pax6a paired box 6a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: pax6aprovided by ZNC
Official Full Name: paired box 6aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-990415-200
See related: Ensembl:ENSDARG00000103379 AllianceGenome:ZFIN:ZDB-GENE-990415-200
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: pax6; cb280; pax-a; Pax6.1; paxzfa; PAXZF-A; fc20e07; zfpax-6a; zfpax-6b; pax[zf-a]; wu:fc20e07
Summary: Enables DNA-binding transcription factor activity, RNA polymerase II-specific and sequence-specific DNA binding activity. Involved in positive regulation of cell population proliferation; retinal cone cell differentiation; and retinal rod cell differentiation. Acts upstream of or within several processes, including brain development; neural crest cell migration; and positive regulation of transcription by RNA polymerase II. Located in nucleus. Is expressed in several structures, including immature eye; nervous system; neural keel; neural plate; and neural rod. Human ortholog(s) of this gene implicated in bilateral optic nerve hypoplasia; eye disease (multiple); glucose intolerance; and paranoid schizophrenia. Orthologous to human PAX6 (paired box 6). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 25

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	25	NC_007136.7 (15029041..15049748, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	25	NC_007136.6 (14932646..14953350, complement)

Chromosome 25 - NC_007136.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Unique activities of two overlapping PAX6 retinal enhancers.
Title: Unique activities of two overlapping PAX6 retinal enhancers.
Pax6 organizes the anterior eye segment by guiding two distinct neural crest waves.
Title: Pax6 organizes the anterior eye segment by guiding two distinct neural crest waves.
Study finds that Pax6 is initially distributed contiguously throughout a large domain of the anterior neural plate of zebrafish, including the presumptive eye fields and the dorsal diencephalon. After evagination of the optic vesicle, Pax6 becomes restricted to all proliferating cells of the pigment epithelial and neural layers of the retina.
Title: Distribution of Pax6 protein during eye development suggests discrete roles in proliferative and differentiated visual cells.
Pax6 has an evolutionarily conserved function in establishing the temporospatial expression of Shh in the mid-diencephalic organizer in vertebrates.
Title: Pax6 regulates the formation of the habenular nuclei by controlling the temporospatial expression of Shh in the diencephalon in vertebrates.
loss of Pax6b or Hb9 independently results in the loss of insulin expression, the data reveal a novel cross-talk between the two essential regulators of early beta-cell differentiation.
Title: Characterization and regulation of the hb9/mnx1 beta-cell progenitor specific enhancer in zebrafish.
morpholino depletion of zebrafish Pax6.2 resulted in a "small eye" phenotype, supporting a role in retinal development.
Title: Sequencing of Pax6 loci from the elephant shark reveals a family of Pax6 genes in vertebrate genomes, forged by ancient duplications and divergences.
This study supports the hypothesis that the Pax6 transcription factor is also a signaling molecule with direct non-cell autonomous activity.
Title: Direct non-cell autonomous Pax6 activity regulates eye development in the zebrafish.
following a postulated whole-genome duplication event in an ancestral teleost, duplicates pax6a and pax6b encode transcription factors required for eye, brain, olfactory system, and pancreas development
Title: Subfunctionalization of duplicated zebrafish pax6 genes by cis-regulatory divergence.
The results suggest that decreased Pax6 expression is permissive for axon regeneration and extensive searching, while higher levels of Pax6 are associated with restoration of topography.
Title: Changing Pax6 expression correlates with axon outgrowth and restoration of topography during optic nerve regeneration.
Pax6 interacts with itself via both the paired domain and the homeodomain. Pax6 interaction with itself superactivates Pax6 mediated transactivation.
Title: Superactivation of Pax6-mediated transactivation from paired domain-binding sites by dna-independent recruitment of different homeodomain proteins.

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General gene information

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Markers

PAX6 (e-PCR)
- UniSTS:205448

STS1.B06 (e-PCR)
- UniSTS:205709

fc68h11.y1 (e-PCR)
- UniSTS:194267

fc20e07.x1 (e-PCR)
- UniSTS:193002

fc20e07.x1 (e-PCR)
- UniSTS:193003

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within anterior/posterior pattern specification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in brain development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within epithalamus development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in forebrain development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within forebrain development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within habenula development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hindbrain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural crest cell migration	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of gene expression	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in retina development in camera-type eye	IBA Inferred from Biological aspect of Ancestor more info
involved_in retinal cone cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in retinal rod cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sensory organ development	IBA Inferred from Biological aspect of Ancestor more info
involved_in type B pancreatic cell differentiation	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: paired box protein Pax-6

Names: etID309716.25; paired box gene 6a; paired box homeotic gene 6; paired box protein Pax[Zf-a]; pax-6

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_131304.1 → NP_571379.1 paired box protein Pax-6

See identical proteins and their annotated locations for NP_571379.1

Status: PROVISIONAL

Source sequence(s)

X63183

UniProtKB/Swiss-Prot

P26630

Related

ENSDARP00000135767.1, ENSDART00000164384.2

Conserved Domains (2) summary

smart00351
Location:23 → 161

PAX; Paired Box domain

pfam00046
Location:247 → 299

Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCz11 Primary Assembly

Genomic

NC_007136.7 Reference GRCz11 Primary Assembly

Range

15029041..15049748 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_009297883.4 → XP_009296158.1 paired box protein Pax-6 isoform X5

See identical proteins and their annotated locations for XP_009296158.1

UniProtKB/Swiss-Prot

A2AUN5, P26630

UniProtKB/TrEMBL

A0A8M9P6C7

Related

ENSDARP00000139430.1, ENSDART00000162485.2

Conserved Domains (2) summary

smart00351
Location:23 → 147

PAX; Paired Box domain

pfam00046
Location:233 → 285

Homeobox; Homeobox domain
XM_068217313.1 → XP_068073414.1 paired box protein Pax-6 isoform X2
XM_009297878.4 → XP_009296153.1 paired box protein Pax-6 isoform X1

UniProtKB/TrEMBL

A0A8M3AZJ7

Conserved Domains (3) summary

smart00351
Location:31 → 169

PAX; Paired Box domain

pfam00046
Location:255 → 307

Homeobox; Homeobox domain

cl25836
Location:341 → 459

Retinal; Retinal protein
XM_009297885.4 → XP_009296160.1 paired box protein Pax-6 isoform X7

UniProtKB/TrEMBL

A0A8M3APL7

Conserved Domains (2) summary

smart00351
Location:5 → 129

PAX; Paired Box domain

pfam00046
Location:215 → 267

Homeobox; Homeobox domain
XM_009297884.4 → XP_009296159.1 paired box protein Pax-6 isoform X6

UniProtKB/TrEMBL

A0A8M3B718

Conserved Domains (2) summary

smart00351
Location:5 → 143

PAX; Paired Box domain

pfam00046
Location:229 → 281

Homeobox; Homeobox domain
XM_009297882.4 → XP_009296157.1 paired box protein Pax-6 isoform X4

UniProtKB/TrEMBL

A0A0R4IXU2, A0A8M3AWF6

Related

ENSDARP00000140503.1, ENSDART00000165774.2

Conserved Domains (2) summary

smart00351
Location:13 → 151

PAX; Paired Box domain

pfam00046
Location:237 → 289

Homeobox; Homeobox domain
XM_021470447.2 → XP_021326122.1 paired box protein Pax-6 isoform X5

UniProtKB/Swiss-Prot

A2AUN5, P26630

UniProtKB/TrEMBL

A0A8M9P6C7

Conserved Domains (2) summary

smart00351
Location:23 → 147

PAX; Paired Box domain

pfam00046
Location:233 → 285

Homeobox; Homeobox domain
XM_021470448.2 → XP_021326123.1 paired box protein Pax-6 isoform X7

UniProtKB/TrEMBL

A0A8M3APL7

Conserved Domains (2) summary

smart00351
Location:5 → 129

PAX; Paired Box domain

pfam00046
Location:215 → 267

Homeobox; Homeobox domain
XM_068217314.1 → XP_068073415.1 paired box protein Pax-6 isoform X3

UniProtKB/TrEMBL

A0A8M6YYD0
XM_009297886.4 → XP_009296161.1 paired box protein Pax-6 isoform X8

See identical proteins and their annotated locations for XP_009296161.1

UniProtKB/TrEMBL

A0A8M2BGP0, A0A8M3AP00

Conserved Domains (1) summary

pfam00046
Location:78 → 130

Homeobox; Homeobox domain
XM_068217316.1 → XP_068073417.1 paired box protein Pax-6 isoform X8

UniProtKB/TrEMBL

A0A8M2BGP0, A0A8M3AP00
XM_009297889.4 → XP_009296164.1 paired box protein Pax-6 isoform X8

See identical proteins and their annotated locations for XP_009296164.1

UniProtKB/TrEMBL

A0A8M2BGP0, A0A8M3AP00

Conserved Domains (1) summary

pfam00046
Location:78 → 130

Homeobox; Homeobox domain
XM_009297888.4 → XP_009296163.1 paired box protein Pax-6 isoform X8

See identical proteins and their annotated locations for XP_009296163.1

UniProtKB/TrEMBL

A0A8M2BGP0, A0A8M3AP00

Conserved Domains (1) summary

pfam00046
Location:78 → 130

Homeobox; Homeobox domain
XM_009297887.4 → XP_009296162.1 paired box protein Pax-6 isoform X8

See identical proteins and their annotated locations for XP_009296162.1

UniProtKB/TrEMBL

A0A8M2BGP0, A0A8M3AP00

Conserved Domains (1) summary

pfam00046
Location:78 → 130

Homeobox; Homeobox domain