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P56224 (P3F3A_DANRE) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 113. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:pou3f3a
Synonyms:brn-1.1, brn1.1, pou12, tai-ji, zp12, zp12pou
ORF Names:si:dkeyp-118h3.2
OrganismDanio rerio (Zebrafish) (Brachydanio rerio) [Reference proteome]
Taxonomic identifier7955 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio

Protein attributes

Sequence length438 AA.
Sequence statusComplete.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

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

Subcellular location

Nucleus.

Tissue specificity

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. Ref.1 Ref.3 Ref.7

Developmental stage

Isoform 2 is expressed both maternally and zygotically, and is the major isoform inadults. 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. Ref.1 Ref.2 Ref.3 Ref.7

Sequence similarities

Belongs to the POU transcription factor family. Class-3 subfamily.

Contains 1 homeobox DNA-binding domain.

Contains 1 POU-specific domain.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   DomainHomeobox
   LigandDNA-binding
   Molecular functionDevelopmental protein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processmulticellular organismal development

Inferred from electronic annotation. Source: UniProtKB-KW

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentnucleus

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionsequence-specific DNA binding

Inferred from electronic annotation. Source: InterPro

sequence-specific DNA binding transcription factor activity

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Alternative products

This entry describes 4 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: P56224-1)

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.
Isoform 2 (identifier: P56224-2)

Also known as: U;

The sequence of this isoform differs from the canonical sequence as follows:
     425-438: EFCGRLLKRCKFER → MFTET
Isoform 3 (identifier: P56224-3)

Also known as: B;

The sequence of this isoform differs from the canonical sequence as follows:
     411-438: VSADTPPPSMDCKREFCGRLLKRCKFER → GSFVVDYLKGASLKDEPDSNHNVTTASSYGQEILVH
Isoform 4 (identifier: P56224-4)

The sequence of this isoform differs from the canonical sequence as follows:
     402-438: EDVYTHAGNVSADTPPPSMDCKREFCGRLLKRCKFER → KDMDQCRQTLNIKQWKNLPQDTYQFYAQELYYSF
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 438438POU domain, class 3, transcription factor 3-A
PRO_0000100731

Regions

Domain242 – 31675POU-specific
DNA binding334 – 39360Homeobox
Compositional bias85 – 10016Ala-rich
Compositional bias209 – 23931His-rich

Natural variations

Alternative sequence402 – 43837EDVYT…CKFER → KDMDQCRQTLNIKQWKNLPQ DTYQFYAQELYYSF in isoform 4.
VSP_012010
Alternative sequence411 – 43828VSADT…CKFER → GSFVVDYLKGASLKDEPDSN HNVTTASSYGQEILVH in isoform 3.
VSP_002339
Alternative sequence425 – 43814EFCGR…CKFER → MFTET in isoform 2.
VSP_002340

Experimental info

Sequence conflict261S → F in AAH65961. Ref.5
Sequence conflict2221Missing in CAA69212. Ref.1
Sequence conflict2221Missing in CAA69213. Ref.1
Sequence conflict2221Missing in AAC41300. Ref.2
Sequence conflict2221Missing in AAB84079. Ref.3
Sequence conflict2221Missing in AAH44354. Ref.5
Sequence conflict2221Missing in AAH70001. Ref.5
Sequence conflict2221Missing in AAI65334. Ref.5
Sequence conflict2221Missing in AAB92590. Ref.6
Sequence conflict3011M → I in AAH70001. Ref.5

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (A) [UniParc].

Last modified November 24, 2009. Version 2.
Checksum: DFC0E59F41D3E0CA

FASTA43847,216
        10         20         30         40         50         60 
MATAASNPYL ASSTILSSAS LVHSESGGGG MQPGSGAVTS VSGGYRGDPT VKMVQSDFMQ 

        70         80         90        100        110        120 
GAMAASNGGH MLSHAHQWVT SLPHAAAAAA AAAAAAAAEA GSPWSSSPVG MAGSPQQQDV 

       130        140        150        160        170        180 
KSSSNREDLH SGTALHHRPS HLGAHQSHQS AWGGTTASHI STITGGQQQS QQSLIYSQPG 

       190        200        210        220        230        240 
GFTVNGMLNP PGSLVHPGLM RGESPEMDHH HHHHHHQQQH PHHHHHHQHH AGVNSHDSHS 

       250        260        270        280        290        300 
DEDTPTSDDL EQFAKQFKQR RIKLGFTQAD VGLALGTLYG NVFSQTTICR FEALQLSFKN 

       310        320        330        340        350        360 
MCKLKPLLNK WLEEADSTTG SPTSIDKIAA QGRKRKKRTS IEVSVKGALE SHFLKCPKPS 

       370        380        390        400        410        420 
AQEITSLADN LQLEKEVVRV WFCNRRQKEK RMTPPGVPQT PEDVYTHAGN VSADTPPPSM 

       430 
DCKREFCGRL LKRCKFER 

« Hide

Isoform 2 (U) [UniParc].

Checksum: D755C0B19A342CC7
Show »

FASTA42946,058
Isoform 3 (B) [UniParc].

Checksum: A192568963882A9D
Show »

FASTA44647,824
Isoform 4 [UniParc].

Checksum: 63CD45022F05E9B8
Show »

FASTA43547,266

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_571225.1. NM_131150.1.
XP_005167492.1. XM_005167435.1.
UniGeneDr.75085.

3D structure databases

ProteinModelPortalP56224.
SMRP56224. Positions 248-394.
ModBaseSearch...
MobiDBSearch...

Proteomic databases

PRIDEP56224.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSDART00000061593; ENSDARP00000061592; ENSDARG00000042032. [P56224-3]
ENSDART00000113914; ENSDARP00000103222; ENSDARG00000042032. [P56224-1]
ENSDART00000133178; ENSDARP00000117406; ENSDARG00000042032. [P56224-2]
GeneID30386.
KEGGdre:30386.

Organism-specific databases

CTD30386.
ZFINZDB-GENE-980526-220. pou3f3a.

Phylogenomic databases

GeneTreeENSGT00730000110809.
HOVERGENHBG053120.
InParanoidP56224.
OrthoDBEOG7DJSMG.
PhylomeDBP56224.
TreeFamTF316413.

Gene expression databases

BgeeP56224.

Family and domain databases

Gene3D1.10.10.60. 1 hit.
1.10.260.40. 1 hit.
InterProIPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR010982. Lambda_DNA-bd_dom.
IPR013847. POU.
IPR000327. POU_specific.
IPR016362. Transcription_factor_POU.
[Graphical view]
PfamPF00046. Homeobox. 1 hit.
PF00157. Pou. 1 hit.
[Graphical view]
PIRSFPIRSF002629. Transcription_factor_POU. 1 hit.
PRINTSPR00028. POUDOMAIN.
SMARTSM00389. HOX. 1 hit.
SM00352. POU. 1 hit.
[Graphical view]
SUPFAMSSF46689. SSF46689. 1 hit.
SSF47413. SSF47413. 1 hit.
PROSITEPS00027. 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]
ProtoNetSearch...

Other

NextBio20806799.

Entry information

Entry nameP3F3A_DANRE
AccessionPrimary (citable) accession number: P56224
Secondary accession number(s): B0S7I5 expand/collapse secondary AC list , B0S7I6, B0S7I7, B5DDP9, O57514, Q6IS23, Q6NZU9, Q6PE22, Q7ZU57, Q90433, Q90436
Entry history
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: November 24, 2009
Last modified: April 16, 2014
This is version 113 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families