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TIMD4 T cell immunoglobulin and mucin domain containing 4 [ Homo sapiens (human) ]

Gene ID: 91937, updated on 5-Mar-2024

Summary

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Official Symbol
TIMD4provided by HGNC
Official Full Name
T cell immunoglobulin and mucin domain containing 4provided by HGNC
Primary source
HGNC:HGNC:25132
See related
Ensembl:ENSG00000145850 MIM:610096; AllianceGenome:HGNC:25132
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TIM4; SMUCKLER
Summary
Predicted to enable phosphatidylserine binding activity. Predicted to act upstream of or within apoptotic cell clearance. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in lymph node (RPKM 8.4), testis (RPKM 2.6) and 5 other tissues See more
Orthologs
all
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Genomic context

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Location:
5q33.3
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (156919292..156963226, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (157438332..157482246, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (156346303..156390237, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 556, pseudogene Neighboring gene PPP1R2 family member B Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:156339619-156340818 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:156340819-156341764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23495 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23496 Neighboring gene apolipoprotein O pseudogene 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:156441149-156441653 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:156441654-156442157 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:156477155-156477714 Neighboring gene hepatitis A virus cellular receptor 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:156499176-156500375 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23497 Neighboring gene hepatitis A virus cellular receptor 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. TIM-4 orchestrates mitochondrial homeostasis to promote lung cancer progression via ANXA2/PI3K/AKT/OPA1 axis. Wang Y, et al. Cell Death Dis, 2023 Feb 20. PMID 36806050, Free PMC Article
  2. Tim-4 expressing monocytes as a novel indicator to assess disease activity and severity of ulcerative colitis. Xue G, et al. Life Sci, 2021 Mar 15. PMID 33465392
  3. TIMD4 exhibits regulatory capability on the proliferation and apoptosis of diffuse large B-cell lymphoma cells via the Wnt/β-catenin pathway. Li Y, et al. J Gene Med, 2020 Aug. PMID 32187802
  4. TIMD4 rs6882076 SNP Is Associated with Decreased Levels of Triglycerides and the Risk of Coronary Heart Disease and Ischemic Stroke. Khounphinith E, et al. Int J Med Sci, 2019. PMID 31337960, Free PMC Article
  5. Tim-4 expression increases in ischemic stroke patients and is associated with poor outcome. Xu L, et al. J Neuroimmunol, 2018 Mar 15. PMID 29233585

See all (64) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. TIM-4 orchestrates mitochondrial homeostasis to promote lung cancer progression via ANXA2/PI3K/AKT/OPA1 axis.
    Title: TIM-4 orchestrates mitochondrial homeostasis to promote lung cancer progression via ANXA2/PI3K/AKT/OPA1 axis.
  2. Overexpression of Nuclear Enriched Autosomal Transcript 1 Facilitates Cell Proliferation, Migration Invasion, and Suppresses Apoptosis in Endometrial Cancer by Targeting MicroRNA-202-3p/T Cell Immunoglobulin and Mucin Domain 4 Axis.
    Title: Overexpression of Nuclear Enriched Autosomal Transcript 1 Facilitates Cell Proliferation, Migration Invasion, and Suppresses Apoptosis in Endometrial Cancer by Targeting MicroRNA-202-3p/T Cell Immunoglobulin and Mucin Domain 4 Axis.
  3. TIM-4 in macrophages contributes to nasal polyp formation through the TGF-beta1-mediated epithelial to mesenchymal transition in nasal epithelial cells.
    Title: TIM-4 in macrophages contributes to nasal polyp formation through the TGF-β1-mediated epithelial to mesenchymal transition in nasal epithelial cells.
  4. Tim4 recognizes carbon nanotubes and mediates phagocytosis leading to granuloma formation.
    Title: Tim4 recognizes carbon nanotubes and mediates phagocytosis leading to granuloma formation.
  5. Platelet-derived extracellular vesicles are increased in sera of Alzheimer's disease patients, as revealed by Tim4-based assays.
    Title: Platelet-derived extracellular vesicles are increased in sera of Alzheimer's disease patients, as revealed by Tim4-based assays.
  6. Tim-4(+) cavity-resident macrophages impair anti-tumor CD8(+) T cell immunity.
    Title: Tim-4(+) cavity-resident macrophages impair anti-tumor CD8(+) T cell immunity.
  7. EphA2 Interacts with Tim-4 through Association between Its FN3 Domain and the IgV Domain of Tim-4.
    Title: EphA2 Interacts with Tim-4 through Association between Its FN3 Domain and the IgV Domain of Tim-4.
  8. TIMD4 exhibits regulatory capability on the proliferation and apoptosis of diffuse large B-cell lymphoma cells via the Wnt/beta-catenin pathway.
    Title: TIMD4 exhibits regulatory capability on the proliferation and apoptosis of diffuse large B-cell lymphoma cells via the Wnt/β-catenin pathway.
  9. The expression of Tim-1 and Tim-4 molecules in regulatory T cells in type 1 diabetes.
    Title: The expression of Tim-1 and Tim-4 molecules in regulatory T cells in type 1 diabetes.
  10. Tim4 regulates NALP3 inflammasome expression and activity during monocyte/macrophage dysfunction in septic shock patients.
    Title: Tim4 regulates NALP3 inflammasome expression and activity during monocyte/macrophage dysfunction in septic shock patients.
Submit: New GeneRIF Correction See all GeneRIFs (49)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Biological, clinical and population relevance of 95 loci for blood lipids.
EBI GWAS Catalog
Common variants at 30 loci contribute to polygenic dyslipidemia.
EBI GWAS Catalog
Discovery and refinement of loci associated with lipid levels.
EBI GWAS Catalog
Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
capsid gag TIM-4 inhibits the release of HIV-1 in terms of reduced levels of CA and RT activity in virus particles, and induces the accumulation of cell-associated CA PubMed
reverse transcriptase gag-pol TIM-4 inhibits the release of HIV-1 in terms of reduced levels of CA and RT activity in virus particles, and induces the accumulation of cell-associated CA PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ27515

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables phosphatidylserine binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in apoptotic cell clearance IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cytoskeletal rearrangement involved in phagocytosis, engulfment IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
T-cell immunoglobulin and mucin domain-containing protein 4
Names
T-cell immunoglobulin mucin receptor 4
T-cell membrane protein 4
TIM-4
TIMD-4

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001146726.2 → NP_001140198.1  T-cell immunoglobulin and mucin domain-containing protein 4 isoform 2 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an exon in the coding region compared to variant 1. The encoded isoform (2) is shorter compared to isoform 1.
    Source sequence(s)
    AA843555, AC008491, AC026777, BC008988
    Consensus CDS
    CCDS54943.1
    UniProtKB/Swiss-Prot
    Q96H15
    Related
    ENSP00000385973.3, ENST00000407087.4
    Conserved Domains (2) summary
    cd00096
    Location:36 → 40
    Ig; Ig strand B [structural motif]
    cl11960
    Location:28 → 129
    Ig; Immunoglobulin domain

  2. NM_138379.3 → NP_612388.2  T-cell immunoglobulin and mucin domain-containing protein 4 isoform 1 precursor

    See identical proteins and their annotated locations for NP_612388.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AA843555, AC008491, BC008988
    Consensus CDS
    CCDS4332.1
    UniProtKB/Swiss-Prot
    B5MCL9, Q96H15
    Related
    ENSP00000274532.2, ENST00000274532.7
    Conserved Domains (2) summary
    smart00410
    Location:27 → 115
    IG_like; Immunoglobulin like
    pfam07686
    Location:23 → 128
    V-set; Immunoglobulin V-set domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    156919292..156963226 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017010021.2 → XP_016865510.1  T-cell immunoglobulin and mucin domain-containing protein 4 isoform X1

  2. XM_011534694.3 → XP_011532996.1  T-cell immunoglobulin and mucin domain-containing protein 4 isoform X2

    Conserved Domains (1) summary
    pfam07686
    Location:23 → 128
    V-set; Immunoglobulin V-set domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    157438332..157482246 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054353790.1 → XP_054209765.1  T-cell immunoglobulin and mucin domain-containing protein 4 isoform X1

  2. XM_054353791.1 → XP_054209766.1  T-cell immunoglobulin and mucin domain-containing protein 4 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96H15.2 GenPept UniProtKB/Swiss-Prot:Q96H15

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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