ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1276961820  13 IGVNFKNKDLLKVAMVHRSYINEHpSFALNHNERLEFLGDAVLELVVTEYLYQNY-QNPEGELTNWRAALVNGGSLAEVA 91
Cdd:TIGR02191   5 LGYKFKNPELLEQALTHRSYANEH-HKDVKNNERLEFLGDAVLGLVVAEYLFKNFpDASEGELSRLRAALVSEESLAEVA 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1276961820  92 EEFGLYDYLYLSRGEAKDaNPKARNYILANATEALIGAIYLDMGWQTAKEFITEHLLVKLPHILKNKLYLDAKSHFQELA 171
Cdd:TIGR02191  84 RELGLGDFLLLGKGEEKS-GGRRRDSILADAFEALIGAIYLDSGLEAARKFILKLLIPRIDAIIKEETLKDYKTALQEWA 162

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1276961820 172 QEKVGITPSYRVLSESGPDHAKDFVIGVYLDDELVAEGNGTSKQEAQMDAARRALE 227
Cdd:TIGR02191 163 QARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGEPYGEGKGKSKKEAEQNAAKAALE 218

Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA processing. They probably also cleave a stem-loop structure at the 3' end of U2 snRNA to ensure formation of the correct U2 3' end; they are involved in polyadenylation-independent transcription termination. Some members may be mitochondrial ribosomal protein subunit L15, others may be 60S ribosomal protein L3.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1276961820  20 KDLLKVAMVHRSYINEHpsfaLNHNERLEFLGDAVLELVVTEYLYQNYQNPEGELTNWRAALVNGGSLAEVAEEFGLYDY 99
Cdd:pfam14622   1 EELLLQALTHKSYANGR----KPYNERLEFLGDAVLELSVSEYLFKKPDLDEGGLTKLRASIVSEESLAEIAREIGLGKY 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1276961820 100 LYLSRGEakdANPKARNY--ILANATEALIGAIYLDMGWQTAKEFITEHLLVKL 151
Cdd:pfam14622  77 LRLGKGE---EETGGSGResILADALEALIGAIYLDGGFEVAKEFILKKILPDL 127

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1276961820  13 IGVNFKNKDLLKVAMVHRSYINEHpSFALNHNERLEFLGDAVLELVVTEYLYQNY-QNPEGELTNWRAALVNGGSLAEVA 91
Cdd:TIGR02191   5 LGYKFKNPELLEQALTHRSYANEH-HKDVKNNERLEFLGDAVLGLVVAEYLFKNFpDASEGELSRLRAALVSEESLAEVA 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1276961820  92 EEFGLYDYLYLSRGEAKDaNPKARNYILANATEALIGAIYLDMGWQTAKEFITEHLLVKLPHILKNKLYLDAKSHFQELA 171
Cdd:TIGR02191  84 RELGLGDFLLLGKGEEKS-GGRRRDSILADAFEALIGAIYLDSGLEAARKFILKLLIPRIDAIIKEETLKDYKTALQEWA 162

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1276961820 172 QEKVGITPSYRVLSESGPDHAKDFVIGVYLDDELVAEGNGTSKQEAQMDAARRALE 227
Cdd:TIGR02191 163 QARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGEPYGEGKGKSKKEAEQNAAKAALE 218

Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA processing. They probably also cleave a stem-loop structure at the 3' end of U2 snRNA to ensure formation of the correct U2 3' end; they are involved in polyadenylation-independent transcription termination. Some members may be mitochondrial ribosomal protein subunit L15, others may be 60S ribosomal protein L3.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1276961820  20 KDLLKVAMVHRSYINEHpsfaLNHNERLEFLGDAVLELVVTEYLYQNYQNPEGELTNWRAALVNGGSLAEVAEEFGLYDY 99
Cdd:pfam14622   1 EELLLQALTHKSYANGR----KPYNERLEFLGDAVLELSVSEYLFKKPDLDEGGLTKLRASIVSEESLAEIAREIGLGKY 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1276961820 100 LYLSRGEakdANPKARNY--ILANATEALIGAIYLDMGWQTAKEFITEHLLVKL 151
Cdd:pfam14622  77 LRLGKGE---EETGGSGResILADALEALIGAIYLDGGFEVAKEFILKKILPDL 127

Ribonuclease III domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1276961820  45 ERLEFLGDAVLELVVTEYLYQNYQN-PEGELTNWRAALVNGGSLAEVAEEFGLYDYL------YLSRGEAKDANPK---A 114
Cdd:pfam00636   1 ERLEFLGDAVLELYVREYLFEKFPDlREGDLHRLRSALVSNEALAKLARKLGLEKFLteeeldIRRRNNALGKGPKradG 80

                          90       100
                  ....*....|....*....|.
gi 1276961820 115 RNYILANATEALIGAIYLDMG 135
Cdd:pfam00636  81 KEKVLADAFEALIGALYLDGG 101

Double-stranded RNA binding motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1276961820  163 AKSHFQELAQeKVGITPSYRVLSESGPDHAKDFVIGVYLDDELVAEGNGTSKQEAQMDAARRALEE 228
Cdd:smart00358   1 PKSLLQELAQ-KRKLPPEYELVKEEGPDHAPRFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRS 65

double-stranded RNA binding motif of metazoan ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as Drosha, or ribonuclease 3) is a double-stranded RNA (dsRNA)-specific endoribonuclease that is involved in the initial step of microRNA (miRNA) biogenesis. It is a component of the microprocessor complex that is required to process primary miRNA transcripts (pri-miRNAs) to release precursor miRNA (pre-miRNA) in the nucleus. Within the microprocessor complex, RNase III cleaves the 3' and 5' strands of a stem-loop in pri-miRNAs (processing center 11 bp from the dsRNA-ssRNA junction) to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. It is also involved in pre-rRNA processing. Metazoan RNase III is a larger protein than bacterial RNase III. It contains two RNase III domains in the C-terminal half of the protein followed by a 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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1276961820 161 LDAKSHFQE--LAQEKVGIT----PSYRVLSESGPDHAKDFVIGVYLDDELVAEGNGTSKQEAQMDAARRALEEK 229
Cdd:cd19877     1 NDPKSQLQQccLTLRTEGKKepdiPEYKVLQKSGPTNTRVYTVAVYFRGERIATGTGSSIQQAEMNAAEKALEKL 75

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 1276961820 165 SHFQELAQeKVGITPSYRVLSESGPDHAKDFVIGVYLDDeLVAEGNGTSKQEAQMDAARRALE 227
Cdd:cd19862     5 SVLQELCA-KRGITPKYELISSEGAVHEPTFTFRVTVGD-ITATGSGTSKKKAKHAAAENALE 65

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
                  ....*....|....*....|....*....|....*....|....*...
gi 1276961820 180 SYRVLSESGPDHAKDFVIGVYLDDElVAEGNGTSKQEAQMDAARRALE 227
Cdd:cd19865    15 QYKLTSQTGPVHAPVFTMSVEVNGQ-TFEGTGRSKKKAKLEAAEKALR 61

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 1276961820 165 SHFQELAQeKVGITPSYRVLSESGPDHAKDFVIGVYLdDELVAEGNGTSKQEAQMDAARRALEE 228
Cdd:cd19859     3 SLVHEIAL-KRNLTVNFEVLRESGPPHMKNFITRCTV-GSFVTEGEGNSKKVSKKRAAEKMLEE 64

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1276961820 168 QELAQEKVGITPSYRVLSESGPDHAKDFVIGVYLdDELVAEGNGTSKQEAQMDAARRAL 226
Cdd:cd19863     7 QELCVQRRWRLPEYEVEQESGPPHEKEFTIACRV-ENFSETGSGKSKKLAKRAAAEKML 64

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        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1276961820 181 YRVLSESGPDHAKDFVIGVYLDDElVAEGNGTSKQEAQMDAARRALEE 228
Cdd:cd19866    16 YKCLSESGESHAKSFVMSVTVDGQ-TFEGTGRSKKLAKAAAAQAALAK 62

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
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1276961820 172 QEKVGITPSYRVLSESGPDHAKDFVIGVYLDDELVAEGNGTSKQEAQMDAARRALEE 228
Cdd:cd19903    11 CQKQKVVLDYVEVPTSGPSHDPRFTFQVVIDGKEYPEGEGKSKKEAKQAAAKLALEI 67

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1276961820 177 ITPSYRVLSESGPDHAKDFVIGVYLDDElVAEGNGTSKQEAQMDAARRAL 226
Cdd:cd19880    20 IQPQYKLLNERGPAHAKIFTVQLTLGEQ-TWEAEGSSIKKAQHAAASKAL 68

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 1276961820 165 SHFQELAQeKVGITPSYRVLSESGPDHAKDFVIGVYLDDELVAEGNGTSKQEAQMDAARRAL 226
Cdd:cd19902     5 SALMEYAQ-SRGVTAEIEVLSQSGPPHNPRFKAAVFVGGRRFPSVEASSKKDAKQEAADLAL 65

double-stranded RNA binding motif of mL44 subfamily proteins; The mitochondrion-specific ribosomal protein mL44 subfamily is composed of mitochondrial 54S ribosomal protein L3 (MRPL3) and mitochondrial 39S ribosomal protein L44 (MRPL44). MRPL3 (also known as mitochondrial large ribosomal subunit protein mL44) is a component of the mitochondrial ribosome (mitoribosome), a dedicated translation machinery responsible for the synthesis of mitochondrial genome-encoded proteins, including at least some of the essential transmembrane subunits of the mitochondrial respiratory chain. MRPL44 (also called L44mt, MRP-L44, or mitochondrial large ribosomal subunit protein mL44) is a component of the 39S subunit of mitochondrial ribosome. It may play a role in the assembly/stability of nascent mitochondrial polypeptides exiting the ribosome. Members of this family contain a RNase III-like domain and a 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 1276961820 168 QELAQE--KVGIT-PSYRVLSESGPDHAKD-FVIGVYLDDELVAEGNGTSKQEAQMDAARRAL 226
Cdd:cd20315     5 RELAEIlrREGIEkPVSRLIAESGRLTKSPvYIVGVYCDEETIGEGYGYSIKEAKAEAATDAL 67

second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar proteins; TARBP2 (also known as 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. TARBP2 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
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1276961820 168 QELAQEKVGITPSYRVLSESGPDHAKDFVIGVYLdDELVAEGNGTSKQEAQMDAARRAL 226
Cdd:cd10844     7 QELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRV-ERFIEIGSGTSKKLAKRNAAAKML 64

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 1276961820 164 KSHFQELAQEKVGITPSYRvLSESGPDHAKDFVIGVYLDDELVAEGNGTSKQEAQMDAARRALEE 228
Cdd:cd19878     2 KNLLQEYAQKKKIPLPKYE-SAKSGPSHQPTFVSTVIVLGVRFSSEGAKNKKQAEQSAAKVALKE 65

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 1276961820 169 ELAQeKVGITPSYRVLSESGPDHAKDFVIGVYLDDELVAEGNGTSKQEAQMDAARRALEE 228
Cdd:cd20314     9 EYCQ-KERLTVKYEEEKRSGPTHKPRFFCKYIIDGKEYPEGEGKSKKEAKQAAARLAYEE 67

first double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) and similar proteins; 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. STRBP contains an N-terminal DZF domain and 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
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1276961820 170 LAQEKVGItpSYRVLSESGPDHAKDFVIGVYLDDElVAEGNGTSKQEAQMDAARRALE 227
Cdd:cd19909    12 LNQIRPGL--QYKLLSQSGPVHAPVFTMSVDVDGT-TYEASGPSKKTAKLHVAVKVLQ 66

first double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3). 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. Members of this STRBP/ILF3 group contain an N-terminal DZF domain and 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
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1276961820 170 LAQEKVGITpsYRVLSESGPDHAKDFVIGVYLDDeLVAEGNGTSKQEAQMDAARRALE 227
Cdd:cd19894     7 LNQLRPGLQ--YKLASQTGPVHAPQFTMSVEVDG-VTYEASGPSKKTAKLHVAVKVLQ 61

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 1276961820 168 QELAQEKVGITPSYRVLSESGPDHAKDFVIGVYLDDE----LVAEGNgtsKQEAQMDAARRAL 226
Cdd:cd19870     9 MELCNKRKWGPPEFRLVEESGPPHRKHFLFKVVVNGVeyqpSVASGN---KKDAKAQAATVAL 68

double-stranded RNA binding motif of mitochondrial 39S ribosomal protein L44 (MRPL44) and similar proteins; MRPL44 (also known as L44mt, MRP-L44, or mitochondrial large ribosomal subunit protein mL44) is a component of the 39S subunit of mitochondrial ribosome. It may play a role in the assembly/stability of nascent mitochondrial polypeptides exiting the ribosome. MRPL44 contains a RNase III-like domain and a 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 1276961820 168 QELAQEKVGiTPSYRVLSESGPDHAKD-FVIGVYLDDELVAEGNGTSKQEAQMDAARRAL 226
Cdd:cd19874    20 EILQKRGLP-PPEPRLIRQSGANTVLPvYFVGLYSDKKLIGEGPGESILIAEEMAARDAL 78

second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3). 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. Members of this STRBP/ILF3 group contain an N-terminal DZF domain and 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 1276961820 164 KSHFQELAQEKVGItpSYRVLSESGPDHAKDFVIGVYLDDELVaEGNGTSKQEAQMDAARRALEE 228
Cdd:cd19897     1 KNPVMELNEKRRGL--KYELISETGGSHDKRFVMEVEVDGQKF-QGAGSNKKVAKANAALAALEK 62

second double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and similar proteins; 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. ILF3 contains an N-terminal DZF domain and 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 1276961820 163 AKSHFQELAQEKVGItpSYRVLSESGPDHAKDFVIGVYLDDELVaEGNGTSKQEAQMDAARRALEE 228
Cdd:cd19912     6 GKNPVMELNEKRRGL--KYELISETGGSHDKRFVMEVEVDGQKF-QGAGSNKKVAKAYAALAALEK 68

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1276961820 162 DAKSHFQELAQEKVGITPSYRVLSESGPDHAKDFVIGVYLDDELVaEGNGTSKQEAQMDAA 222
Cdd:TIGR04238   1 NVVGMLQELAVKRGLELPVYEKVGKEGPDHAPTFTIKLTANDIEV-IEAASSKKQAEKLAA 60