CRTAM cytotoxic and regulatory T cell molecule [Homo sapiens (human)] - Gene

Summary

Official Symbol: CRTAMprovided by HGNC
Official Full Name: cytotoxic and regulatory T cell moleculeprovided by HGNC
Primary source: HGNC:HGNC:24313
See related: Ensembl:ENSG00000109943 MIM:612597; AllianceGenome:HGNC:24313
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CD355
Summary: The CRTAM gene is upregulated in CD4 (see MIM 186940)-positive and CD8 (see CD8A; MIM 186910)-positive T cells and encodes a type I transmembrane protein with V and C1-like Ig domains (Yeh et al., 2008 [PubMed 18329370]).[supplied by OMIM, Feb 2009]
Expression: Biased expression in lymph node (RPKM 4.2), spleen (RPKM 1.7) and 11 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11q24.1

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (122838500..122872643)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (122866290..122900405)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (122709208..122743351)

Chromosome 11 - NC_000011.10 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: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CRTAM promotes antitumor immune response in triple negative breast cancer by enhancing CD8+ T cell infiltration.
Title: CRTAM promotes antitumor immune response in triple negative breast cancer by enhancing CD8+ T cell infiltration.
Prokaryotic Expression of the Immunoglobulin's Domains of CRTAM to Characterize a Monoclonal Antibody.
Title: Prokaryotic Expression of the Immunoglobulin's Domains of CRTAM to Characterize a Monoclonal Antibody.
The findings suggest, for the first time, that the tumor microenvironment in acute lymphoblastic leukemia directly contribute to exhaustion of NK cell functions by the CRTAM/Necl-2 interaction, and that the potential regulatory role of exhausted-like NK cells may favor malignant progression at the expense of anti-tumor responses.
Title: CRTAM(+) NK cells endowed with suppressor properties arise in leukemic bone marrow.
These results reveal that CRTAM is critical to instruct the differentiation of CD4(+)CTL through the induction of Eomes and CTL-related gene.
Title: CRTAM determines the CD4+ cytotoxic T lymphocyte lineage.
CRTAM is negatively regulated by ZEB1 in T cells.
Title: CRTAM is negatively regulated by ZEB1 in T cells.
Case-control studies reveal malignant mesothelioma risk associated with variants in the SDK1, CRTAM and RASGRF2 genes.
Title: A genome-wide association study for malignant mesothelioma risk.
The cell adhesion molecule Necl-2 competitively binds the immune receptor CRTAM.
Title: Competition of cell adhesion and immune recognition: insights into the interaction between CRTAM and nectin-like 2.
The expression of CRTAM in activated Vgamma9Vdelta2 T cells is quickly downregulated following interaction with Necl-2 on tumor cells.
Title: CRTAM receptor engagement by Necl-2 on tumor cells triggers cell death of activated Vγ9Vδ2 T cells.
Three common variants in the class I MHC-restricted T cell-associated molecule gene were identified that were associated with an increased rate of asthma exacerbations based on the presence of a low circulating vitamin D level.
Title: Genome-wide association study reveals class I MHC-restricted T cell-associated molecule gene (CRTAM) variants interact with vitamin D levels to affect asthma exacerbations.
Results show that CRTAM is a molecule involved in epithelial cell adhesion.
Title: CRTAM: A molecule involved in epithelial cell adhesion.

Submit: New GeneRIF Correction See all GeneRIFs (13)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

General gene information

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Markers

D11S4402 (e-PCR)
- UniSTS:83298

L77857 (e-PCR)
- UniSTS:17073

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables signaling receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables signaling receptor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
NOT involved_in T cell mediated cytotoxicity	IDA Inferred from Direct Assay more info	PubMed
NOT involved_in activated T cell proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in cell recognition	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell recognition	IDA Inferred from Direct Assay more info	PubMed
involved_in detection of stimulus	IDA Inferred from Direct Assay more info	PubMed
involved_in detection of tumor cell	IBA Inferred from Biological aspect of Ancestor more info
involved_in detection of tumor cell	IDA Inferred from Direct Assay more info	PubMed
involved_in establishment of T cell polarity	ISS Inferred from Sequence or Structural Similarity more info
involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules	ISS Inferred from Sequence or Structural Similarity more info
involved_in lymphocyte migration into lymphoid organs	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of activated T cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cytokine production	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of natural killer cell mediated cytotoxicity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of type II interferon production	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of CD8-positive, alpha-beta T cell activation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of T cell activation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of T cell differentiation	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in immunological synapse	ISS Inferred from Sequence or Structural Similarity more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: cytotoxic and regulatory T-cell molecule

Names: class-I MHC-restricted T-cell-associated molecule

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_001304782.2 → NP_001291711.1 cytotoxic and regulatory T-cell molecule isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) represents use of an alternate promoter and therefore differs in the 5' UTR and 5' coding region, compared to variant 1. These differences cause translation initiation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AB209830, AF001622, AP004318, BC070266, DC305734

Consensus CDS

CCDS76489.1

UniProtKB/TrEMBL

B4DE52

Related

ENSP00000433728.1, ENST00000533709.1
NM_019604.4 → NP_062550.2 cytotoxic and regulatory T-cell molecule isoform 1 precursor

See identical proteins and their annotated locations for NP_062550.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AB209830, AF001622, AP004318, BC070266

Consensus CDS

CCDS8437.1

UniProtKB/Swiss-Prot

O95727, Q59EI1, Q6IRX2

UniProtKB/TrEMBL

B2R902

Related

ENSP00000227348.4, ENST00000227348.9

Conserved Domains (2) summary

smart00410
Location:24 → 114

IG_like; Immunoglobulin like

cl11960
Location:20 → 114

Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

122838500..122872643

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011542900.3 → XP_011541202.1 cytotoxic and regulatory T-cell molecule isoform X1

UniProtKB/TrEMBL

B2R902

Conserved Domains (1) summary

cl11960
Location:20 → 65

Ig; Immunoglobulin domain