Hoxc6 MGI Mouse Gene Detail - MGI:96197

Symbol

Hoxc6
Name

homeobox C6
Synonyms

Hox-3.3, Hox-6.1

Feature Type

protein coding gene
IDs

MGI:96197
NCBI Gene: 15425
Member of

Hoxc cluster
Alliance

genome feature page
Transcription Start Sites

6 TSS

Sequence Map

Chr15:102906689-102920313 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 15, 58.06 cM, cytoband E2
Mapping Data

5 experiments

SNPs within 2kb

170 from dbSNP Build 142
Strain Annotations

19

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_96197	protein coding gene	Chr15:102906658-102920314 (+)
129S1/SvImJ	ENSMUSG00200051719	protein coding gene	Chr15:100131520-100145321 (+)
A/J	ENSMUSG00195044173	protein coding gene	Chr15:100020692-100034497 (+)
AKR/J	ENSMUSG00220044935	protein coding gene	Chr15:99990679-100004488 (+)
BALB/cJ	ENSMUSG00180041670	protein coding gene	Chr15:99904166-99917967 (+)
C3H/HeJ	ENSMUSG00175035771	protein coding gene	Chr15:100227850-100241655 (+)
C57BL/6NJ	ENSMUSG00215051090	protein coding gene	Chr15:99947597-99961397 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0020369	protein coding gene	Chr15:96846631-96860314 (+)
CAST/EiJ	ENSTCUG00005044213	protein coding gene	Chr15:99422177-99435974 (+)
CBA/J	ENSMUSG00210025489	protein coding gene	Chr15:99973678-99987481 (+)
DBA/2J	ENSMUSG00185039592	protein coding gene	Chr15:99990505-100004304 (+)
FVB/NJ	ENSMUSG00205029836	protein coding gene	Chr15:99695271-99709071 (+)
JF1/MsJ	ENSUMUG00000050352	protein coding gene	Chr15:99451190-99464977 (+)
LP/J	ENSMUSG00230005925	protein coding gene	Chr15:103352493-103366298 (+)
NOD/ShiLtJ	ENSMUSG00190046509	protein coding gene	Chr15:99935306-99949105 (+)
NZO/HlLtJ	ENSMUSG00225027530	protein coding gene	Chr15:103536988-103550790 (+)
PWK/PhJ	ENSLUMG00010048615	protein coding gene	Chr15:99661210-99675009 (+)
SPRET/EiJ	ENSMSPG00010039152	protein coding gene	Chr15:101457180-101460286 (+)
WSB/EiJ	ENSIUOG00005030910	protein coding gene	Chr15:100074512-100088312 (+)

Human Ortholog

HOXC6, homeobox C6

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

HOXC6, homeobox C6
Synonyms

CP25, HHO.C8, HOX3, HOX3C
Links

HGNC:5128

NCBI Gene ID: 3223

UniProt: P09630
Chr Location

12q13.13; chr12:53990624-54030823 (+) GRCh38

MGI Vertebrate Homology

Hoxc6 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: HOXC6
Gene Tree

Hoxc6

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References

1 with disease annotations

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Phenotype Summary

6 phenotypes from 1 allele in 1 genetic background
11 phenotypes from multigenic genotypes
35 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

8
Endonuclease-mediated

1
Radiation induced

2
Targeted

5
Genomic Mutations

4 involving Hoxc6
Incidental Mutations

Mutagenetix
Find Mice (IMSR)

9 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for disruptions in this gene display a transformation of thoracic vertebra 2 to a form similar to that of T1. Mammary glands do not develop normally resulting in poor lactation and poor survival of pups.

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All GO Annotations

19
GO References

7

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

1130
Tissues

329
cDNA Data

29
Literature Summary

87

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase hoxc6

ZFIN hoxc6a, hoxc6b

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All Sequences

51
RefSeq

8
UniProt

3
CCDS

CCDS27895.1

Ensembl

ENSMUSG00000001661 (Evidence)
NCBI Gene

15425

			Length	Strain/Species	Flank
genomic	ENSMUSG00000001661	Ensembl Gene Model \| MGI Sequence Detail	13625	C57BL/6J	± kb
transcript	ENSMUST00000001711	Ensembl \| MGI Sequence Detail	1581	Not Applicable
polypeptide	ENSMUSP00000001711	Ensembl \| MGI Sequence Detail	235	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000008713 homeobox protein Hox-C6

(term hierarchy)
InterPro Domains

IPR050296 Antennapedia-type homeobox

IPR017970 Homeobox, conserved site

IPR017995 Homeobox protein, antennapedia type

IPR001827 Homeobox protein, antennapedia type, conserved site

IPR001356 Homeodomain

IPR009057 Homeodomain-like superfamily

IPR020479 Homeodomain, metazoa

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All nucleic 65

Genomic 12

cDNA 30

Primer pair 11

Other 12

Antibodies 4

Microarray probesets 5

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MGD-MRK-10841, MGD-MRK-10865, MGD-MRK-10898

Summaries

All 154

Developmental Gene Expression 87

Diseases 1

Gene Ontology 7

Phenotypes 35
Earliest

J:7688 Lane PW, et al., Association of megacolon with a new dominant spotting gene (Dom) in the mouse. J Hered. 1984 Nov-Dec;75(6):435-9
Latest

J:387680 Ahn B, et al., Disorganization of Transcriptional Regulation and Alteration of Keratin Family Gene Expression in Hairy Ear Mice. Genes (Basel). 2026 Jan 31;17(2)

TSS for Hoxc6:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr133500	Chr15:102906643-102906654 (+)	-40 bp
Tssr133501	Chr15:102906659-102906679 (+)	-20 bp
Tssr133502	Chr15:102917913-102917939 (+)	11,237 bp
Tssr133503	Chr15:102917949-102917976 (+)	11,274 bp
Tssr133504	Chr15:102917977-102917990 (+)	11,295 bp
Tssr133505	Chr15:102918559-102918572 (+)	11,877 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 09/08/2026 MGI 6.24