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P56224

- P3F3A_DANRE

UniProt

P56224 - P3F3A_DANRE

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Protein

POU domain, class 3, transcription factor 3-A

Gene

pou3f3a

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at transcript leveli

Functioni

Transcription factor that may play important roles in patterning the embryonic brain.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi334 – 39360HomeoboxPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. sequence-specific DNA binding Source: InterPro
  2. sequence-specific DNA binding transcription factor activity Source: InterPro

GO - Biological processi

  1. multicellular organismal development Source: UniProtKB-KW
  2. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
POU domain, class 3, transcription factor 3-A
Alternative name(s):
Brain-specific homeobox/POU domain protein 1.1
Short name:
Brain-1.1
Short name:
zfBrn-1.1
Class III POU domain protein taichi
POU domain protein 12
Short name:
ZP-12
Gene namesi
Name:pou3f3a
Synonyms:brn-1.1, brn1.1, pou12, tai-ji, zp12, zp12pou
ORF Names:si:dkeyp-118h3.2
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
ProteomesiUP000000437: Chromosome 9

Organism-specific databases

ZFINiZDB-GENE-980526-220. pou3f3a.

Subcellular locationi

GO - Cellular componenti

  1. nucleus Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 438438POU domain, class 3, transcription factor 3-APRO_0000100731Add
BLAST

Proteomic databases

PRIDEiP56224.

Expressioni

Tissue specificityi

Predominantly expressed in the embryonic and adult central nervous system. In adults, isoform 2 is expressed in the brain, ovary, basal cells of the skin and muscle satellite cells.3 Publications

Developmental stagei

Isoform 2 is expressed both maternally and zygotically, and is the major isoform in adults. Isoform 1 and isoform 3 are expressed zygotically. Maximal expression is after 1 to 2 days of development and becomes down-regulated as cells differentiate.4 Publications

Gene expression databases

BgeeiP56224.

Structurei

3D structure databases

ProteinModelPortaliP56224.
SMRiP56224. Positions 248-394.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini242 – 31675POU-specificPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi85 – 10016Ala-richAdd
BLAST
Compositional biasi209 – 23931His-richAdd
BLAST

Sequence similaritiesi

Contains 1 homeobox DNA-binding domain.PROSITE-ProRule annotation
Contains 1 POU-specific domain.PROSITE-ProRule annotation

Keywords - Domaini

Homeobox

Phylogenomic databases

GeneTreeiENSGT00760000118935.
HOVERGENiHBG053120.
InParanoidiP56224.
OrthoDBiEOG7DJSMG.
PhylomeDBiP56224.
TreeFamiTF316413.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
1.10.260.40. 1 hit.
InterProiIPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR010982. Lambda_DNA-bd_dom.
IPR013847. POU.
IPR000327. POU_specific.
IPR016362. Transcription_factor_POU.
[Graphical view]
PfamiPF00046. Homeobox. 1 hit.
PF00157. Pou. 1 hit.
[Graphical view]
PIRSFiPIRSF002629. Transcription_factor_POU. 1 hit.
PRINTSiPR00028. POUDOMAIN.
SMARTiSM00389. HOX. 1 hit.
SM00352. POU. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
SSF47413. SSF47413. 1 hit.
PROSITEiPS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
PS00035. POU_1. 1 hit.
PS00465. POU_2. 1 hit.
PS51179. POU_3. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: P56224-1) [UniParc]FASTAAdd to Basket

Also known as: A

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MATAASNPYL ASSTILSSAS LVHSESGGGG MQPGSGAVTS VSGGYRGDPT
60 70 80 90 100
VKMVQSDFMQ GAMAASNGGH MLSHAHQWVT SLPHAAAAAA AAAAAAAAEA
110 120 130 140 150
GSPWSSSPVG MAGSPQQQDV KSSSNREDLH SGTALHHRPS HLGAHQSHQS
160 170 180 190 200
AWGGTTASHI STITGGQQQS QQSLIYSQPG GFTVNGMLNP PGSLVHPGLM
210 220 230 240 250
RGESPEMDHH HHHHHHQQQH PHHHHHHQHH AGVNSHDSHS DEDTPTSDDL
260 270 280 290 300
EQFAKQFKQR RIKLGFTQAD VGLALGTLYG NVFSQTTICR FEALQLSFKN
310 320 330 340 350
MCKLKPLLNK WLEEADSTTG SPTSIDKIAA QGRKRKKRTS IEVSVKGALE
360 370 380 390 400
SHFLKCPKPS AQEITSLADN LQLEKEVVRV WFCNRRQKEK RMTPPGVPQT
410 420 430
PEDVYTHAGN VSADTPPPSM DCKREFCGRL LKRCKFER
Length:438
Mass (Da):47,216
Last modified:November 24, 2009 - v2
Checksum:iDFC0E59F41D3E0CA
GO
Isoform 2 (identifier: P56224-2) [UniParc]FASTAAdd to Basket

Also known as: U

The sequence of this isoform differs from the canonical sequence as follows:
     425-438: EFCGRLLKRCKFER → MFTET

Show »
Length:429
Mass (Da):46,058
Checksum:iD755C0B19A342CC7
GO
Isoform 3 (identifier: P56224-3) [UniParc]FASTAAdd to Basket

Also known as: B

The sequence of this isoform differs from the canonical sequence as follows:
     411-438: VSADTPPPSMDCKREFCGRLLKRCKFER → GSFVVDYLKGASLKDEPDSNHNVTTASSYGQEILVH

Show »
Length:446
Mass (Da):47,824
Checksum:iA192568963882A9D
GO
Isoform 4 (identifier: P56224-4) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     402-438: EDVYTHAGNVSADTPPPSMDCKREFCGRLLKRCKFER → KDMDQCRQTLNIKQWKNLPQDTYQFYAQELYYSF

Note: No experimental confirmation available.

Show »
Length:435
Mass (Da):47,266
Checksum:i63CD45022F05E9B8
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti26 – 261S → F in AAH65961. 1 PublicationCurated
Sequence conflicti222 – 2221Missing in CAA69212. (PubMed:9016656)Curated
Sequence conflicti222 – 2221Missing in CAA69213. (PubMed:9016656)Curated
Sequence conflicti222 – 2221Missing in AAC41300. (PubMed:9582430)Curated
Sequence conflicti222 – 2221Missing in AAB84079. (PubMed:9507055)Curated
Sequence conflicti222 – 2221Missing in AAH44354. 1 PublicationCurated
Sequence conflicti222 – 2221Missing in AAH70001. 1 PublicationCurated
Sequence conflicti222 – 2221Missing in AAI65334. 1 PublicationCurated
Sequence conflicti222 – 2221Missing in AAB92590. 1 PublicationCurated
Sequence conflicti301 – 3011M → I in AAH70001. 1 PublicationCurated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei402 – 43837EDVYT…CKFER → KDMDQCRQTLNIKQWKNLPQ DTYQFYAQELYYSF in isoform 4. 1 PublicationVSP_012010Add
BLAST
Alternative sequencei411 – 43828VSADT…CKFER → GSFVVDYLKGASLKDEPDSN HNVTTASSYGQEILVH in isoform 3. 3 PublicationsVSP_002339Add
BLAST
Alternative sequencei425 – 43814EFCGR…CKFER → MFTET in isoform 2. 1 PublicationVSP_002340Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Y07906 mRNA. Translation: CAA69212.1.
Y07906 mRNA. Translation: CAA69213.1.
AF039952 mRNA. Translation: AAC41300.1.
U77736 Genomic DNA. Translation: AAB84079.1.
BX842683 Genomic DNA. Translation: CAQ14274.1.
BX842683 Genomic DNA. Translation: CAQ14275.1.
BX842683 Genomic DNA. Translation: CAQ14276.1.
BC044354 mRNA. Translation: AAH44354.1.
BC058318 mRNA. Translation: AAH58318.1.
BC065961 mRNA. Translation: AAH65961.1.
BC070001 mRNA. Translation: AAH70001.1.
BC165334 mRNA. Translation: AAI65334.1.
U43898 mRNA. Translation: AAB92590.2.
U43656 Genomic DNA. Translation: AAB00433.1.
RefSeqiNP_571225.1. NM_131150.1.
XP_005167492.1. XM_005167435.1. [P56224-1]
UniGeneiDr.75085.

Genome annotation databases

EnsembliENSDART00000061593; ENSDARP00000061592; ENSDARG00000042032. [P56224-3]
ENSDART00000113914; ENSDARP00000103222; ENSDARG00000042032. [P56224-1]
ENSDART00000133178; ENSDARP00000117406; ENSDARG00000042032. [P56224-2]
GeneIDi30386.
KEGGidre:30386.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Y07906 mRNA. Translation: CAA69212.1 .
Y07906 mRNA. Translation: CAA69213.1 .
AF039952 mRNA. Translation: AAC41300.1 .
U77736 Genomic DNA. Translation: AAB84079.1 .
BX842683 Genomic DNA. Translation: CAQ14274.1 .
BX842683 Genomic DNA. Translation: CAQ14275.1 .
BX842683 Genomic DNA. Translation: CAQ14276.1 .
BC044354 mRNA. Translation: AAH44354.1 .
BC058318 mRNA. Translation: AAH58318.1 .
BC065961 mRNA. Translation: AAH65961.1 .
BC070001 mRNA. Translation: AAH70001.1 .
BC165334 mRNA. Translation: AAI65334.1 .
U43898 mRNA. Translation: AAB92590.2 .
U43656 Genomic DNA. Translation: AAB00433.1 .
RefSeqi NP_571225.1. NM_131150.1.
XP_005167492.1. XM_005167435.1. [P56224-1 ]
UniGenei Dr.75085.

3D structure databases

ProteinModelPortali P56224.
SMRi P56224. Positions 248-394.
ModBasei Search...
MobiDBi Search...

Proteomic databases

PRIDEi P56224.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSDART00000061593 ; ENSDARP00000061592 ; ENSDARG00000042032 . [P56224-3 ]
ENSDART00000113914 ; ENSDARP00000103222 ; ENSDARG00000042032 . [P56224-1 ]
ENSDART00000133178 ; ENSDARP00000117406 ; ENSDARG00000042032 . [P56224-2 ]
GeneIDi 30386.
KEGGi dre:30386.

Organism-specific databases

CTDi 30386.
ZFINi ZDB-GENE-980526-220. pou3f3a.

Phylogenomic databases

GeneTreei ENSGT00760000118935.
HOVERGENi HBG053120.
InParanoidi P56224.
OrthoDBi EOG7DJSMG.
PhylomeDBi P56224.
TreeFami TF316413.

Miscellaneous databases

NextBioi 20806799.

Gene expression databases

Bgeei P56224.

Family and domain databases

Gene3Di 1.10.10.60. 1 hit.
1.10.260.40. 1 hit.
InterProi IPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR010982. Lambda_DNA-bd_dom.
IPR013847. POU.
IPR000327. POU_specific.
IPR016362. Transcription_factor_POU.
[Graphical view ]
Pfami PF00046. Homeobox. 1 hit.
PF00157. Pou. 1 hit.
[Graphical view ]
PIRSFi PIRSF002629. Transcription_factor_POU. 1 hit.
PRINTSi PR00028. POUDOMAIN.
SMARTi SM00389. HOX. 1 hit.
SM00352. POU. 1 hit.
[Graphical view ]
SUPFAMi SSF46689. SSF46689. 1 hit.
SSF47413. SSF47413. 1 hit.
PROSITEi PS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
PS00035. POU_1. 1 hit.
PS00465. POU_2. 1 hit.
PS51179. POU_3. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Class III POU genes of zebrafish are predominantly expressed in the central nervous system."
    Spaniol P., Bornmann C., Hauptmann G., Gerster T.
    Nucleic Acids Res. 24:4874-4881(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
    Tissue: Embryo.
  2. "A new splicing variant of a type III POU gene from zebrafish encodes a POU protein with a distinct C-terminal."
    Lim J.H., He J., Korzh V., Gong Z.
    Biochim. Biophys. Acta 1397:253-256(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), DEVELOPMENTAL STAGE.
    Tissue: Embryo.
  3. "Progenitor cells in the adult zebrafish nervous system express a Brn-1-related POU gene, tai-ji."
    Huang S., Sato S.
    Mech. Dev. 71:23-35(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 2), TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
  4. "The zebrafish reference genome sequence and its relationship to the human genome."
    Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.
    , White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M., Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J., Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G., Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M., Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.
    Nature 496:498-503(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Tuebingen.
  5. NIH - Zebrafish Gene Collection (ZGC) project
    Submitted (APR-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 3 AND 4).
    Strain: AB.
    Tissue: Embryo.
  6. "Brn-1.1: an alternatively spliced class III POU domain gene expressed in the nervous system of the zebrafish."
    Shah D., Sampath K., Stuart G.W.
    Submitted (MAR-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 5-438 (ISOFORM 3).
    Tissue: Embryo.
  7. "Developmental expression of class III and IV POU domain genes in the zebrafish."
    Sampath K., Stuart G.W.
    Biochem. Biophys. Res. Commun. 219:565-571(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 265-378, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
    Tissue: Embryo.

Entry informationi

Entry nameiP3F3A_DANRE
AccessioniPrimary (citable) accession number: P56224
Secondary accession number(s): B0S7I5
, B0S7I6, B0S7I7, B5DDP9, O57514, Q6IS23, Q6NZU9, Q6PE22, Q7ZU57, Q90433, Q90436
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: November 24, 2009
Last modified: October 29, 2014
This is version 116 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3