Aliases for TARM1 Gene

Aliases for TARM1 Gene

  • T Cell-Interacting, Activating Receptor On Myeloid Cells 1 2 3 5
  • T-Cell-Interacting, Activating Receptor On Myeloid Cells Protein 1 3 4
  • OSCAR-Like Transcript-2 Protein 3 4
  • OLT-2 3 4
  • TARM1 5

External Ids for TARM1 Gene

Previous GeneCards Identifiers for TARM1 Gene

  • GC19M059265
  • GC19M054573
  • GC19M050888

Summaries for TARM1 Gene

GeneCards Summary for TARM1 Gene

TARM1 (T Cell-Interacting, Activating Receptor On Myeloid Cells 1) is a Protein Coding gene. Diseases associated with TARM1 include Retinitis Pigmentosa. Among its related pathways are Innate Immune System. An important paralog of this gene is IGSF1.

UniProtKB/Swiss-Prot Summary for TARM1 Gene

  • May act as receptor (By similarity). Negatively regulates TCR-mediated CD4(+) T cell proliferation and activation, possibly by binding an unknown ligand on the T cell surface (PubMed:26311901). Enhances Toll-like receptor-mediated production of pro-inflammatory cytokines by macrophages and neutrophils (By similarity).

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TARM1 Gene

Genomics for TARM1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TARM1 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
GH19J054078 Enhancer 0.5 Ensembl 13.3 +2.4 2364 6.8 SPI1 ATF4 TRIM28 ZNF366 ATF3 ZNF24 ZNF512 TARM1 OSCAR VSTM1
GH19J054199 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 1.3 -124.2 -124224 12.4 BCLAF1 SP1 ZNF207 ZNF600 NCOR1 MYC IKZF1 SSRP1 ZNF580 ZNF592 RPS9 HSALNG0127488 PRPF31 LENG8-AS1 LENG8 CNOT3 ZNF525 ENSG00000235681 ZNF845 ZNF761
GH19J054270 Promoter/Enhancer 0.9 FANTOM5 Ensembl ENCODE dbSUPER 1.9 -189.9 -189933 0.2 HSALNG0127502 MN297614 LAIR1 OSCAR LILRB2 MYADM LILRB3 LILRA5 VSTM1 LILRB1
GH19J054373 Promoter/Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 1.1 -293.6 -293552 2.7 YY1 TRIM22 MAFF ZNF316 CBFB SMARCA5 NFE2 MAFK BHLHE40 SPI1 HSALNG0127520 HSALNG0127521 FCAR LAIR1 LILRB2 OSCAR LILRA5 VSTM1 LILRB3 LILRB4
GH19J054018 Enhancer 1.1 FANTOM5 ENCODE 1.3 +60.2 60248 6.8 NCOR1 ZNF654 IKZF1 CEBPA CTCF REST CEBPB BHLHE40 ZEB1 MAX LILRB3 VSTM1 LILRA5 OSCAR MYADM LILRB2 NLRP12 LAIR1 CACNG8 LILRA6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TARM1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TARM1

Genomic Locations for TARM1 Gene

Latest Assembly
chr19:54,069,895-54,081,365
(GRCh38/hg38)
Size:
11,471 bases
Orientation:
Minus strand

Previous Assembly
chr19:54,573,149-54,584,634
(GRCh37/hg19 by Entrez Gene)
Size:
11,486 bases
Orientation:
Minus strand

chr19:54,573,149-54,584,634
(GRCh37/hg19 by Ensembl)
Size:
11,486 bases
Orientation:
Minus strand

Alternative Locations (GRCh38/hg38)

  • chr19(ALT_REF_LOCI_1):44,262-55,747 (-)
  • chr19(ALT_REF_LOCI_2):44,262-55,747 (-)
  • chr19(ALT_REF_LOCI_3):44,262-55,747 (-)
  • chr19(ALT_REF_LOCI_4):44,262-55,747 (-)
  • chr19(ALT_REF_LOCI_5):44,262-55,747 (-)
  • chr19(ALT_REF_LOCI_6):44,262-55,747 (-)
  • chr19(ALT_REF_LOCI_7):44,262-55,747 (-)
  • chr19(ALT_REF_LOCI_8):44,262-55,747 (-)
  • chr19(ALT_REF_LOCI_9):44,262-55,747 (-)

Genomic View for TARM1 Gene

Genes around TARM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TARM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TARM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TARM1 Gene

Proteins for TARM1 Gene

  • Protein details for TARM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    B6A8C7-TARM1_HUMAN
    Recommended name:
    T-cell-interacting, activating receptor on myeloid cells protein 1
    Protein Accession:
    B6A8C7
    Secondary Accessions:
    • B4DWY4

    Protein attributes for TARM1 Gene

    Size:
    271 amino acids
    Molecular mass:
    29474 Da
    Quaternary structure:
    • Interacts with Fc receptor gamma chain FCER1G.

    Alternative splice isoforms for TARM1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TARM1 Gene

Post-translational modifications for TARM1 Gene

Other Protein References for TARM1 Gene

No data available for DME Specific Peptides for TARM1 Gene

Domains & Families for TARM1 Gene

Gene Families for TARM1 Gene

Protein Domains for TARM1 Gene

Suggested Antigen Peptide Sequences for TARM1 Gene

GenScript: Design optimal peptide antigens:
  • OSCAR-like transcript-2 protein (TARM1_HUMAN)
genes like me logo Genes that share domains with TARM1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for TARM1 Gene

Function for TARM1 Gene

Molecular function for TARM1 Gene

UniProtKB/Swiss-Prot Function:
May act as receptor (By similarity). Negatively regulates TCR-mediated CD4(+) T cell proliferation and activation, possibly by binding an unknown ligand on the T cell surface (PubMed:26311901). Enhances Toll-like receptor-mediated production of pro-inflammatory cytokines by macrophages and neutrophils (By similarity).

Phenotypes From GWAS Catalog for TARM1 Gene

Gene Ontology (GO) - Molecular Function for TARM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0034987 immunoglobulin receptor binding IPI 26311901
genes like me logo Genes that share ontologies with TARM1: view
genes like me logo Genes that share phenotypes with TARM1: view

Animal Models for TARM1 Gene

MGI Knock Outs for TARM1:

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TARM1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for TARM1 Gene

Localization for TARM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TARM1 Gene

Cell 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 TARM1 gene
Compartment Confidence
plasma membrane 5
extracellular 1
peroxisome 1
lysosome 0

Gene Ontology (GO) - Cellular Components for TARM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0035579 specific granule membrane TAS --
GO:0070821 tertiary granule membrane TAS --
genes like me logo Genes that share ontologies with TARM1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TARM1 Gene

Pathways & Interactions for TARM1 Gene

PathCards logo

SuperPathways for TARM1 Gene

genes like me logo Genes that share pathways with TARM1: view

Pathways by source for TARM1 Gene

3 Reactome pathways for TARM1 Gene

Interacting Proteins for TARM1 Gene

Gene Ontology (GO) - Biological Process for TARM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002250 adaptive immune response IEA --
GO:0002376 immune system process IEA --
GO:0043312 neutrophil degranulation TAS --
GO:0045087 innate immune response IEA --
GO:2000515 negative regulation of CD4-positive, alpha-beta T cell activation IDA 26311901
genes like me logo Genes that share ontologies with TARM1: view

No data available for SIGNOR curated interactions for TARM1 Gene

Drugs & Compounds for TARM1 Gene

No Compound Related Data Available

Transcripts for TARM1 Gene

mRNA/cDNA for TARM1 Gene

2 REFSEQ mRNAs :
2 NCBI additional mRNA sequence :
2 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 TARM1

Alternative Splicing Database (ASD) splice patterns (SP) for TARM1 Gene

No ASD Table

Relevant External Links for TARM1 Gene

GeneLoc Exon Structure for
TARM1

Expression for TARM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TARM1 Gene

mRNA differential expression in normal tissues according to GTEx for TARM1 Gene

This gene is overexpressed in Whole Blood (x47.1).

Protein differential expression in normal tissues from HIPED for TARM1 Gene

This gene is overexpressed in Fetal gut (35.5) and Kidney (33.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for TARM1 Gene



Protein tissue co-expression partners for TARM1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TARM1

SOURCE GeneReport for Unigene cluster for TARM1 Gene:

Hs.694674

mRNA Expression by UniProt/SwissProt for TARM1 Gene:

B6A8C7-TARM1_HUMAN
Tissue specificity: Expressed in fetal and adult liver, lung, testis, thymus and spleen. Expressed in blood neutrophils.

Evidence on tissue expression from TISSUES for TARM1 Gene

  • Bone marrow(4.2)
genes like me logo Genes that share expression patterns with TARM1: view

Primer products for research

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 TARM1 Gene

Orthologs for TARM1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for TARM1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia TARM1 29 30
  • 99.14 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LOC484314 29
  • 74.3 (n)
-- 30
  • 56 (a)
OneToMany
-- 30
  • 38 (a)
OneToMany
Cow
(Bos Taurus)
Mammalia TARM1 29 30
  • 69.05 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Tarm1 29 16 30
  • 65.65 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Tarm1 29
  • 64.95 (n)
Oppossum
(Monodelphis domestica)
Mammalia -- 30
  • 38 (a)
OneToMany
-- 30
  • 32 (a)
OneToMany
-- 30
  • 32 (a)
OneToMany
-- 30
  • 30 (a)
OneToMany
-- 30
  • 28 (a)
OneToMany
-- 30
  • 23 (a)
OneToMany
-- 30
  • 22 (a)
OneToMany
-- 30
  • 21 (a)
OneToMany
-- 30
  • 20 (a)
OneToMany
-- 30
  • 18 (a)
OneToMany
-- 30
  • 18 (a)
OneToMany
-- 30
  • 18 (a)
OneToMany
-- 30
  • 18 (a)
OneToMany
-- 30
  • 17 (a)
OneToMany
-- 30
  • 15 (a)
OneToMany
-- 30
  • 15 (a)
OneToMany
-- 30
  • 12 (a)
OneToMany
Platypus
(Ornithorhynchus anatinus)
Mammalia TARM1 30
  • 23 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 12 (a)
OneToMany
Species where no ortholog for TARM1 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)
  • Chicken (Gallus gallus)
  • 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 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 TARM1 Gene

ENSEMBL:
Gene Tree for TARM1 (if available)
TreeFam:
Gene Tree for TARM1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TARM1: view image
Alliance of Genome Resources:
Additional Orthologs for TARM1

Paralogs for TARM1 Gene

(3) SIMAP similar genes for TARM1 Gene using alignment to 1 proteins:

  • TARM1_HUMAN
genes like me logo Genes that share paralogs with TARM1: view

Variants for TARM1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TARM1 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
rs17305269 -- p.Ser37Pro
rs77768804 -- p.Arg258Trp
rs80087697 -- p.Arg111His

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TARM1 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 TARM1 Gene

Variant ID Type Subtype PubMed ID
dgv3653n100 CNV gain 25217958
esv2718812 CNV deletion 23290073
esv2718852 CNV deletion 23290073
esv29726 CNV gain 19812545
esv3379140 CNV insertion 20981092
esv3893246 CNV gain 25118596
nsv1056177 CNV gain 25217958
nsv182 CNV deletion 15895083
nsv2542 CNV deletion 18451855
nsv458782 CNV gain 19166990
nsv470157 CNV loss 18288195
nsv510773 CNV deletion 20534489
nsv580110 CNV gain 21841781
nsv833877 CNV loss 17160897

Variation tolerance for TARM1 Gene

Gene Damage Index Score: 4.31; 62.91% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TARM1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TARM1
Leiden Open Variation Database (LOVD)
TARM1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TARM1 Gene

Disorders for TARM1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for TARM1 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
retinitis pigmentosa
  • rp
- elite association - COSMIC cancer census association via MalaCards
Search TARM1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for TARM1

genes like me logo Genes that share disorders with TARM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TARM1 Gene

Publications for TARM1 Gene

  1. TARM1 Is a Novel Leukocyte Receptor Complex-Encoded ITAM Receptor That Costimulates Proinflammatory Cytokine Secretion by Macrophages and Neutrophils. (PMID: 26311901) Radjabova V … Barrow AD (Journal of immunology (Baltimore, Md. : 1950) 2015) 3 4
  2. Breakpoint characterization of a novel approximately 59 kb genomic deletion on 19q13.42 in autosomal-dominant retinitis pigmentosa with incomplete penetrance. (PMID: 19050727) Köhn L … Golovleva I (European journal of human genetics : EJHG 2009) 3
  3. The DNA sequence and biology of human chromosome 19. (PMID: 15057824) Grimwood J … Lucas SM (Nature 2004) 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 4

Products for TARM1 Gene

Sources for TARM1 Gene