Aliases for TRAT1 Gene

Aliases for TRAT1 Gene

  • T Cell Receptor Associated Transmembrane Adaptor 1 2 3 5
  • TCRIM 2 3 4
  • TRIM 2 3 4
  • T-Cell Receptor-Associated Transmembrane Adapter 1 3 4
  • HSPC062 2 3
  • Pp29/30 3 4
  • T Cell Receptor Interacting Molecule 3
  • T-Cell Receptor-Interacting Molecule 4
  • TRAT1 5

External Ids for TRAT1 Gene

Previous HGNC Symbols for TRAT1 Gene


Previous GeneCards Identifiers for TRAT1 Gene

  • GC03P110026
  • GC03P108541
  • GC03P105915

Summaries for TRAT1 Gene

GeneCards Summary for TRAT1 Gene

TRAT1 (T Cell Receptor Associated Transmembrane Adaptor 1) is a Protein Coding gene. Diseases associated with TRAT1 include Autosomal Recessive Limb-Girdle Muscular Dystrophy Type 2H and Inclusion Conjunctivitis. Among its related pathways are RET signaling and Signaling by GPCR. Gene Ontology (GO) annotations related to this gene include transmembrane receptor protein tyrosine kinase adaptor activity.

UniProtKB/Swiss-Prot Summary for TRAT1 Gene

  • Stabilizes the TCR (T-cell antigen receptor)/CD3 complex at the surface of T-cells.

Gene Wiki entry for TRAT1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TRAT1 Gene

Genomics for TRAT1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TRAT1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J108820 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE dbSUPER 250.7 +1.6 1624 8.4 FEZF1 ZNF384 L3MBTL2 PKNOX1 CTBP1 POLR2A MNT HSALNG0027923 TRAT1 DZIP3 RETNLB MYH15 CIP2A HSALNG0027924 GUCA1C
GH03J108862 Enhancer 0.8 Ensembl ENCODE dbSUPER 11.4 +40.6 40579 1.9 JUND USF2 MAFK TOE1 FOS EP300 CEBPB HSALNG0027927 TRAT1 HSALNG0027924 lnc-GUCA1C-2 HSALNG0027926 GUCA1C
GH03J108915 Enhancer 0.8 Ensembl ENCODE 10.9 +92.4 92375 0.7 ZNF654 REST TRIM22 CTCF SIN3A RAD21 RFX5 IRF4 SMC3 YY1 lnc-TRAT1-7 TRAT1 RF00017-3672 GUCA1C
GH03J108833 Enhancer 0.5 FANTOM5 ENCODE dbSUPER 7.9 +11.8 11844 2.7 TRAT1 HSALNG0027923 HSALNG0027924 GUCA1C
GH03J108859 Enhancer 0.3 Ensembl dbSUPER 11.4 +37.2 37231 0.4 TRAT1 HSALNG0027927 HSALNG0027924 GUCA1C
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TRAT1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TRAT1

Top Transcription factor binding sites by QIAGEN in the TRAT1 gene promoter:
  • AML1a
  • AREB6
  • c-Myc
  • Max
  • MyoD
  • Sox5
  • STAT3
  • TBP

Genomic Locations for TRAT1 Gene

Latest Assembly
32,236 bases
Plus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
32,220 bases
Plus strand

(GRCh37/hg19 by Ensembl)
32,308 bases
Plus strand

Genomic View for TRAT1 Gene

Genes around TRAT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRAT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRAT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TRAT1 Gene

Proteins for TRAT1 Gene

  • Protein details for TRAT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    T-cell receptor-associated transmembrane adapter 1
    Protein Accession:
    Secondary Accessions:
    • Q9NZX5

    Protein attributes for TRAT1 Gene

    186 amino acids
    Molecular mass:
    21211 Da
    Quaternary structure:
    • Homodimer; disulfide-linked. Interacts with CD3Z. When phosphorylated, interacts with PIK3R1.
    • Sequence=AAF29034.1; Type=Frameshift; Evidence={ECO:0000305};

neXtProt entry for TRAT1 Gene

Post-translational modifications for TRAT1 Gene

  • Phosphorylated on tyrosines by LCK or FYN upon TCR activation.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for TRAT1 Gene

No data available for DME Specific Peptides for TRAT1 Gene

Domains & Families for TRAT1 Gene

Gene Families for TRAT1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for TRAT1 Gene

Suggested Antigen Peptide Sequences for TRAT1 Gene

GenScript: Design optimal peptide antigens:
  • pp29/30 (TRAT1_HUMAN)
genes like me logo Genes that share domains with TRAT1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for TRAT1 Gene

Function for TRAT1 Gene

Molecular function for TRAT1 Gene

UniProtKB/Swiss-Prot Function:
Stabilizes the TCR (T-cell antigen receptor)/CD3 complex at the surface of T-cells.

Phenotypes From GWAS Catalog for TRAT1 Gene

Gene Ontology (GO) - Molecular Function for TRAT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005068 transmembrane receptor protein tyrosine kinase adaptor activity TAS 9687533
GO:0005515 protein binding IPI 32296183
genes like me logo Genes that share ontologies with TRAT1: view
genes like me logo Genes that share phenotypes with TRAT1: view

Animal Models for TRAT1 Gene

MGI Knock Outs for TRAT1:

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRAT1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for TRAT1 Gene

Localization for TRAT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TRAT1 Gene

Cell membrane. Single-pass type III membrane protein.

Subcellular locations from

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 TRAT1 gene
Compartment Confidence
plasma membrane 5
extracellular 4
endoplasmic reticulum 3
cytoskeleton 2
mitochondrion 2
nucleus 2
endosome 2
cytosol 2
lysosome 2
peroxisome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Centriolar satellite (4)
  • Plasma membrane (4)
  • Mitotic spindle (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TRAT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IDA,TAS --
GO:0005887 integral component of plasma membrane TAS 9687533
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0034451 centriolar satellite IDA --
genes like me logo Genes that share ontologies with TRAT1: view

Pathways & Interactions for TRAT1 Gene

genes like me logo Genes that share pathways with TRAT1: view

Pathways by source for TRAT1 Gene

3 GeneGo (Thomson Reuters) pathways for TRAT1 Gene
  • Immune response ICOS pathway in T-helper cell
  • Immune response NFAT in immune response
  • Immune response T cell receptor signaling pathway
3 Qiagen pathways for TRAT1 Gene
  • CTLA4 Signaling
  • ICos-ICosL Pathway in T-Helper Cell
  • TCR Signaling

Gene Ontology (GO) - Biological Process for TRAT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001920 negative regulation of receptor recycling IDA 11390434
GO:0002250 adaptive immune response IEA --
GO:0002376 immune system process IEA --
GO:0006968 cellular defense response TAS 9687533
GO:0007165 signal transduction TAS 9687533
genes like me logo Genes that share ontologies with TRAT1: view

No data available for SIGNOR curated interactions for TRAT1 Gene

Drugs & Compounds for TRAT1 Gene

No Compound Related Data Available

Transcripts for TRAT1 Gene

mRNA/cDNA for TRAT1 Gene

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

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRAT1

Alternative Splicing Database (ASD) splice patterns (SP) for TRAT1 Gene

No ASD Table

Relevant External Links for TRAT1 Gene

GeneLoc Exon Structure for

Expression for TRAT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TRAT1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for TRAT1 Gene

This gene is overexpressed in Whole Blood (x20.8), Spleen (x6.3), and Small Intestine - Terminal Ileum (x4.9).

Protein differential expression in normal tissues from HIPED for TRAT1 Gene

This gene is overexpressed in CD8 Tcells (30.3), CD4 Tcells (26.0), and Peripheral blood mononuclear cells (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TRAT1 Gene

Protein tissue co-expression partners for TRAT1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TRAT1

SOURCE GeneReport for Unigene cluster for TRAT1 Gene:


mRNA Expression by UniProt/SwissProt for TRAT1 Gene:

Tissue specificity: Strongly expressed in thymus, and to a lesser extent in spleen, lymph node and peripheral blood lymphocytes. Present in T-cells and NK cells, but not B-cells (at protein level).

Evidence on tissue expression from TISSUES for TRAT1 Gene

  • Blood(4.5)
  • Pancreas(4.2)
  • Lymph node(2.6)
  • Spleen(2.6)
  • Intestine(2.4)
  • Lung(2.2)
  • Skin(2.1)
  • Nervous system(2)
genes like me logo Genes that share expression patterns with TRAT1: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for TRAT1 Gene

Orthologs for TRAT1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for TRAT1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia TRAT1 29 30
  • 99.28 (n)
(Canis familiaris)
Mammalia TRAT1 29 30
  • 82.34 (n)
(Mus musculus)
Mammalia Trat1 29 16 30
  • 80.54 (n)
(Rattus norvegicus)
Mammalia Trat1 29
  • 79.35 (n)
(Bos Taurus)
Mammalia TRAT1 29 30
  • 79.17 (n)
(Monodelphis domestica)
Mammalia TRAT1 30
  • 51 (a)
(Ornithorhynchus anatinus)
Mammalia TRAT1 30
  • 49 (a)
(Gallus gallus)
Aves TRAT1 29 30
  • 58.16 (n)
Species where no ortholog for TRAT1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Lizard (Anolis carolinensis)
  • 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 Vase (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)
  • Zebrafish (Danio rerio)

Evolution for TRAT1 Gene

Gene Tree for TRAT1 (if available)
Gene Tree for TRAT1 (if available)
Evolutionary constrained regions (ECRs) for TRAT1: view image
Alliance of Genome Resources:
Additional Orthologs for TRAT1

Paralogs for TRAT1 Gene

No data available for Paralogs for TRAT1 Gene

Variants for TRAT1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TRAT1 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
rs144073270 Benign: not provided 108,849,207(+) C/T
NM_016388.4(TRAT1):c.256C>T (p.Pro86Ser)
rs57744779 -- p.Asp137Gly
rs61585973 -- p.Ser148Pro

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TRAT1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for TRAT1 Gene

Variant ID Type Subtype PubMed ID
dgv4834n100 CNV loss 25217958
dgv4835n100 CNV gain 25217958
esv3568956 CNV loss 25503493
esv3597329 CNV gain 21293372
esv3597330 CNV gain 21293372
esv3597331 CNV loss 21293372
nsv508236 CNV deletion 20534489
nsv521830 CNV loss 19592680
nsv522119 CNV gain 19592680
nsv829661 CNV gain 17160897
nsv829662 CNV gain 17160897

Variation tolerance for TRAT1 Gene

Residual Variation Intolerance Score: 82.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.80; 47.50% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TRAT1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
Leiden Open Variation Database (LOVD)

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRAT1 Gene

Disorders for TRAT1 Gene

MalaCards: The human disease database

(5) MalaCards diseases for TRAT1 Gene - From: COP

Disorder Aliases PubMed IDs
autosomal recessive limb-girdle muscular dystrophy type 2h
  • lgmd2h
inclusion conjunctivitis
  • adult inclusion conjunctivitis
opitz-gbbb syndrome
  • opitz g/bbb syndrome
mulibrey nanism
  • muscle-liver-brain-eye nanism
bone cancer
  • bone neoplasm
- elite association - COSMIC cancer census association via MalaCards
Search TRAT1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for TRAT1

genes like me logo Genes that share disorders with TRAT1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TRAT1 Gene

Publications for TRAT1 Gene

  1. Genomic organization and chromosomal localization of the human gene encoding the T-cell receptor-interacting molecule (TRIM). (PMID: 10663578) Hübener C … Bruyns E (Immunogenetics 2000) 2 3 22
  2. T cell receptor (TCR) interacting molecule (TRIM), a novel disulfide-linked dimer associated with the TCR-CD3-zeta complex, recruits intracellular signaling proteins to the plasma membrane. (PMID: 9687533) Bruyns E … Schraven B (The Journal of experimental medicine 1998) 2 3 4
  3. Transmembrane adaptor molecules: a new category of lymphoid-cell markers. (PMID: 16160011) Tedoldi S … Horejsí V (Blood 2006) 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. The transmembrane adaptor protein TRIM regulates T cell receptor (TCR) expression and TCR-mediated signaling via an association with the TCR zeta chain. (PMID: 11390434) Kirchgessner H … Schraven B (The Journal of experimental medicine 2001) 3 4

Products for TRAT1 Gene

Sources for TRAT1 Gene