pax6b paired box 6b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: pax6bprovided by ZNC
Official Full Name: paired box 6bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-001031-1
See related: Ensembl:ENSDARG00000045936 AllianceGenome:ZFIN:ZDB-GENE-001031-1
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: cb566; Pax6.2; fc09c10; id:ibd5095; wu:fc09c10; wu:fc33g08
Summary: Enables DNA-binding transcription factor activity, RNA polymerase II-specific. Acts upstream of or within several processes, including brain development; camera-type eye development; and enteroendocrine cell differentiation. Predicted to be located in nucleus. Is expressed in several structures, including anterior neural keel; endocrine system; immature eye; nervous system; and neural plate. 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, Nov 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 7

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	7	NC_007118.7 (15871383..15897078)
105	previous assembly	GRCz10 (GCF_000002035.5)	7	NC_007118.6 (15619410..15647807)

Chromosome 7 - NC_007118.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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 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?

Pancreatic and intestinal endocrine cells in zebrafish share common transcriptomic signatures and regulatory programmes.
Title: Pancreatic and intestinal endocrine cells in zebrafish share common transcriptomic signatures and regulatory programmes.
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.
Lack of pax6b function leads to severe disturbance of the corneal gene regulatory programme
Title: Molecular description of eye defects in the zebrafish Pax6b mutant, sunrise, reveals a Pax6b-dependent genetic network in the developing anterior chamber.
The Pax6b homeodomain is dispensable for pancreatic endocrine cell differentiation in zebrafish.
Title: The Pax6b homeodomain is dispensable for pancreatic endocrine cell differentiation in zebrafish.
data indicate a conserved role of enhancers A and C in the pancreatic expression of pax6b and emphasize the importance of the homeoproteins PBX and PREP cooperating with PDX1, in activating pax6b expression in endocrine pancreatic cells
Title: Expression of zebrafish pax6b in pancreas is regulated by two enhancers containing highly conserved cis-elements bound by PDX1, PBX and PREP factors.
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.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

fc09c10.x1 (e-PCR)
- UniSTS:188018

fa06h02.s1 (e-PCR)
- UniSTS:202234

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

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 cornea development in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within enteroendocrine cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within epithalamus development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within eye development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in forebrain development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within hindbrain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lens development in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lens morphogenesis in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nervous system development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neural crest cell migration	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within pancreatic A cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pancreatic D cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pancreatic epsilon cell differentiation	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 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
acts_upstream_of_or_within type B pancreatic cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: paired box protein Pax-6b

Names: paired box gene 6b; sri(l)

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_131641.1 → NP_571716.1 paired box protein Pax-6b

See identical proteins and their annotated locations for NP_571716.1

Status: PROVISIONAL

Source sequence(s)

AF061252

UniProtKB/TrEMBL

A0A286Y952, A0A8M1P8P3, F1QKK6, Q9YHZ8

Related

ENSDARP00000019067.7, ENSDART00000014572.8

Conserved Domains (2) summary

smart00351
Location:23 → 147

PAX; Paired Box domain

pfam00046
Location:233 → 285

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_007118.7 Reference GRCz11 Primary Assembly

Range

15871383..15897078

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005168822.5 → XP_005168879.1 paired box protein Pax-6b isoform X4

UniProtKB/TrEMBL

A0A8M2BG41

Conserved Domains (2) summary

smart00351
Location:23 → 160

PAX; Paired Box domain

pfam00046
Location:246 → 298

Homeobox; Homeobox domain
XM_009302973.4 → XP_009301248.1 paired box protein Pax-6b isoform X5

UniProtKB/TrEMBL

A0A8M3B3W1

Conserved Domains (2) summary

smart00351
Location:23 → 147

PAX; Paired Box domain

pfam00046
Location:233 → 285

Homeobox; Homeobox domain
XM_005168819.5 → XP_005168876.1 paired box protein Pax-6b isoform X1

See identical proteins and their annotated locations for XP_005168876.1

UniProtKB/TrEMBL

A0A0R4IQL7, A0A8M6Z765

Related

ENSDARP00000115545.3, ENSDART00000145946.4

Conserved Domains (2) summary

smart00351
Location:23 → 160

PAX; Paired Box domain

pfam00046
Location:246 → 298

Homeobox; Homeobox domain
XM_021477603.2 → XP_021333278.1 paired box protein Pax-6b isoform X3

UniProtKB/TrEMBL

A0A8M9Q1T3

Conserved Domains (2) summary

smart00351
Location:5 → 129

PAX; Paired Box domain

pfam00046
Location:215 → 267

Homeobox; Homeobox domain
XM_017356906.3 → XP_017212395.1 paired box protein Pax-6b isoform X1

UniProtKB/TrEMBL

A0A0R4IQL7, A0A8M6Z765

Related

ENSDARP00000152284.1, ENSDART00000192252.1

Conserved Domains (2) summary

smart00351
Location:23 → 160

PAX; Paired Box domain

pfam00046
Location:246 → 298

Homeobox; Homeobox domain
XM_068222401.1 → XP_068078502.1 paired box protein Pax-6b isoform X2
XM_021477602.2 → XP_021333277.1 paired box protein Pax-6b isoform X2

UniProtKB/TrEMBL

A0A8M9PP46

Conserved Domains (2) summary

smart00351
Location:5 → 142

PAX; Paired Box domain

pfam00046
Location:228 → 280

Homeobox; Homeobox domain