Hoxc13 MGI Mouse Gene Detail - MGI:99560

Symbol

Hoxc13
Name

homeobox C13
Synonyms

N

Feature Type

protein coding gene
IDs

MGI:99560
NCBI Gene: 15422
Member of

Hoxc cluster
Alliance

gene page
Transcription Start Sites

6 TSS

Sequence Map

Chr15:102829566-102837249 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 15, Syntenic
Mapping Data

18 experiments

SNPs within 2kb

178 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_99560	protein coding gene	Chr15:102829538-102837249 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0022424	protein coding gene	Chr15:105155371-105163078 (+)
A/J	MGP_AJ_G0022386	protein coding gene	Chr15:100999798-101007603 (+)
AKR/J	MGP_AKRJ_G0022361	protein coding gene	Chr15:104069070-104076767 (+)
BALB/cJ	MGP_BALBcJ_G0022390	protein coding gene	Chr15:101047145-101054856 (+)
C3H/HeJ	MGP_C3HHeJ_G0022157	protein coding gene	Chr15:104144523-104152928 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0022839	protein coding gene	Chr15:109047774-109057225 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0020362	protein coding gene	Chr15:96769350-96777179 (+)
CAST/EiJ	MGP_CASTEiJ_G0021683	protein coding gene	Chr15:105015504-105025127 (+)
CBA/J	MGP_CBAJ_G0022126	protein coding gene	Chr15:112882663-112890374 (+)
DBA/2J	MGP_DBA2J_G0022257	protein coding gene	Chr15:100269937-100277676 (+)
FVB/NJ	MGP_FVBNJ_G0022233	protein coding gene	Chr15:99339465-99347150 (+)
LP/J	MGP_LPJ_G0022326	protein coding gene	Chr15:105290987-105298694 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0022255	protein coding gene	Chr15:116399253-116406950 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0022851	protein coding gene	Chr15:104107798-104115510 (+)
PWK/PhJ	MGP_PWKPhJ_G0021423	protein coding gene	Chr15:100448202-100456335 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0021255	protein coding gene	Chr15:103936809-103945457 (+)
WSB/EiJ	MGP_WSBEiJ_G0021733	protein coding gene	Chr15:104722292-104729853 (+)

Human Ortholog

HOXC13, homeobox C13

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

HOXC13, homeobox C13
Synonyms

ECTD9, HOX3, HOX3G
Links

HGNC:5125

NCBI Gene ID: 3229

neXtProt AC: NX_P31276

UniProt: P31276
Chr Location

12q13.13; chr12:53938831-53946544 (+) GRCh38

MGI Vertebrate Homology

Hoxc13 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: HOXC13
Gene Tree

Hoxc13

Diseases

1 with human HOXC13 associations

				Human Disease	Mouse Models
				ectodermal dysplasia 9 IDs ectodermal dysplasia 9 DOID:0111656 OMIM:614931

Click on a disease name to see all genes associated with that disease.

References

1 with disease annotations

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Phenotype Summary

45 phenotypes from 7 alleles in 6 genetic backgrounds
49 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

21
Endonuclease-mediated

5
Gene trapped

1
Radiation induced

2
Spontaneous

1
Targeted

8
Transgenic

4
Genomic Mutations

4 involving Hoxc13
Incidental Mutations

CvDC
Find Mice (IMSR)

15 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygotes for targeted null mutations exhibit alopecia due to brittle hair, poor growth, abnormalities of caudal vertebrae, nails, and tongue filiform papillae, and lethality in the second week. Rare survivors recover, but lack hair.

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All GO Annotations

19
GO References

5

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

855
Tissues

76
cDNA Data

12
Literature Summary

41

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase hoxc13

ZFIN hoxc13a, hoxc13b

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All Sequences

28
RefSeq

2
UniProt

1
CCDS

CCDS27890.1

Ensembl

ENSMUSG00000001655 (Evidence)
NCBI Gene

15422

			Length	Strain/Species	Flank
genomic	15422	NCBI Gene Model \| MGI Sequence Detail	7684	C57BL/6J	± kb
transcript	NM_010464	RefSeq \| MGI Sequence Detail	2433	ZRU/MplStud
polypeptide	P50207	UniProt \| EBI \| MGI Sequence Detail	328	Not Applicable

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UniProt

1 Sequence
Protein Ontology

PR:000008710 homeobox protein Hox-C13

(term hierarchy)
InterPro Domains

IPR051003 Anterior-posterior axis regulatory homeobox

IPR017970 Homeobox, conserved site

IPR001356 Homeobox domain

IPR009057 Homeobox-like domain superfamily

IPR022067 Homeobox protein Hox1A3 N-terminal

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All nucleic 30

Genomic 3

cDNA 14

Primer pair 9

Other 4

Microarray probesets 2

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MGD-MRK-12776, MGD-MRK-16338, MGI:97277

Summaries

All 115

Developmental Gene Expression 41

Diseases 1

Gene Ontology 5

Phenotypes 49
Earliest

J:14939 Lebedinsky NG, et al., Atrichosis und ihre Vererbung bei der albinotischen Hausmaus. Biol Zentralbl. 1927;47:748-52
Latest

J:332853 Castilla-Ibeas A, et al., Failure of digit tip regeneration in the absence of Lmx1b suggests Lmx1b functions disparate from dorsoventral polarity. Cell Rep. 2023 Jan 13;42(1):111975

TSS for Hoxc13:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr133470	Chr15:102829556-102829567 (+)	-4 bp
Tssr133471	Chr15:102829572-102829577 (+)	9 bp
Tssr133472	Chr15:102829582-102829604 (+)	27 bp
Tssr133473	Chr15:102829607-102829634 (+)	55 bp
Tssr133474	Chr15:102836521-102836527 (+)	6,958 bp
Tssr4741	Chr15:102836589-102836635 (+)	7,046 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)
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