Q90435 (PO4F3_DANRE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
POU domain, class 4, transcription factor 3

Alternative name(s):
Brain-specific homeobox/POU domain protein 3.1
Short name=Brain-3.1
Short name=zfBrn-3.1

Gene names

Name:	pou4f3
Synonyms:	brn-3.1, brn-3c, brn3.1, brn3c

Organism

Danio rerio (Zebrafish) (Brachydanio rerio)

Taxonomic identifier

7955 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Actinopterygii › Neopterygii › Teleostei › Ostariophysi › Cypriniformes › Cyprinidae › Danio

Protein attributes

Sequence length	331 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	May play a role in specifying terminally differentiated neuronal phenotypes By similarity.
Subcellular location	Nucleus.
Tissue specificity	Expressed in the nervous system. Expressed in the otic vesicle during embryogenesis. Expressed in the adult retina in a subset of retinal ganglion cells (RGCs), and at a lower level in the adult tectum. Not expressed in the adult olfactory bulb. Ref.1 Ref.2 Ref.3
Developmental stage	Weakly expressed during embryogenesis, with stronger expression in the adult eye. Ref.2 Ref.3
Sequence similarities	Belongs to the POU transcription factor family. Class-4 subfamily. Contains 1 homeobox DNA-binding domain. Contains 1 POU-specific domain.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Domain	Homeobox
Ligand	DNA-binding
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	brain development Inferred from expression pattern Ref.3. Source: ZFIN transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	sequence-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...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 331	331	POU domain, class 4, transcription factor 3		PRO_0000100745
Regions
	Domain	172 – 249	78	POU-specific
	DNA binding	267 – 326	60	Homeobox
	Compositional bias	76 – 124	49	Ser-rich
	Compositional bias	99 – 164	66	His-rich
Experimental info
	Sequence conflict	299	1	A → R in AAB00435. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	Q90435 [UniParc]. Last modified November 24, 2009. Version 2. Checksum: 26E3487CCCC7533A	FASTA	331	36,550
	10 20 30 40 50 60 MMTMNGKQHF SMHPALHPSS EGMRRVCLPA PQLQGNIFSG FDESLLARAE ALAAADIVSH 70 80 90 100 110 120 GKSHPFKTDV TYHTMSSVPC TSSSSTVPIS HPSSNLPSHH HHHLSHQTLE GDLLDHISSS 130 140 150 160 170 180 LSVSGMGAPP DPSVMTTQAH QHHLQMGHLH QAMAMGHPHT LSVHNGMACV NDVESDPREL 190 200 210 220 230 240 EAFAERFKQR RIKLGVTQAD VGSALANLKI PGVGSLSQST ICRFESLTLS HNNMIALKPV 250 260 270 280 290 300 LQAWLEEAEA AYREKNGKPD LFNGNERKRK RTSIAAPEKR SLEAYFAIQP RPSSEKIAAI 310 320 330 AEKLDLKKNV VRVWFCNQRQ KQKRMKYSAV H

References

[1]	"A GFP-based genetic screen reveals mutations that disrupt the architecture of the zebrafish retinotectal projection." Xiao T., Roeser T., Staub W., Baier H. Development 132:2955-2967(2005) [PubMed: 15930106] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
[2]	"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: 8605028] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 196-311, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
[3]	"Developmental expression of the POU domain transcription factor Brn-3b (Pou4f2) in the lateral line and visual system of zebrafish." DeCarvalho A.C., Cappendijk S.L., Fadool J.M. Dev. Dyn. 229:869-876(2004) [PubMed: 15042710] [Abstract] Cited for: TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AY995217 mRNA. Translation: AAX86839.1. U43658 Genomic DNA. Translation: AAB00435.1.
IPI	IPI01023984.
RefSeq	NP_571353.1. NM_131278.1.
UniGene	Dr.93311.
3D structure databases
ProteinModelPortal	Q90435.
ModBase	Search...
Protein-protein interaction databases
STRING	Q90435.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSDART00000149175; ENSDARP00000124728; ENSDARG00000006206.
GeneID	30534.
KEGG	dre:30534.
Organism-specific databases
CTD	5459.
ZFIN	ZDB-GENE-990415-24. pou4f3.
Phylogenomic databases
GeneTree	ENSGT00580000081294.
HOVERGEN	HBG053120.
InParanoid	Q90435.
OMA	SHGKSHP.
OrthoDB	EOG4NP745.
Gene expression databases
Bgee	Q90435.
Family and domain databases
InterPro	IPR001356. Homeobox. IPR017970. Homeobox_CS. IPR009057. Homeodomain-like. IPR012287. Homeodomain-rel. IPR010982. Lambda_DNA-bd. IPR013847. POU. IPR015584. POU4-related. IPR000327. POU_specific. [Graphical view]
Gene3D	G3DSA:1.10.260.40. G3DSA:1.10.260.40. 1 hit. G3DSA:1.10.10.60. Homeodomain-rel. 1 hit.
KO	K09366.
PANTHER	PTHR11636:SF10. POU_4_related. 1 hit.
Pfam	PF00046. Homeobox. 1 hit. PF00157. Pou. 1 hit. [Graphical view]
PRINTS	PR00028. POUDOMAIN.
SMART	SM00389. HOX. 1 hit. SM00352. POU. 1 hit. [Graphical view]
SUPFAM	SSF46689. Homeodomain_like. 1 hit. SSF47413. Lambda_like_DNA. 1 hit.
PROSITE	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]
ProtoNet	Search...

Entry information

Entry name

PO4F3_DANRE

Accession

Primary (citable) accession number: Q90435
Secondary accession number(s): Q52NV5

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 24, 2009
Last modified:	December 14, 2011
This is version 91 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program