Free for academic non-profit institutions. Other users need a Commercial license

Aliases for TIMD4 Gene

Aliases for TIMD4 Gene

  • T Cell Immunoglobulin And Mucin Domain Containing 4 2 3 5
  • T-Cell Immunoglobulin Mucin Receptor 4 3 4
  • T-Cell Membrane Protein 4 3 4
  • TIMD-4 3 4
  • TIM-4 3 4
  • TIM4 3 4
  • T-Cell Immunoglobulin And Mucin Domain-Containing Protein 4 3
  • T-Cell Immunoglobulin And Mucin Domain Containing 4 2
  • SMUCKLER 3

External Ids for TIMD4 Gene

Previous GeneCards Identifiers for TIMD4 Gene

  • GC05M156278
  • GC05M151439
  • GC05M156346

Summaries for TIMD4 Gene

GeneCards Summary for TIMD4 Gene

TIMD4 (T Cell Immunoglobulin And Mucin Domain Containing 4) is a Protein Coding gene. Among its related pathways are T Cell Co-Signaling Pathway: Ligand-Receptor Interactions. An important paralog of this gene is HAVCR1.

UniProtKB/Swiss-Prot for TIMD4 Gene

  • Phosphatidylserine receptor that enhances the engulfment of apoptotic cells. Involved in regulating T-cell proliferation and lymphotoxin signaling. Ligand for HAVCR1/TIMD1 (By similarity).

Additional gene information for TIMD4 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TIMD4 Gene

Genomics for TIMD4 Gene

GeneHancer (GH) Regulatory Elements for TIMD4 Gene

Promoters and enhancers for TIMD4 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
GH05J156972 Promoter 0.5 EPDnew 650.7 -0.1 -58 0.1 TIMD4 HAVCR1
GH05J156963 Promoter 0.5 EPDnew 650.4 +9.1 9064 0.1 TIMD4 GC05M156933
GH05J157105 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 10.1 -135.9 -135923 5.1 HDGF KLF1 SMAD1 RB1 EBF1 IRF4 POLR2A EED ATF7 IKZF2 HAVCR2 ITK MED7 TIMD4 HAVCR1 ENSG00000254246 PIR42544
GH05J156912 Enhancer 1.1 Ensembl ENCODE dbSUPER 11.1 +58.4 58364 3 PKNOX1 SIN3A ETS1 POLR2A EED ATF7 ETV6 IKZF2 ZNF687 NANOG TIMD4 GC05P156904 APOOP1
GH05J157069 Promoter/Enhancer 1.1 EPDnew ENCODE 10.6 -97.6 -97555 1.2 CTCF ZNF3 HLF CEBPB CEBPG RAD21 NFIL3 CEBPA KDM1A NR2F6 HAVCR1 TIMD4 ITK MED7 HAVCR2 GC05P157080
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TIMD4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TIMD4 gene promoter:
  • IRF-1
  • HNF-4alpha2
  • HNF-4alpha1
  • Evi-1
  • PPAR-gamma2
  • PPAR-gamma1
  • Nkx2-5
  • AP-1
  • XBP-1
  • ISGF-3

Genomic Locations for TIMD4 Gene

Genomic Locations for TIMD4 Gene
chr5:156,919,282-156,972,310
(GRCh38/hg38)
Size:
53,029 bases
Orientation:
Minus strand
chr5:156,346,293-156,390,266
(GRCh37/hg19)
Size:
43,974 bases
Orientation:
Minus strand

Genomic View for TIMD4 Gene

Genes around TIMD4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TIMD4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TIMD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TIMD4 Gene

Proteins for TIMD4 Gene

  • Protein details for TIMD4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96H15-TIMD4_HUMAN
    Recommended name:
    T-cell immunoglobulin and mucin domain-containing protein 4
    Protein Accession:
    Q96H15
    Secondary Accessions:
    • B5MCL9

    Protein attributes for TIMD4 Gene

    Size:
    378 amino acids
    Molecular mass:
    41578 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for TIMD4 Gene

    Alternative splice isoforms for TIMD4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TIMD4 Gene

Post-translational modifications for TIMD4 Gene

  • Glycosylation at posLast=291291
  • Modification sites at PhosphoSitePlus

Other Protein References for TIMD4 Gene

No data available for DME Specific Peptides for TIMD4 Gene

Domains & Families for TIMD4 Gene

Gene Families for TIMD4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted membrane proteins

Protein Domains for TIMD4 Gene

Suggested Antigen Peptide Sequences for TIMD4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96H15

UniProtKB/Swiss-Prot:

TIMD4_HUMAN :
  • Recognizes phosphatidyl serine via its immunoglobulin domain.
  • Belongs to the immunoglobulin superfamily. TIM family.
Domain:
  • Recognizes phosphatidyl serine via its immunoglobulin domain.
Family:
  • Belongs to the immunoglobulin superfamily. TIM family.
genes like me logo Genes that share domains with TIMD4: view

Function for TIMD4 Gene

Molecular function for TIMD4 Gene

UniProtKB/Swiss-Prot Function:
Phosphatidylserine receptor that enhances the engulfment of apoptotic cells. Involved in regulating T-cell proliferation and lymphotoxin signaling. Ligand for HAVCR1/TIMD1 (By similarity).

Phenotypes From GWAS Catalog for TIMD4 Gene

genes like me logo Genes that share phenotypes with TIMD4: view

Animal Models for TIMD4 Gene

MGI Knock Outs for TIMD4:

Animal Model Products

miRNA for TIMD4 Gene

miRTarBase miRNAs that target TIMD4

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for TIMD4 Gene

Localization for TIMD4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TIMD4 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 TIMD4 gene
Compartment Confidence
plasma membrane 4
cytosol 3
extracellular 2
peroxisome 1

Gene Ontology (GO) - Cellular Components for TIMD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with TIMD4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TIMD4 Gene

Pathways & Interactions for TIMD4 Gene

genes like me logo Genes that share pathways with TIMD4: view

Pathways by source for TIMD4 Gene

1 R&D Systems pathway for TIMD4 Gene

Interacting Proteins for TIMD4 Gene

STRING Interaction Network Preview (showing 3 interactants - click image to see details)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000274532%0d%0a9606.ENSP00000399168%0d%0a9606.ENSP00000320084%0d%0a9606.ENSP00000255324%0d%0a
Selected Interacting proteins: Q96H15-TIMD4_HUMAN ENSP00000274532 for TIMD4 Gene via IID STRING

Gene Ontology (GO) - Biological Process for TIMD4 Gene

None

No data available for SIGNOR curated interactions for TIMD4 Gene

Drugs & Compounds for TIMD4 Gene

No Compound Related Data Available

Transcripts for TIMD4 Gene

mRNA/cDNA for TIMD4 Gene

Unigene Clusters for TIMD4 Gene

T-cell immunoglobulin and mucin domain containing 4:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TIMD4 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b · 8c ^ 9 ^ 10
SP1: - -
SP2: -
SP3:

Relevant External Links for TIMD4 Gene

GeneLoc Exon Structure for
TIMD4
ECgene alternative splicing isoforms for
TIMD4

Expression for TIMD4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TIMD4 Gene

mRNA differential expression in normal tissues according to GTEx for TIMD4 Gene

This gene is overexpressed in Testis (x31.0) and Spleen (x5.2).

Protein differential expression in normal tissues from HIPED for TIMD4 Gene

This gene is overexpressed in Synovial fluid (45.7) and Peripheral blood mononuclear cells (23.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for TIMD4 Gene



Protein tissue co-expression partners for TIMD4 Gene

NURSA nuclear receptor signaling pathways regulating expression of TIMD4 Gene:

TIMD4

SOURCE GeneReport for Unigene cluster for TIMD4 Gene:

Hs.334907

Evidence on tissue expression from TISSUES for TIMD4 Gene

  • Nervous system(4)
  • Lymph node(2.7)
  • Spleen(2.5)
genes like me logo Genes that share expression patterns with TIMD4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TIMD4 Gene

Orthologs for TIMD4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for TIMD4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TIMD4 34 33
  • 98.94 (n)
OneToOne
dog
(Canis familiaris)
Mammalia TIMD4 34 33
  • 72.33 (n)
OneToOne
cow
(Bos Taurus)
Mammalia TIMD4 34 33
  • 72.01 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Timd4 16 34 33
  • 67.94 (n)
rat
(Rattus norvegicus)
Mammalia Timd4 33
  • 64.81 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 42 (a)
OneToMany
-- 34
  • 22 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia TIMD4 34
  • 38 (a)
OneToOne
chicken
(Gallus gallus)
Aves TIMD4 34 33
  • 46.88 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TIMD4 34
  • 24 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii timd4 34
  • 13 (a)
OneToMany
Species where no ortholog for TIMD4 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 TIMD4 Gene

ENSEMBL:
Gene Tree for TIMD4 (if available)
TreeFam:
Gene Tree for TIMD4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TIMD4: view image

Paralogs for TIMD4 Gene

Paralogs for TIMD4 Gene

genes like me logo Genes that share paralogs with TIMD4: view

Variants for TIMD4 Gene

Sequence variations from dbSNP and Humsavar for TIMD4 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1000049921 -- 156,931,639(-) A/G genic_downstream_transcript_variant, intron_variant
rs1000092440 -- 156,950,438(-) G/T intron_variant
rs1000126875 -- 156,944,104(-) C/T genic_downstream_transcript_variant, intron_variant
rs1000143931 -- 156,943,367(-) T/A genic_downstream_transcript_variant, intron_variant
rs1000148924 -- 156,944,321(-) G/C genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for TIMD4 Gene

Variant ID Type Subtype PubMed ID
esv2674952 CNV deletion 23128226
esv2730953 CNV deletion 23290073
esv3607302 CNV gain 21293372
esv3607303 CNV loss 21293372
esv3607304 CNV gain 21293372
esv3607305 CNV gain 21293372

Variation tolerance for TIMD4 Gene

Residual Variation Intolerance Score: 88.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.39; 63.64% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TIMD4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TIMD4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TIMD4 Gene

Disorders for TIMD4 Gene

Additional Disease Information for TIMD4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for TIMD4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for TIMD4 Gene

Publications for TIMD4 Gene

  1. Significant association between TIM1 promoter polymorphisms and protection against cerebral malaria in Thailand. (PMID: 18294362) Nuchnoi P … Patarapotikul J (Annals of human genetics 2008) 3 22 44 58
  2. Biological, clinical and population relevance of 95 loci for blood lipids. (PMID: 20686565) Teslovich TM … Kathiresan S (Nature 2010) 3 44 58
  3. Increased expression of human T-cell immunoglobulin- and mucin-domain-containing molecule-4 in peripheral blood mononuclear cells from patients with system lupus erythematosus. (PMID: 20140011) Zhao P … Gao L (Cellular & molecular immunology 2010) 3 22 58
  4. Association of TIM4 promoter polymorphism -1419G>A with childhood asthma in a Chinese Han population. (PMID: 19392790) Cai PC … Wu QW (Tissue antigens 2009) 3 44 58
  5. Common variants at 30 loci contribute to polygenic dyslipidemia. (PMID: 19060906) Kathiresan S … Cupples LA (Nature genetics 2009) 3 44 58

Products for TIMD4 Gene

Sources for TIMD4 Gene

Content
Loading form....