Cd4 MGI Mouse Gene Detail - MGI:88335

Symbol

Cd4
Name

CD4 antigen
Synonyms

L3T4, Ly-4

Feature Type

protein coding gene
IDs

MGI:88335
NCBI Gene: 12504
Alliance

gene page
Transcription Start Sites

3 TSS
Regulated by

Rr95, Rr96, Rr386 ... (5 regulatory regions)

Sequence Map

Chr6:124841655-124865184 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 6, 59.17 cM
Mapping Data

26 experiments

SNPs within 2kb

748 from dbSNP Build 142
Strain Annotations

18
PCR

6
RFLP

2

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_88335	protein coding gene	Chr6:124841655-124865210 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0031275	protein coding gene	Chr6:128175215-128201064 (-)
A/J	MGP_AJ_G0031245	protein coding gene	Chr6:123350831-123399534 (-)
AKR/J	MGP_AKRJ_G0031173	protein coding gene	Chr6:126716376-126767792 (-)
BALB/cJ	MGP_BALBcJ_G0031253	protein coding gene	Chr6:122951280-123000174 (-)
C3H/HeJ	MGP_C3HHeJ_G0030976	protein coding gene	Chr6:126765836-126816990 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0031709	protein coding gene	Chr6:131555640-131579161 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0028859	protein coding gene	Chr6:120560733-120584382 (-)
CAST/EiJ	MGP_CASTEiJ_G0030357	protein coding gene	Chr6:126972854-126997851 (-)
CBA/J	MGP_CBAJ_G0030937	protein coding gene	Chr6:136586635-136641341 (-)
DBA/2J	MGP_DBA2J_G0031093	protein coding gene	Chr6:122277926-122328994 (-)
FVB/NJ	MGP_FVBNJ_G0031043	protein coding gene	Chr6:121181258-121204968 (-)
LP/J	MGP_LPJ_G0031173	protein coding gene	Chr6:128342209-128368722 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0031081	protein coding gene	Chr6:140646584-140670114 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0031744	protein coding gene	Chr6:126609060-126632474 (-)
PWK/PhJ	MGP_PWKPhJ_G0030072	protein coding gene	Chr6:120509096-120533619 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0029901	protein coding gene	Chr6:124693735-124717341 (-)
WSB/EiJ	MGP_WSBEiJ_G0030442	protein coding gene	Chr6:126970685-126994213 (-)

Human Ortholog

CD4, CD4 molecule

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

CD4, CD4 molecule
Synonyms

CD4mut, IMD79, Leu-3, OKT4D, T4
Links

HGNC:1678

NCBI Gene ID: 920

neXtProt AC: NX_P01730

UniProt: P01730
Chr Location

12p13.31; chr12:6786858-6820799 (+) GRCh38

MGI Vertebrate Homology

Cd4 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: CD4
Gene Tree

Cd4

Diseases

1 with human CD4 associations

				Human Disease	Mouse Models
				immunodeficiency 79 IDs immunodeficiency 79 DOID:0112277 OMIM:619238

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

Mutations/Alleles

2 with disease annotations

References

2 with disease annotations

less

Phenotype Summary

30 phenotypes from 11 alleles in 16 genetic backgrounds
37 phenotypes from multigenic genotypes
399 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

46
Chemically induced (ENU)

5
Endonuclease-mediated

18
Gene trapped

5
Spontaneous

3
Targeted

14
Transgenic

1
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

84 strains or lines available
Comparison Matrix

Gene Expression + Phenotype
Recombinase Activity

Comparison Matrix Gene Expression + Recombinase Activity

Mice homozygous for knock-out alleles exhibit abnormal immune system morphology and physiology.

less

All GO Annotations

98
GO References

64

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.

less

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

878
Tissues

58
cDNA Data

35
Literature Summary

56

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

ZFIN cd4-1

less

All Sequences

49
RefSeq

6
UniProt

4
CCDS

CCDS20535.1

Ensembl

ENSMUSG00000023274 (Evidence)
NCBI Gene

12504

			Length	Strain/Species	Flank
genomic	ENSMUSG00000023274	Ensembl Gene Model \| MGI Sequence Detail	23530	C57BL/6J	± kb
transcript	ENSMUST00000024044	Ensembl \| MGI Sequence Detail	3108	Not Applicable
polypeptide	ENSMUSP00000024044	Ensembl \| MGI Sequence Detail	457	Not Applicable

less

UniProt

4 Sequences
Protein Ontology

PR:000001004 CD4 molecule

(term hierarchy)
InterPro Domains

IPR015274 CD4, extracellular

IPR013151 Immunoglobulin

IPR008424 Immunoglobulin C2-set

IPR007110 Immunoglobulin-like domain

IPR036179 Immunoglobulin-like domain superfamily

IPR013783 Immunoglobulin-like fold

IPR003599 Immunoglobulin subtype

IPR013106 Immunoglobulin V-set domain

IPR021963 T cell CD4 receptor C-terminal region

IPR000973 T-cell surface antigen CD4
GlyGen

P06332 7 sites

less

All nucleic 54

Genomic 15

cDNA 35

Primer pair 4

Microarray probesets 3

less

MGD-MRK-11981, MGD-MRK-1858

Summaries

All 730

Developmental Gene Expression 56

Diseases 2

Gene Ontology 64

Phenotypes 399
Earliest

J:5358 Snell GD, et al., Ly-4, a new locus determining a lymphocyte cell-surface alloantigen in mice. Proc Natl Acad Sci U S A. 1973 Apr;70(4):1108-11
Latest

J:359567 Al-Omari AA, et al., Modi-2 a vaccine stimulating CD4 responses to homocitrullinated self epitopes as therapy for solid cancers. NPJ Vaccines. 2024 Nov 27;9(1):236

Cd4 expression regulated by:

Feature	Feature Type	Location	Reference
Rr95, regulatory region 95	enhancer	Chr6:124862196-124862560	J:267930
Rr96, regulatory region 96	silencer	Chr6:124862841-124863329	J:191711
Rr386, regulatory region 386	enhancer	Chr6:124878778-124879162	J:333574
Rr94, regulatory region 94	enhancer	Chr6, Syntenic	J:158962
Rr112, regulatory region 112	enhancer	Chr6, Syntenic	J:158962

TSS for Cd4:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr63208	Chr6:124865155-124865180 (-)	16 bp
Tssr63207	Chr6:124865128-124865144 (-)	48 bp
Tssr63206	Chr6:124847484-124847492 (-)	17,696 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 03/25/2025 MGI 6.24