NCBI Conserved Domain Search

fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...

512-588

3.82e-22

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: 91.30 E-value: 3.82e-22

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 571553410 512 VNPVSRLDQIQQAKREKEPVYNLIEEKGAPRRKEFVMEVTMGQHSAQGIGPNKKLAKRAAAEALLAQLGYSKPQPQP 588
Cdd:cd19885   10 MNPISRLAQIQQAKKEKEPEYTLITERGLPRRREFVMQVKVGNQTAEGMGPNKKVAKRNAAEKMLELLGFKVPQPQP 86

DSRM_STAU2_rpt2

cd19882

second double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...

276-367

7.72e-21

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: 87.08 E-value: 7.72e-21

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571553410 276 VELNALAMKRGEATVYTFRQAPPagLQQYVTNSlgHFPRIFNPRFptynrgFHAEPQLYLVSLKVGEREFIGRGLTGQAA 355
Cdd:cd19882    1 VELNGLAMKRGEPAIYRPIDPKP--PPNYRPNY--NFRGMYNQRY------HYPMPKTFYVSLTVGNREFIGEGRTRQAA 70

                         90
                 ....*....|..
gi 571553410 356 RHDAASKALEQL 367
Cdd:cd19882   71 RHNAAMKALQAL 82

Staufen_C

pfam16482

Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of ...

658-743

6.17e-17

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: 77.25 E-value: 6.17e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571553410  658 AEELRGQQQQNP----PTVSPKDQLKYLSQLFNFSVEFNDFPKGAvNKEYLSLVTLSTDPPQVCHGNGPTRTASRNEAAL 733
Cdd:pfam16482  22 AEAILKNNGKTGavpcGLVQPSQQLEYLARVQGFQVEYSDFPRQN-KNEFLSLLTLSSQPVQMTHGIGSSLEASHDQAAL 100

                          90
                  ....*....|
gi 571553410  734 KALCTLSKLG 743
Cdd:pfam16482 101 SALKQLSEQG 110

DSRM

Double-stranded RNA binding motif;

180-243

1.04e-16

Double-stranded RNA binding motif;

Pssm-ID: 214634 [Multi-domain] Cd Length: 67 Bit Score: 74.99 E-value: 1.04e-16

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 571553410   180 PMCLLNELARFNKIQHQYRLTNEQGPAHKKRFTVTLKLGEEEY-VAEGPSIKKAQHSAATEALTK 243
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGKRTgEGEGSSKKEAKQRAAEAALRS 65

DSRM

Double-stranded RNA binding motif;

400-464

2.08e-16

Double-stranded RNA binding motif;

Pssm-ID: 214634 [Multi-domain] Cd Length: 67 Bit Score: 74.22 E-value: 2.08e-16

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571553410   400 PVSLVHEKALKRGLPVSFEVVSEIGKPHIRTFRTKCTVGDKVT-LGEGPSKKVSKKHAAEFMLEEL 464
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGKRTgEGEGSSKKEAKQRAAEAALRSL 66

dsrm

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...

180-243

5.08e-14

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: 67.26 E-value: 5.08e-14

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 571553410  180 PMCLLNELARFNKIQHQYRLTNEQGPAHKKRFTVTLKLGEEEY-VAEGPSIKKAQHSAATEALTK 243
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYgSGTGSSKKEAEQLAAEKALEK 65

dsrm

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...

400-464

9.52e-12

Pssm-ID: 425434 [Multi-domain] Cd Length: 66 Bit Score: 60.71 E-value: 9.52e-12

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571553410  400 PVSLVHEKALKRGLPVSFEVVSEIGKPHIRTFRTKCTVGDKVTL-GEGPSKKVSKKHAAEFMLEEL 464
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYGsGTGSSKKEAEQLAAEKALEKL 66

Rnc

dsRNA-specific ribonuclease [Transcription];

196-243

7.93e-11

dsRNA-specific ribonuclease [Transcription];

Pssm-ID: 440336 [Multi-domain] Cd Length: 229 Bit Score: 62.81 E-value: 7.93e-11

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 571553410 196 QYRLTNEQGPAHKKRFTVTLKLGEEEY-VAEGPSIKKAQHSAATEALTK 243
Cdd:COG0571  176 EYEVVEEEGPDHAKTFTVEVLVGGKVLgEGTGRSKKEAEQAAAKAALEK 224

seadorna_dsRNA

TIGR04238

seadornavirus double-stranded RNA-binding protein; This protein family occurs in the ...

400-464

3.28e-09

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: 57.26 E-value: 3.28e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571553410  400 PVSLVHEKALKRGLPV-SFEVVSEIGKPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAAEFMLEEL 464
Cdd:TIGR04238   2 VVGMLQELAVKRGLELpVYEKVGKEGPDHAPTFTIKLTANDIEVIEAASSKKQAEKLAAATIYEDM 67

Rnc

dsRNA-specific ribonuclease [Transcription];

386-466

9.85e-09

dsRNA-specific ribonuclease [Transcription];

Pssm-ID: 440336 [Multi-domain] Cd Length: 229 Bit Score: 56.65 E-value: 9.85e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571553410 386 TLGEAKDPIAELKspvslvhEKALKRGLPV-SFEVVSEIGKPHIRTFRTKCTVGDKV-TLGEGPSKKVSKKHAAEFMLEE 463
Cdd:COG0571  152 PGGAGKDYKTALQ-------EWLQARGLPLpEYEVVEEEGPDHAKTFTVEVLVGGKVlGEGTGRSKKEAEQAAAKAALEK 224


                 ...
gi 571553410 464 LNR 466
Cdd:COG0571  225 LGK 227

RNaseIII

TIGR02191

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...

165-243

5.25e-08

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

Pssm-ID: 274024 [Multi-domain] Cd Length: 220 Bit Score: 54.13 E-value: 5.25e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571553410  165 INVTDSALANMKEKTPMCLLNELA-RFNKIQHQYRLTNEQGPAHKKRFTVTLKLGEEEYV-AEGPSIKKAQHSAATEALT 242
Cdd:TIGR02191 139 IPRIDAIIKEETLKDYKTALQEWAqARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGEPYGeGKGKSKKEAEQNAAKAALE 218


                  .
gi 571553410  243 K 243
Cdd:TIGR02191 219 K 219

Rnc

dsRNA-specific ribonuclease [Transcription];

493-563

5.90e-05

dsRNA-specific ribonuclease [Transcription];

Pssm-ID: 440336 [Multi-domain] Cd Length: 229 Bit Score: 45.09 E-value: 5.90e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 571553410 493 RNLIKVYQEPRSESDAAEEV--NPVSRLDQIQQAKREKEPVYNLIEEKGAPRRKEFVMEVTM-GQHSAQGIGPN 563
Cdd:COG0571  136 RKFVLRLFEPRLEEIAPGGAgkDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVgGKVLGEGTGRS 209

DSRM

Double-stranded RNA binding motif;

514-568

1.94e-04

Double-stranded RNA binding motif;

Pssm-ID: 214634 [Multi-domain] Cd Length: 67 Bit Score: 40.32 E-value: 1.94e-04

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 571553410   514 PVSRLDQIQQaKREKEPVYNLIEEKGAPRRKEFVMEVTM-GQHSAQGIGPNKKLAK 568
Cdd:smart00358   1 PKSLLQELAQ-KRKLPPEYELVKEEGPDHAPRFTVTVKVgGKRTGEGEGSSKKEAK 55

Name

Accession

Description

Interval

E-value

DSRM_STAU_rpt1

cd19857

first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...

179-241

1.04e-31

Pssm-ID: 380686 Cd Length: 64 Bit Score: 117.75 E-value: 1.04e-31

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 571553410 179 TPMCLLNELARFNKIQHQYRLTNEQGPAHKKRFTVTLKLG-EEEYVAEGPSIKKAQHSAATEAL 241
Cdd:cd19857    1 TPMCLLNELARFNKIRPQYTLVDEEGPAHKKTFTVKLTLGdEEEYEASGSSIKKAQHAAAEKAL 64

DSRM_STAU1_rpt1

cd19879

first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...

176-241

1.74e-28

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: 108.63 E-value: 1.74e-28

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571553410 176 KEKTPMCLLNELARFNKIQHQYRLTNEQGPAHKKRFTVTLKLGEEEYVAEGPSIKKAQHSAATEAL 241
Cdd:cd19879    1 KEKTPMCLVNELARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTSIKKAQHAAAAKAL 66

DSRM_STAU2_rpt1

cd19880

first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...

174-241

4.04e-28

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: 107.50 E-value: 4.04e-28

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 571553410 174 NMKEKTPMCLLNELARFNKIQHQYRLTNEQGPAHKKRFTVTLKLGEEEYVAEGPSIKKAQHSAATEAL 241
Cdd:cd19880    1 NPKEKTPMCLVNELARFNRIQPQYKLLNERGPAHAKIFTVQLTLGEQTWEAEGSSIKKAQHAAASKAL 68

DSRM_STAU_rpt5

cd19861

fifth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...

674-742

2.92e-26

Pssm-ID: 380690 Cd Length: 68 Bit Score: 102.30 E-value: 2.92e-26

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 571553410 674 PKDQLKYLSQLFNFSVEFNDFPKGAvNKEYLSLVTLSTDPPQVCHGNGPTRTASRNEAALKALCTLSKL 742
Cdd:cd19861    1 PKEQLEYLAKVLGFSVEFTDFPKGN-KSEYLSLVSLGTEPPQVCHGSGSSVEESRDAAALNALKLLKEL 68

DSRM_STAU_rpt3

cd19859

third double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...

400-464

1.29e-25

Pssm-ID: 380688 Cd Length: 65 Bit Score: 100.17 E-value: 1.29e-25

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 571553410 400 PVSLVHEKALKRGLPVSFEVVSEIGKPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAAEFMLEEL 464
Cdd:cd19859    1 EISLVHEIALKRNLTVNFEVLRESGPPHMKNFITRCTVGSFVTEGEGNSKKVSKKRAAEKMLEEL 65

DSRM_STAU1_rpt4

fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...

512-588

3.82e-22

Pssm-ID: 380714 Cd Length: 86 Bit Score: 91.30 E-value: 3.82e-22

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 571553410 512 VNPVSRLDQIQQAKREKEPVYNLIEEKGAPRRKEFVMEVTMGQHSAQGIGPNKKLAKRAAAEALLAQLGYSKPQPQP 588
Cdd:cd19885   10 MNPISRLAQIQQAKKEKEPEYTLITERGLPRRREFVMQVKVGNQTAEGMGPNKKVAKRNAAEKMLELLGFKVPQPQP 86

DSRM_STAU_rpt4

cd19860

fourth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...

513-564

4.45e-22

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: 90.08 E-value: 4.45e-22

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 571553410 513 NPVSRLDQIQQAKREKEPVYNLIEEKGAPRRKEFVMEVTMGQHSAQGIGPNK 564
Cdd:cd19860    1 NPISRLIQIQQARKEKEPVYSLVAERGTPRRREFVMQVTVGDKTATGTGPNK 52

DSRM_STAU2_rpt2

cd19882

second double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...

276-367

7.72e-21

Pssm-ID: 380711 Cd Length: 82 Bit Score: 87.08 E-value: 7.72e-21

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571553410 276 VELNALAMKRGEATVYTFRQAPPagLQQYVTNSlgHFPRIFNPRFptynrgFHAEPQLYLVSLKVGEREFIGRGLTGQAA 355
Cdd:cd19882    1 VELNGLAMKRGEPAIYRPIDPKP--PPNYRPNY--NFRGMYNQRY------HYPMPKTFYVSLTVGNREFIGEGRTRQAA 70

                         90
                 ....*....|..
gi 571553410 356 RHDAASKALEQL 367
Cdd:cd19882   71 RHNAAMKALQAL 82

DSRM_STAU2_rpt4

cd19886

fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...

512-591

4.40e-19

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: 82.31 E-value: 4.40e-19

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571553410 512 VNPVSRLDQIQQAKREKEPVYNLIEEKGAPRRKEFVMEVTMGQHSAQGIGPNKKLAKRAAAEALLAQLGYSKPQPQPTKP 591
Cdd:cd19886    3 MNPISRLAQIQQAKKEKEPEYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKRNAAEAMLLQLGYKASTPLQDQT 82

DSRM_STAU1_rpt3

cd19883

third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...

398-464

2.39e-18

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: 79.67 E-value: 2.39e-18

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 571553410 398 KSPVSLVHEKALKRGLPVSFEVVSEIGKPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAAEFMLEEL 464
Cdd:cd19883    1 KSEISQVFEIALKRNMPVNFEVTKETGPPHMKSFVTKVSVGEFAGEGEGKSKKISKKNAAIAVLEEL 67

DSRM_STAU2_rpt3

cd19884

third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...

398-464

3.86e-18

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: 78.90 E-value: 3.86e-18

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 571553410 398 KSPVSLVHEKALKRGLPVSFEVVSEIGKPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAAEFMLEEL 464
Cdd:cd19884    1 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVTVGEFTAEGEGNSKKLSKKRAATSVLQEL 67

Staufen_C

pfam16482

Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of ...

658-743

6.17e-17

Pssm-ID: 465131 Cd Length: 110 Bit Score: 77.25 E-value: 6.17e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571553410  658 AEELRGQQQQNP----PTVSPKDQLKYLSQLFNFSVEFNDFPKGAvNKEYLSLVTLSTDPPQVCHGNGPTRTASRNEAAL 733
Cdd:pfam16482  22 AEAILKNNGKTGavpcGLVQPSQQLEYLARVQGFQVEYSDFPRQN-KNEFLSLLTLSSQPVQMTHGIGSSLEASHDQAAL 100

                          90
                  ....*....|
gi 571553410  734 KALCTLSKLG 743
Cdd:pfam16482 101 SALKQLSEQG 110

DSRM

Double-stranded RNA binding motif;

180-243

1.04e-16

Double-stranded RNA binding motif;

Pssm-ID: 214634 [Multi-domain] Cd Length: 67 Bit Score: 74.99 E-value: 1.04e-16

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 571553410   180 PMCLLNELARFNKIQHQYRLTNEQGPAHKKRFTVTLKLGEEEY-VAEGPSIKKAQHSAATEALTK 243
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGKRTgEGEGSSKKEAKQRAAEAALRS 65

DSRM

Double-stranded RNA binding motif;

400-464

2.08e-16

Double-stranded RNA binding motif;

Pssm-ID: 214634 [Multi-domain] Cd Length: 67 Bit Score: 74.22 E-value: 2.08e-16

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571553410   400 PVSLVHEKALKRGLPVSFEVVSEIGKPHIRTFRTKCTVGDKVT-LGEGPSKKVSKKHAAEFMLEEL 464
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGKRTgEGEGSSKKEAKQRAAEAALRSL 66

dsrm

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...

180-243

5.08e-14

Pssm-ID: 425434 [Multi-domain] Cd Length: 66 Bit Score: 67.26 E-value: 5.08e-14

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 571553410  180 PMCLLNELARFNKIQHQYRLTNEQGPAHKKRFTVTLKLGEEEY-VAEGPSIKKAQHSAATEALTK 243
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYgSGTGSSKKEAEQLAAEKALEK 65

DSRM_PRKRA-like_rpt1

cd19862

first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...

398-467

5.27e-14

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: 67.29 E-value: 5.27e-14

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571553410 398 KSPVSLVHEKALKRGLPVSFEVVSEIGKPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAAEFMLEELNRL 467
Cdd:cd19862    1 KTPISVLQELCAKRGITPKYELISSEGAVHEPTFTFRVTVGDITATGSGTSKKKAKHAAAENALEQLKGS 70

DSRM_PRKRA-like_rpt3

cd19864

third double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family ...

673-739

5.60e-14

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

Pssm-ID: 380693 Cd Length: 72 Bit Score: 67.25 E-value: 5.60e-14

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 571553410 673 SPKDQLKYLSQLFNFSVEFNDFPKGAVNKEYLSLVTLSTDPPQVCHGNGPTRTASRNEAALKALCTL 739
Cdd:cd19864    2 DYCELLQELAEEQKFKVTYVDIEELSSSGKYQCLVQLSTLPPTVCHGSGASLEEAKEEAARNALEYL 68

DSRM_STAU_rpt2

cd19858

second double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...

303-365

6.62e-13

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: 64.35 E-value: 6.62e-13

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 571553410 303 QYVTNSLGHFPRIFNPRFPTYNRGFHAePQLYLVSLKVGEREFIGRGLTGQAARHDAASKALE 365
Cdd:cd19858    6 NYNNYGMPQRRGDYRFRYPYPNNPSGP-PPPFYVTLTVGEREFIGEGRTRQAARHDAASKALK 67

dsrm

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...

400-464

9.52e-12

Pssm-ID: 425434 [Multi-domain] Cd Length: 66 Bit Score: 60.71 E-value: 9.52e-12

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571553410  400 PVSLVHEKALKRGLPVSFEVVSEIGKPHIRTFRTKCTVGDKVTL-GEGPSKKVSKKHAAEFMLEEL 464
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYGsGTGSSKKEAEQLAAEKALEKL 66

Rnc

dsRNA-specific ribonuclease [Transcription];

196-243

7.93e-11

dsRNA-specific ribonuclease [Transcription];

Pssm-ID: 440336 [Multi-domain] Cd Length: 229 Bit Score: 62.81 E-value: 7.93e-11

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 571553410 196 QYRLTNEQGPAHKKRFTVTLKLGEEEY-VAEGPSIKKAQHSAATEALTK 243
Cdd:COG0571  176 EYEVVEEEGPDHAKTFTVEVLVGGKVLgEGTGRSKKEAEQAAAKAALEK 224

DSRM_SF

cd00048

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...

405-461

1.17e-10

Pssm-ID: 380679 [Multi-domain] Cd Length: 57 Bit Score: 57.29 E-value: 1.17e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 571553410 405 HEKALKRGLP-VSFEVVSEIGkPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAAEFML 461
Cdd:cd00048    1 NELCQKNKWPpPEYETVEEGG-PHNPRFTCTVTVNGQTFEGEGKSKKEAKQAAAEKAL 57

DSRM_EIF2AK2-like

cd19875

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...

398-464

1.19e-10

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: 57.66 E-value: 1.19e-10

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 571553410 398 KSPVSLVHEKALKRGLPVSFEVVSEiGKPHIRTFRTKCTVGDKV-TLGEGPSKKVSKKHAAEFMLEEL 464
Cdd:cd19875    1 KNPVSALNEYCQKRGLSLEFVDVSV-GPDHCPGFTASATIDGIVfASATGTSKKEAKRAAAKLALKKL 67

DSRM_RNAse_III_family

cd10845

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...

196-243

2.96e-10

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: 56.73 E-value: 2.96e-10

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 571553410 196 QYRLTNEQGPAHKKRFTVTLKLGEEEY-VAEGPSIKKAQHSAATEALTK 243
Cdd:cd10845   20 EYELVEEEGPDHNKTFTVEVKVNGKVIgEGTGRSKKEAEQAAAKAALEK 68

DSRM_STAU_rpt4

cd19860

fourth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...

414-464

5.95e-10

Pssm-ID: 380689 Cd Length: 68 Bit Score: 55.80 E-value: 5.95e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 571553410 414 PVsFEVVSEIGKPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAAEFMLEEL 464
Cdd:cd19860   18 PV-YSLVAERGTPRRREFVMQVTVGDKTATGTGPNKKLAKRNAAEAMLELL 67

DSRM_EIF2AK2-like

cd19875

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...

178-243

1.12e-09

Pssm-ID: 380704 Cd Length: 67 Bit Score: 54.97 E-value: 1.12e-09

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 571553410 178 KTPMCLLNELARFNKIQHQYRLTnEQGPAHKKRFTVTLKLGEEEYV-AEGPSIKKAQHSAATEALTK 243
Cdd:cd19875    1 KNPVSALNEYCQKRGLSLEFVDV-SVGPDHCPGFTASATIDGIVFAsATGTSKKEAKRAAAKLALKK 66

DSRM_SF

cd00048

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...

185-241

1.71e-09

Pssm-ID: 380679 [Multi-domain] Cd Length: 57 Bit Score: 54.21 E-value: 1.71e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 571553410 185 NELA-RFNKIQHQYRLTnEQGPAHKKRFTVTLKLGEEEYVAEGPSIKKAQHSAATEAL 241
Cdd:cd00048    1 NELCqKNKWPPPEYETV-EEGGPHNPRFTCTVTVNGQTFEGEGKSKKEAKQAAAEKAL 57

DSRM_PRKRA_rpt1

cd19889

first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...

398-464

2.45e-09

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: 54.15 E-value: 2.45e-09

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 571553410 398 KSPVSLVHEKALKRGLPVSFEVVSEIGKPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAAEFMLEEL 464
Cdd:cd19889    2 KTPIQLLHEYGTKTGNIPVYELEKSEGQAHLPSFTFRVTVGDITCTGEGTSKKLAKHRAAEAALNIL 68

seadorna_dsRNA

TIGR04238

seadornavirus double-stranded RNA-binding protein; This protein family occurs in the ...

400-464

3.28e-09

Pssm-ID: 275074 [Multi-domain] Cd Length: 201 Bit Score: 57.26 E-value: 3.28e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571553410  400 PVSLVHEKALKRGLPV-SFEVVSEIGKPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAAEFMLEEL 464
Cdd:TIGR04238   2 VVGMLQELAVKRGLELpVYEKVGKEGPDHAPTFTIKLTANDIEVIEAASSKKQAEKLAAATIYEDM 67

Rnc

dsRNA-specific ribonuclease [Transcription];

386-466

9.85e-09

dsRNA-specific ribonuclease [Transcription];

Pssm-ID: 440336 [Multi-domain] Cd Length: 229 Bit Score: 56.65 E-value: 9.85e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571553410 386 TLGEAKDPIAELKspvslvhEKALKRGLPV-SFEVVSEIGKPHIRTFRTKCTVGDKV-TLGEGPSKKVSKKHAAEFMLEE 463
Cdd:COG0571  152 PGGAGKDYKTALQ-------EWLQARGLPLpEYEVVEEEGPDHAKTFTVEVLVGGKVlGEGTGRSKKEAEQAAAKAALEK 224


                 ...
gi 571553410 464 LNR 466
Cdd:COG0571  225 LGK 227

DSRM_PRKRA-like_rpt1

cd19862

first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...

178-241

1.03e-08

Pssm-ID: 380691 [Multi-domain] Cd Length: 70 Bit Score: 52.26 E-value: 1.03e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 571553410 178 KTPMCLLNELARFNKIQHQYRLTNEQGPAHKKRFTVTLKLGEEEYVAEGPSIKKAQHSAATEAL 241
Cdd:cd19862    1 KTPISVLQELCAKRGITPKYELISSEGAVHEPTFTFRVTVGDITATGSGTSKKKAKHAAAENAL 64

DSRM_RNAse_III_family

cd10845

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...

398-464

1.27e-08

Pssm-ID: 380682 [Multi-domain] Cd Length: 69 Bit Score: 52.11 E-value: 1.27e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 571553410 398 KSPVSLVHEKALKRGLP-VSFEVVSEIGKPHIRTFRTKCTVGDKVT-LGEGPSKKVSKKHAAEFMLEEL 464
Cdd:cd10845    1 KDYKTALQEYLQKRGLPlPEYELVEEEGPDHNKTFTVEVKVNGKVIgEGTGRSKKEAEQAAAKAALEKL 69

DSRM_STAU1_rpt5

cd19887

fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...

674-742

2.12e-08

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

Pssm-ID: 380716 Cd Length: 70 Bit Score: 51.59 E-value: 2.12e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 571553410 674 PKDQLKYLSQLFNFSVEFNDFPKGAVNkEYLSLVTLSTDPPQVCHGNGPTRTASRNEAALKALCTLSKL 742
Cdd:cd19887    2 PSEQLDYLSRVQGLQVEYKDFPKNNKN-EFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSEL 69

DSRM_PRKRA-like_rpt2

cd19863

second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family ...

400-464

3.81e-08

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: 50.84 E-value: 3.81e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 571553410 400 PVSLVHEKALKRG--LPvSFEVVSEIGKPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAAEFMLEEL 464
Cdd:cd19863    2 PVGILQELCVQRRwrLP-EYEVEQESGPPHEKEFTIACRVENFSETGSGKSKKLAKRAAAEKMLTRL 67

RNaseIII

TIGR02191

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...

165-243

5.25e-08

Pssm-ID: 274024 [Multi-domain] Cd Length: 220 Bit Score: 54.13 E-value: 5.25e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 571553410  165 INVTDSALANMKEKTPMCLLNELA-RFNKIQHQYRLTNEQGPAHKKRFTVTLKLGEEEYV-AEGPSIKKAQHSAATEALT 242
Cdd:TIGR02191 139 IPRIDAIIKEETLKDYKTALQEWAqARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGEPYGeGKGKSKKEAEQNAAKAALE 218


                  .
gi 571553410  243 K 243
Cdd:TIGR02191 219 K 219

DSRM_STRBP_RED-like_rpt2

cd19866

second double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...

398-464

1.27e-07

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: 49.09 E-value: 1.27e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 571553410 398 KSPVSLVHEkaLKRGLpvSFEVVSEIGKPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAAEFMLEEL 464
Cdd:cd19866    1 KNPVMLLNE--LRPGL--KYKCLSESGESHAKSFVMSVTVDGQTFEGTGRSKKLAKAAAAQAALAKL 63

DSRM_STRBP_RED-like_rpt1

cd19865

first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...

178-241

2.23e-07

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: 48.50 E-value: 2.23e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 571553410 178 KTPMCLLNELarfnKIQHQYRLTNEQGPAHKKRFTVTLKLGEEEYVAEGPSIKKAQHSAATEAL 241
Cdd:cd19865    1 KNALMQLNEL----RPGLQYKLTSQTGPVHAPVFTMSVEVNGQTFEGTGRSKKKAKLEAAEKAL 60

DSRM_TARBP2_rpt3

cd19893

third double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar ...

678-736

3.29e-07

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

Pssm-ID: 380722 Cd Length: 72 Bit Score: 48.37 E-value: 3.29e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 571553410 678 LKYLSQLFNFSVEFNDFPKGAVNKEYLSLVTLSTDPPQVCHGNGPTRTASRNEAALKAL 736
Cdd:cd19893    7 LRELSEEQAFHISYLDIEELSLSGLCQCLVELSTQPATVCHGSATTRDAARANAAHNAL 65

DSRM_STAU1_rpt2

cd19881

second double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...

313-365

3.55e-07

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: 48.34 E-value: 3.55e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 571553410 313 PRIFNPRFPTynrgfhaEPQLYLVSLKVGEREFIGRGLTGQAARHDAASKALE 365
Cdd:cd19881   34 PRYFYPFPPV-------GPVLYQVELSIGGQQFHGKGRTRQAAKHDAAAKALK 79

DSRM_DCL_plant

cd19869

double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant ...

196-241

6.32e-07

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: 47.36 E-value: 6.32e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 571553410 196 QYRLTNEQGPAHKKRFT--VTLKLGEEEYVAEG-----PSIKKAQHSAATEAL 241
Cdd:cd19869   13 VYRCVEEEGPAHAKRFTymVRVKIPERGWTIECegepmRSKKRAKDSAALLLL 65

DSRM_PRKRA_rpt3

cd19892

third double-stranded RNA binding motif of protein activator of the interferon-induced protein ...

678-736

1.58e-06

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

Pssm-ID: 380721 Cd Length: 72 Bit Score: 46.42 E-value: 1.58e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 571553410 678 LKYLSQLFNFSVEFNDFPKGAVNKEYLSLVTLSTDPPQVCHGNGPTRTASRNEAALKAL 736
Cdd:cd19892    7 LGEVAEEQGFNVTYLDIDELSVNGQYQCLAELSTSPVTVCHGTGISCGNAHNDAAHNAL 65

DSRM_EIF2AK2

cd20314

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...

401-464

1.68e-06

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: 46.23 E-value: 1.68e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 571553410 401 VSLVHEKALKRGLPVSFEVVSEIGKPHIRTFRTKCTVGDK-VTLGEGPSKKVSKKHAAEFMLEEL 464
Cdd:cd20314    4 VSLLNEYCQKERLTVKYEEEKRSGPTHKPRFFCKYIIDGKeYPEGEGKSKKEAKQAAARLAYEEL 68

DSRM_STAU2_rpt5

cd19888

fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...

672-743

2.75e-06

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: 45.33 E-value: 2.75e-06

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 571553410 672 VSPKDQLKYLSQLFNFSVEFNDFPKGavnKEYLSLVTLStdPPQVC-HGNGPTRTASRNEAALKALCTLSKLG 743
Cdd:cd19888    1 VQPSKQLEYLARIQGFQVQYSDRQNG---KECMTCLTLS--PVQMTfHGIGSSIEASHDQAALSALKQLSEQG 68

DSRM_PRKRA_rpt2

cd19891

second double-stranded RNA binding motif of protein activator of the interferon-induced ...

400-464

5.43e-06

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: 44.55 E-value: 5.43e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 571553410 400 PVSLVHEKALKRG--LPvSFEVVSEIGKPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAAEFMLEEL 464
Cdd:cd19891    2 PIGSLQELAVQKGwrLP-EYTLAQESGPPHKREFTITCRVETFVETGTGTSKKVAKRNAAEKLLAKF 67

DSRM_STAU_rpt2

cd19858

second double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...

189-242

5.47e-06

Pssm-ID: 380687 Cd Length: 67 Bit Score: 44.71 E-value: 5.47e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 571553410 189 RFNKIQHQYRLTNEQGPAhKKRFTVTLKLGEEEYVAEGPSIKKAQHSAATEALT 242
Cdd:cd19858   15 RRGDYRFRYPYPNNPSGP-PPPFYVTLTVGEREFIGEGRTRQAARHDAASKALK 67

DSRM_STAU2_rpt4

cd19886

fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...

419-464

6.01e-06

Pssm-ID: 380715 Cd Length: 86 Bit Score: 44.95 E-value: 6.01e-06

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 571553410 419 VVSEIGKPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAAEFMLEEL 464
Cdd:cd19886   25 LLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKRNAAEAMLLQL 70

DSRM_DRADA

cd19902

double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) ...

398-464

7.06e-06

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: 44.20 E-value: 7.06e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 571553410 398 KSPVSLVHEKALKRGLPVSFEVVSEIGKPHIRTFRTKCTVGDK-VTLGEGPSKKVSKKHAAEFMLEEL 464
Cdd:cd19902    1 KNPVSALMEYAQSRGVTAEIEVLSQSGPPHNPRFKAAVFVGGRrFPSVEASSKKDAKQEAADLALRAL 68

DSRM_STAU1_rpt4

fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...

399-472

7.64e-06

Pssm-ID: 380714 Cd Length: 86 Bit Score: 44.69 E-value: 7.64e-06

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 571553410 399 SPVS-LVHEKALKRGLPVSFEVVSEIGKPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAAEFMLEELNRLPPLPE 472
Cdd:cd19885   11 NPISrLAQIQQAKKEKEPEYTLITERGLPRRREFVMQVKVGNQTAEGMGPNKKVAKRNAAEKMLELLGFKVPQPQ 85

DSRM_DRADA_rpt2

cd19914

second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...

178-241

8.12e-06

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: 44.07 E-value: 8.12e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 571553410 178 KTPMCLLNELARFNKIQHQYRLTNEQGPAHKKRFTVTLKLGEEEY-VAEGPSIKKAQHSAATEAL 241
Cdd:cd19914    1 KNPISVLMEHSQKSGNMCEFQLLSQEGPPHDPKFTYCVKVGEQTFpSVVANSKKVAKQMAAEEAV 65

DSRM_SON-like

cd19870

double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...

398-468

9.11e-06

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: 44.19 E-value: 9.11e-06

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 571553410 398 KSPVSLVHEKALKRGL-PVSFEVVSEIGKPHIRTFRTKCTVGDKV--TLGEGPSKKVSKKHAAEFMLEELNRLP 468
Cdd:cd19870    2 KHPVSALMELCNKRKWgPPEFRLVEESGPPHRKHFLFKVVVNGVEyqPSVASGNKKDAKAQAATVALQALGLVP 75

DSRM_TARBP2_rpt1

cd19890

first double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar ...

398-464

1.17e-05

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: 43.97 E-value: 1.17e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 571553410 398 KSPVSLVHEKALKRGLPVSFEVVSEIGKPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAAEFMLEEL 464
Cdd:cd19890    3 KTPISLLQEYGTRIGKTPVYDLLKAEGQAHQPNFTFRVTVGDISCTGQGPSKKAAKHKAAEVALKLL 69

DSRM_DRADA_rpt2

cd19914

second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...

398-464

1.21e-05

Pssm-ID: 380743 Cd Length: 71 Bit Score: 43.68 E-value: 1.21e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 571553410 398 KSPVSLVHEKALKRGLPVSFEVVSEIGKPHIRTFRTKCTVGDKV-TLGEGPSKKVSKKHAAEFMLEEL 464
Cdd:cd19914    1 KNPISVLMEHSQKSGNMCEFQLLSQEGPPHDPKFTYCVKVGEQTfPSVVANSKKVAKQMAAEEAVKEL 68

DSRM_PRKRA_rpt1

cd19889

first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...

178-241

1.73e-05

Pssm-ID: 380718 [Multi-domain] Cd Length: 71 Bit Score: 43.36 E-value: 1.73e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 571553410 178 KTPMCLLNELARFNKIQHQYRLTNEQGPAHKKRFTVTLKLGEEEYVAEGPSIKKAQHSAATEAL 241
Cdd:cd19889    2 KTPIQLLHEYGTKTGNIPVYELEKSEGQAHLPSFTFRVTVGDITCTGEGTSKKLAKHRAAEAAL 65

DSRM_RNAse_III_family

cd10845

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...

513-563

1.75e-05

Pssm-ID: 380682 [Multi-domain] Cd Length: 69 Bit Score: 43.25 E-value: 1.75e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 571553410 513 NPVSRLDQIQQAKREKEPVYNLIEEKGAPRRKEFVMEVTM-GQHSAQGIGPN 563
Cdd:cd10845    2 DYKTALQEYLQKRGLPLPEYELVEEEGPDHNKTFTVEVKVnGKVIGEGTGRS 53

DSRM_EIF2AK2_rpt1

cd19903

first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha ...

181-241

1.88e-05

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: 43.15 E-value: 1.88e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 571553410 181 MCLLNELARFNKIQHQYRLTNEQGPAHKKRFTVTLKLGEEEY-VAEGPSIKKAQHSAATEAL 241
Cdd:cd19903    4 MGKLNEYCQKQKVVLDYVEVPTSGPSHDPRFTFQVVIDGKEYpEGEGKSKKEAKQAAAKLAL 65

DSRM_STRBP_rpt1

cd19909

first double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...

183-246

2.44e-05

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: 43.48 E-value: 2.44e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571553410 183 LLNELARFNKIQH--QYRLTNEQGPAHKKRFTVTLKLGEEEYVAEGPSIKKAQHSAATEALTKTWY 246
Cdd:cd19909    5 PMNALMRLNQIRPglQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGY 70

DSRM_STRBP-like_rpt1

cd19894

first double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family ...

184-241

2.48e-05

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: 42.76 E-value: 2.48e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 571553410 184 LNELARFNKIQH--QYRLTNEQGPAHKKRFTVTLKLGEEEYVAEGPSIKKAQHSAATEAL 241
Cdd:cd19894    1 MNALMRLNQLRPglQYKLASQTGPVHAPQFTMSVEVDGVTYEASGPSKKTAKLHVAVKVL 60

DSRM_STAU_rpt3

cd19859

third double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...

180-241

4.32e-05

Pssm-ID: 380688 Cd Length: 65 Bit Score: 42.00 E-value: 4.32e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 571553410 180 PMCLLNELARFNKIQHQYRLTNEQGPAHKKRFTVTLKLGEEEYVAEGPSIKKAQHSAATEAL 241
Cdd:cd19859    1 EISLVHEIALKRNLTVNFEVLRESGPPHMKNFITRCTVGSFVTEGEGNSKKVSKKRAAEKML 62

DSRM_STRBP-like_rpt2

cd19897

second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family ...

398-464

4.66e-05

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: 41.96 E-value: 4.66e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 571553410 398 KSPVSLVHEKalKRGLpvSFEVVSEIGKPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAAEFMLEEL 464
Cdd:cd19897    1 KNPVMELNEK--RRGL--KYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKANAALAALEKL 63

DSRM_DRADA_rpt1

cd19913

first double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...

178-245

5.04e-05

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: 42.17 E-value: 5.04e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 571553410 178 KTPMCLLNELARFNKIQHQYRLTNEQGPAHKKRFTVTLKLGEEEY-VAEGPSIKKAQHSAATEALTKTW 245
Cdd:cd19913    1 KNPVSGLMEYAQFLGQTCEFLLLEQSGPSHDPRFKFQAVIDGRRFpPAEASSKKVAKKDAAAIALKILL 69

Rnc

dsRNA-specific ribonuclease [Transcription];

493-563

5.90e-05

dsRNA-specific ribonuclease [Transcription];

Pssm-ID: 440336 [Multi-domain] Cd Length: 229 Bit Score: 45.09 E-value: 5.90e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 571553410 493 RNLIKVYQEPRSESDAAEEV--NPVSRLDQIQQAKREKEPVYNLIEEKGAPRRKEFVMEVTM-GQHSAQGIGPN 563
Cdd:COG0571  136 RKFVLRLFEPRLEEIAPGGAgkDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVgGKVLGEGTGRS 209

DSRM_PRKRA_rpt2

cd19891

second double-stranded RNA binding motif of protein activator of the interferon-induced ...

180-243

1.03e-04

Pssm-ID: 380720 Cd Length: 67 Bit Score: 41.08 E-value: 1.03e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 571553410 180 PMCLLNELArfnkIQH-----QYRLTNEQGPAHKKRFTVTLKLGEEEYVAEGPSIKKAQHSAATEALTK 243
Cdd:cd19891    2 PIGSLQELA----VQKgwrlpEYTLAQESGPPHKREFTITCRVETFVETGTGTSKKVAKRNAAEKLLAK 66

DSRM_STRBP_RED-like_rpt1

cd19865

first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...

398-462

1.15e-04

Pssm-ID: 380694 Cd Length: 63 Bit Score: 40.79 E-value: 1.15e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 571553410 398 KSPVSLVHEkaLKRGLpvSFEVVSEIGKPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAAEFMLE 462
Cdd:cd19865    1 KNALMQLNE--LRPGL--QYKLTSQTGPVHAPVFTMSVEVNGQTFEGTGRSKKKAKLEAAEKALR 61

DSRM_STRBP_RED-like_rpt2

cd19866

second double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...

178-243

1.25e-04

Pssm-ID: 380695 Cd Length: 63 Bit Score: 40.61 E-value: 1.25e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571553410 178 KTPMCLLNELARFNKiqhqYRLTNEQGPAHKKRFTVTLKLGEEEYVAEGPSIKKAQHSAATEALTK 243
Cdd:cd19866    1 KNPVMLLNELRPGLK----YKCLSESGESHAKSFVMSVTVDGQTFEGTGRSKKLAKAAAAQAALAK 62

DSRM_EIF2AK2_rpt2

cd19904

second double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha ...

401-464

1.61e-04

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: 40.57 E-value: 1.61e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 571553410 401 VSLVHEKALKRGLPVSFEVVSEIGKPHIRTFRTKCTVGDKV-TLGEGPSKKVSKKHAAEFMLEEL 464
Cdd:cd19904    4 ISLLNQYAQKKRLTVNYEQCASTGVPGPPRFSCKCKIGQKEyGIGTGSTKQEAKQAAAKEAYEQL 68

DSRM

Double-stranded RNA binding motif;

514-568

1.94e-04

Double-stranded RNA binding motif;

Pssm-ID: 214634 [Multi-domain] Cd Length: 67 Bit Score: 40.32 E-value: 1.94e-04

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 571553410   514 PVSRLDQIQQaKREKEPVYNLIEEKGAPRRKEFVMEVTM-GQHSAQGIGPNKKLAK 568
Cdd:smart00358   1 PKSLLQELAQ-KRKLPPEYELVKEEGPDHAPRFTVTVKVgGKRTGEGEGSSKKEAK 55

DSRM_RED2_rpt1

cd19896

first double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar proteins; ...

185-249

2.29e-04

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: 40.08 E-value: 2.29e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 571553410 185 NELARFNKIQH--QYRLTNEQGPAHKKRFTVTLKLGEEEYVAEGPSIKKAQHSAATEALtKTWYQRP 249
Cdd:cd19896    7 NALVQLNELKPglQYRMVSQTGPVHAPVFAVAVEVNGLTFEGTGPTKKKAKMRAAEMAL-KSFVQFP 72

DSRM_STRBP_rpt2

cd19911

second double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...

178-243

2.46e-04

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: 39.73 E-value: 2.46e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571553410 178 KTPMCLLNELARFNKiqhqYRLTNEQGPAHKKRFTVTLKLGEEEYVAEGPSIKKAQHSAATEALTK 243
Cdd:cd19911    1 KNPVMELNEKRRGLK----YELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEK 62

DSRM_ILF3_rpt1

cd19910

first double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and ...

180-241

3.14e-04

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

Pssm-ID: 380739 Cd Length: 73 Bit Score: 39.74 E-value: 3.14e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 571553410 180 PMCLLNELARFNKIQH--QYRLTNEQGPAHKKRFTVTLKLGEEEYVAEGPSIKKAQHSAATEAL 241
Cdd:cd19910    2 PPQAMNALMRLNQLKPglQYKLISQTGPVHAPVFTMSVEVDGKTFEASGPSKKTAKLHVAVKVL 65

DSRM_TARBP2_rpt1

cd19890

first double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar ...

178-242

3.67e-04

Pssm-ID: 380719 Cd Length: 72 Bit Score: 39.73 E-value: 3.67e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 571553410 178 KTPMCLLNELARFNKIQHQYRLTNEQGPAHKKRFTVTLKLGEEEYVAEGPSIKKAQHSAATEALT 242
Cdd:cd19890    3 KTPISLLQEYGTRIGKTPVYDLLKAEGQAHQPNFTFRVTVGDISCTGQGPSKKAAKHKAAEVALK 67

DSRM_TARBP2_rpt2

cd10844

second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and ...

196-243

4.98e-04

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: 38.93 E-value: 4.98e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 571553410 196 QYRLTNEQGPAHKKRFTVTLKLGEEEYVAEGPSIKKAQHSAATEALTK 243
Cdd:cd10844   19 EYTVTQESGPAHRKEFTMTCRVERFIEIGSGTSKKLAKRNAAAKMLLR 66

DSRM_SON-like

cd19870

double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...

178-241

5.23e-04

Pssm-ID: 380699 Cd Length: 75 Bit Score: 39.19 E-value: 5.23e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 571553410 178 KTPMCLLNELARFNK-IQHQYRLTNEQGPAHKKRFTVTLKLGEEEYVAEGPSIKK--AQHSAATEAL 241
Cdd:cd19870    2 KHPVSALMELCNKRKwGPPEFRLVEESGPPHRKHFLFKVVVNGVEYQPSVASGNKkdAKAQAATVAL 68

DSRM_STRBP_rpt2

cd19911

second double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...

398-464

5.69e-04

Pssm-ID: 380740 Cd Length: 64 Bit Score: 38.96 E-value: 5.69e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 571553410 398 KSPVSLVHEKalKRGLpvSFEVVSEIGKPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAAEFMLEEL 464
Cdd:cd19911    1 KNPVMELNEK--RRGL--KYELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEKL 63

DSRM_RED1_rpt2

cd19898

second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar ...

398-469

6.56e-04

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: 38.63 E-value: 6.56e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 571553410 398 KSPVSLVHEkaLKRGLpvSFEVVSEIGKPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAAEFMLEELNRLPP 469
Cdd:cd19898    3 KNPVMILNE--LRPGL--KYEFVSESGESHAKNFVMSVTVDGQTFEGSGRNKKLAKARAAQAALAKLFNLQL 70

DSRM_RED1_rpt1

cd19895

first double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins; ...

180-249

7.21e-04

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: 38.91 E-value: 7.21e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 571553410 180 PMCLLNELARFNKIQH--QYRLTNEQGPAHKKRFTVTLKLGEEEYVAEGPSIKKAQHSAATEALtKTWYQRP 249
Cdd:cd19895    2 PVLPKNALMQLNEIKPglQYKLLSQTGPVHAPVFVMSVEVNGQVFEGSGPTKKKAKLHAAEKAL-RSFVQFP 72

DSRM_ILF3_rpt2

cd19912

second double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and ...

398-464

7.22e-04

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: 38.86 E-value: 7.22e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 571553410 398 KSPVSLVHEKalKRGLpvSFEVVSEIGKPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAAEFMLEEL 464
Cdd:cd19912    7 KNPVMELNEK--RRGL--KYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKAYAALAALEKL 69

DSRM_DRADA

cd19902

double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) ...

178-243

7.39e-04

Pssm-ID: 380731 Cd Length: 71 Bit Score: 38.81 E-value: 7.39e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 571553410 178 KTPMCLLNELARFNKIQHQYRLTNEQGPAHKKRFTVTLKLGEEEY-VAEGPSIKKAQHSAATEALTK 243
Cdd:cd19902    1 KNPVSALMEYAQSRGVTAEIEVLSQSGPPHNPRFKAAVFVGGRRFpSVEASSKKDAKQEAADLALRA 67

DSRM_EIF2AK2

cd20314

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...

181-243

7.54e-04

Pssm-ID: 380746 Cd Length: 68 Bit Score: 38.53 E-value: 7.54e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 571553410 181 MCLLNELARFNKIQHQYRLTNEQGPAHKKRFTVTLKLGEEEY-VAEGPSIKKAQHSAATEALTK 243
Cdd:cd20314    4 VSLLNEYCQKERLTVKYEEEKRSGPTHKPRFFCKYIIDGKEYpEGEGKSKKEAKQAAARLAYEE 67

DSRM_PRKRA-like_rpt1

cd19862

first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...

513-569

1.60e-03

Pssm-ID: 380691 [Multi-domain] Cd Length: 70 Bit Score: 37.62 E-value: 1.60e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 571553410 513 NPVSRLDQIQqAKREKEPVYNLIEEKGAPRRKEFVMEVTMGQHSAQGIGPNKKLAKR 569
Cdd:cd19862    2 TPISVLQELC-AKRGITPKYELISSEGAVHEPTFTFRVTVGDITATGSGTSKKKAKH 57

DSRM_STRBP_RED-like_rpt2

cd19866

second double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...

513-563

2.00e-03

Pssm-ID: 380695 Cd Length: 63 Bit Score: 37.15 E-value: 2.00e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 571553410 513 NPVSRLDQIQQAKRekepvYNLIEEKGAPRRKEFVMEVTMGQHSAQGIGPN 563
Cdd:cd19866    2 NPVMLLNELRPGLK-----YKCLSESGESHAKSFVMSVTVDGQTFEGTGRS 47

DSRM_STRBP-like_rpt2

cd19897

second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family ...

178-243

3.50e-03

Pssm-ID: 380726 Cd Length: 64 Bit Score: 36.57 E-value: 3.50e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 571553410 178 KTPMCLLNELARFNKiqhqYRLTNEQGPAHKKRFTVTLKLGEEEYVAEGPSIKKAQHSAATEALTK 243
Cdd:cd19897    1 KNPVMELNEKRRGLK----YELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKANAALAALEK 62

DSRM_TARBP2_rpt2

cd10844

second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and ...

399-461

5.13e-03

Pssm-ID: 380681 Cd Length: 67 Bit Score: 36.24 E-value: 5.13e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 571553410 399 SPVSLVHEKALKRG--LPvSFEVVSEIGKPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAAEFML 461
Cdd:cd10844    1 NPVGALQELVVQKGwrLP-EYTVTQESGPAHRKEFTMTCRVERFIEIGSGTSKKLAKRNAAAKML 64

DSRM_STAU1_rpt1

cd19879

first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...

398-457

5.26e-03

Pssm-ID: 380708 Cd Length: 66 Bit Score: 36.21 E-value: 5.26e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 571553410 398 KSPVSLVHEKALKRGLPVSFEVVSEIGKPHIRTFRTKCTVGDKVTLGEGPSKKVSKKHAA 457
Cdd:cd19879    3 KTPMCLVNELARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTSIKKAQHAAA 62

DSRM_EIF2AK2_rpt1

cd19903

first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha ...

401-464

5.79e-03

Pssm-ID: 380732 Cd Length: 68 Bit Score: 36.21 E-value: 5.79e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 571553410 401 VSLVHEKALKRGLPVSFEVVSEIGKPHIRTFRTKCTV-GDKVTLGEGPSKKVSKKHAAEFMLEEL 464
Cdd:cd19903    4 MGKLNEYCQKQKVVLDYVEVPTSGPSHDPRFTFQVVIdGKEYPEGEGKSKKEAKQAAAKLALEIL 68

DSRM_STAU1_rpt4