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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
  • 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. Diseases associated with TIMD4 include Histiocytic Sarcoma. 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

Regulatory Elements for TIMD4 Gene

Enhancers for TIMD4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05H156912 1.2 Ensembl ENCODE dbSUPER 11.1 +58.4 58365 2 PKNOX1 ZNF687 MAZ ELF1 DPF2 ETS1 POLR2A EED IKZF1 POU5F1 TIMD4 GC05P156904 APOOP1
GH05H156919 1.1 ENCODE dbSUPER 11.1 +51.7 51684 1 HDGF TBL1XR1 BACH1 BMI1 EBF1 BATF RELA EED ATF7 RUNX3 APOOP1 TIMD4 GC05P156904
GH05H157105 1.2 Ensembl ENCODE dbSUPER 10.1 -135.9 -135924 5 HDGF KLF1 TBL1XR1 RB1 POLR2A EED ATF7 RUNX3 IKZF2 CREM ITK HAVCR2 MED7 TIMD4 HAVCR1 ENSG00000254246 PIR42544
GH05H157058 0.9 ENCODE 9.9 -86.9 -86891 1 ELF3 FOXA2 ARID4B SIN3A RAD21 ZSCAN9 RARA MIXL1 REST PPARG ENSG00000254246 TIMD4 HAVCR1 ADAM19
GH05H156798 0.8 ENCODE dbSUPER 9.5 +170.8 170839 6 POLR2A MAX POU5F1 REST TIMD4 ENSG00000248544 GC05P156815 GC05P156760
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TIMD4 on UCSC Golden Path with GeneCards custom track

Genomic Location for TIMD4 Gene

Chromosome:
5
Start:
156,919,282 bp from pter
End:
156,972,310 bp from pter
Size:
53,029 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

Antibody Products

  • Abcam antibodies for TIMD4
  • Santa Cruz Biotechnology (SCBT) Antibodies for TIMD4

Protein Products

  • Abcam proteins for TIMD4

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

Gene Ontology (GO) - Molecular Function for TIMD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001786 phosphatidylserine binding IEA --
genes like me logo Genes that share ontologies with TIMD4: view
genes like me logo Genes that share phenotypes with TIMD4: view

Animal Models for TIMD4 Gene

MGI Knock Outs for TIMD4:

Animal Model Products

CRISPR Products

miRNA for TIMD4 Gene

miRTarBase miRNAs that target TIMD4

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for TIMD4
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , 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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TIMD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with TIMD4: view

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: ENSP00000274532 Q96H15-TIMD4_HUMAN for TIMD4 Gene via STRING IID

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

Unigene Clusters for TIMD4 Gene

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

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for TIMD4
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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, PaxDb, 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

Primer Products

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 33 34
  • 98.94 (n)
dog
(Canis familiaris)
Mammalia TIMD4 33 34
  • 72.33 (n)
cow
(Bos Taurus)
Mammalia TIMD4 33 34
  • 72.01 (n)
mouse
(Mus musculus)
Mammalia Timd4 33 16 34
  • 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 33 34
  • 46.88 (n)
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)

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 Sequence Context AA Info Type
rs1000049921 -- 156,931,639(+) TTAGT(A/G)AATTG intron-variant
rs1000092440 -- 156,950,438(+) TTAGG(G/T)TTCAT intron-variant
rs1000126875 -- 156,944,104(+) ATAGG(C/T)GAAAA intron-variant
rs1000143931 -- 156,943,367(+) GAAAC(A/T)GAGAT intron-variant
rs1000148924 -- 156,944,321(+) CCCCA(C/G)AAAAA 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)

Relevant External Links for TIMD4 Gene

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

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

Disorders for TIMD4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for TIMD4 Gene - From: GeneCards

Disorder Aliases PubMed IDs
histiocytic sarcoma
- elite association - COSMIC cancer census association via MalaCards
Search TIMD4 in MalaCards View complete list of genes associated with diseases

Relevant External Links for TIMD4

Genetic Association Database (GAD)
TIMD4
Human Genome Epidemiology (HuGE) Navigator
TIMD4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TIMD4
genes like me logo Genes that share disorders with TIMD4: view

No data available for 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 45 60
  2. Biological, clinical and population relevance of 95 loci for blood lipids. (PMID: 20686565) Teslovich TM … Kathiresan S (Nature 2010) 3 45 60
  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 60
  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 45 60
  5. Common variants at 30 loci contribute to polygenic dyslipidemia. (PMID: 19060906) Kathiresan S … Cupples LA (Nature genetics 2009) 3 45 60

Products for TIMD4 Gene

Sources for TIMD4 Gene

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