Cd3d CD3 antigen, delta polypeptide [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Cd3dprovided by MGI
Official Full Name: CD3 antigen, delta polypeptideprovided by MGI
Primary source: MGI:MGI:88331
See related: Ensembl:ENSMUSG00000032094 AllianceGenome:MGI:88331
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: T3d
Summary: Predicted to enable identical protein binding activity and transmembrane signaling receptor activity. Involved in positive thymic T cell selection. Part of alpha-beta T cell receptor complex. Is expressed in thymus primordium. Human ortholog(s) of this gene implicated in immunodeficiency 19 and severe combined immunodeficiency. Orthologous to human CD3D (CD3 delta subunit of T-cell receptor complex). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in thymus adult (RPKM 78.5), spleen adult (RPKM 9.8) and 1 other tissue See more
Orthologs: human all
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Genomic context

Location:: 9 A5.2; 9 24.84 cM

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	9	NC_000075.7 (44893067..44898350)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	9	NC_000075.6 (44981769..44987052)

Chromosome 9 - NC_000075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Mutation of Cd3d not only impairs the proper development of amacrine cells expressing Cd3d but also those not expressing Cd3d . In contrast to effects of Major histocompatibility complex and its receptor, PirB, on other neurons, mutation of Cd3d has no effect on retinal ganglion cells death and starburst amacrine cells degeneration after optic nerve crush.
Title: The effects of immune protein CD3ζ development and degeneration of retinal neurons after optic nerve injury.
CD3/CD28-inducible MNSFbeta-Bcl-G complex may be involved in the regulation of T cell function and survival.
Title: Ubiquitin-like protein MNSFβ negatively regulates T cell function and survival.
Polymorphisms of the CD3delta ectodomain exist in mice,some of which lead to amino acid substitutions which cause structural changes and affect anti-CD3 antibody binding.
Title: Polymorphisms of the T cell receptor CD3delta and CD3epsilon chains affect anti-CD3 antibody binding and T cell activation.
CD3gammaepsilon dimers predominated over CD3deltaepsilon dimers at the early stage of T cell development.
Title: Dynamics of CD3gammaepsilon and CD3deltaepsilon dimer expression during murine T cell development.
CD3delta transgene rescues gammadelta T cell development in mice lacking both mouse CD3delta and CD3gamma.
Title: Different composition of the human and the mouse gammadelta T cell receptor explains different phenotypes of CD3gamma and CD3delta immunodeficiencies.
CD3delta and CD3gamma play a different role in humans and mice in pre-TCR and TCR function during alphabeta T-cell development
Title: Overlapping functions of human CD3delta and mouse CD3gamma in alphabeta T-cell development revealed in a humanized CD3gamma-mouse.
mouse CD3delta has a T-cell specific expression pattern
Title: T cell-specific expression of the murine CD3delta promoter.
A human CD3 transgene that encodes full length CD3delta and a truncated but functional form of CD3epsilon restored the defective preTCR function in not only CD3epsilon- but CD3gamma- and CD3gammadelta-deficient mice as well.
Title: Different role for mouse and human CD3delta/epsilon heterodimer in preT cell receptor (preTCR) function: human CD3delta/epsilon heterodimer restores the defective preTCR function in CD3gamma- and CD3gammadelta-deficient mice.
there is one molecule each of CD3delta and CD3gamma in the surface TCR/CD3 complex
Title: Biochemical evidence for the presence of a single CD3delta and CD3gamma chain in the surface T cell receptor/CD3 complex.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1)
Targeted (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D9Mit23 (e-PCR), detects polymorphism
- UniSTS:131792

Cd3d (e-PCR), detects polymorphism
- UniSTS:141280

D9Mit255 (e-PCR), detects polymorphism
- UniSTS:131825

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transmembrane signaling receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables transmembrane signaling receptor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in T cell activation	NAS Non-traceable Author Statement more info	PubMed
involved_in adaptive immune response	IEA Inferred from Electronic Annotation more info
involved_in cell surface receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell surface receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in positive thymic T cell selection	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive thymic T cell selection	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein-containing complex assembly	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of T cell receptor complex	ISO Inferred from Sequence Orthology more info
part_of T cell receptor complex	NAS Non-traceable Author Statement more info	PubMed
part_of alpha-beta T cell receptor complex	IBA Inferred from Biological aspect of Ancestor more info
part_of alpha-beta T cell receptor complex	IDA Inferred from Direct Assay more info	PubMed
part_of alpha-beta T cell receptor complex	ISO Inferred from Sequence Orthology more info
is_active_in external side of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: T-cell surface glycoprotein CD3 delta chain

Names: T-cell receptor T3 delta chain

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_013487.3 → NP_038515.3 T-cell surface glycoprotein CD3 delta chain precursor

See identical proteins and their annotated locations for NP_038515.3

Status: VALIDATED

Source sequence(s)

AK042172, BB237678, BC062807, BY576367

Consensus CDS

CCDS23124.1

UniProtKB/Swiss-Prot

P04235

UniProtKB/TrEMBL

Q3U4T1, Q3V3B4, Q6P5P1

Related

ENSMUSP00000034602.8, ENSMUST00000034602.9

Conserved Domains (2) summary

pfam02189
Location:146 → 165

ITAM; Immunoreceptor tyrosine-based activation motif

pfam16680
Location:31 → 95

Ig_4; T-cell surface glycoprotein CD3 delta chain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000075.7 Reference GRCm39 C57BL/6J

Range

44893067..44898350

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006509965.1 → XP_006510028.1 T-cell surface glycoprotein CD3 delta chain isoform X1

Conserved Domains (2) summary

pfam02189
Location:201 → 220

ITAM; Immunoreceptor tyrosine-based activation motif

pfam16680
Location:85 → 158

Ig_4; T-cell surface glycoprotein CD3 delta chain