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] See more...

Aliases for CRTAM Gene

Aliases for CRTAM Gene

  • Cytotoxic And Regulatory T Cell Molecule 2 3 5
  • Class-I MHC-Restricted T-Cell-Associated Molecule 3 4
  • Cytotoxic And Regulatory T-Cell Molecule 3 4
  • Class I MHC Restricted T Cell Associated Molecule 2
  • CD355 Antigen 4
  • CD355 3

External Ids for CRTAM Gene

Previous GeneCards Identifiers for CRTAM Gene

  • GC11P124710
  • GC11P124222
  • GC11P122743
  • GC11P122246
  • GC11P122214
  • GC11P118652

Summaries for CRTAM Gene

Entrez Gene Summary for CRTAM Gene

  • 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]

GeneCards Summary for CRTAM Gene

CRTAM (Cytotoxic And Regulatory T Cell Molecule) is a Protein Coding gene. Among its related pathways are Class I MHC mediated antigen processing and presentation and Innate Immune System. Gene Ontology (GO) annotations related to this gene include signaling receptor binding. An important paralog of this gene is CADM3.

UniProtKB/Swiss-Prot Summary for CRTAM Gene

  • Interaction with CADM1 promotes natural killer (NK) cell cytotoxicity and interferon-gamma (IFN-gamma) secretion by CD8+ cells in vitro as well as NK cell-mediated rejection of tumors expressing CADM3 in vivo.

Additional gene information for CRTAM Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CRTAM Gene

Genomics for CRTAM Gene

GeneHancer (GH) Regulatory Elements for CRTAM Gene

Promoters and enhancers for CRTAM Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J122837 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE dbSUPER 500.7 +1.1 1053 3 CREB1 ZBTB17 ZFHX2 ATF2 JUND ATF7 EGR2 ATF3 JUN CTCF CRTAM JHY ENSG00000285909
GH11J122882 Promoter/Enhancer 1.5 Ensembl ENCODE CraniofacialAtlas 19.2 +44.7 44670 2.6 PHF8 ZFX ZIC2 CLOCK ZBTB26 TRIM28 SAP30 RFX1 EZH2 POLR2A JHY CRTAM BSX RF00017-1055
GH11J122748 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 15.7 -89.3 -89306 1.2 FOS ZNF316 MEF2B NFE2 NR3C1 EZH2 BATF GATA3 MAFK POU2F2 CRTAM ENSG00000239079 UBASH3B lnc-BSX-1
GH11J122812 Enhancer 0.7 Ensembl ENCODE 22.9 -25.6 -25630 4.4 CTCF USF1 RAD21 POLR2A SMC3 GTF2F1 TBP NANOG TAF7 CEBPB CRTAM JHY lnc-BSX-1 ENSG00000285909 ENSG00000239079 UBASH3B
GH11J122815 Enhancer 0.8 Ensembl ENCODE dbSUPER 19.2 -21.4 -21449 2 CTBP1 DPF2 NFIB JUND CREB1 SP1 POLR2A CRTAM JHY lnc-BSX-1 ENSG00000285909 ENSG00000239079
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CRTAM on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CRTAM

Top Transcription factor binding sites by QIAGEN in the CRTAM gene promoter:
  • AML1a
  • IRF-1
  • IRF-2
  • NF-kappaB
  • NF-kappaB1
  • NF-kappaB2
  • Nkx2-5
  • RORalpha1

Genomic Locations for CRTAM Gene

Genomic Locations for CRTAM Gene
chr11:122,838,431-122,872,643
(GRCh38/hg38)
Size:
34,213 bases
Orientation:
Plus strand
chr11:122,709,208-122,743,347
(GRCh37/hg19)
Size:
34,140 bases
Orientation:
Plus strand

Genomic View for CRTAM Gene

Genes around CRTAM on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CRTAM Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CRTAM Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CRTAM Gene

Proteins for CRTAM Gene

  • Protein details for CRTAM Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95727-CRTAM_HUMAN
    Recommended name:
    Cytotoxic and regulatory T-cell molecule
    Protein Accession:
    O95727
    Secondary Accessions:
    • Q59EI1
    • Q6IRX2

    Protein attributes for CRTAM Gene

    Size:
    393 amino acids
    Molecular mass:
    44641 Da
    Quaternary structure:
    • Interacts with CADM1.
    SequenceCaution:
    • Sequence=BAD93067.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CRTAM Gene

    Alternative splice isoforms for CRTAM Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CRTAM Gene

Post-translational modifications for CRTAM Gene

  • Glycosylation at Asn21, Asn87, and Asn178
  • Modification sites at PhosphoSitePlus

Other Protein References for CRTAM Gene

No data available for DME Specific Peptides for CRTAM Gene

Domains & Families for CRTAM Gene

Gene Families for CRTAM Gene

Protein Domains for CRTAM Gene

Suggested Antigen Peptide Sequences for CRTAM Gene

GenScript: Design optimal peptide antigens:
  • Class-I MHC-restricted T-cell-associated molecule (CRTAM_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O95727

UniProtKB/Swiss-Prot:

CRTAM_HUMAN :
  • Belongs to the nectin family.
Family:
  • Belongs to the nectin family.
genes like me logo Genes that share domains with CRTAM: view

Function for CRTAM Gene

Molecular function for CRTAM Gene

UniProtKB/Swiss-Prot Function:
Interaction with CADM1 promotes natural killer (NK) cell cytotoxicity and interferon-gamma (IFN-gamma) secretion by CD8+ cells in vitro as well as NK cell-mediated rejection of tumors expressing CADM3 in vivo.

Phenotypes From GWAS Catalog for CRTAM Gene

Gene Ontology (GO) - Molecular Function for CRTAM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005102 signaling receptor binding IPI 15811952
genes like me logo Genes that share ontologies with CRTAM: view
genes like me logo Genes that share phenotypes with CRTAM: view

Animal Models for CRTAM Gene

MGI Knock Outs for CRTAM:

Animal Model Products

  • Taconic Biosciences Mouse Models for CRTAM

miRNA for CRTAM Gene

miRTarBase miRNAs that target CRTAM

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CRTAM Gene

Localization for CRTAM Gene

Subcellular locations from UniProtKB/Swiss-Prot for CRTAM Gene

Membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CRTAM gene
Compartment Confidence
plasma membrane 5
extracellular 2
cytoskeleton 1
peroxisome 1
nucleus 1
endoplasmic reticulum 1
cytosol 1

Gene Ontology (GO) - Cellular Components for CRTAM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS,IDA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with CRTAM: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CRTAM Gene

Pathways & Interactions for CRTAM Gene

genes like me logo Genes that share pathways with CRTAM: view

Pathways by source for CRTAM Gene

Gene Ontology (GO) - Biological Process for CRTAM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001913 NOT T cell mediated cytotoxicity IDA 15811952
GO:0002355 detection of tumor cell IDA 15811952
GO:0002376 immune system process IEA --
GO:0002860 positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target IDA 15811952
GO:0008037 cell recognition IDA 15811952
genes like me logo Genes that share ontologies with CRTAM: view

No data available for SIGNOR curated interactions for CRTAM Gene

Drugs & Compounds for CRTAM Gene

No Compound Related Data Available

Transcripts for CRTAM Gene

mRNA/cDNA for CRTAM Gene

2 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CRTAM Gene

No ASD Table

Relevant External Links for CRTAM Gene

GeneLoc Exon Structure for
CRTAM

Expression for CRTAM Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CRTAM Gene

mRNA differential expression in normal tissues according to GTEx for CRTAM Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x26.3) and Brain - Cerebellum (x22.3).

Protein differential expression in normal tissues from HIPED for CRTAM Gene

This gene is overexpressed in CD8 Tcells (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CRTAM Gene



Protein tissue co-expression partners for CRTAM Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CRTAM

SOURCE GeneReport for Unigene cluster for CRTAM Gene:

Hs.159523

mRNA Expression by UniProt/SwissProt for CRTAM Gene:

O95727-CRTAM_HUMAN
Tissue specificity: In the immune system, expression is restricted to activated class-I MHC-restricted cells, including NKT and CD8 cells. Strongly expressed in spleen, thymus, small intestine, peripheral blood leukocyte, and in Purkinje neurons in cerebellum. Expressed at much lower levels in testis, ovary, colon, lung and lymphoid tissues.

Evidence on tissue expression from TISSUES for CRTAM Gene

  • Nervous system(2.8)
  • Blood(2)
genes like me logo Genes that share expression patterns with CRTAM: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for CRTAM Gene

Orthologs for CRTAM Gene

This gene was present in the common ancestor of chordates.

Orthologs for CRTAM Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CRTAM 31 30
  • 99.07 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CRTAM 31 30
  • 84.9 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CRTAM 31 30
  • 83.5 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Crtam 17 31 30
  • 77.46 (n)
rat
(Rattus norvegicus)
Mammalia Crtam 30
  • 75.45 (n)
oppossum
(Monodelphis domestica)
Mammalia CRTAM 31
  • 61 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CRTAM 31
  • 53 (a)
OneToOne
chicken
(Gallus gallus)
Aves CRTAM 31 30
  • 56.29 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CRTAM 31
  • 35 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii LOC101884219 30
  • 47.12 (n)
BX120005.1 31
  • 26 (a)
OneToOne
Species where no ortholog for CRTAM was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CRTAM Gene

ENSEMBL:
Gene Tree for CRTAM (if available)
TreeFam:
Gene Tree for CRTAM (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CRTAM: view image

Paralogs for CRTAM Gene

genes like me logo Genes that share paralogs with CRTAM: view

Variants for CRTAM Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CRTAM Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
776673 Benign: not provided 122,851,732(+) C/A MISSENSE_VARIANT
776674 Benign: not provided 122,854,037(+) G/A SYNONYMOUS_VARIANT
776675 Benign: not provided 122,855,783(+) G/A SYNONYMOUS_VARIANT
778566 Benign: not provided 122,855,722(+) A/G MISSENSE_VARIANT
781238 Benign: not provided 122,850,068(+) A/C MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for CRTAM Gene

Structural Variations from Database of Genomic Variants (DGV) for CRTAM Gene

Variant ID Type Subtype PubMed ID
esv3627947 CNV gain 21293372
nsv1133175 CNV tandem duplication 24896259
nsv1140492 CNV tandem duplication 24896259
nsv480269 CNV novel sequence insertion 20440878
nsv520988 CNV gain 19592680
nsv556481 CNV loss 21841781
nsv556482 CNV loss 21841781

Variation tolerance for CRTAM Gene

Residual Variation Intolerance Score: 46.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.36; 76.90% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CRTAM Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CRTAM

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CRTAM Gene

Disorders for CRTAM Gene

Additional Disease Information for CRTAM

No disorders were found for CRTAM Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CRTAM Gene

Publications for CRTAM Gene

  1. Human class-I restricted T cell associated molecule is highly expressed in the cerebellum and is a marker for activated NKT and CD8+ T lymphocytes. (PMID: 16300832) Patiño-Lopez G … Zlotnik A (Journal of neuroimmunology 2006) 2 3 4 54
  2. A molecular analysis of NKT cells: identification of a class-I restricted T cell-associated molecule (CRTAM). (PMID: 10811014) Kennedy J … Zlotnik A (Journal of leukocyte biology 2000) 2 3 4 54
  3. Characterization of CRTAM gene promoter: AP-1 transcription factor control its expression in human T CD8 lymphocytes. (PMID: 19695707) Valle-Rios R … Ortiz-Navarrete V (Molecular immunology 2009) 3 23 54
  4. Nectin-like protein 2 defines a subset of T-cell zone dendritic cells and is a ligand for class-I-restricted T-cell-associated molecule. (PMID: 15781451) Galibert L … Yan W (The Journal of biological chemistry 2005) 3 4 54
  5. The tumor suppressor TSLC1/NECL-2 triggers NK-cell and CD8+ T-cell responses through the cell-surface receptor CRTAM. (PMID: 15811952) Boles KS … Colonna M (Blood 2005) 3 4 54

Products for CRTAM Gene

Sources for CRTAM Gene