TDRD6_DANRE
ID TDRD6_DANRE Reviewed; 2117 AA.
AC F1R237; F1RE34;
DT 11-DEC-2019, integrated into UniProtKB/Swiss-Prot.
DT 13-NOV-2013, sequence version 2.
DT 03-AUG-2022, entry version 70.
DE RecName: Full=Tudor domain-containing 6 {ECO:0000305};
GN Name=tdrd6 {ECO:0000312|ZFIN:ZDB-GENE-041001-210};
GN Synonyms=tdrd6a {ECO:0000303|PubMed:30086300};
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955 {ECO:0000312|Proteomes:UP000000437};
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [2]
RP FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH BUC, DISRUPTION PHENOTYPE,
RP TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, AND DOMAIN.
RX PubMed=30086300; DOI=10.1016/j.devcel.2018.07.009;
RA Roovers E.F., Kaaij L.J.T., Redl S., Bronkhorst A.W., Wiebrands K.,
RA de Jesus Domingues A.M., Huang H.Y., Han C.T., Riemer S., Dosch R.,
RA Salvenmoser W., Gruen D., Butter F., van Oudenaarden A., Ketting R.F.;
RT "Tdrd6a Regulates the Aggregation of Buc into Functional Subcellular
RT Compartments that Drive Germ Cell Specification.";
RL Dev. Cell 46:285-301(2018).
CC -!- FUNCTION: Tudor domain-containing protein involved in germ cell
CC development, more specifically the formation of chromatoid body (during
CC spermiogenesis), Balbiani body (during oogenesis), germ plasm (upon
CC fertilization), and for proper miRNA expression and spliceosome
CC maturation (By similarity) (PubMed:30086300). Required for Balbiani
CC body and germ plasm formation and mobility through interaction with
CC dimethylated arginines in the prion-like protein Bucky ball (buc)
CC (PubMed:30086300). Coordinates transcript deposition into future
CC primordial germ cells (PubMed:30086300). Interacts with known germ
CC plasm mRNAs such as vasa, dazl, nanos3 and hook2 (PubMed:30086300).
CC {ECO:0000250|UniProtKB:P61407, ECO:0000269|PubMed:30086300}.
CC -!- SUBUNIT: Interacts (via Tudor domain) with buc (when dimethylated on
CC arginine residues); and may be responsible for recruitment of different
CC protein complexes to germ plasm. {ECO:0000269|PubMed:30086300}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:30086300}.
CC Note=Presents in chromatoid body (CB) of spermatids, also named
CC processing bodies (P-bodies) in somatic cells. Detected in the
CC multilobular cytoplasmic CBs (also called intermitochondrial cementin)
CC in pachytene spermatocytes and as a single perinuclear CB in haploid
CC round spermatids (By similarity). Localizes to nuage, the Balbiani body
CC during oogenesis, and in the grem plasm upon fertilization
CC (PubMed:30086300). {ECO:0000250|UniProtKB:P61407,
CC ECO:0000269|PubMed:30086300}.
CC -!- DEVELOPMENTAL STAGE: Expressed in the ovary, where it localizes to
CC nuage and to the Balbiani body (PubMed:30086300). Maternally provided
CC and localized to the germ plasm in 4-cell stage embryos
CC (PubMed:30086300). 24 hours post-fertilization, restricted to
CC primordial germ cells, where it localizes to nuage (a peri-nuclear
CC protein-RNA aggregate that associates closely with mitochondria)
CC (PubMed:30086300). {ECO:0000269|PubMed:30086300}.
CC -!- DOMAIN: The tudor domains recognize and bind to proteins with
CC dimethylated arginine or lysine residues (Probable). Plays an important
CC role in the protein functions through its direct binding to the target
CC proteins (Probable). {ECO:0000305|PubMed:30086300}.
CC -!- DISRUPTION PHENOTYPE: Knockout oocytes exhibit significant defects in
CC germ cell development, leading to reduction in primordial germ cell
CC number in the offspring, irrespective of the genotype of the father
CC (PubMed:30086300). Barely affects piRNA populations (PubMed:30086300).
CC {ECO:0000269|PubMed:30086300}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; BX510920; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; XP_694024.6; XM_688932.8.
DR AlphaFoldDB; F1R237; -.
DR SMR; F1R237; -.
DR STRING; 7955.ENSDARP00000093281; -.
DR PaxDb; F1R237; -.
DR PRIDE; F1R237; -.
DR Ensembl; ENSDART00000102504; ENSDARP00000093281; ENSDARG00000070052.
DR Ensembl; ENSDART00000124497; ENSDARP00000112268; ENSDARG00000070052.
DR GeneID; 565665; -.
DR KEGG; dre:565665; -.
DR CTD; 221400; -.
DR ZFIN; ZDB-GENE-041001-210; tdrd6.
DR eggNOG; KOG2039; Eukaryota.
DR GeneTree; ENSGT00940000159049; -.
DR HOGENOM; CLU_001126_1_0_1; -.
DR OMA; VDYGQTK; -.
DR OrthoDB; 496838at2759; -.
DR PRO; PR:F1R237; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 20.
DR Bgee; ENSDARG00000070052; Expressed in testis and 21 other tissues.
DR ExpressionAtlas; F1R237; baseline.
DR GO; GO:0033391; C:chromatoid body; IDA:UniProtKB.
DR GO; GO:0060293; C:germ plasm; IMP:ZFIN.
DR GO; GO:0032019; C:mitochondrial cloud; IMP:ZFIN.
DR GO; GO:0043186; C:P granule; IDA:UniProtKB.
DR GO; GO:0007281; P:germ cell development; IDA:UniProtKB.
DR GO; GO:0070925; P:organelle assembly; IMP:ZFIN.
DR GO; GO:1903863; P:P granule assembly; IDA:UniProtKB.
DR GO; GO:0030719; P:P granule organization; IBA:GO_Central.
DR GO; GO:0034587; P:piRNA metabolic process; IBA:GO_Central.
DR GO; GO:1905879; P:regulation of oogenesis; IDA:UniProtKB.
DR GO; GO:0007283; P:spermatogenesis; IDA:UniProtKB.
DR CDD; cd04508; TUDOR; 7.
DR Gene3D; 2.40.50.90; -; 7.
DR InterPro; IPR035437; SNase_OB-fold_sf.
DR InterPro; IPR002999; Tudor.
DR Pfam; PF00567; TUDOR; 7.
DR SMART; SM00333; TUDOR; 7.
DR PROSITE; PS50304; TUDOR; 6.
PE 1: Evidence at protein level;
KW Cytoplasm; Differentiation; Oogenesis; Reference proteome; Spermatogenesis.
FT CHAIN 1..2117
FT /note="Tudor domain-containing 6"
FT /id="PRO_0000448683"
FT DOMAIN 62..118
FT /note="Tudor 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00211"
FT DOMAIN 291..350
FT /note="Tudor 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00211"
FT DOMAIN 527..584
FT /note="Tudor 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00211"
FT DOMAIN 757..816
FT /note="Tudor 4"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00211"
FT DOMAIN 974..1030
FT /note="Tudor 5"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00211"
FT DOMAIN 1282..1340
FT /note="Tudor 6"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00211"
FT DOMAIN 1485..1543
FT /note="Tudor 7"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00211"
FT REGION 1125..1216
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1131..1155
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1156..1205
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 2117 AA; 236512 MW; 44DC08FDD896AB57 CRC64;
MCSIPGLPSK GSNVPVLITR VNLNPSCVLV EFWGNFDEDR KFAYQQLKKE IQYPRECFSE
SDGNPGDLCL VQVYETWYRA RIVSRDSDEY SVFLIDEGRT LRAAVNTLAW GKSDFFYLPP
EVEFCILANA LPLSPENNWS SMALEFMKTF CGRRVNATVQ DVLVAHRTFL LDIPCLSRQM
FEMGFAKKLY SDQFMEFVVR SLQASTGTSD LKRISSIRTK PVEIIEQKEK QQAYMFPELQ
TDTVETVVIT EVTSPFRIFC QLKVFSQELK KLTEQITQYY EGRVGSYFAR AENLGSPCAS
RGSDGKWYRS VLQQVMSANN VVEVLHVDYG KKQFVQVENV KPLASEFFRM PVVTYVCSLH
GIVDKGVGWT ASQIDYLKSL LLNRTVIAKF QYQSLSEGVH YVTLYGEENT NINKLFELKP
KCSLDSDMTL ADFAVQKSPS SQKSKISRTT ESTHINETYS DLKVNKPVFF TETLTPNSTH
MAVVQHVDSP GKFWIQTQRY ADEFDLLMNG LGNLYSDPTS TESLIRKPVV GLICAAKAQD
GVFYRAAVYK VIDKTAEVYF LDYGNTEVVD SFNLRQLPLR FQQLPAVAVK CSLHGVKPRL
KLWEERATLF FSKLVRDRII DLHVQDKQQD THIVQLVDPS LDGEKDVSKL LCNAGFAVSE
KSIVDYSATR SCGLKTTHAS GVFLTGTQPQ TPCSSSVVMD SASAFKEYLF PIGSSLEVTV
SYIENPNDFW CQKARNAACL EVLMQDIQRF YSHSEFEPLL EAACVARHPE TGIWYRALVI
QKHQTPHVDV LFIDYGQTKK VAIEDLRKIT PAFLKMKGQA FRCSLYNLIH PVLHSSSDWS
TEATLEFQEF VDAAASMNVP LKCTIFAVMY DSQKVVFNVV DLETPFQSIC NLLVQRRLAD
RAPSKRSPLP PFRLDTYYYS THGVKTGCDE KVSITCVKGV NQFFCHLARN SDEVEKLAEK
VNFLCHQLEA TKCPQTFGTV CFAKYTDGLW YRGQIKSTKP SVVINFVDYG DTLEVDKSDL
LPVPIEAGDI MSVPVQAIEC GLSDMPEELP CEVDNWFRKF ADSHCFTALI VAKEPAGKLI
LELYDGKTQV NALIKQKFHN EIHKNDASTF KIYGLKSRAA ESVEASACKK ESSTGPKRDA
IDQVPKSRES HAIQRSNDVA SKQPQSRWGF STNGRPEPTR DSGTINNCQK QPELRTSQGN
LRHPCTSSKP EVVKPKPQAL LKESALPIKS IKPGLEAEVF ISHCNSPCSF FVQFATDEDD
IYSLVEKLNA DQSRCRNIDS SDIHEGDLVC AMFPDDSSWY RAVVRKNTNE KIDVEFVDFG
NTAVISSKNV CHLGQSFASF PRYSIHCSVH KLNVDSKDQE LAPNFKQVLE QNIEKVICTF
VKMSGTMWEV RLDVNGVVLG SVCKDHVKPE IAIPDLKDAA SEIKVCTYYK NPDISIGQVI
TGYTSYIKGP QLFWCQYVAM DKLQEISDML QNIGNASETT LREDCMPVGS ACIALFTEDN
LWYRAKVTSK DLDTLSITFV DYGNESKVKI GDVKALPPKL SDVPPHAFDC QLEGFDVSEG
FWDETADDAF YELVHDKPLN ITIEKMGNSE MPHIVKLDCD GVDINTTMKS HWKTRNPETP
PAELFNGAEM ASDDDYVASK VNIDSVVTFD TDTDPADNET CTSALEMELS EQENLLSSTG
VENEAQIDPL KMATENVTLP ITESTVLSET HKKLETITED EPVLGFTGLS DTNQHAVSKE
TDVGLPQHSE GASSVTIDSF LMNNTDSQLC IVEEPEAPSY EIIQSNLGCL RRATEKKPVG
SECVIWSQVR RSWCTARVLK VSEEATLVLL EKYDSEVVVD PINIFEIMPE KPLQIACIEA
AIANDDATKE TDATLENSAS KLYQTEVSDA NGIAVALESE DLNGKEETFI DQMAPNDELA
GQPQEEESVS CSAFLEDSKA KHMLVEGAQV HDLVQGLCPD DVESKDPQDD LNTSFEEQND
GAKMSTAVDL LLDFLDTAPR DKVQDVSETD ALLEEFNIHV TEDLIVLTSD DGAESDTASD
GTLHGDAVAM EVGPDTEESS CFQERSNASD CTSAEDSQVT HLTLKVEDAS DDVIFVGVLQ
ESQAVVHEPE SEKEKRD
