irx3a iroquois homeobox 3a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: irx3aprovided by ZNC
Official Full Name: iroquois homeobox 3aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-991119-5
See related: Ensembl:ENSDARG00000101076 AllianceGenome:ZFIN:ZDB-GENE-991119-5
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: iro3; irx3; zehn0543; id:ibd3380; wu:fk88a03; zgc:109805; hm:zehn0543
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 endocrine pancreas development and gastrulation. Predicted to be active in nucleus. Is expressed in several structures, including digestive system; germ ring; hindbrain neural keel; nervous system; and neural rod. Orthologous to human IRX3 (iroquois homeobox 3). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 7

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	7	NC_007118.7 (36041491..36044827)
105	previous assembly	GRCz10 (GCF_000002035.5)	7	NC_007118.6 (35770014..35773350)

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:

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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?

Data show that human fat mass and obesity associated protein FTO BAC:GFP transgenic zebrafish larvae expressed GFP in the the posterior hypothalamus and the anterior brainstem, which are also expression domains of zebrafish protein irx3a.
Title: BAC transgenic zebrafish reveal hypothalamic enhancer activity around obesity associated SNP rs9939609 within the human FTO gene.
Olig2 is required for repression of iro3 expression in the progenitor domain of ventral spinal cord
Title: Regulation of iro3 expression in the zebrafish spinal cord.

Submit: New GeneRIF Correction

General gene information

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Markers

fk88a03.x1 (e-PCR)
- UniSTS:201660

fa91c03.y1 (e-PCR)
- UniSTS:189631

fc78e02.y1 (e-PCR)
- UniSTS:194519

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
involved_in cell development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within endocrine pancreas development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within gastrulation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor 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

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: iroquois-class homeodomain protein IRX-3a

Names: iroquois homeobox protein 3a

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_001320125.1 → NP_001307054.1 iroquois-class homeodomain protein IRX-3a

Status: VALIDATED

Source sequence(s)

CR384080

UniProtKB/TrEMBL

A0A8M1P883, Q90Z68

Related

ENSDARP00000139882.1, ENSDART00000162850.3

Conserved Domains (2) summary

COG5576
Location:103 → 191

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam05920
Location:123 → 162

Homeobox_KN; Homeobox KN 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

36041491..36044827

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_131267.1: Suppressed sequence

Description

NM_131267.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.