Cd3d MGI Mouse Gene Detail - MGI:88331 - CD3 antigen, delta polypeptide

Symbol

Cd3d
Name

CD3 antigen, delta polypeptide
Synonyms

T3d

Feature Type

protein coding gene
IDs

MGI:88331
NCBI Gene: 12500
Alliance

genome feature page
Transcription Start Sites

6 TSS

Sequence Map

Chr9:44893067-44898350 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 9, 24.84 cM
Mapping Data

12 experiments

SNPs within 2kb

258 from dbSNP Build 142
Strain Annotations

19
PCR

3
RFLP

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_88331	protein coding gene	Chr9:44893067-44898637 (+)
129S1/SvImJ	ENSMUSG00200018070	protein coding gene	Chr9:41969047-41974601 (+)
A/J	ENSMUSG00195023908	protein coding gene	Chr9:41728219-41733775 (+)
AKR/J	ENSMUSG00220039490	protein coding gene	Chr9:41810742-41816330 (+)
BALB/cJ	ENSMUSG00180026965	protein coding gene	Chr9:41839938-41845508 (+)
C3H/HeJ	ENSMUSG00175015210	protein coding gene	Chr9:41851831-41857397 (+)
C57BL/6NJ	ENSMUSG00215013408	protein coding gene	Chr9:41813418-41818973 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0032133	protein coding gene	Chr9:41856481-41861833 (+)
CAST/EiJ	ENSTCUG00005013938	protein coding gene	Chr9:41799012-41804609 (+)
CBA/J	ENSMUSG00210016674	protein coding gene	Chr9:41894468-41900023 (+)
DBA/2J	ENSMUSG00185010241	protein coding gene	Chr9:41966505-41972075 (+)
FVB/NJ	ENSMUSG00205039466	protein coding gene	Chr9:42210154-42215729 (+)
JF1/MsJ	ENSUMUG00000023027	protein coding gene	Chr9:42008798-42014352 (+)
LP/J	ENSMUSG00230041758	protein coding gene	Chr9:42259498-42264277 (+)
NOD/ShiLtJ	ENSMUSG00190018796	protein coding gene	Chr9:42045466-42051026 (+)
NZO/HlLtJ	ENSMUSG00225042735	protein coding gene	Chr9:42223709-42229275 (+)
PWK/PhJ	ENSLUMG00010018157	protein coding gene	Chr9:41968775-41974377 (+)
SPRET/EiJ	ENSMSPG00010009415	protein coding gene	Chr9:42730877-42736542 (+)
WSB/EiJ	ENSIUOG00005019960	protein coding gene	Chr9:41454943-41460518 (+)

Human Ortholog

CD3D, CD3 delta subunit of T-cell receptor complex

Vertebrate Orthologs

2

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

CD3D, CD3 delta subunit of T-cell receptor complex
Synonyms

CD3-DELTA, CD3DELTA, IMD19, T3D
Links

HGNC:1673

NCBI Gene ID: 915

UniProt: P04234
Chr Location

11q23.3; chr11:118334537-118342705 (-) GRCh38

MGI Vertebrate Homology

Cd3d stringent orthology
1 human;1 mouse;1 rat
HCOP

vertebrate homology predictions: CD3D
Gene Tree

Cd3d

Diseases

2 with human CD3D associations

				Human Disease	Mouse Models
				immunodeficiency 19 IDs immunodeficiency 19 DOID:0111972 OMIM:615617 UMLS_CUI:C3810147
				severe combined immunodeficiency IDs severe combined immunodeficiency DOID:627 MESH:D016511 NCI:C3472 UMLS_CUI:C0085110

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

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Phenotype Summary

3 phenotypes from 1 allele in 1 genetic background
22 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

14
Gene trapped

5
Targeted

9
Genomic Mutations

4 involving Cd3d
Incidental Mutations

CvDC
Find Mice (IMSR)

13 strains or lines available

Homozygotes for targeted null mutations exhibit impaired early thymic development, small numbers of peripheral TCR-alpha/beta+ T cells, and failure of T lymphocyte transition from double-positive to single-positive developmental stages.

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All GO Annotations

29
GO References

10

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

604
Tissues

1
cDNA Data

17
Literature Summary

4

Images

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GEO

Expression Atlas

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All Sequences

52
RefSeq

4
UniProt

8
CCDS

CCDS23124.1

Ensembl

ENSMUSG00000032094 (Evidence)
NCBI Gene

12500

			Length	Strain/Species	Flank
genomic	12500	NCBI Gene Model \| MGI Sequence Detail	5284	C57BL/6J	± kb
transcript	NM_013487	RefSeq \| MGI Sequence Detail	1330	ZRU/MplStud
polypeptide	P04235	UniProt \| EBI \| MGI Sequence Detail	173	Not Applicable

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UniProt

8 Sequences
Protein Ontology

PR:000001019 CD3 delta

(term hierarchy)
InterPro Domains

IPR032052 CD3 gamma/delta subunit, Ig-like domain

IPR015484 CD3 protein, epsilon/gamma/delta subunit

IPR036179 Immunoglobulin-like domain superfamily

IPR013783 Immunoglobulin-like fold

IPR003110 Phosphorylated immunoreceptor signalling ITAM
GlyGen

P04235 3 sites

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All nucleic 28

Genomic 9

cDNA 17

Primer pair 2

Microarray probesets 5

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MGD-MRK-14696, MGD-MRK-1852

Summaries

All 74

Developmental Gene Expression 4

Gene Ontology 10

Phenotypes 22
Earliest

J:7832 van den Elsen P, et al., Isolation and characterization of a cDNA clone encoding the murine homologue of the human 20K T3/T-cell receptor glycoprotein. Nature. 1985 Apr 11-17;314(6011):542-4
Latest

J:359311 Lin F, et al., Multimodal targeting chimeras enable integrated immunotherapy leveraging tumor-immune microenvironment. Cell. 2024 Nov 2;

TSS for Cd3d:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr84704	Chr9:44891834-44891856 (+)	-1,222 bp
Tssr84705	Chr9:44893077-44893096 (+)	20 bp
Tssr84706	Chr9:44893099-44893132 (+)	49 bp
Tssr84707	Chr9:44893145-44893162 (+)	87 bp
Tssr84708	Chr9:44894957-44894961 (+)	1,892 bp
Tssr84709	Chr9:44896733-44896752 (+)	3,676 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 09/01/2026 MGI 6.24