Cd247 CD247 antigen [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Cd247provided by MGI
Official Full Name: CD247 antigenprovided by MGI
Primary source: MGI:MGI:88334
See related: Ensembl:ENSMUSG00000005763 AllianceGenome:MGI:88334
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: Cd3; T3z; Cd3h; Cd3z; Tcrk; Tcrz; Cd3-eta; Cd3zeta; Cd3-zeta; 4930549J05Rik; A430104F18Rik
Summary: Predicted to enable protein heterodimerization activity; protein homodimerization activity; and protein tyrosine kinase binding activity. Acts upstream of or within T cell receptor signaling pathway and positive regulation of protein localization to cell surface. Located in Golgi apparatus and plasma membrane. Part of alpha-beta T cell receptor complex. Is expressed in several structures, including alimentary system; brain; genitourinary system; hemolymphoid system gland; and liver and biliary system. Human ortholog(s) of this gene implicated in immunodeficiency 25. Orthologous to human CD247 (CD247 molecule). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in thymus adult (RPKM 43.2), spleen adult (RPKM 5.1) and 2 other tissues See more
Orthologs: human all
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Genomic context

Location:: 1 H2.3; 1 73.14 cM

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	1	NC_000067.7 (165607514..165698722)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	1	NC_000067.6 (165779952..165871153)

Chromosome 1 - NC_000067.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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?

Alternatively Spliced Variants of Murine CD247 Influence T Cell Development and Activation, Revealing the Importance of the CD3zeta C-Terminal Region.
Title: Alternatively Spliced Variants of Murine CD247 Influence T Cell Development and Activation, Revealing the Importance of the CD3ζ C-Terminal Region.
CD3zeta ITAMs enable ligand discrimination and antagonism by inhibiting TCR signaling in response to low-affinity peptides.
Title: CD3ζ ITAMs enable ligand discrimination and antagonism by inhibiting TCR signaling in response to low-affinity peptides.
The CD3zeta adaptor structure determines functional differences between human and mouse CD16 Fc receptor signaling.
Title: The CD3ζ adaptor structure determines functional differences between human and mouse CD16 Fc receptor signaling.
Study findings underline the important roles of p38 and STAT3 in the regulation of PD-L1 expression and prove that IFNalpha induces STAT3/p38-mediated expression of PD-L1 and thereby a reduced stimulatory ability of dendritic cells.
Title: Interferon-α Up-Regulates the Expression of PD-L1 Molecules on Immune Cells Through STAT3 and p38 Signaling.
ITAM sequence diversity is required for optimal TCR signal transduction and subsequent T cell maturation
Title: Cutting Edge: CD3 ITAM Diversity Is Required for Optimal TCR Signaling and Thymocyte Development.
Comprehensive Survey of miRNA-mRNA Interactions Reveals That Ccr7 and Cd247 (CD3 zeta) are Posttranscriptionally Controlled in Pancreas Infiltrating T Lymphocytes of Non-Obese Diabetic (NOD) Mice
Title: Comprehensive Survey of miRNA-mRNA Interactions Reveals That Ccr7 and Cd247 (CD3 zeta) are Posttranscriptionally Controlled in Pancreas Infiltrating T Lymphocytes of Non-Obese Diabetic (NOD) Mice.
There is an early (within seconds) interaction between CD3zeta and the coreceptor CD8 that is independent of the binding of CD8 to MHC.
Title: Ligand-engaged TCR is triggered by Lck not associated with CD8 coreceptor.
The resting TCR localized in the disordered domain of giant plasma membrane (PM) vesicles (GPMVs) and PM spheres (PMSs) and single and nanoclustered TCRs are found in the high-density fractions in sucrose gradients.
Title: Nanoclusters of the resting T cell antigen receptor (TCR) localize to non-raft domains.
When Ly108 is engaged in trans during cell-cell interactions, Ly108-CD3zeta interactions are promoted in a manner that uniquely depends on Ly108 TM domain, leading to more efficient CD3zeta dephosphorylation.
Title: SAP-regulated T Cell-APC adhesion and ligation-dependent and -independent Ly108-CD3ζ interactions.
Two transcription factor binding sites and a long non-coding RNA are identified within the Cd247 gene.
Title: Spatially conserved regulatory elements identified within human and mouse Cd247 gene using high-throughput sequencing data from the ENCODE project.

Submit: New GeneRIF Correction See all GeneRIFs (39)

Variation

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Alleles

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

Chemically induced (ENU) (1)
Endonuclease-mediated (2)
Targeted (7) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AW552088 (e-PCR)
- UniSTS:178499

J04967 (e-PCR)
- UniSTS:178503

RH94658 (e-PCR)
- UniSTS:119905

J03297 (e-PCR)
- UniSTS:124852

L03353 (e-PCR)
- UniSTS:163269

Cd3z (e-PCR), detects polymorphism
- UniSTS:141281

D1Mit144 (e-PCR), detects polymorphism
- UniSTS:128481

PMC197251P5 (e-PCR)
- UniSTS:271854

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	IEA Inferred from Electronic Annotation more info
enables protein heterodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein tyrosine kinase binding	IEA Inferred from Electronic Annotation more info
enables protein tyrosine kinase binding	ISO Inferred from Sequence Orthology more info
enables transmembrane signaling receptor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in Fc-gamma receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in Fc-gamma receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in T cell receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within T cell receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in T cell receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in adaptive immune response	IEA Inferred from Electronic Annotation more info
involved_in cell surface receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within interleukin-2 production	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within positive regulation of protein localization to cell surface	IDA Inferred from Direct Assay more info	PubMed
involved_in protein complex oligomerization	IEA Inferred from Electronic Annotation more info
involved_in protein complex oligomerization	ISO Inferred from Sequence Orthology more info
involved_in protein-containing complex assembly	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of Fc-gamma receptor III complex	ISO Inferred from Sequence Orthology more info
part_of Fc-gamma receptor III complex	ISS Inferred from Sequence or Structural Similarity more info
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
part_of T cell receptor complex	ISO Inferred from Sequence Orthology more info
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
located_in cytoplasm	ISO Inferred from Sequence Orthology more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	ISO Inferred from Sequence Orthology more info	PubMed

General protein information

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Preferred Names: CD247 antigen

Names: CD3 antigen, zeta polypeptide; CD3-zeta/eta; T-cell receptor T3 eta chain; T-cell surface glycoprotein CD3 zeta 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_001113391.2 → NP_001106862.1 CD247 antigen isoform zeta precursor

See identical proteins and their annotated locations for NP_001106862.1

Status: VALIDATED

Description

Transcript Variant: This variant (zeta) encodes the shortest isoform (zeta).

Source sequence(s)

AC093371, AK138774, BC052824, BM240376

Consensus CDS

CCDS48427.1

UniProtKB/Swiss-Prot

P24161, P29020, Q9D3G3

Related

ENSMUSP00000005907.6, ENSMUST00000005907.12

Conserved Domains (3) summary

smart00077
Location:69 → 89

ITAM; Immunoreceptor tyrosine-based activation motif

pfam02189
Location:139 → 158

ITAM; Immunoreceptor tyrosine-based activation motif

pfam11628
Location:28 → 58

TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain
NM_001113392.2 → NP_001106863.1 CD247 antigen isoform iota precursor

See identical proteins and their annotated locations for NP_001106863.1

Status: VALIDATED

Description

Transcript Variant: This variant (iota) has alternate exon structure in the 3' coding region and 3' UTR, compared to variant zeta. The resulting isoform (iota) has a distinct C-terminus and is longer than isoform zeta.

Source sequence(s)

AC093371, AK138774

Consensus CDS

CCDS48429.1

UniProtKB/TrEMBL

Q3UU54

Related

ENSMUSP00000124297.2, ENSMUST00000161971.8

Conserved Domains (2) summary

smart00077
Location:69 → 89

ITAM; Immunoreceptor tyrosine-based activation motif

pfam11628
Location:28 → 58

TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain
NM_001113393.2 → NP_001106864.2 CD247 antigen isoform theta precursor

See identical proteins and their annotated locations for NP_001106864.2

Status: VALIDATED

Description

Transcript Variant: This variant (theta) uses an alternate in-frame splice site in the central coding region, and has alternate exon structure in the 3' coding region and 3' UTR, compared to variant zeta. The resulting isoform (theta) has a distinct C-terminus and is longer than isoform zeta.

Source sequence(s)

AC093371, AC124587

Consensus CDS

CCDS48428.2

UniProtKB/TrEMBL

A2MZG6, E7EXC2, J3QMU3

Related

ENSMUSP00000124299.3, ENSMUST00000161559.3

Conserved Domains (2) summary

smart00077
Location:69 → 89

ITAM; Immunoreceptor tyrosine-based activation motif

pfam11628
Location:28 → 58

TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain
NM_031162.4 → NP_112439.1 CD247 antigen isoform eta precursor

See identical proteins and their annotated locations for NP_112439.1

Status: VALIDATED

Description

Transcript Variant: This variant (eta) has alternate exon structure in the 3' coding region and 3' UTR, compared to variant zeta. The resulting isoform (eta) has a distinct C-terminus and is longer than isoform zeta. Variants eta and kappa encode the same isoform.

Source sequence(s)

AC093371, AC124587, BF020526

Consensus CDS

CCDS15443.1

UniProtKB/TrEMBL

J3QMU3

Related

ENSMUSP00000027849.5, ENSMUST00000027849.11

Conserved Domains (2) summary

smart00077
Location:69 → 89

ITAM; Immunoreceptor tyrosine-based activation motif

pfam11628
Location:28 → 58

TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain

RNA

NR_103716.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (kappa) differs at the 3' end compared to variant zeta. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant zeta, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC093371, AC124587

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_000067.7 Reference GRCm39 C57BL/6J

Range

165607514..165698722

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011238745.4 → XP_011237047.1 CD247 antigen isoform X1

See identical proteins and their annotated locations for XP_011237047.1

UniProtKB/Swiss-Prot

P24161, P29020, Q9D3G3

Conserved Domains (3) summary

smart00077
Location:69 → 89

ITAM; Immunoreceptor tyrosine-based activation motif

pfam02189
Location:139 → 158

ITAM; Immunoreceptor tyrosine-based activation motif

pfam11628
Location:28 → 58

TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain
XM_011238746.2 → XP_011237048.1 CD247 antigen isoform X2

Conserved Domains (2) summary

smart00077
Location:69 → 89

ITAM; Immunoreceptor tyrosine-based activation motif

pfam11628
Location:28 → 58

TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain
XM_036156509.1 → XP_036012402.1 CD247 antigen isoform X1

UniProtKB/Swiss-Prot

P24161, P29020, Q9D3G3

Conserved Domains (3) summary

smart00077
Location:69 → 89

ITAM; Immunoreceptor tyrosine-based activation motif

pfam02189
Location:139 → 158

ITAM; Immunoreceptor tyrosine-based activation motif

pfam11628
Location:28 → 58

TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain
XM_017313285.2 → XP_017168774.1 CD247 antigen isoform X1

UniProtKB/Swiss-Prot

P24161, P29020, Q9D3G3

Conserved Domains (3) summary

smart00077
Location:69 → 89

ITAM; Immunoreceptor tyrosine-based activation motif

pfam02189
Location:139 → 158

ITAM; Immunoreceptor tyrosine-based activation motif

pfam11628
Location:28 → 58

TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain
XM_036156498.1 → XP_036012391.1 CD247 antigen isoform X1

UniProtKB/Swiss-Prot

P24161, P29020, Q9D3G3

Conserved Domains (3) summary

smart00077
Location:69 → 89

ITAM; Immunoreceptor tyrosine-based activation motif

pfam02189
Location:139 → 158

ITAM; Immunoreceptor tyrosine-based activation motif

pfam11628
Location:28 → 58

TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001113394.2: Suppressed sequence

Description

NM_001113394.2: This RefSeq was permanently suppressed because the transcript is a nonsense-mediated mRNA decay (NMD) candidate when it uses a supported upstream start codon.