otx1 orthodenticle homeobox 1 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: otx1provided by ZNC
Official Full Name: orthodenticle homeobox 1provided by ZNC
Primary source: ZFIN:ZDB-GENE-980526-400
See related: Ensembl:ENSDARG00000094992 AllianceGenome:ZFIN:ZDB-GENE-980526-400
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: cb769; otx1b; zOtx1; fj99f05; wu:fj99f05
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 inner ear morphogenesis; lateral semicircular canal development; and retinal pigment epithelium development. Predicted to be active in nucleus. Is expressed in several structures, including germ ring; immature eye; nervous system; neural keel; and presumptive neural plate. Orthologous to human OTX1 (orthodenticle homeobox 1). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 17

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	17	NC_007128.7 (24318768..24324415)
105	previous assembly	GRCz10 (GCF_000002035.5)	17	NC_007128.6 (24300367..24306014)

Chromosome 17 - NC_007128.7 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.
Foxa1 binds to the otx1b non-conserved enhancer to direct its activity in forebrain and otic vesicle of zebrafish at 24 hpf.
Title: Conserved and non-conserved enhancers direct tissue specific transcription in ancient germ layer specific developmental control genes.
Results suggest that for transcriptional activation of at least one gene in the cell aggregation pathway, zOtx1 need not bind directly to DNA, but does require helix 1 and 2 of its homeodomain to interact with an as yet undefined DNA binding protein.
Title: Molecular dissection of Otx1 functional domains in the zebrafish embryo.
otx1 expression can account for all major patterning differences between zebrafish and lampreys.
Title: The developing lamprey ear closely resembles the zebrafish otic vesicle: otx1 expression can account for all major patterning differences.

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General gene information

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Markers

fj99f05.x1 (e-PCR)
- UniSTS:200477

OTX1 (e-PCR)
- UniSTS:205405

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 inner ear morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lateral semicircular canal development	IMP Inferred from Mutant Phenotype 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 B

Names: orthodenticle homeobox 1b; orthodenticle homolog 1b

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.