double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known as Bax antagonist selected in saccharomyces 1 (BASS1), negative regulatory element-binding protein (NRE-binding protein), or protein DBP-5, or SON3) is an RNA-binding protein which acts as an mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. It specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Members of this group contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1126170404 676 GKHPVSALMEICNKRKWMPPEFVLVHDSGPDHKKNFLFKVRINSEEYQPTIASPNKKHAKAQAATVALQAMGLIP 750
Cdd:cd19870     1 GKHPVSALMELCNKRKWGPPEFRLVEESGPPHRKHFLFKVVVNGVEYQPSVASGNKKDAKAQAATVALQALGLVP 75

Arginine/Serine-Rich protein 1; RSRP1 is an eukaryotic protein family. Its function is unknown.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1126170404 229 GECRSRSLSKDRLKSQEHRSGSGKHSRSRSKSHDRHHKHRHRSSSRERHRHKGSSRHRSRSRHRSRSRQGSRHRSRSRHR 308
Cdd:pfam17069  26 SSSRLSSRSRSRSSSRSSRSHSRSSSRFSSRSRSRPRRSRSRSRSRRRHQRKYRRYSRSYSRSRSRSRRRRYYRRSRYRY 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1126170404 309 SGSHDRYRHRSRSHEKHRHRSRS------GERYPNRAKERH------HRSRSPNHSRSRTP--TERIDKAKLLEIAKANA 374
Cdd:pfam17069 106 SRRYYRSPSRSRSRSRSRSRGRSyyaiwrGSRYYGFGRTVYpersprWRSRSRTRSRSRTPfrLSEKERMELLEIAKANA 185

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1126170404 375 INQFRAGMIPAHLPIPSMTPEEELAKKSGGKTVEELTKFCKFLSEKEKAGDEDE 428
Cdd:pfam17069 186 AKALGTQNLDLPASLREMEQAKERSRGGVSSSGDKEERVRVDLSEQKTADDEAE 239

double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known as Bax antagonist selected in saccharomyces 1 (BASS1), negative regulatory element-binding protein (NRE-binding protein), or protein DBP-5, or SON3) is an RNA-binding protein which acts as an mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. It specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Members of this group contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1126170404 676 GKHPVSALMEICNKRKWMPPEFVLVHDSGPDHKKNFLFKVRINSEEYQPTIASPNKKHAKAQAATVALQAMGLIP 750
Cdd:cd19870     1 GKHPVSALMELCNKRKWGPPEFRLVEESGPPHRKHFLFKVVVNGVEYQPSVASGNKKDAKAQAATVALQALGLVP 75

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1126170404 608 QGGMGMQLMKKMGWKPGEGLGKGQTGVLEPLTLDVKTDRRGL 649
Cdd:pfam01585   1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGL 42

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1126170404  606 PVQGGMGMQLMKKMGWKPGEGLGKGQTGVLEPLTLDVKTDRRGL 649
Cdd:smart00443   1 ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGL 44

Arginine/Serine-Rich protein 1; RSRP1 is an eukaryotic protein family. Its function is unknown.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1126170404 229 GECRSRSLSKDRLKSQEHRSGSGKHSRSRSKSHDRHHKHRHRSSSRERHRHKGSSRHRSRSRHRSRSRQGSRHRSRSRHR 308
Cdd:pfam17069  26 SSSRLSSRSRSRSSSRSSRSHSRSSSRFSSRSRSRPRRSRSRSRSRRRHQRKYRRYSRSYSRSRSRSRRRRYYRRSRYRY 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1126170404 309 SGSHDRYRHRSRSHEKHRHRSRS------GERYPNRAKERH------HRSRSPNHSRSRTP--TERIDKAKLLEIAKANA 374
Cdd:pfam17069 106 SRRYYRSPSRSRSRSRSRSRGRSyyaiwrGSRYYGFGRTVYpersprWRSRSRTRSRSRTPfrLSEKERMELLEIAKANA 185

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1126170404 375 INQFRAGMIPAHLPIPSMTPEEELAKKSGGKTVEELTKFCKFLSEKEKAGDEDE 428
Cdd:pfam17069 186 AKALGTQNLDLPASLREMEQAKERSRGGVSSSGDKEERVRVDLSEQKTADDEAE 239

double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known as Bax antagonist selected in saccharomyces 1 (BASS1), negative regulatory element-binding protein (NRE-binding protein), or protein DBP-5, or SON3) is an RNA-binding protein which acts as an mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. It specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Members of this group contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1126170404 676 GKHPVSALMEICNKRKWMPPEFVLVHDSGPDHKKNFLFKVRINSEEYQPTIASPNKKHAKAQAATVALQAMGLIP 750
Cdd:cd19870     1 GKHPVSALMELCNKRKWGPPEFRLVEESGPPHRKHFLFKVVVNGVEYQPSVASGNKKDAKAQAATVALQALGLVP 75

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1126170404 608 QGGMGMQLMKKMGWKPGEGLGKGQTGVLEPLTLDVKTDRRGL 649
Cdd:pfam01585   1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGL 42

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1126170404  606 PVQGGMGMQLMKKMGWKPGEGLGKGQTGVLEPLTLDVKTDRRGL 649
Cdd:smart00443   1 ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGL 44

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; The family includes EIF2AK2 and adenosine deaminase domain-containing proteins, ADAD1 and ADAD2. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. ADAD1 (also called testis nuclear RNA-binding protein (TENR)) and ADAD2 (also called testis nuclear RNA-binding protein-like (TENRL)) are phylogenetically related to a family of adenosine deaminases involved in RNA editing. ADAD1 plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs. ADAD2 is a double-stranded RNA binding protein with unclear biological function. Members of this group contains varying numbers of double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1126170404 677 KHPVSALMEICNKRKwMPPEFVLVhDSGPDHKKNFLFKVRINSEEYQPTIASpNKKHAKAQAATVALQ 744
Cdd:cd19875     1 KNPVSALNEYCQKRG-LSLEFVDV-SVGPDHCPGFTASATIDGIVFASATGT-SKKEAKRAAAKLALK 65

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1126170404 684 MEICNKRKWMPPEFVLVHdSGPDHKKNFLFKVRINSEEYQPTiaSPNKKHAKAQAATVAL 743
Cdd:cd00048     1 NELCQKNKWPPPEYETVE-EGGPHNPRFTCTVTVNGQTFEGE--GKSKKEAKQAAAEKAL 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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1126170404 678 HPVSALMEICNKRKWMPPEFVLVHDSGPDHKKNFLFKVRInsEEYQPTIASPNKKHAKAQAA 739
Cdd:cd19863     1 NPVGILQELCVQRRWRLPEYEVEQESGPPHEKEFTIACRV--ENFSETGSGKSKKLAKRAAA 60

double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF) and similar proteins; A1CF (also known as APOBEC1-stimulating protein) is an essential component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the posttranscriptional editing of a CAA codon for Gln to a UAA codon for stop in APOB mRNA. A1CF binds to APOB mRNA and is probably responsible for docking the catalytic subunit, APOBEC1, to the mRNA to allow it to deaminate its target cytosine. It contains three RNA recognition motifs (RRMs) and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1126170404 677 KHPVSALMEICNKRKWMPPEFVLVHDSGPDHKKNFLFKVRI--------NSEEYQPTIASPNKKHAKAQAATVALQAMGL 748
Cdd:cd19900     1 KSPPQILEEICQKNNWGQPVYQLHSTIGPDQRQLFLYKVTIpalasqypNITPFQPNKLCRSVEEAKSYAAEYTLQQLGI 80

dsRNA-specific ribonuclease [Transcription];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1126170404 668 DTTGKDLSGKHPVSALMEICNKRKWMPPEFVLVHDSGPDHKKNFLFKVRINSEEYqpTIAS-PNKKHAKAQAATVALQAM 746
Cdd:COG0571   148 EEIAPGGAGKDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGGKVL--GEGTgRSKKEAEQAAAKAALEKL 225

                  .
gi 1126170404 747 G 747
Cdd:COG0571   226 G 226

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1126170404 677 KHPVSALMEICNKRKWmPPEFVLVHDSGPDHKKNFLFKVRInsEEYQPTIASPNKKHAKAQAATVALQAM 746
Cdd:cd19862     1 KTPISVLQELCAKRGI-TPKYELISSEGAVHEPTFTFRVTV--GDITATGSGTSKKKAKHAAAENALEQL 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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1126170404 678 HPVSALMEICNKRKWMPPEFVLVHDSGPDHKKNFLFKVRINSEeyQPTIASPNKKHAKAQAATVALQAMG 747
Cdd:cd19860     1 NPISRLIQIQQARKEKEPVYSLVAERGTPRRREFVMQVTVGDK--TATGTGPNKKLAKRNAAEAMLELLG 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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1126170404 677 KHPVSALMEICnKRKWMPPEFVLVHDSGPDHKKNFLFKVRINSEEYQPTIASpNKKHAKAQAATVALQ 744
Cdd:cd19913     1 KNPVSGLMEYA-QFLGQTCEFLLLEQSGPSHDPRFKFQAVIDGRRFPPAEAS-SKKVAKKDAAAIALK 66

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1126170404 680 VSALMEICNKRKWMPpEFVLVHDSGPDHKKNFLFKVRINSEEYqPTIASPNKKHAKAQAATVALQAM 746
Cdd:cd19903     4 MGKLNEYCQKQKVVL-DYVEVPTSGPSHDPRFTFQVVIDGKEY-PEGEGKSKKEAKQAAAKLALEIL 68

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1126170404 683 LMEICNKRKwMPPEFVlVHDSGPDHKKNFLFKVRINSEEYQPTIASPNKKHAKAQAA 739
Cdd:cd19854     6 LYAWCGKKK-LTPEYD-IKEAGNKHRQRFKCEVRVEGFDYVGTGNATNKKDAQTNAA 60

second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins; RED1 (EC 3.5.4.37; also known as double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. It contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the second DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1126170404 675 SGKHPVSALMEIcnkRKWMPPEFVlvHDSGPDHKKNFLFKVRINSEEYQPTiaSPNKKHAKAQAATVALQAM 746
Cdd:cd19898     1 SGKNPVMILNEL---RPGLKYEFV--SESGESHAKNFVMSVTVDGQTFEGS--GRNKKLAKARAAQAALAKL 65

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1126170404 676 GKHPVSALMEICNKRKWMPPEFVLVHDSGPDHKKNFLFKVRINSEeyQPTIASPNKKHAKAQAATVALQAMG 747
Cdd:cd19886     2 GMNPISRLAQIQQAKKEKEPEYVLLSERGMPRRREFVMQVKVGNE--VATGTGPNKKIAKRNAAEAMLLQLG 71

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1126170404 676 GKHPVSALMEICNKRKWMPPEFVLVHDSGPDHKKNFLFKVRINSEEYQPTiaSPNKKHAKAQAATVALQAMGL-IPKDAP 754
Cdd:cd19885     9 GMNPISRLAQIQQAKKEKEPEYTLITERGLPRRREFVMQVKVGNQTAEGM--GPNKKVAKRNAAEKMLELLGFkVPQPQP 86

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1126170404 681 SALMEICNKRKWMPPEFVLVHdSGPDHKKNFLFKVRINSEEYQPTIASPNKKHAKAQAATVALQAM 746
Cdd:cd19907     4 SQLQEYAQKSCLNLPVYACIR-EGPDHAPRFRATVTFNGVIFESPPGFPTLKAAEHSAAEVALNSL 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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1126170404 679 PVSALMEICNKRKwMPPEFVLVHDSGPDHKKNFLFKVRINSEE-YQPTIASPNK-KHAKAQAA 739
Cdd:cd19857     2 PMCLLNELARFNK-IRPQYTLVDEEGPAHKKTFTVKLTLGDEEeYEASGSSIKKaQHAAAEKA 63

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1126170404 680 VSALMEICNKRKwMPPEFVLVHDSGPDHKKNFLFKVRINSEEYqPTIASPNKKHAKAQAATVALQAM 746
Cdd:cd20314     4 VSLLNEYCQKER-LTVKYEEEKRSGPTHKPRFFCKYIIDGKEY-PEGEGKSKKEAKQAAARLAYEEL 68

third double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins; Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1126170404 679 PVSALMEICNKRKwMPPEFVLVHDSGPDHKKNFLFKVRINSEEYQPTIASpnKKHAKAQAATVALQAM 746
Cdd:cd19859     1 EISLVHEIALKRN-LTVNFEVLRESGPPHMKNFITRCTVGSFVTEGEGNS--KKVSKKRAAEKMLEEL 65

second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3). STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. Members of this STRBP/ILF3 group contain an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1126170404 677 KHPVsalMEICNKRKWMPPEfvLVHDSGPDHKKNFLFKVRINSEEYQPtiASPNKKHAKAQAATVALQAM 746
Cdd:cd19897     1 KNPV---MELNEKRRGLKYE--LISETGGSHDKRFVMEVEVDGQKFQG--AGSNKKVAKANAALAALEKL 63

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1126170404 238 KDRLKSQEhRSGSGKHSRSRSKshdrhhkhrhrsssrERHRHKGSSRHRS------RSRHRSRSRQGSRHRSRSRHRSGS 311
Cdd:TIGR01642   1 RDEEPDRE-REKSRGRDRDRSS---------------ERPRRRSRDRSRFrdrhrrSRERSYREDSRPRDRRRYDSRSPR 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1126170404 312 HDRYRHRSRSHEKHRHRSRSGERypNRAKERHHRSRSPNHSRSRTPTERI--DKAKL-LEIAKANAINQFRAGMIPAHLP 388
Cdd:TIGR01642  65 SLRYSSVRRSRDRPRRRSRSVRS--IEQHRRRLRDRSPSNQWRKDDKKRSlwDIKPPgYELVTADQAKASQVFSVPGTAP 142

                         170
                  ....*....|
gi 1126170404 389 IPSMTPEEEL 398
Cdd:TIGR01642 143 RPAMTDPEKL 152

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1126170404 681 SALMEICNKRKWMPPEFVLVHDsGPDHKKNFLFKVRINSEEYQPTIAsPNKKHAKAQAATVALQAMG 747
Cdd:cd19878     3 NLLQEYAQKKKIPLPKYESAKS-GPSHQPTFVSTVIVLGVRFSSEGA-KNKKQAEQSAAKVALKELG 67