hoxa13a homeobox A13a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: hoxa13aprovided by ZNC
Official Full Name: homeobox A13aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-990415-5
See related: Ensembl:ENSDARG00000100312 AllianceGenome:ZFIN:ZDB-GENE-990415-5
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: hoxa13
Summary: Enables DNA-binding transcription factor activity, RNA polymerase II-specific. Acts upstream of or within fin development and negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Is expressed in several structures, including central nervous system; gut; pectoral fin; pectoral fin bud; and tail bud. Human ortholog(s) of this gene implicated in Guttmacher syndrome and hand-foot-genital syndrome. Orthologous to human HOXA13 (homeobox A13). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs: all
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Genomic context

Location:: chromosome: 19

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	19	NC_007130.7 (19729512..19731291)
105	previous assembly	GRCz10 (GCF_000002035.5)	19	NC_007130.6 (20156561..20158340)

Chromosome 19 - NC_007130.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

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 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.
Results describe the latent build up of molecular changes in Hoxa13A, which is associated with the development of a novel feature in a very diverse group of fishes.
Title: Hypermutability of HoxA13A and functional divergence from its paralog are associated with the origin of a novel developmental feature in zebrafish and related taxa (Cypriniformes).
We re-analyzed the expression patterns of hox9-13 genes during development of pectoral fins in zebrafish. Expression occurs in three distinct phases, in which the most distal/third phase is correlated with the development of the fin blade.
Title: Tri-phasic expression of posterior Hox genes during development of pectoral fins in zebrafish: implications for the evolution of vertebrate paired appendages.

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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	IDA Inferred from Direct Assay more info	PubMed
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 fin development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within fin development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
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-A13a

Names: homeo box A13a; homeobox gene A-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.

mRNA and Protein(s)

NM_001085494.1 → NP_001078963.1 homeobox protein Hox-A13a

See identical proteins and their annotated locations for NP_001078963.1

Status: PROVISIONAL

Source sequence(s)

BC133882

UniProtKB/Swiss-Prot

Q1L974, Q6W990, Q9YGT9

UniProtKB/TrEMBL

A3KNK0

Related

ENSDARP00000135830.1, ENSDART00000171610.2

Conserved Domains (2) summary

cd00086
Location:245 → 301

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam12284
Location:29 → 146

HoxA13_N; Hox protein A13 N terminal