hoxd13a homeobox D13a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: hoxd13aprovided by ZNC
Official Full Name: homeobox D13aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-990415-119
See related: Ensembl:ENSDARG00000059256 AllianceGenome:ZFIN:ZDB-GENE-990415-119
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: hoxd13; hoxd-13; zgc:110511
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 regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of DNA-templated transcription. Predicted to be located in nucleus. Is expressed in several structures, including cloaca; mesenchyme; pectoral fin bud; periderm; and tail bud. Human ortholog(s) of this gene implicated in brachydactyly-syndactyly syndrome; clubfoot; cryptorchidism; and dysostosis (multiple). Orthologous to human HOXD13 (homeobox D13). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs: 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 (1987370..1990311, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	9	NC_007120.6 (1986573..1989514, 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?

Hoxd13/Bmp2-mediated mechanism involved in zebrafish finfold design.
Title: Hoxd13/Bmp2-mediated mechanism involved in zebrafish finfold design.
Hox13 genes are required for mesoderm formation and axis elongation during early zebrafish development.
Title: Hox13 genes are required for mesoderm formation and axis elongation during early zebrafish development.
results support the idea that modulation of 5'Hoxd gene expression, by acquisition of novel enhancer elements, offered the substrate for the evolution of fins and the origin of tetrapod limbs
Title: Hoxd13 contribution to the evolution of vertebrate appendages.
Data show that cis-regulatory elements driving Hoxd gene expression in distal limbs are present in fish.
Title: Appendage expression driven by the Hoxd Global Control Region is an ancient gnathostome feature.

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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, 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 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
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: homeobox protein Hox-D13a

Names: homeo box D13a; homeobox gene D-13

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.