otx2a orthodenticle homeobox 2a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: otx2aprovided by ZNC
Official Full Name: orthodenticle homeobox 2aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-980526-27
See related: Ensembl:ENSDARG00000030703 AllianceGenome:ZFIN:ZDB-GENE-980526-27
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: otx3; otx1a; otx1l
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within brain development and retinal pigment epithelium development. Predicted to be active in nucleus. Is expressed in several structures, including anterior neural keel; axis; brain; immature eye; and neural plate. Orthologous to human OTX1 (orthodenticle homeobox 1). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 1

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	1	NC_007112.7 (50921266..50929957)
105	previous assembly	GRCz10 (GCF_000002035.5)	1	NC_007112.6 (50275678..50286298)

Chromosome 1 - NC_007112.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

These findings suggest that one or more Otx targets in addition to mitfa and mitfb, possibly another mitf family member, are necessary for development of the retinal pigmented epithelium in zebrafish.
Title: Otx but not Mitf transcription factors are required for zebrafish retinal pigment epithelium development.
The Zona limitans intrathalamica is induced within the competence area established by Otx1l/2, and is posteriorly restricted by Irx1b.
Title: Otx1l, Otx2 and Irx1b establish and position the ZLI in the diencephalon.

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General gene information

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Markers

otx3 (e-PCR)
- UniSTS:187014

fb26d12 (e-PCR)
- UniSTS:204733

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	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	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 cerebellum development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within hindbrain development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within midbrain development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within midbrain-hindbrain boundary development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within retinal pigment epithelium development	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: homeobox protein OTX1 A

Names: homeobox protein Otx1l; orthodenticle homeobox 1a; orthodenticle homolog 1 like; orthodenticle homolog 1a; orthodenticle homolog 3; zOTX3

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.