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

gene 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

76 from dbSNP Build 142
Strain Annotations

18
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	MGP_129S1SvImJ_G0034725	protein coding gene	Chr9:43516692-43521952 (+)
A/J	MGP_AJ_G0034706	protein coding gene	Chr9:42294935-42306258 (+)
AKR/J	MGP_AKRJ_G0034633	protein coding gene	Chr9:43172615-43180247 (+)
BALB/cJ	MGP_BALBcJ_G0034697	protein coding gene	Chr9:42033621-42039276 (+)
C3H/HeJ	MGP_C3HHeJ_G0034408	protein coding gene	Chr9:43623510-43628971 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0035218	protein coding gene	Chr9:44797817-44803075 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0032133	protein coding gene	Chr9:41856481-41861833 (+)
CAST/EiJ	MGP_CASTEiJ_G0033730	protein coding gene	Chr9:43487164-43493946 (+)
CBA/J	MGP_CBAJ_G0034380	protein coding gene	Chr9:46430307-46438466 (+)
DBA/2J	MGP_DBA2J_G0034539	protein coding gene	Chr9:42189369-42194816 (+)
FVB/NJ	MGP_FVBNJ_G0034480	protein coding gene	Chr9:41451688-41456695 (+)
LP/J	MGP_LPJ_G0034620	protein coding gene	Chr9:43814107-43819367 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0034524	protein coding gene	Chr9:48267600-48272758 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0035239	protein coding gene	Chr9:43093565-43100452 (+)
PWK/PhJ	MGP_PWKPhJ_G0033435	protein coding gene	Chr9:42077342-42082923 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0033271	protein coding gene	Chr9:43385563-43393721 (+)
WSB/EiJ	MGP_WSBEiJ_G0033843	protein coding gene	Chr9:43121396-43127687 (+)

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

CD3DELTA, CD3-DELTA, IMD19, T3D
Links

HGNC:1673

NCBI Gene ID: 915

neXtProt AC: NX_P04234

UniProt: P04234
Chr Location

11q23.3; chr11:118338954-118342705 (-) 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
19 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

10
Gene trapped

5
Targeted

5
Genomic Mutations

2 involving Cd3d
Incidental Mutations

CvDC
Find Mice (IMSR)

26 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

17
GO References

8

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	non-membrane-bounded 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

713
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

51
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

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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 68

Developmental Gene Expression 4

Gene Ontology 8

Phenotypes 19
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:340980 Chora AF, et al., Interplay between liver and blood stages of Plasmodium infection dictates malaria severity via gammadelta T cells and IL-17-promoted stress erythropoiesis. Immunity. 2023 Mar 14;56(3):592-605.e8

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)
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