....|....*
gi 568957773  239 ALGTGSSSCAG-WLEFSGRRLHDCHGLVIARRALL 272
Cdd:pfam02137   1 ALGTGTKCIGGsKLSPSGRVLNDSHAEVIARRSLL 35

Double-stranded RNA binding motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568957773    94 AVALLTQCMANLGVSLTFLEDQTAGPGSS--FSVCADLDGLVCPAGTGSSKLEAKQQAALSALQYIQ 158
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELVKEEGPDHAprFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRSLK 67

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 568957773  92 AQAVALLTQCMANLGVSLTFLEDQTAGP--GSSFSVCADLDGLVCPAGTGSSKLEAKQQAALSALQ 155
Cdd:cd19905    1 KNPVSALHEYAQMTRLKLSFKETVTTGNvaGPYFAFCAVVDGIEYPTGVGKTKKEAKANAAKIALD 66

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 568957773 101 CMANLGVSLTFLEDQTAGPGS-SFSVCADLDGLVCpAGTGSSKLEAKQQAALSAL 154
Cdd:cd00048    4 CQKNKWPPPEYETVEEGGPHNpRFTCTVTVNGQTF-EGEGKSKKEAKQAAAEKAL 57

third double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The 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. The 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 third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                         10        20
                 ....*....|....*....|....*.
gi 568957773 133 VCPaGTGSSKLEAKQQAALSALQYIQ 158
Cdd:cd19864   45 VCH-GSGASLEEAKEEAARNALEYLK 69

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 568957773  94 AVALLTQCMANLGVSLTF-LEDQTAGPGS-SFSVCADLDGLVCPAGTGSSKLEAKQQAALSALQ 155
Cdd:cd19902    3 PVSALMEYAQSRGVTAEIeVLSQSGPPHNpRFKAAVFVGGRRFPSVEASSKKDAKQEAADLALR 66

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
                 ....*....|....*....|....*....|....*
gi 568957773 123 FSVCADLDGLVCPAGTGSSKLEAKQQAALSALQYI 157
Cdd:cd10845   35 FTVEVKVNGKVIGEGTGRSKKEAEQAAAKAALEKL 69