ID   NANOG_CHICK             Reviewed;         309 AA.
AC   A7Y7W3; R4GLF7;
DT   16-SEP-2015, integrated into UniProtKB/Swiss-Prot.
DT   16-SEP-2015, sequence version 2.
DT   03-AUG-2022, entry version 82.
DE   RecName: Full=Homeobox protein NANOG;
DE   AltName: Full=Homeobox transcription factor Nanog;
DE            Short=cNanog;
GN   Name=NANOG;
OS   Gallus gallus (Chicken).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
OC   Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes; Phasianidae;
OC   Phasianinae; Gallus.
OX   NCBI_TaxID=9031 {ECO:0000312|EMBL:ABK27429.1};
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, DEVELOPMENTAL STAGE, AND INDUCTION.
RX   PubMed=17827181; DOI=10.1242/dev.006569;
RA   Lavial F., Acloque H., Bertocchini F., MacLeod D.J., Boast S.,
RA   Bachelard E., Montillet G., Thenot S., Sang H.M., Stern C.D., Samarut J.,
RA   Pain B.;
RT   "The Oct4 homologue PouV and Nanog regulate pluripotency in chicken
RT   embryonic stem cells.";
RL   Development 134:3549-3563(2007).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Red jungle fowl;
RX   PubMed=15592404; DOI=10.1038/nature03154;
RA   Hillier L.W., Miller W., Birney E., Warren W., Hardison R.C., Ponting C.P.,
RA   Bork P., Burt D.W., Groenen M.A.M., Delany M.E., Dodgson J.B.,
RA   Chinwalla A.T., Cliften P.F., Clifton S.W., Delehaunty K.D., Fronick C.,
RA   Fulton R.S., Graves T.A., Kremitzki C., Layman D., Magrini V.,
RA   McPherson J.D., Miner T.L., Minx P., Nash W.E., Nhan M.N., Nelson J.O.,
RA   Oddy L.G., Pohl C.S., Randall-Maher J., Smith S.M., Wallis J.W.,
RA   Yang S.-P., Romanov M.N., Rondelli C.M., Paton B., Smith J., Morrice D.,
RA   Daniels L., Tempest H.G., Robertson L., Masabanda J.S., Griffin D.K.,
RA   Vignal A., Fillon V., Jacobbson L., Kerje S., Andersson L.,
RA   Crooijmans R.P., Aerts J., van der Poel J.J., Ellegren H., Caldwell R.B.,
RA   Hubbard S.J., Grafham D.V., Kierzek A.M., McLaren S.R., Overton I.M.,
RA   Arakawa H., Beattie K.J., Bezzubov Y., Boardman P.E., Bonfield J.K.,
RA   Croning M.D.R., Davies R.M., Francis M.D., Humphray S.J., Scott C.E.,
RA   Taylor R.G., Tickle C., Brown W.R.A., Rogers J., Buerstedde J.-M.,
RA   Wilson S.A., Stubbs L., Ovcharenko I., Gordon L., Lucas S., Miller M.M.,
RA   Inoko H., Shiina T., Kaufman J., Salomonsen J., Skjoedt K., Wong G.K.-S.,
RA   Wang J., Liu B., Wang J., Yu J., Yang H., Nefedov M., Koriabine M.,
RA   Dejong P.J., Goodstadt L., Webber C., Dickens N.J., Letunic I., Suyama M.,
RA   Torrents D., von Mering C., Zdobnov E.M., Makova K., Nekrutenko A.,
RA   Elnitski L., Eswara P., King D.C., Yang S.-P., Tyekucheva S.,
RA   Radakrishnan A., Harris R.S., Chiaromonte F., Taylor J., He J.,
RA   Rijnkels M., Griffiths-Jones S., Ureta-Vidal A., Hoffman M.M., Severin J.,
RA   Searle S.M.J., Law A.S., Speed D., Waddington D., Cheng Z., Tuzun E.,
RA   Eichler E., Bao Z., Flicek P., Shteynberg D.D., Brent M.R., Bye J.M.,
RA   Huckle E.J., Chatterji S., Dewey C., Pachter L., Kouranov A.,
RA   Mourelatos Z., Hatzigeorgiou A.G., Paterson A.H., Ivarie R., Brandstrom M.,
RA   Axelsson E., Backstrom N., Berlin S., Webster M.T., Pourquie O.,
RA   Reymond A., Ucla C., Antonarakis S.E., Long M., Emerson J.J., Betran E.,
RA   Dupanloup I., Kaessmann H., Hinrichs A.S., Bejerano G., Furey T.S.,
RA   Harte R.A., Raney B., Siepel A., Kent W.J., Haussler D., Eyras E.,
RA   Castelo R., Abril J.F., Castellano S., Camara F., Parra G., Guigo R.,
RA   Bourque G., Tesler G., Pevzner P.A., Smit A., Fulton L.A., Mardis E.R.,
RA   Wilson R.K.;
RT   "Sequence and comparative analysis of the chicken genome provide unique
RT   perspectives on vertebrate evolution.";
RL   Nature 432:695-716(2004).
RN   [3]
RP   SUBCELLULAR LOCATION, AND DEVELOPMENTAL STAGE.
RX   PubMed=25846318; DOI=10.1111/dgd.12205;
RA   Nakanoh S., Fuse N., Takahashi Y., Agata K.;
RT   "Verification of chicken Nanog as an epiblast marker and identification of
RT   chicken PouV as Pou5f3 by newly raised antibodies.";
RL   Dev. Growth Differ. 57:251-263(2015).
CC   -!- FUNCTION: Transcription factor required for the maintenance of
CC       pluripotency and self-renewal of embryonic stem cells.
CC       {ECO:0000250|UniProtKB:Q9H9S0, ECO:0000269|PubMed:17827181}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:25846318}.
CC   -!- DEVELOPMENTAL STAGE: During embryonic development, expressed
CC       preferentially in epiblastic cells and germ cells. In pre-streak
CC       embryos, detected in the whole epiblast, but not in the forming
CC       hypoblast (stages XI through XIII) (at protein level). As the primitive
CC       streak starts to form, disappears from the primitive streak epiblast,
CC       but still expressed throughout the area pellucida epiblast (stage XIV
CC       -> 3+). At the end of gastrulation (stage 4+), quickly decreases in the
CC       epiblast and persists in a crescent anterior to the emerging head
CC       process (stages 4+ through 6). At stage 5, strongly expressed in some
CC       of the cells in the germinal crescent, probably corresponding
CC       primordial germ cells. At stage 7 (neurula stage), undetectable in
CC       differentiated cells (at protein level). As the neural plate forms
CC       (stages 6-8), expression in the epiblast is restricted to the anterior
CC       neural plate. At stage 33, still expressed in germ cells. At stages 42-
CC       43, expressed in gonads, as well as in brain, kidney and heart, but at
CC       much lower levels than in proliferating embryonic stem cells.
CC       {ECO:0000269|PubMed:17827181, ECO:0000269|PubMed:25846318}.
CC   -!- INDUCTION: Strongly down-regulated during embryonic stem cell
CC       differentiation, induced either by retinoic acid treatment, or by cell
CC       adhesion prevention leading to embryoid body formation.
CC       {ECO:0000269|PubMed:17827181}.
CC   -!- SIMILARITY: Belongs to the Nanog homeobox family. {ECO:0000305}.
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DR   EMBL; DQ867025; ABK27429.1; -; mRNA.
DR   EMBL; AADN03000707; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   RefSeq; NP_001139614.1; NM_001146142.1.
DR   AlphaFoldDB; A7Y7W3; -.
DR   SMR; A7Y7W3; -.
DR   STRING; 9031.ENSGALP00000043037; -.
DR   GeneID; 100272166; -.
DR   KEGG; gga:100272166; -.
DR   CTD; 79923; -.
DR   VEuPathDB; HostDB:geneid_100272166; -.
DR   eggNOG; KOG0491; Eukaryota.
DR   OrthoDB; 1141558at2759; -.
DR   PRO; PR:A7Y7W3; -.
DR   Proteomes; UP000000539; Unplaced.
DR   GO; GO:0005634; C:nucleus; IDA:AgBase.
DR   GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IBA:GO_Central.
DR   GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; IBA:GO_Central.
DR   GO; GO:0000976; F:transcription cis-regulatory region binding; ISS:UniProtKB.
DR   GO; GO:1902459; P:positive regulation of stem cell population maintenance; IMP:UniProtKB.
DR   GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR   GO; GO:0019827; P:stem cell population maintenance; ISS:UniProtKB.
DR   CDD; cd00086; homeodomain; 1.
DR   InterPro; IPR009057; Homeobox-like_sf.
DR   InterPro; IPR017970; Homeobox_CS.
DR   InterPro; IPR001356; Homeobox_dom.
DR   Pfam; PF00046; Homeodomain; 1.
DR   SMART; SM00389; HOX; 1.
DR   SUPFAM; SSF46689; SSF46689; 1.
DR   PROSITE; PS00027; HOMEOBOX_1; 1.
DR   PROSITE; PS50071; HOMEOBOX_2; 1.
PE   1: Evidence at protein level;
KW   DNA-binding; Homeobox; Nucleus; Reference proteome; Transcription;
KW   Transcription regulation.
FT   CHAIN           1..309
FT                   /note="Homeobox protein NANOG"
FT                   /id="PRO_0000433627"
FT   DNA_BIND        98..157
FT                   /note="Homeobox"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00108"
FT   REGION          24..104
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        40..80
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        82..98
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   CONFLICT        194
FT                   /note="T -> A (in Ref. 1; ABK27429)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   309 AA;  34310 MW;  4532E7BA928159A6 CRC64;
     MSAHLAMPSY GSVRCGHYYW PSPGSMDSAS AAEAPAADLS LTTEQKTPCH PDASPASSSS
     GTLIQYTPDS ATSPTADHPS HRPTFQKVKD KGESGTRKAK SRTAFSQEQL QTLHQRFQSQ
     KYLSPHQIRE LAAALGLTYK QVKTWFQNQR MKFKRCQKES QWVDKGIYLP QNGFHQAAYL
     DMTPTFHQGF PVVTNRNLQA VTSAHQAYSS GQTYGNGQGL YPFMAVEDEG FFGKGGTSCN
     TQQAMGLLSQ QMNFYHGYST NVDYDSLQAE DTYSFQSTSD SITQFSSSPV RHQYQAPWHT
     LGTQNGYET