hoxc9a homeobox C9a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: hoxc9aprovided by ZNC
Official Full Name: homeobox C9aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-000328-5
See related: Ensembl:ENSDARG00000092809 AllianceGenome:ZFIN:ZDB-GENE-000328-5
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: bz39; BZ-39; hoxc9; zgc:109844
Summary: Predicted to enable DNA-binding transcription factor activity and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within negative regulation of vasculogenesis and positive regulation of lymphangiogenesis. Predicted to be active in nucleus. Is expressed in several structures, including CNS interneuron; axial vasculature; neural tube; pectoral fin bud; and spinal cord. Orthologous to human HOXC9 (homeobox C9). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 23

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	23	NC_007134.7 (36095306..36097769)
105	previous assembly	GRCz10 (GCF_000002035.5)	23	NC_007134.6 (35996503..35998966)

Chromosome 23 - NC_007134.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

HOXC9 regulates formation of parachordal lymphangioplasts and the thoracic duct in zebrafish via stabilin 2.
Title: HOXC9 regulates formation of parachordal lymphangioplasts and the thoracic duct in zebrafish via stabilin 2.
The data identify HOXC9 as an endothelial cell active transcriptional repressor promoting the resting, antiangiogenic endothelial cell phenotype in an interleukin 8-dependent manner
Title: The transcription factor HOXC9 regulates endothelial cell quiescence and vascular morphogenesis in zebrafish via inhibition of interleukin 8.

Submit: New GeneRIF Correction

General gene information

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Markers

hoxc9a (e-PCR), detects polymorphism
- UniSTS:205604

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	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 DNA-templated transcription	IEA Inferred from Electronic Annotation more info
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 negative regulation of vasculogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within positive regulation of lymphangiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in proximal/distal pattern formation	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-C9a

Names: homeo box C9a; homeobox gene C-9; hox-C9

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_131528.3 → NP_571603.3 homeobox protein Hox-C9a

Status: VALIDATED

Source sequence(s)

BX005254, EH591454

UniProtKB/Swiss-Prot

O57370, Q4PR87, Q4VBV5, Q9YGS6

UniProtKB/TrEMBL

A0A8M1P8A4, A2BE65

Related

ENSDARP00000105244.2, ENSDART00000127384.3

Conserved Domains (2) summary

smart00389
Location:202 → 251

HOX; Homeodomain

pfam04617
Location:11 → 189

Hox9_act; Hox9 activation region