Hoxc4 MGI Mouse Gene Detail - MGI:96195

Symbol

Hoxc4
Name

homeobox C4
Synonyms

Hox-3.5

Feature Type

protein coding gene
IDs

MGI:96195
NCBI Gene: 15423
Member of

Hoxc cluster
Alliance

gene page
Transcription Start Sites

4 TSS

Sequence Map

Chr15:102927366-102945278 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 15, 58.08 cM
Mapping Data

4 experiments

SNPs within 2kb

280 from dbSNP Build 142
Strain Annotations

18
RFLP

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_96195	protein coding gene	Chr15:102926531-102945281 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0022432	protein coding gene	Chr15:105254223-105274265 (+)
A/J	MGP_AJ_G0022394	protein coding gene	Chr15:101098025-101116465 (+)
AKR/J	MGP_AKRJ_G0022369	protein coding gene	Chr15:104168413-104186315 (+)
BALB/cJ	MGP_BALBcJ_G0022398	protein coding gene	Chr15:101146154-101164258 (+)
C3H/HeJ	MGP_C3HHeJ_G0022165	protein coding gene	Chr15:104246230-104266435 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0022847	protein coding gene	Chr15:109150065-109168505 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0020370	protein coding gene	Chr15:96867392-96884980 (+)
CAST/EiJ	MGP_CASTEiJ_G0021691	protein coding gene	Chr15:105120536-105141440 (+)
CBA/J	MGP_CBAJ_G0022134	protein coding gene	Chr15:112985558-113008382 (+)
DBA/2J	MGP_DBA2J_G0022265	protein coding gene	Chr15:100368608-100386847 (+)
FVB/NJ	MGP_FVBNJ_G0022241	protein coding gene	Chr15:99437545-99455448 (+)
LP/J	MGP_LPJ_G0022334	protein coding gene	Chr15:105390860-105409894 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0022263	protein coding gene	Chr15:116499197-116519858 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0022859	protein coding gene	Chr15:104207344-104227467 (+)
PWK/PhJ	MGP_PWKPhJ_G0021431	protein coding gene	Chr15:100548353-100567189 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0021263	protein coding gene	Chr15:104038091-104057993 (+)
WSB/EiJ	MGP_WSBEiJ_G0021741	protein coding gene	Chr15:104820461-104841819 (+)

Human Ortholog

HOXC4, homeobox C4

Vertebrate Orthologs

2

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

HOXC4, homeobox C4
Synonyms

cp19, HOX3, HOX3E
Links

HGNC:5126

NCBI Gene ID: 3221

neXtProt AC: NX_P09017

UniProt: P09017
Chr Location

12q13.13; chr12:54016888-54056030 (+) GRCh38

MGI Vertebrate Homology

Hoxc4 stringent orthology
1 human;1 mouse;1 zebrafish
HCOP

vertebrate homology predictions: HOXC4
Gene Tree

Hoxc4

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References

1 with disease annotations

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Phenotype Summary

27 phenotypes from 3 alleles in 3 genetic backgrounds
33 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

11
Endonuclease-mediated

4
Radiation induced

2
Targeted

5
Genomic Mutations

4 involving Hoxc4
Incidental Mutations

APF
Find Mice (IMSR)

9 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit some postnatal lethality (in the case of one allele but no the other), transformations of thoracic vertebrae, and abnormal rib attachment and sternebra morphology.

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All GO Annotations

21
GO References

6

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

830
Tissues

80
cDNA Data

16
Literature Summary

45

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase hoxc4

ZFIN hoxc4a

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All Sequences

48
RefSeq

12
UniProt

3
CCDS

CCDS27897.1

Ensembl

ENSMUSG00000075394 (Evidence)
NCBI Gene

15423

			Length	Strain/Species	Flank
genomic	ENSMUSG00000075394	Ensembl Gene Model \| MGI Sequence Detail	17913	C57BL/6J	± kb
transcript	ENSMUST00000100164	Ensembl \| MGI Sequence Detail	1983	Not Applicable
polypeptide	ENSMUSP00000097740	Ensembl \| MGI Sequence Detail	264	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000008711 homeobox protein Hox-C4

(term hierarchy)
InterPro Domains

IPR050609 Antp homeobox family, Deformed subfamily

IPR017970 Homeobox, conserved site

IPR001356 Homeobox domain

IPR020479 Homeobox domain, metazoa

IPR009057 Homeobox-like domain superfamily

IPR017995 Homeobox protein, antennapedia type

IPR001827 Homeobox protein, antennapedia type, conserved site

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All nucleic 35

Genomic 7

cDNA 17

Primer pair 6

Other 5

Microarray probesets 3

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MGD-MRK-10843, MGD-MRK-10896

Summaries

All 97

Developmental Gene Expression 45

Diseases 1

Gene Ontology 6

Phenotypes 33
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:338694 Kumar S, et al., Sf3b4 regulates chromatin remodeler splicing and Hox expression. Differentiation. 2023 May-Jun;131:59-73

TSS for Hoxc4:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr133509	Chr15:102927396-102927405 (+)	35 bp
Tssr133510	Chr15:102943043-102943068 (+)	15,690 bp
Tssr133511	Chr15:102943083-102943102 (+)	15,727 bp
Tssr133512	Chr15:102943126-102943146 (+)	15,770 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 12/17/2024 MGI 6.24