TDRD9_RAT
ID TDRD9_RAT Reviewed; 1384 AA.
AC Q3MHU3;
DT 20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT 02-MAR-2010, sequence version 3.
DT 03-AUG-2022, entry version 110.
DE RecName: Full=ATP-dependent RNA helicase TDRD9 {ECO:0000305};
DE EC=3.6.4.13 {ECO:0000250|UniProtKB:Q14BI7};
DE AltName: Full=Tudor domain-containing protein 9 {ECO:0000305};
GN Name=Tdrd9 {ECO:0000312|RGD:1306942};
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway;
RX PubMed=15057822; DOI=10.1038/nature02426;
RA Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J.,
RA Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G.,
RA Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G.,
RA Morgan M., Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G.,
RA Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S.,
RA Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T.,
RA Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D.,
RA Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L.,
RA Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D.,
RA Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M.,
RA Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C.,
RA Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J.,
RA Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H.,
RA Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X.,
RA Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q.,
RA Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P.,
RA Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A.,
RA Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C.,
RA Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J.,
RA Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J.,
RA Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F.,
RA Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A.,
RA Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A.,
RA Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J.,
RA Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E.,
RA Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M.,
RA Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C.,
RA Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L.,
RA Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W.,
RA Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y.,
RA Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V.,
RA Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M.,
RA Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S.,
RA Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B.,
RA Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R.,
RA Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J.,
RA Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D.,
RA Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S.,
RA Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S.,
RA Mockrin S., Collins F.S.;
RT "Genome sequence of the Brown Norway rat yields insights into mammalian
RT evolution.";
RL Nature 428:493-521(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC TISSUE=Thymus;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
CC -!- FUNCTION: ATP-binding RNA helicase which plays a central role during
CC spermatogenesis by repressing transposable elements and preventing
CC their mobilization, which is essential for the germline integrity. Acts
CC via the piRNA metabolic process, which mediates the repression of
CC transposable elements during meiosis by forming complexes composed of
CC piRNAs and Piwi proteins and governs the methylation and subsequent
CC repression of transposons. Acts downstream of piRNA biogenesis:
CC exclusively required for transposon silencing in the nucleus,
CC suggesting that it acts as a nuclear effector in the nucleus together
CC with PIWIL4. {ECO:0000250|UniProtKB:Q14BI7}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;
CC Evidence={ECO:0000250|UniProtKB:Q14BI7};
CC -!- SUBUNIT: Interacts with piRNA-associated proteins PIWIL1 and PIWIL4.
CC {ECO:0000250|UniProtKB:Q14BI7}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q14BI7}. Nucleus
CC {ECO:0000250|UniProtKB:Q14BI7}. Note=Component of the nuage, also named
CC P granule, a germ-cell-specific organelle required to repress
CC transposon activity during meiosis. Specifically localizes to piP-
CC bodies, a subset of the nuage which contains secondary piRNAs. PIWIL2
CC is required for its localization to piP-bodies.
CC {ECO:0000250|UniProtKB:Q14BI7}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q3MHU3-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q3MHU3-2; Sequence=VSP_033556, VSP_033557;
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DEAH subfamily.
CC {ECO:0000305}.
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DR EMBL; AABR03050289; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AABR03048647; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AABR03049552; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AABR03049859; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AABR03050293; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AABR03051941; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC104675; AAI04676.1; -; mRNA.
DR RefSeq; XP_001072421.2; XM_001072421.4. [Q3MHU3-1]
DR RefSeq; XP_008763208.1; XM_008764986.1. [Q3MHU3-1]
DR AlphaFoldDB; Q3MHU3; -.
DR SMR; Q3MHU3; -.
DR STRING; 10116.ENSRNOP00000017118; -.
DR jPOST; Q3MHU3; -.
DR PaxDb; Q3MHU3; -.
DR PRIDE; Q3MHU3; -.
DR Ensembl; ENSRNOT00000086594; ENSRNOP00000073728; ENSRNOG00000053631. [Q3MHU3-1]
DR GeneID; 299343; -.
DR KEGG; rno:299343; -.
DR UCSC; RGD:1306942; rat. [Q3MHU3-1]
DR CTD; 122402; -.
DR RGD; 1306942; Tdrd9.
DR eggNOG; KOG0920; Eukaryota.
DR GeneTree; ENSGT00940000157035; -.
DR HOGENOM; CLU_002601_1_0_1; -.
DR InParanoid; Q3MHU3; -.
DR OMA; DPCRTVY; -.
DR OrthoDB; 278674at2759; -.
DR PhylomeDB; Q3MHU3; -.
DR TreeFam; TF324869; -.
DR PRO; PR:Q3MHU3; -.
DR Proteomes; UP000002494; Chromosome 6.
DR Bgee; ENSRNOG00000053631; Expressed in thymus and 6 other tissues.
DR GO; GO:0005737; C:cytoplasm; ISO:RGD.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0071547; C:piP-body; ISS:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; ISS:UniProtKB.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0003724; F:RNA helicase activity; IEA:UniProtKB-EC.
DR GO; GO:0030154; P:cell differentiation; IEA:UniProtKB-KW.
DR GO; GO:0043046; P:DNA methylation involved in gamete generation; ISS:UniProtKB.
DR GO; GO:0009566; P:fertilization; ISS:UniProtKB.
DR GO; GO:0031047; P:gene silencing by RNA; IEA:UniProtKB-KW.
DR GO; GO:0007141; P:male meiosis I; ISS:UniProtKB.
DR GO; GO:0007140; P:male meiotic nuclear division; ISS:UniProtKB.
DR GO; GO:0010529; P:negative regulation of transposition; ISS:UniProtKB.
DR GO; GO:0034587; P:piRNA metabolic process; ISS:UniProtKB.
DR GO; GO:0007283; P:spermatogenesis; ISS:UniProtKB.
DR CDD; cd04508; TUDOR; 1.
DR Gene3D; 2.40.50.90; -; 1.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR007502; Helicase-assoc_dom.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR035437; SNase_OB-fold_sf.
DR InterPro; IPR002999; Tudor.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF04408; HA2; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF00567; TUDOR; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00847; HA2; 1.
DR SMART; SM00490; HELICc; 1.
DR SMART; SM00333; TUDOR; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS50304; TUDOR; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; ATP-binding; Cytoplasm; Developmental protein;
KW Differentiation; Helicase; Hydrolase; Meiosis; Nucleotide-binding; Nucleus;
KW Reference proteome; RNA-mediated gene silencing; Spermatogenesis.
FT CHAIN 1..1384
FT /note="ATP-dependent RNA helicase TDRD9"
FT /id="PRO_0000333815"
FT DOMAIN 144..310
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 379..546
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT DOMAIN 946..1006
FT /note="Tudor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00211"
FT REGION 35..60
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 256..259
FT /note="DEAH box"
FT /evidence="ECO:0000250|UniProtKB:Q14BI7"
FT BINDING 157..164
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT VAR_SEQ 1..837
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_033556"
FT VAR_SEQ 908
FT /note="E -> EVALCAHTLLLQ (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_033557"
SQ SEQUENCE 1384 AA; 156156 MW; 2EA55FD2520DFE32 CRC64;
MLRKLTVDQI NDWFTIGKTV TNVELLGLPP AFPAEAPREE VQRSEEVPSE APTAQAQDPV
KATALARPAS AFGRSLSQRS SEVEYINKYR QLEAQELDIY GQDQPPSGPG LRSPLAKISN
VACIPETTYK YPDLPINRCK EEVISLIESN SVVIIHGATG SGKSTQLPQY VLDHYTQRSA
FCNIVVTQPR KIGASSIARW ISKERSWTLG GLVGYQVGLE KTATEDTRLI YMTTGVLLQK
IVSAKSLMEF THVFIDEVHE RTEEMDFLLL VVRKLLRTNS RFVKVILMSA TINCKQFADY
FAVPVQNKMN PAYVFEVEGK PHTIEQYYLN DLGHIYHSGL PPYRLEEPVI TKDVYEVAVS
LIQMFDDLDM KESGNKTWSG AQFVSERSSV LVFLPGLGEI NYMHELLTNM IHKRLQVYPL
HSSVTLEEQN NVFLSPVPGY RKIILSTNIA ESSVTVPDVK YVIDFCLTRT LVCDEDTNYQ
SLRLSWASKT SCDQRKGRAG RVSKGYCYRL IHRDFWDSAI PDHVVPEMLR CPLGSTVLKV
KLLDMGEPRA LLATALSPPS LSDIERTILL LKEVGALAVS GQREDENPHD GELTFLGRVL
AQLPVSQQLG KLIVLGHVFG CLDECLIIAA ALSLKNFFTM PFRQHLDGYR NKVHFSGSSR
SDCLALVEAF RAWQACRQRG ELRHPKDELD WGRLNYIQIK RIREVAELYE ELKNRISQFN
MFVDPRHPVL DQEYPYKQRF ILQVVLAGAF YPNYFTFGQP DEEMAVRELA GRDPKTTVVL
KHIPPYGFLY YKQLQSLFRQ CGQVKSIVFD GAKAFVEFSR NPTERFKTLP AVNLAVKMSQ
LKVSLELSIH AAEEIEGKVQ GGSVSKLRNT RVNVDFQKQT VDPMQVSFNT LDRPRTVADL
LLTVDVTEVV EVGHFWGYRI DERNAELLRQ LTAEINRLEL VPLPIHPHPD LVCLAPFTDY
NKESYFRAQI LYVSGNSAEV FFVDYGNRSH VDLDLLREIP CQLLELPFQA LEFKICKMRP
SAKSLICGEH WSGGANGRFA ALVSGCPLLV KVFSIVHSVL HVDVYRYSGA QDAVNIRDVL
IREGYAELAE ESYESKQSYE VLKGFFAKSV DTMPDGSVSS PMKDDEKHLI QILLESFASN
RLGAPNCKAV LHGPFNPYEL KCHSLTRISK FRCVWIEKES INSVVISDSP ADLHQRMLVA
ASLSVNETGS TMLLRETSLM PHIPGLPALL SMLFAPVMEL RVDREGKCYT GVLCGLGWNS
TTEAPILPEH DIELAFDVCF NVEDIVEINI LRAAINKLAC DGPHGPKYLG PERIAQLQEN
ARQKLLGLFC RLKPREKITP QWHEKPYEWN QVDPRLVIEQ AEREGGPGKS TCLYQLHTPV
VLSP
