P3F3A_DANRE
ID P3F3A_DANRE Reviewed; 438 AA.
AC P56224; B0S7I5; B0S7I6; B0S7I7; B5DDP9; O57514; Q6IS23; Q6NZU9; Q6PE22;
AC Q7ZU57; Q90433; Q90436;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 24-NOV-2009, sequence version 2.
DT 03-AUG-2022, entry version 156.
DE RecName: Full=POU domain, class 3, transcription factor 3-A;
DE AltName: Full=Brain-specific homeobox/POU domain protein 1.1;
DE Short=Brain-1.1;
DE Short=zfBrn-1.1;
DE AltName: Full=Class III POU domain protein taichi;
DE AltName: Full=POU domain protein 12;
DE Short=ZP-12;
GN Name=pou3f3a; Synonyms=brn-1.1, brn1.1, pou12, tai-ji, zp12, zp12pou;
GN ORFNames=si:dkeyp-118h3.2;
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;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), TISSUE SPECIFICITY, AND
RP DEVELOPMENTAL STAGE.
RC TISSUE=Embryo;
RX PubMed=9016656; DOI=10.1093/nar/24.24.4874;
RA Spaniol P., Bornmann C., Hauptmann G., Gerster T.;
RT "Class III POU genes of zebrafish are predominantly expressed in the
RT central nervous system.";
RL Nucleic Acids Res. 24:4874-4881(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), AND DEVELOPMENTAL STAGE.
RC TISSUE=Embryo;
RX PubMed=9582430; DOI=10.1016/s0167-4781(98)00032-3;
RA Lim J.H., He J., Korzh V., Gong Z.;
RT "A new splicing variant of a type III POU gene from zebrafish encodes a POU
RT protein with a distinct C-terminal.";
RL Biochim. Biophys. Acta 1397:253-256(1998).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 2), TISSUE SPECIFICITY, AND
RP DEVELOPMENTAL STAGE.
RX PubMed=9507055; DOI=10.1016/s0925-4773(97)00199-8;
RA Huang S., Sato S.;
RT "Progenitor cells in the adult zebrafish nervous system express a Brn-1-
RT related POU gene, tai-ji.";
RL Mech. Dev. 71:23-35(1998).
RN [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 3 AND 4).
RC STRAIN=AB; TISSUE=Embryo;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (APR-2008) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 5-438 (ISOFORM 3).
RC TISSUE=Embryo;
RA Shah D., Sampath K., Stuart G.W.;
RT "Brn-1.1: an alternatively spliced class III POU domain gene expressed in
RT the nervous system of the zebrafish.";
RL Submitted (MAR-1999) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 265-378, TISSUE SPECIFICITY, AND
RP DEVELOPMENTAL STAGE.
RC TISSUE=Embryo;
RX PubMed=8605028; DOI=10.1006/bbrc.1996.0274;
RA Sampath K., Stuart G.W.;
RT "Developmental expression of class III and IV POU domain genes in the
RT zebrafish.";
RL Biochem. Biophys. Res. Commun. 219:565-571(1996).
CC -!- FUNCTION: Transcription factor that may play important roles in
CC patterning the embryonic brain.
CC -!- SUBCELLULAR LOCATION: Nucleus.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=4;
CC Name=1; Synonyms=A;
CC IsoId=P56224-1; Sequence=Displayed;
CC Name=2; Synonyms=U;
CC IsoId=P56224-2; Sequence=VSP_002340;
CC Name=3; Synonyms=B;
CC IsoId=P56224-3; Sequence=VSP_002339;
CC Name=4;
CC IsoId=P56224-4; Sequence=VSP_012010;
CC -!- TISSUE SPECIFICITY: Predominantly expressed in the embryonic and adult
CC central nervous system. In adults, isoform 2 is expressed in the brain,
CC ovary, basal cells of the skin and muscle satellite cells.
CC {ECO:0000269|PubMed:8605028, ECO:0000269|PubMed:9016656,
CC ECO:0000269|PubMed:9507055}.
CC -!- DEVELOPMENTAL STAGE: Isoform 2 is expressed both maternally and
CC zygotically, and is the major isoform in adults. Isoform 1 and isoform
CC 3 are expressed zygotically. Maximal expression is after 1 to 2 days of
CC development and becomes down-regulated as cells differentiate.
CC {ECO:0000269|PubMed:8605028, ECO:0000269|PubMed:9016656,
CC ECO:0000269|PubMed:9507055, ECO:0000269|PubMed:9582430}.
CC -!- SIMILARITY: Belongs to the POU transcription factor family. Class-3
CC subfamily. {ECO:0000305}.
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DR EMBL; Y07906; CAA69212.1; -; mRNA.
DR EMBL; Y07906; CAA69213.1; -; mRNA.
DR EMBL; AF039952; AAC41300.1; -; mRNA.
DR EMBL; U77736; AAB84079.1; -; Genomic_DNA.
DR EMBL; BX842683; CAQ14274.1; -; Genomic_DNA.
DR EMBL; BX842683; CAQ14275.1; -; Genomic_DNA.
DR EMBL; BX842683; CAQ14276.1; -; Genomic_DNA.
DR EMBL; BC044354; AAH44354.1; -; mRNA.
DR EMBL; BC058318; AAH58318.1; -; mRNA.
DR EMBL; BC065961; AAH65961.1; -; mRNA.
DR EMBL; BC070001; AAH70001.1; -; mRNA.
DR EMBL; BC165334; AAI65334.1; -; mRNA.
DR EMBL; U43898; AAB92590.2; -; mRNA.
DR EMBL; U43656; AAB00433.1; -; Genomic_DNA.
DR RefSeq; NP_001299616.1; NM_001312687.1. [P56224-1]
DR RefSeq; NP_571225.2; NM_131150.2. [P56224-3]
DR AlphaFoldDB; P56224; -.
DR SMR; P56224; -.
DR STRING; 7955.ENSDARP00000061592; -.
DR PaxDb; P56224; -.
DR Ensembl; ENSDART00000061593; ENSDARP00000061592; ENSDARG00000042032. [P56224-3]
DR Ensembl; ENSDART00000113914; ENSDARP00000103222; ENSDARG00000042032. [P56224-1]
DR Ensembl; ENSDART00000133178; ENSDARP00000117406; ENSDARG00000042032. [P56224-2]
DR GeneID; 30386; -.
DR KEGG; dre:30386; -.
DR CTD; 30386; -.
DR ZFIN; ZDB-GENE-980526-220; pou3f3a.
DR eggNOG; KOG3802; Eukaryota.
DR GeneTree; ENSGT00940000164385; -.
DR HOGENOM; CLU_013065_1_2_1; -.
DR InParanoid; P56224; -.
DR OMA; IGAHQSH; -.
DR OrthoDB; 752252at2759; -.
DR PhylomeDB; P56224; -.
DR TreeFam; TF316413; -.
DR PRO; PR:P56224; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 9.
DR Bgee; ENSDARG00000042032; Expressed in hypothalamus and 35 other tissues.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
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:0007420; P:brain development; IEA:InterPro.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR CDD; cd00086; homeodomain; 1.
DR Gene3D; 1.10.260.40; -; 1.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR017970; Homeobox_CS.
DR InterPro; IPR001356; Homeobox_dom.
DR InterPro; IPR010982; Lambda_DNA-bd_dom_sf.
DR InterPro; IPR013847; POU.
DR InterPro; IPR000327; POU_dom.
DR InterPro; IPR016362; TF_POU_3.
DR Pfam; PF00046; Homeodomain; 1.
DR Pfam; PF00157; Pou; 1.
DR PIRSF; PIRSF002629; Transcription_factor_POU; 1.
DR PRINTS; PR00028; POUDOMAIN.
DR SMART; SM00389; HOX; 1.
DR SMART; SM00352; POU; 1.
DR SUPFAM; SSF46689; SSF46689; 1.
DR SUPFAM; SSF47413; SSF47413; 1.
DR PROSITE; PS00027; HOMEOBOX_1; 1.
DR PROSITE; PS50071; HOMEOBOX_2; 1.
DR PROSITE; PS00035; POU_1; 1.
DR PROSITE; PS00465; POU_2; 1.
DR PROSITE; PS51179; POU_3; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Developmental protein; DNA-binding; Homeobox;
KW Nucleus; Reference proteome; Transcription; Transcription regulation.
FT CHAIN 1..438
FT /note="POU domain, class 3, transcription factor 3-A"
FT /id="PRO_0000100731"
FT DOMAIN 242..316
FT /note="POU-specific"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00530"
FT DNA_BIND 334..393
FT /note="Homeobox"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00108"
FT REGION 22..43
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 102..172
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 186..248
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 107..122
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 144..172
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 211..232
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 233..248
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 402..438
FT /note="EDVYTHAGNVSADTPPPSMDCKREFCGRLLKRCKFER -> KDMDQCRQTLN
FT IKQWKNLPQDTYQFYAQELYYSF (in isoform 4)"
FT /evidence="ECO:0000303|Ref.5"
FT /id="VSP_012010"
FT VAR_SEQ 411..438
FT /note="VSADTPPPSMDCKREFCGRLLKRCKFER -> GSFVVDYLKGASLKDEPDSN
FT HNVTTASSYGQEILVH (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:9582430, ECO:0000303|Ref.5,
FT ECO:0000303|Ref.6"
FT /id="VSP_002339"
FT VAR_SEQ 425..438
FT /note="EFCGRLLKRCKFER -> MFTET (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:9016656"
FT /id="VSP_002340"
FT CONFLICT 26
FT /note="S -> F (in Ref. 5; AAH65961)"
FT /evidence="ECO:0000305"
FT CONFLICT 222
FT /note="Missing (in Ref. 1; CAA69212/CAA69213, 2; AAC41300,
FT 3; AAB84079, 5; AAH44354/AAH70001/AAI65334 and 6;
FT AAB92590)"
FT /evidence="ECO:0000305"
FT CONFLICT 301
FT /note="M -> I (in Ref. 5; AAH70001)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 438 AA; 47216 MW; DFC0E59F41D3E0CA CRC64;
MATAASNPYL ASSTILSSAS LVHSESGGGG MQPGSGAVTS VSGGYRGDPT VKMVQSDFMQ
GAMAASNGGH MLSHAHQWVT SLPHAAAAAA AAAAAAAAEA GSPWSSSPVG MAGSPQQQDV
KSSSNREDLH SGTALHHRPS HLGAHQSHQS AWGGTTASHI STITGGQQQS QQSLIYSQPG
GFTVNGMLNP PGSLVHPGLM RGESPEMDHH HHHHHHQQQH PHHHHHHQHH AGVNSHDSHS
DEDTPTSDDL EQFAKQFKQR RIKLGFTQAD VGLALGTLYG NVFSQTTICR FEALQLSFKN
MCKLKPLLNK WLEEADSTTG SPTSIDKIAA QGRKRKKRTS IEVSVKGALE SHFLKCPKPS
AQEITSLADN LQLEKEVVRV WFCNRRQKEK RMTPPGVPQT PEDVYTHAGN VSADTPPPSM
DCKREFCGRL LKRCKFER
