rx3 retinal homeobox gene 3 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: rx3provided by ZNC
Official Full Name: retinal homeobox gene 3provided by ZNC
Primary source: ZFIN:ZDB-GENE-990415-238
See related: Ensembl:ENSDARG00000052893 AllianceGenome:ZFIN:ZDB-GENE-990415-238
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
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 several processes, including camera-type eye development; diencephalon development; and neural crest cell migration. Predicted to be located in nucleus. Is expressed in several structures, including forebrain; neural keel; neural plate; presumptive neural plate; and retina. Human ortholog(s) of this gene implicated in isolated microphthalmia 3. Orthologous to human RAX (retina and anterior neural fold homeobox). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 21

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	21	NC_007132.7 (10756265..10759223)
105	previous assembly	GRCz10 (GCF_000002035.5)	21	NC_007132.6 (10663637..10666595)

Chromosome 21 - NC_007132.7 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 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?

Holoprosencephaly with a Special Form of Anophthalmia Result from Experimental Induction of bmp4, Oversaturating BMP Antagonists in Zebrafish.
Title: Holoprosencephaly with a Special Form of Anophthalmia Result from Experimental Induction of bmp4, Oversaturating BMP Antagonists in Zebrafish.
Shh and Rx3 govern formation of a distinct progenitor domain that elaborates patterning through its anisotropic growth and differentiation.
Title: Rx3 and Shh direct anisotropic growth and specification in the zebrafish tuberal/anterior hypothalamus.
lmo4b has an essential role in forebrain development as a modulator of six3 and rx3 expression, and thus indirectly influences neural cell fate commitment, cell proliferation and tissue growth in the anterior CNS.
Title: A zebrafish LMO4 ortholog limits the size of the forebrain and eyes through negative regulation of six3b and rx3.
rx3 mutation leads to microphthalmia, incomplete eye maturation, and dramatic increases in apoptotic eye progenitors
Title: Zebrafish rx3 and mab21l2 are required during eye morphogenesis.
In addition to controlling optic lobe evagination and proliferation, chk/rx3 also determines cellular fate.
Title: chokh/rx3 specifies the retinal pigment epithelium fate independently of eye morphogenesis.
The process segregating the telencephalic and eye fields is isolated from diencephalic patterning, and is mediated by Rx3.
Title: Segregation of telencephalic and eye-field identities inside the zebrafish forebrain territory is controlled by Rx3.

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General gene information

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Markers

AF001909 (e-PCR)
- UniSTS:187030

AF001909 (e-PCR)
- UniSTS:205514

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	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 adenohypophysis development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within camera-type eye morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell fate specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic camera-type eye morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within eye development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within eye field cell fate commitment involved in camera-type eye formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within forebrain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hypothalamus development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural crest cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
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 retina development in camera-type eye	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: retinal homeobox protein Rx3

Names: chk; chokh; eyes missing; eym

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.