hoxd3a homeobox D3a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: hoxd3aprovided by ZNC
Official Full Name: homeobox D3aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-990415-120
See related: Ensembl:ENSDARG00000059280 AllianceGenome:ZFIN:ZDB-GENE-990415-120
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: Z-56; hoxd3; im:7144208
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. Predicted to be involved in anterior/posterior pattern specification; embryonic skeletal system morphogenesis; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of DNA-templated transcription. Predicted to be active in nucleus. Is expressed in several structures, including hindbrain; hindbrain neural keel; neural tube; pectoral fin bud; and spinal cord. Orthologous to human HOXD3 (homeobox D3). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 9

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	9	NC_007120.7 (1931420..1959600, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	9	NC_007120.6 (1936255..1938293, 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?

Oculomotor circuits in hindbrain rhombomeres 5-6 develop and function independently of hox3 genes.
Title: Development of oculomotor circuitry independent of hox3 genes.
hoxd3 gene is mainly expressed in nervous system of wide-type zebrafish embryos.
Title: [Expression pattern of hoxd3 gene during early development of wild-type zebrafish embryos].

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General gene information

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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
involved_in anterior/posterior pattern specification	IBA Inferred from Biological aspect of Ancestor more info
involved_in embryonic skeletal system morphogenesis	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: homeobox protein Hox-D3a

Names: homeo box D3a; homeobox gene D-3; hox-D3

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_131125.1 → NP_571200.1 homeobox protein Hox-D3a

See identical proteins and their annotated locations for NP_571200.1

Status: VALIDATED

Source sequence(s)

BX322661

UniProtKB/Swiss-Prot

B0S5Y4, O42370

UniProtKB/TrEMBL

A0A8M9PRW4

Related

ENSDARP00000120633.1, ENSDART00000146131.2

Conserved Domains (3) summary

pfam00046
Location:165 → 217

Homeobox; Homeobox domain

pfam13293
Location:333 → 394

DUF4074; Domain of unknown function (DUF4074)

cl27820
Location:116 → 237

Abdominal-A; Homeobox protein

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_007120.7 Reference GRCz11 Primary Assembly

Range

1931420..1959600 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_021478602.2 → XP_021334277.1 homeobox protein Hox-D3a isoform X1

UniProtKB/Swiss-Prot

B0S5Y4, O42370

UniProtKB/TrEMBL

A0A8M9PRW4

Related

ENSDARP00000093704.3, ENSDART00000082359.5

Conserved Domains (3) summary

pfam00046
Location:165 → 217

Homeobox; Homeobox domain

pfam13293
Location:333 → 394

DUF4074; Domain of unknown function (DUF4074)

cl27820
Location:116 → 237

Abdominal-A; Homeobox protein