hoxd4a homeobox D4a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: hoxd4aprovided by ZNC
Official Full Name: homeobox D4aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-980526-214
See related: Ensembl:ENSDARG00000059276 AllianceGenome:ZFIN:ZDB-GENE-980526-214
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: hoxd4; fb36c05; wu:fb36c05; etID37000.9; etID309823.9
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 blood vessel morphogenesis and hemopoiesis. Predicted to be located in nucleus. Predicted to be active in nucleoplasm. Is expressed in several structures, including nervous system; neural keel; neural plate; presumptive structure; and vasculature. Orthologous to human HOXD4 (homeobox D4). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 9

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	9	NC_007120.7 (1949366..1951004, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	9	NC_007120.6 (1940730..1950930, complement)

Chromosome 9 - NC_007120.7 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?

A zebrafish hox gene acts before gastrulation to specify the hemangioblast.
Title: A zebrafish hox gene acts before gastrulation to specify the hemangioblast.
Zebrafish hoxd4a acts upstream of meis1.1 to direct vasculogenesis, angiogenesis and hematopoiesis.
Title: Zebrafish hoxd4a acts upstream of meis1.1 to direct vasculogenesis, angiogenesis and hematopoiesis.
hoxb4a in combination with its paralogs hoxa4a and hoxd4a may play a significant role in the development of precerebellar, vagal, and pectoral fin neuronal subtypes
Title: Enhancer detection in zebrafish permits the identification of neuronal subtypes that express Hox4 paralogs.
The sequence of regulatory elements, including a DR5 type retinoic acid response element (RARE) required for Hoxd4 neural enhancer activity, are highly conserved, zebrafish and mouse neural enhancers function identically in transgenic mouse embryos.
Title: The role of a retinoic acid response element in establishing the anterior neural expression border of Hoxd4 transgenes.

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General gene information

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Markers

hoxd4 (e-PCR)
- UniSTS:205603

hoxd4 (e-PCR)
- UniSTS:186976

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 angiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in anterior/posterior pattern specification	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within definitive hemopoiesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in embryonic skeletal system morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within hemangioblast cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within primitive hemopoiesis	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
acts_upstream_of_or_within vasculogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in nucleoplasm	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 Hox-D4a

Names: homeo box D4a; homeobox gene D-4; hox-D4

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.