NCBI Conserved Domain Search

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

Pssm-ID: 380711 Cd Length: 82 Bit Score: 187.61 E-value: 1.50e-58

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039729204  66 VELNGLAMKRGEPAIYRPLDPKPFPNYRANYNFRGMYNQRYHCPMPKIFYVQLTVGNNEFFGEGKTRQAARHNAAMKALQ 145
Cdd:cd19882     1 VELNGLAMKRGEPAIYRPIDPKPPPNYRPNYNFRGMYNQRYHYPMPKTFYVSLTVGNREFIGEGRTRQAARHNAAMKALQ 80


                  ..
gi 1039729204 146 AL 147
Cdd:cd19882    81 AL 82

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

Pssm-ID: 380715 Cd Length: 86 Bit Score: 172.06 E-value: 1.46e-52

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039729204 272 QGMNPISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQLGYKASTSLQD 351
Cdd:cd19886     1 QGMNPISRLAQIQQAKKEKEPEYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKRNAAEAMLLQLGYKASTPLQD 80


                  ....*.
gi 1039729204 352 PLDKTG 357
Cdd:cd19886    81 QTEKSG 86

fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; 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 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

Pssm-ID: 380714 Cd Length: 86 Bit Score: 135.21 E-value: 1.71e-38

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1039729204 268 PDYGQGMNPISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQLGYK 344
Cdd:cd19885     4 PEYGQGMNPISRLAQIQQAKKEKEPEYTLITERGLPRRREFVMQVKVGNQTAEGMGPNKKVAKRNAAEKMLELLGFK 80

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

Pssm-ID: 380689 Cd Length: 68 Bit Score: 134.00 E-value: 2.17e-38

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039729204 275 NPISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQLG 342
Cdd:cd19860     1 NPISRLIQIQQARKEKEPVYSLVAERGTPRRREFVMQVTVGDKTATGTGPNKKLAKRNAAEAMLELLG 68

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.

Pssm-ID: 380713 Cd Length: 67 Bit Score: 132.44 E-value: 9.91e-38

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1039729204 174 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 240
Cdd:cd19884     1 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVTVGEFTAEGEGNSKKLSKKRAATSVLQEL 67

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.

Pssm-ID: 380688 Cd Length: 65 Bit Score: 125.20 E-value: 3.93e-35

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1039729204 176 EISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 240
Cdd:cd19859     1 EISLVHEIALKRNLTVNFEVLRESGPPHMKNFITRCTVGSFVTEGEGNSKKVSKKRAAEKMLEEL 65

third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; 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 1 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.

Pssm-ID: 380712 Cd Length: 67 Bit Score: 118.96 E-value: 9.24e-33

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1039729204 174 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 240
Cdd:cd19883     1 KSEISQVFEIALKRNMPVNFEVTKETGPPHMKSFVTKVSVGEFAGEGEGKSKKISKKNAAIAVLEEL 67

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

Pssm-ID: 380687 Cd Length: 67 Bit Score: 85.92 E-value: 9.17e-21

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039729204  90 PNYRANYNF--RGMYNQRYHCP-----MPKIFYVQLTVGNNEFFGEGKTRQAARHNAAMKALQ 145
Cdd:cd19858     5 PNYNNYGMPqrRGDYRFRYPYPnnpsgPPPPFYVTLTVGEREFIGEGRTRQAARHDAASKALK 67

Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of an N-terminal Staufen-swapping motif (SSM) comprising two alpha helices, connected by a linker region to a dsRNA-binding-like domain ('RBD'). The 'RBD' has the fold of a functional dsRNA-binding domain, but lacks the residues required to bind RNA. This domain is responsible for dimerization, the SSM from one molecule interacts with the 'RBD' of another.

Pssm-ID: 465131 Cd Length: 110 Bit Score: 79.18 E-value: 6.12e-18

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1039729204 433 ARELLMNGTSPTAEAI-GLKGSSPTSPCSSVQPSKQLEYLARIQGFQ 478
Cdd:pfam16482  10 ARELLYGGTSPTAEAIlKNNGKTGAVPCGLVQPSQQLEYLARVQGFQ 56

second double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; 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 1 contains five 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.

Pssm-ID: 380710 Cd Length: 79 Bit Score: 78.00 E-value: 6.74e-18

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1039729204  73 MKRGEPAIYRPLDPKPFPNYRANYNFRGM--YNQRYHCPMPKI----FYVQLTVGNNEFFGEGKTRQAARHNAAMKALQ 145
Cdd:cd19881     1 MKLGKKPIYKPIDPYTGMRSAYNYNMRGNgaYPPRYFYPFPPVgpvlYQVELSIGGQQFHGKGRTRQAAKHDAAAKALK 79

Double-stranded RNA binding motif;

Pssm-ID: 214634 [Multi-domain] Cd Length: 67 Bit Score: 76.15 E-value: 2.23e-17

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039729204  276 PISRLAQIQQARKeKEPDYILLSERGMPRRREFVMQVKV-GNEVATGTGPNKKIAKKNAAEAMLLQLG 342
Cdd:smart00358   1 PKSLLQELAQKRK-LPPEYELVKEEGPDHAPRFTVTVKVgGKRTGEGEGSSKKEAKQRAAEAALRSLK 67

Double-stranded RNA binding motif;

Pssm-ID: 214634 [Multi-domain] Cd Length: 67 Bit Score: 73.84 E-value: 1.56e-16

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1039729204  177 ISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFS-AEGEGNSKKLSKKRAATTVLQELK 241
Cdd:smart00358   2 KSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGKRtGEGEGSSKKEAKQRAAEAALRSLK 67

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.

Pssm-ID: 380691 [Multi-domain] Cd Length: 70 Bit Score: 69.60 E-value: 5.76e-15

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039729204 174 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQELK 241
Cdd:cd19862     1 KTPISVLQELCAKRGITPKYELISSEGAVHEPTFTFRVTVGDITATGSGTSKKKAKHAAAENALEQLK 68

dsRNA-specific ribonuclease [Transcription];

Pssm-ID: 440336 [Multi-domain] Cd Length: 229 Bit Score: 72.05 E-value: 2.81e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039729204 255 FFKKRPKTIVKAGPdygqGMNPISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNEV-ATGTGPNKKIAKKNA 333
Cdd:COG0571   142 LFEPRLEEIAPGGA----GKDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGGKVlGEGTGRSKKEAEQAA 217


                  ....*....
gi 1039729204 334 AEAMLLQLG 342
Cdd:COG0571   218 AKAALEKLG 226

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.

Pssm-ID: 380682 [Multi-domain] Cd Length: 69 Bit Score: 67.13 E-value: 4.03e-14

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1039729204 274 MNPISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNEV-ATGTGPNKKIAKKNAAEAMLLQL 341
Cdd:cd10845     1 KDYKTALQEYLQKRGLPLPEYELVEEEGPDHNKTFTVEVKVNGKViGEGTGRSKKEAEQAAAKAALEKL 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.

Pssm-ID: 425434 [Multi-domain] Cd Length: 66 Bit Score: 65.33 E-value: 1.70e-13

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1039729204 276 PISRLAQIQQaRKEKEPDYILLSERGMPRRREFVMQVKV-GNEVATGTGPNKKIAKKNAAEAMLLQL 341
Cdd:pfam00035   1 PKSLLQEYAQ-KNGKPPPYEYVSEEGPPHSPKFTVTVKVdGKLYGSGTGSSKKEAEQLAAEKALEKL 66

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.

Pssm-ID: 380692 Cd Length: 67 Bit Score: 63.94 E-value: 4.88e-13

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1039729204 275 NPISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 341
Cdd:cd19863     1 NPVGILQELCVQRRWRLPEYEVEQESGPPHEKEFTIACRVENFSETGSGKSKKLAKRAAAEKMLTRL 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.

Pssm-ID: 380709 Cd Length: 68 Bit Score: 63.20 E-value: 9.21e-13

                          10        20        30
                  ....*....|....*....|....*....|...
gi 1039729204   6 QMFSVQLSLGEQTWESEGSSIKKAQQAVANKAL 38
Cdd:cd19880    36 KIFTVQLTLGEQTWEAEGSSIKKAQHAAASKAL 68

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.

Pssm-ID: 425434 [Multi-domain] Cd Length: 66 Bit Score: 62.63 E-value: 1.53e-12

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1039729204 177 ISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFS-AEGEGNSKKLSKKRAATTVLQEL 240
Cdd:pfam00035   2 KSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLyGSGTGSSKKEAEQLAAEKALEKL 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.

Pssm-ID: 380679 [Multi-domain] Cd Length: 57 Bit Score: 59.99 E-value: 9.64e-12

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1039729204 282 QIQQARKEKEPDYILLSERGmPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAML 338
Cdd:cd00048     2 ELCQKNKWPPPEYETVEEGG-PHNPRFTCTVTVNGQTFEGEGKSKKEAKQAAAEKAL 57

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.

Pssm-ID: 380699 Cd Length: 75 Bit Score: 58.45 E-value: 4.77e-11

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1039729204 173 NKSEISLVFEIALKRN-MPVSFEVIKESGPPHMKSFVTRVSVG--EFSAEGEGNSKKLSKKRAATTVLQELKKLP 244
Cdd:cd19870     1 GKHPVSALMELCNKRKwGPPEFRLVEESGPPHRKHFLFKVVVNgvEYQPSVASGNKKDAKAQAATVALQALGLVP 75

dsRNA-specific ribonuclease [Transcription];

Pssm-ID: 440336 [Multi-domain] Cd Length: 229 Bit Score: 62.04 E-value: 7.66e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039729204 161 ESGKEMDDDKDAnKSEISlvfEIALKRNMPV-SFEVIKESGPPHMKSFVTRVSV-GEFSAEGEGNSKKLSKKRAATTVLQ 238
Cdd:COG0571   148 EEIAPGGAGKDY-KTALQ---EWLQARGLPLpEYEVVEEEGPDHAKTFTVEVLVgGKVLGEGTGRSKKEAEQAAAKAALE 223


                  ....
gi 1039729204 239 ELKK 242
Cdd:COG0571   224 KLGK 227

second double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; 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. PRKRA 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.

Pssm-ID: 380720 Cd Length: 67 Bit Score: 56.49 E-value: 1.87e-10

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1039729204 275 NPISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 341
Cdd:cd19891     1 NPIGSLQELAVQKGWRLPEYTLAQESGPPHKREFTITCRVETFVETGTGTSKKVAKRNAAEKLLAKF 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.

Pssm-ID: 380682 [Multi-domain] Cd Length: 69 Bit Score: 56.35 E-value: 2.65e-10

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1039729204 178 SLVFEIALKRNMP-VSFEVIKESGPPHMKSFVTRVSV-GEFSAEGEGNSKKLSKKRAATTVLQEL 240
Cdd:cd10845     5 TALQEYLQKRGLPlPEYELVEEEGPDHNKTFTVEVKVnGKVIGEGTGRSKKEAEQAAAKAALEKL 69

first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; This family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)), participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. This family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

Pssm-ID: 380691 [Multi-domain] Cd Length: 70 Bit Score: 56.11 E-value: 2.67e-10

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1039729204 275 NPISRLAQIQqARKEKEPDYILLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 341
Cdd:cd19862     2 TPISVLQELC-AKRGITPKYELISSEGAVHEPTFTFRVTVGDITATGSGTSKKKAKHAAAENALEQL 67

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.

Pssm-ID: 380695 Cd Length: 63 Bit Score: 53.71 E-value: 1.63e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1039729204 275 NPISRLAQIQQARKekepdYILLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 341
Cdd:cd19866     2 NPVMLLNELRPGLK-----YKCLSESGESHAKSFVMSVTVDGQTFEGTGRSKKLAKAAAAQAALAKL 63

first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; 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 1 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.

Pssm-ID: 380708 Cd Length: 66 Bit Score: 53.93 E-value: 1.63e-09

                          10        20        30
                  ....*....|....*....|....*....|...
gi 1039729204   6 QMFSVQLSLGEQTWESEGSSIKKAQQAVANKAL 38
Cdd:cd19879    34 KVFTVQLTLGDQHWEAEGTSIKKAQHAAAAKAL 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.

Pssm-ID: 380699 Cd Length: 75 Bit Score: 53.82 E-value: 2.01e-09

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039729204 273 GMNPISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNEV--ATGTGPNKKIAKKNAAEAMLLQLG 342
Cdd:cd19870     1 GKHPVSALMELCNKRKWGPPEFRLVEESGPPHRKHFLFKVVVNGVEyqPSVASGNKKDAKAQAATVALQALG 72

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.

Pssm-ID: 380679 [Multi-domain] Cd Length: 57 Bit Score: 53.06 E-value: 2.37e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1039729204 181 FEIALKRNMP-VSFEVIkESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVL 237
Cdd:cd00048     1 NELCQKNKWPpPEYETV-EEGGPHNPRFTCTVTVNGQTFEGEGKSKKEAKQAAAEKAL 57

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.

Pssm-ID: 380692 Cd Length: 67 Bit Score: 51.99 E-value: 8.92e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039729204 182 EIALKRN-MPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 240
Cdd:cd19863     8 ELCVQRRwRLPEYEVEQESGPPHEKEFTIACRVENFSETGSGKSKKLAKRAAAEKMLTRL 67

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

Pssm-ID: 380689 Cd Length: 68 Bit Score: 51.56 E-value: 1.24e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1039729204 184 ALKRNMPVsFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 240
Cdd:cd19860    12 ARKEKEPV-YSLVAERGTPRRREFVMQVTVGDKTATGTGPNKKLAKRNAAEAMLELL 67

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

Pssm-ID: 380686 Cd Length: 64 Bit Score: 51.11 E-value: 1.46e-08

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1039729204   5 NQMFSVQLSLGEQ-TWESEGSSIKKAQQAVANKAL 38
Cdd:cd19857    30 KKTFTVKLTLGDEeEYEASGSSIKKAQHAAAEKAL 64

first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; 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. PRKRA 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.

Pssm-ID: 380718 [Multi-domain] Cd Length: 71 Bit Score: 49.91 E-value: 4.41e-08

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039729204 174 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQELK 241
Cdd:cd19889     2 KTPIQLLHEYGTKTGNIPVYELEKSEGQAHLPSFTFRVTVGDITCTGEGTSKKLAKHRAAEAALNILK 69

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.

Pssm-ID: 380695 Cd Length: 63 Bit Score: 49.47 E-value: 5.21e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1039729204 191 VSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 240
Cdd:cd19866    14 LKYKCLSESGESHAKSFVMSVTVDGQTFEGTGRSKKLAKAAAAQAALAKL 63

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.

Pssm-ID: 380681 Cd Length: 67 Bit Score: 47.79 E-value: 2.49e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1039729204 275 NPISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 341
Cdd:cd10844     1 NPVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFIEIGSGTSKKLAKRNAAAKMLLRI 67

Double-stranded RNA binding motif;

Pssm-ID: 214634 [Multi-domain] Cd Length: 67 Bit Score: 47.64 E-value: 2.54e-07

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039729204   64 PTVELNGLAMKRGEPAIYRPLDPKPFPnyranynfrgmynqryHCPMpkiFYVQLTVGNNEFF-GEGKTRQAARHNAAMK 142
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELVKEEGPD----------------HAPR---FTVTVKVGGKRTGeGEGSSKKEAKQRAAEA 61


                   ....*.
gi 1039729204  143 ALQALQ 148
Cdd:smart00358  62 ALRSLK 67

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.

Pssm-ID: 380704 Cd Length: 67 Bit Score: 47.26 E-value: 4.18e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039729204 174 KSEISLVFEIALKRNMPVSFEVIkESGPPHMKSFVTRVSVGEFS-AEGEGNSKKLSKKRAATTVLQEL 240
Cdd:cd19875     1 KNPVSALNEYCQKRGLSLEFVDV-SVGPDHCPGFTASATIDGIVfASATGTSKKEAKRAAAKLALKKL 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.

Pssm-ID: 380679 [Multi-domain] Cd Length: 57 Bit Score: 46.51 E-value: 4.89e-07

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1039729204 109 PMPKIFYVQLTVGNNEFFGEGKTRQAARHNAAMKAL 144
Cdd:cd00048    22 PHNPRFTCTVTVNGQTFEGEGKSKKEAKQAAAEKAL 57

double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant Dicer-like (DCL) proteins and other ribonuclease (RNase) III-like (RTL) proteins. DCLs are endoribonucleases involved in RNA-mediated post-transcriptional gene silencing (PTGS). They function in the microRNA (miRNA) biogenesis pathway by cleaving primary miRNAs (pri-miRNAs) and precursor miRNAs (pre-miRNAs). Family members 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.

Pssm-ID: 380698 Cd Length: 70 Bit Score: 46.59 E-value: 6.16e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039729204 182 EIALKRN--MPVsFEVIKESGPPHMKSFVTRVSV------GEFSAEGEG-NSKKLSKKRAATTVLQELKK 242
Cdd:cd19869     2 EICLKRRwpMPV-YRCVEEEGPAHAKRFTYMVRVkipergWTIECEGEPmRSKKRAKDSAALLLLEYLKK 70

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.

Pssm-ID: 380731 Cd Length: 71 Bit Score: 46.51 E-value: 7.80e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039729204 275 NPISRLAQIQQARKEkEPDYILLSERGMPRRREFVMQVKVG-NEVATGTGPNKKIAKKNAAEAMLLQL 341
Cdd:cd19902     2 NPVSALMEYAQSRGV-TAEIEVLSQSGPPHNPRFKAAVFVGgRRFPSVEASSKKDAKQEAADLALRAL 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.

Pssm-ID: 380727 Cd Length: 70 Bit Score: 45.95 E-value: 1.06e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1039729204 193 FEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQELKKLPP 245
Cdd:cd19898    18 YEFVSESGESHAKNFVMSVTVDGQTFEGSGRNKKLAKARAAQAALAKLFNLQL 70

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.

Pssm-ID: 380704 Cd Length: 67 Bit Score: 45.72 E-value: 1.51e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039729204 275 NPISRLAQIqqARKEKEPDYILLSERGMPRRREFVMQVKVGNEV-ATGTGPNKKIAKKNAAEAMLLQL 341
Cdd:cd19875     2 NPVSALNEY--CQKRGLSLEFVDVSVGPDHCPGFTASATIDGIVfASATGTSKKEAKRAAAKLALKKL 67

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.

Pssm-ID: 380731 Cd Length: 71 Bit Score: 45.36 E-value: 2.18e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039729204 174 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFS-AEGEGNSKKLSKKRAATTVLQEL 240
Cdd:cd19902     1 KNPVSALMEYAQSRGVTAEIEVLSQSGPPHNPRFKAAVFVGGRRfPSVEASSKKDAKQEAADLALRAL 68

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.

Pssm-ID: 380726 Cd Length: 64 Bit Score: 45.04 E-value: 2.45e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1039729204 275 NPISRLAQIQQARKekepdYILLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 341
Cdd:cd19897     2 NPVMELNEKRRGLK-----YELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKANAALAALEKL 63

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.

Pssm-ID: 380727 Cd Length: 70 Bit Score: 44.79 E-value: 3.42e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039729204 272 QGMNPISRLAQIQQARKekepdYILLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 341
Cdd:cd19898     1 SGKNPVMILNELRPGLK-----YEFVSESGESHAKNFVMSVTVDGQTFEGSGRNKKLAKARAAQAALAKL 65

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.

Pssm-ID: 380732 Cd Length: 68 Bit Score: 44.30 E-value: 4.02e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039729204 275 NPISRLAQIQQARKEKEpDYILLSERGMPRRREFVMQVKV-GNEVATGTGPNKKIAKKNAAEAMLLQL 341
Cdd:cd19903     2 NYMGKLNEYCQKQKVVL-DYVEVPTSGPSHDPRFTFQVVIdGKEYPEGEGKSKKEAKQAAAKLALEIL 68

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

Pssm-ID: 380686 Cd Length: 64 Bit Score: 44.18 E-value: 4.58e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039729204 177 ISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSA-EGEGNSKKLSKKRAATTVL 237
Cdd:cd19857     3 MCLLNELARFNKIRPQYTLVDEEGPAHKKTFTVKLTLGDEEEyEASGSSIKKAQHAAAEKAL 64

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.

Pssm-ID: 380694 Cd Length: 63 Bit Score: 43.87 E-value: 4.95e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1039729204 274 MNPISRLAQIQQARKekepdYILLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAML 338
Cdd:cd19865     1 KNALMQLNELRPGLQ-----YKLTSQTGPVHAPVFTMSVEVNGQTFEGTGRSKKKAKLEAAEKAL 60

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

Pssm-ID: 380719 Cd Length: 72 Bit Score: 44.35 E-value: 5.57e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039729204 174 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQELK 241
Cdd:cd19890     3 KTPISLLQEYGTRIGKTPVYDLLKAEGQAHQPNFTFRVTVGDISCTGQGPSKKAAKHKAAEVALKLLK 70

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.

Pssm-ID: 380743 Cd Length: 71 Bit Score: 43.68 E-value: 8.39e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039729204 174 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGE-FSAEGEGNSKKLSKKRAATTVLQEL 240
Cdd:cd19914     1 KNPISVLMEHSQKSGNMCEFQLLSQEGPPHDPKFTYCVKVGEqTFPSVVANSKKVAKQMAAEEAVKEL 68

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

Pssm-ID: 380719 Cd Length: 72 Bit Score: 43.58 E-value: 8.58e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1039729204 273 GMNPISrLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 341
Cdd:cd19890     2 GKTPIS-LLQEYGTRIGKTPVYDLLKAEGQAHQPNFTFRVTVGDISCTGQGPSKKAAKHKAAEVALKLL 69

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.

Pssm-ID: 380741 Cd Length: 72 Bit Score: 43.49 E-value: 1.06e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039729204 272 QGMNPISRLAQIQQARKekepdYILLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 341
Cdd:cd19912     5 HGKNPVMELNEKRRGLK-----YELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKAYAALAALEKL 69

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.

Pssm-ID: 275074 [Multi-domain] Cd Length: 201 Bit Score: 46.09 E-value: 1.39e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039729204 177 ISLVFEIALKRNMPV-SFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQELKKLPPLPVVEKPKLF 255
Cdd:TIGR04238   3 VGMLQELAVKRGLELpVYEKVGKEGPDHAPTFTIKLTANDIEVIEAASSKKQAEKLAAATIYEDMKENGLLEVHDTRKSV 82


                  ..
gi 1039729204 256 FK 257
Cdd:TIGR04238  83 SI 84

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.

Pssm-ID: 380746 Cd Length: 68 Bit Score: 42.38 E-value: 1.87e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1039729204 177 ISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVG--EFSaEGEGNSKKLSKKRAATTVLQEL 240
Cdd:cd20314     4 VSLLNEYCQKERLTVKYEEEKRSGPTHKPRFFCKYIIDgkEYP-EGEGKSKKEAKQAAARLAYEEL 68

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.

Pssm-ID: 380738 Cd Length: 84 Bit Score: 43.10 E-value: 1.94e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1039729204 269 DYGQGMNPISRLAQIQQARKekepdYILLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQLGY 343
Cdd:cd19909     1 DANQPMNALMRLNQIRPGLQ-----YKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGY 70

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

Pssm-ID: 380717 Cd Length: 68 Bit Score: 42.25 E-value: 2.10e-05

                          10
                  ....*....|....*..
gi 1039729204 462 VQPSKQLEYLARIQGFQ 478
Cdd:cd19888     1 VQPSKQLEYLARIQGFQ 17

fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; 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 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

Pssm-ID: 380714 Cd Length: 86 Bit Score: 42.77 E-value: 2.24e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1039729204 186 KRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL--KKLPPLP 247
Cdd:cd19885    23 KKEKEPEYTLITERGLPRRREFVMQVKVGNQTAEGMGPNKKVAKRNAAEKMLELLgfKVPQPQP 86

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

Pssm-ID: 380740 Cd Length: 64 Bit Score: 41.66 E-value: 3.10e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1039729204 275 NPISRLAQIQQARKekepdYILLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 341
Cdd:cd19911     2 NPVMELNEKRRGLK-----YELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEKL 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.

Pssm-ID: 380683 Cd Length: 69 Bit Score: 41.10 E-value: 5.67e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1039729204 287 RKEKEPDYiLLSERGMPRRREFVMQVKVGN--EVATGTGPNKKIAKKNAA 334
Cdd:cd19854    12 KKKLTPEY-DIKEAGNKHRQRFKCEVRVEGfdYVGTGNATNKKDAQTNAA 60

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.

Pssm-ID: 380694 Cd Length: 63 Bit Score: 40.79 E-value: 7.15e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1039729204 191 VSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQ 238
Cdd:cd19865    14 LQYKLTSQTGPVHAPVFTMSVEVNGQTFEGTGRSKKKAKLEAAEKALR 61

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.

Pssm-ID: 380728 Cd Length: 74 Bit Score: 40.63 E-value: 8.89e-05

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1039729204 203 HMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 240
Cdd:cd19899    33 HIKSFVMAVRVDGRTFEGSGRSKKLAKAQAAQAALQAL 70

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

Pssm-ID: 380684 Cd Length: 75 Bit Score: 40.66 E-value: 1.00e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1039729204 186 KRNMPVSFEvIKESGPPHMKSFVTRVSV------GEFSAEGEGNSKKLSKKRAATTVLQEL 240
Cdd:cd19855    14 KNKIPAEYK-YTSVGPDHNRSFIAELSIfvkqlgKTIYARETGSNKKLASQSCALSLVRQL 73

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.

Pssm-ID: 380681 Cd Length: 67 Bit Score: 40.48 E-value: 1.03e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1039729204 171 DANKSEISLVFEIALKrnMPvSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVL 237
Cdd:cd10844     1 NPVGALQELVVQKGWR--LP-EYTVTQESGPAHRKEFTMTCRVERFIEIGSGTSKKLAKRNAAAKML 64

second double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; 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. PRKRA 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.

Pssm-ID: 380720 Cd Length: 67 Bit Score: 40.31 E-value: 1.04e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1039729204 182 EIALKRN--MPvSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 240
Cdd:cd19891     8 ELAVQKGwrLP-EYTLAQESGPPHKREFTITCRVETFVETGTGTSKKVAKRNAAEKLLAKF 67

first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and similar proteins; DGCR8 is a component of the microprocessor complex that acts as an RNA- and heme-binding protein that is involved in the initial step of microRNA (miRNA) biogenesis. Within the microprocessor complex, DGCR8 functions as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs DROSHA to cleave 11bp away from the junction to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. DGCR8 contains two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

Pssm-ID: 380696 Cd Length: 74 Bit Score: 40.39 E-value: 1.38e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1039729204 269 DYGQGMNPISRLAQIQQARKEKEPDYI--LLSERGMPrrreFVMQVKV-GNEVATGTGPNKKIAKKNAAEAMLLQLG 342
Cdd:cd19867     1 INPDGKSPVCILHEYCQRVLKVQPEYNftETENAATP----FSAEVFInGVEYGSGEASSKKLAKQKAARATLEILI 73

first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; 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 1 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.

Pssm-ID: 380708 Cd Length: 66 Bit Score: 39.68 E-value: 1.68e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1039729204 174 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVL 237
Cdd:cd19879     3 KTPMCLVNELARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTSIKKAQHAAAAKAL 66

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.

Pssm-ID: 380709 Cd Length: 68 Bit Score: 39.70 E-value: 2.05e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1039729204 174 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVL 237
Cdd:cd19880     5 KTPMCLVNELARFNRIQPQYKLLNERGPAHAKIFTVQLTLGEQTWEAEGSSIKKAQHAAASKAL 68

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

Pssm-ID: 380686 Cd Length: 64 Bit Score: 39.56 E-value: 2.05e-04

                          10        20        30
                  ....*....|....*....|....*....|....
gi 1039729204 112 KIFYVQLTVGNNE-FFGEGKTRQAARHNAAMKAL 144
Cdd:cd19857    31 KTFTVKLTLGDEEeYEASGSSIKKAQHAAAEKAL 64

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.

Pssm-ID: 380732 Cd Length: 68 Bit Score: 38.91 E-value: 3.20e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1039729204 191 VSFEVIKESGPPHMKSFVTRVSVGEFS-AEGEGNSKKLSKKRAATTVLQEL 240
Cdd:cd19903    18 LDYVEVPTSGPSHDPRFTFQVVIDGKEyPEGEGKSKKEAKQAAAKLALEIL 68

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.

Pssm-ID: 380733 Cd Length: 69 Bit Score: 38.65 E-value: 4.04e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1039729204 177 ISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVGE-FSAEGEGNSKKLSKKRAATTVLQEL 240
Cdd:cd19904     4 ISLLNQYAQKKRLTVNYEQCASTGVPGPPRFSCKCKIGQkEYGIGTGSTKQEAKQAAAKEAYEQL 68

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.

Pssm-ID: 380679 [Multi-domain] Cd Length: 57 Bit Score: 38.42 E-value: 4.34e-04

                          10        20        30
                  ....*....|....*....|....*....|....
gi 1039729204   5 NQMFSVQLSLGEQTWESEGSSIKKAQQAVANKAL 38
Cdd:cd00048    24 NPRFTCTVTVNGQTFEGEGKSKKEAKQAAAEKAL 57

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.

Pssm-ID: 425434 [Multi-domain] Cd Length: 66 Bit Score: 38.37 E-value: 5.10e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1039729204 109 PMPKIFYVQLTVGNNEFF-GEGKTRQAARHNAAMKALQAL 147
Cdd:pfam00035  27 PHSPKFTVTVKVDGKLYGsGTGSSKKEAEQLAAEKALEKL 66

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.

Pssm-ID: 380743 Cd Length: 71 Bit Score: 38.29 E-value: 7.02e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039729204 275 NPISRLAQIQQaRKEKEPDYILLSERGMPRRREFVMQVKVGNEV-ATGTGPNKKIAKKNAAEAMLLQL 341
Cdd:cd19914     2 NPISVLMEHSQ-KSGNMCEFQLLSQEGPPHDPKFTYCVKVGEQTfPSVVANSKKVAKQMAAEEAVKEL 68

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.

Pssm-ID: 380726 Cd Length: 64 Bit Score: 38.11 E-value: 7.38e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1039729204 180 VFEIALKRNmPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 240
Cdd:cd19897     4 VMELNEKRR-GLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKANAALAALEKL 63

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.

Pssm-ID: 380728 Cd Length: 74 Bit Score: 38.32 E-value: 7.70e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1039729204 294 YILLSERGMPRR-REFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 341
Cdd:cd19899    22 YVCLSETAEKQHiKSFVMAVRVDGRTFEGSGRSKKLAKAQAAQAALQAL 70

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.

Pssm-ID: 380694 Cd Length: 63 Bit Score: 37.71 E-value: 8.78e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1039729204 107 HCPmpkIFYVQLTVGNNEFFGEGKTRQAARHNAAMKALQAL 147
Cdd:cd19865    26 HAP---VFTMSVEVNGQTFEGTGRSKKKAKLEAAEKALRSF 63

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

Pssm-ID: 380715 Cd Length: 86 Bit Score: 38.40 E-value: 9.55e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1039729204 195 VIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQELKKLPPLPVVEKP 252
Cdd:cd19886    25 LLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKRNAAEAMLLQLGYKASTPLQDQT 82

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.

Pssm-ID: 380683 Cd Length: 69 Bit Score: 37.64 E-value: 1.05e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1039729204 186 KRNMPVSFEvIKESGPPHMKSFVTRVSVGEFS--AEGEGNSKKLSKKRAATTVLQELKK 242
Cdd:cd19854    12 KKKLTPEYD-IKEAGNKHRQRFKCEVRVEGFDyvGTGNATNKKDAQTNAARDFLNYLVR 69

double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant Dicer-like (DCL) proteins and other ribonuclease (RNase) III-like (RTL) proteins. DCLs are endoribonucleases involved in RNA-mediated post-transcriptional gene silencing (PTGS). They function in the microRNA (miRNA) biogenesis pathway by cleaving primary miRNAs (pri-miRNAs) and precursor miRNAs (pre-miRNAs). Family members 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.

Pssm-ID: 380698 Cd Length: 70 Bit Score: 37.73 E-value: 1.09e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1039729204 285 QARKEKEPDYILLSERGMPRRREFVMQVKVGNEVATGT----G---PNKKIAKKNAAEAMLLQLG 342
Cdd:cd19869     5 LKRRWPMPVYRCVEEEGPAHAKRFTYMVRVKIPERGWTieceGepmRSKKRAKDSAALLLLEYLK 69

first double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar proteins; RED2 (also known as double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA but also to ssRNA. RED2 contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the first DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. RED2 lacks editing activity for currently known substrate RNAs, and may have an inactive editase domain.

Pssm-ID: 380725 Cd Length: 74 Bit Score: 37.77 E-value: 1.18e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1039729204 191 VSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQELKKLP 244
Cdd:cd19896    19 LQYRMVSQTGPVHAPVFAVAVEVNGLTFEGTGPTKKKAKMRAAEMALKSFVQFP 72

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

Pssm-ID: 380686 Cd Length: 64 Bit Score: 36.86 E-value: 1.45e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1039729204 275 NPISRLAQIqqARKEK-EPDYILLSERGMPRRREFVMQVKVGNEVA-TGTGPNKKIAKKNAAEAML 338
Cdd:cd19857     1 TPMCLLNEL--ARFNKiRPQYTLVDEEGPAHKKTFTVKLTLGDEEEyEASGSSIKKAQHAAAEKAL 64

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

Pssm-ID: 380724 Cd Length: 72 Bit Score: 37.37 E-value: 1.50e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1039729204 294 YILLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAML 338
Cdd:cd19895    21 YKLLSQTGPVHAPVFVMSVEVNGQVFEGSGPTKKKAKLHAAEKAL 65

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.

Pssm-ID: 380682 [Multi-domain] Cd Length: 69 Bit Score: 37.09 E-value: 1.73e-03

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1039729204 112 KIFYVQLTVGNNEFF-GEGKTRQAARHNAAMKALQAL 147
Cdd:cd10845    33 KTFTVEVKVNGKVIGeGTGRSKKEAEQAAAKAALEKL 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.

Pssm-ID: 380697 Cd Length: 69 Bit Score: 36.88 E-value: 2.01e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1039729204 303 PRRREFVMqvKVGNEVATGTGPNKKIAKKNAAEAMLLQLG 342
Cdd:cd19868    31 HQKHEYTM--TVGKHTVTVICKNKKEGKQLAAQAILKKLH 68

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.

Pssm-ID: 380706 Cd Length: 75 Bit Score: 36.48 E-value: 2.63e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1039729204 282 QIQQA----RKE--KEPD---YILLSERGMPRRREFVMQVKV-GNEVATGTGPNKKIAKKNAAEAML 338
Cdd:cd19877     6 QLQQCcltlRTEgkKEPDipeYKVLQKSGPTNTRVYTVAVYFrGERIATGTGSSIQQAEMNAAEKAL 72

first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; 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. PRKRA 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.

Pssm-ID: 380718 [Multi-domain] Cd Length: 71 Bit Score: 36.04 E-value: 3.67e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1039729204 290 KEPDYILLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAML 338
Cdd:cd19889    17 NIPVYELEKSEGQAHLPSFTFRVTVGDITCTGEGTSKKLAKHRAAEAAL 65

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

Pssm-ID: 380687 Cd Length: 67 Bit Score: 35.85 E-value: 4.61e-03

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1039729204   5 NQMFSVQLSLGEQTWESEGSSIKKAQQAVANKALT 39
Cdd:cd19858    33 PPPFYVTLTVGEREFIGEGRTRQAARHDAASKALK 67

double-stranded RNA binding motif of Saccharomyces cerevisiae ribonuclease 3 (RNT1p) and similar proteins; RNT1p (EC 3.1.26.3; also known as ribonuclease III (RNase III)) is a dsRNA-specific nuclease that cleaves eukaryotic pre-ribosomal RNA at the U3 snoRNP-dependent A0 site in the 5'-external transcribed spacer (ETS) and in the 3'-ETS. RNT1p contains 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.

Pssm-ID: 380705 Cd Length: 69 Bit Score: 35.78 E-value: 4.70e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1039729204 292 PDYILLsERGMPRRREFVMQVKVGNE-VATGTGPNKKIAKKNAAEAML 338
Cdd:cd19876    19 PEYVVV-KKEGGNDPNYTVACRINGEvLGTGVGRSIKKAGQRAAMSAL 65

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.

Pssm-ID: 380723 Cd Length: 63 Bit Score: 35.44 E-value: 5.03e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039729204 274 MNPISRLAQIQQARKekepdYILLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKKNAAEAMLLQL 341
Cdd:cd19894     1 MNALMRLNQLRPGLQ-----YKLASQTGPVHAPQFTMSVEVDGVTYEASGPSKKTAKLHVAVKVLQAM 63

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.

Pssm-ID: 380741 Cd Length: 72 Bit Score: 35.78 E-value: 5.07e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1039729204 180 VFEIALKRNmPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 240
Cdd:cd19912    10 VMELNEKRR-GLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKAYAALAALEKL 69

first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; 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 1 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.

Pssm-ID: 380708 Cd Length: 66 Bit Score: 35.44 E-value: 5.62e-03

                          10        20        30
                  ....*....|....*....|....*....|...
gi 1039729204 112 KIFYVQLTVGNNEFFGEGKTRQAARHNAAMKAL 144
Cdd:cd19879    34 KVFTVQLTLGDQHWEAEGTSIKKAQHAAAAKAL 66

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

Pssm-ID: 380740 Cd Length: 64 Bit Score: 35.11 E-value: 6.59e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1039729204 180 VFEIALKRNmPVSFEVIKESGPPHMKSFVTRVSVGEFSAEGEGNSKKLSKKRAATTVLQEL 240
Cdd:cd19911     4 VMELNEKRR-GLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEKL 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.

Pssm-ID: 380746 Cd Length: 68 Bit Score: 35.06 E-value: 9.41e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1039729204 275 NPISRLAQIQQarKEKEP-DYILLSERGMPRRREFVMQVKV-GNEVATGTGPNKKIAKKNAAEAMLLQL 341
Cdd:cd20314     2 NYVSLLNEYCQ--KERLTvKYEEEKRSGPTHKPRFFCKYIIdGKEYPEGEGKSKKEAKQAAARLAYEEL 68

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.

Pssm-ID: 380742 Cd Length: 71 Bit Score: 34.85 E-value: 9.72e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1039729204 174 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVSVG--EFSAeGEGNSKKLSKKRAATTVLQEL 240
Cdd:cd19913     1 KNPVSGLMEYAQFLGQTCEFLLLEQSGPSHDPRFKFQAVIDgrRFPP-AEASSKKVAKKDAAAIALKIL 68