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Timd4 T cell immunoglobulin and mucin domain containing 4 [ Mus musculus (house mouse) ]

Gene ID: 276891, updated on 12-Nov-2024

Summary

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Official Symbol
Timd4provided by MGI
Official Full Name
T cell immunoglobulin and mucin domain containing 4provided by MGI
Primary source
MGI:MGI:2445125
See related
Ensembl:ENSMUSG00000055546 AllianceGenome:MGI:2445125
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Tim4; TIM-4; B430010N18Rik
Summary
Enables phosphatidylserine binding activity. Acts upstream of or within apoptotic cell clearance. Predicted to be located in membrane. Is expressed in aorta-gonad-mesonephros; brain; gonad; liver; and lung. Used to study systemic lupus erythematosus. Orthologous to human TIMD4 (T cell immunoglobulin and mucin domain containing 4). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in spleen adult (RPKM 8.5), mammary gland adult (RPKM 5.8) and 10 other tissues See more
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Genomic context

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See Timd4 in Genome Data Viewer
Location:
11 B1.1; 11 28.09 cM
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (46701613..46735160)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (46810786..46844333)

Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_29336 Neighboring gene hepatitis A virus cellular receptor 1 Neighboring gene STARR-seq mESC enhancer starr_29337 Neighboring gene predicted gene, 39817 Neighboring gene STARR-seq mESC enhancer starr_29339 Neighboring gene STARR-seq mESC enhancer starr_29340 Neighboring gene STARR-seq mESC enhancer starr_29341 Neighboring gene sarcoglycan, delta (dystrophin-associated glycoprotein) Neighboring gene STARR-seq mESC enhancer starr_29342 Neighboring gene STARR-seq mESC enhancer starr_29343 Neighboring gene STARR-seq mESC enhancer starr_29344 Neighboring gene 40S ribosomal protein S2 pseudogene Neighboring gene STARR-seq mESC enhancer starr_29346 Neighboring gene predicted gene, 23039

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Molecular mechanism for differential recognition of membrane phosphatidylserine by the immune regulatory receptor Tim4. Tietjen GT, et al. Proc Natl Acad Sci U S A, 2014 Apr 15. PMID 24706780, Free PMC Article
  2. Tim-4 Inhibits NLRP3 Inflammasome via the LKB1/AMPKα Pathway in Macrophages. Liu W, et al. J Immunol, 2019 Aug 15. PMID 31263038
  3. Tissue-resident macrophages in the intestine are long lived and defined by Tim-4 and CD4 expression. Shaw TN, et al. J Exp Med, 2018 Jun 4. PMID 29789388, Free PMC Article
  4. Mouse macrophages show different requirements for phosphatidylserine receptor Tim4 in efferocytosis. Yanagihashi Y, et al. Proc Natl Acad Sci U S A, 2017 Aug 15. PMID 28768810, Free PMC Article
  5. TIM-4 is expressed on invariant NKT cells but dispensable for their development and function. Zhang X, et al. Oncotarget, 2016 Nov 1. PMID 27662666, Free PMC Article

See all (84) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Tim-4 alleviates acute hepatic injury by modulating homeostasis and function of NKT cells.
    Title: Tim-4 alleviates acute hepatic injury by modulating homeostasis and function of NKT cells.
  2. Tim4 enables large peritoneal macrophages to cross-present tumor antigens at early stages of tumorigenesis.
    Title: Tim4 enables large peritoneal macrophages to cross-present tumor antigens at early stages of tumorigenesis.
  3. Tim4 deficiency reduces CD301b[+] macrophage and aggravates periodontitis bone loss.
    Title: Tim4 deficiency reduces CD301b(+) macrophage and aggravates periodontitis bone loss.
  4. T-cell immunoglobulin- and mucin-domain-containing molecule-4 maintains adipose tissue homeostasis by orchestrating M2 macrophage polarization via nuclear factor kappa B pathway.
    Title: T-cell immunoglobulin- and mucin-domain-containing molecule-4 maintains adipose tissue homeostasis by orchestrating M2 macrophage polarization via nuclear factor kappa B pathway.
  5. 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.
  6. Three tissue resident macrophage subsets coexist across organs with conserved origins and life cycles.
    Title: Three tissue resident macrophage subsets coexist across organs with conserved origins and life cycles.
  7. Tim4 recognizes carbon nanotubes and mediates phagocytosis leading to granuloma formation.
    Title: Tim4 recognizes carbon nanotubes and mediates phagocytosis leading to granuloma formation.
  8. Role of Tim4 in the regulation of ABCA1(+) adipose tissue macrophages and post-prandial cholesterol levels.
    Title: Role of Tim4 in the regulation of ABCA1(+) adipose tissue macrophages and post-prandial cholesterol levels.
  9. 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.
  10. Autophagic adaptation to oxidative stress alters peritoneal residential macrophage survival and ovarian cancer metastasis.
    Title: Autophagic adaptation to oxidative stress alters peritoneal residential macrophage survival and ovarian cancer metastasis.
Submit: New GeneRIF Correction See all GeneRIFs (54)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (6) 
  • Targeted (4)  1 citation

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables phosphatidylserine binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables phosphatidylserine binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in apoptotic cell clearance IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within apoptotic cell clearance IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cytoskeletal rearrangement involved in phagocytosis, engulfment IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in 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
TIMD-4
smuckler
spleen, mucin-containing, knockout of lymphotoxin protein

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_178759.4 → NP_848874.3  T-cell immunoglobulin and mucin domain-containing protein 4 precursor

    See identical proteins and their annotated locations for NP_848874.3

    Status: VALIDATED

    Source sequence(s)
    AK046560, AK080212, AY376716
    Consensus CDS
    CCDS36137.1
    UniProtKB/Swiss-Prot
    Q6U7R3, Q6U7R4, Q8CIC7
    Related
    ENSMUSP00000069456.7, ENSMUST00000068877.7
    Conserved Domains (2) summary
    smart00410
    Location:27 → 130
    IG_like; Immunoglobulin like
    pfam07686
    Location:32 → 114
    V-set; Immunoglobulin V-set domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000077.7 Reference GRCm39 C57BL/6J

    Range
    46701613..46735160
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006533479.4 → XP_006533542.1  T-cell immunoglobulin and mucin domain-containing protein 4 isoform X1

    Conserved Domains (1) summary
    pfam07686
    Location:24 → 114
    V-set; Immunoglobulin V-set domain

  2. XM_006533480.4 → XP_006533543.1  T-cell immunoglobulin and mucin domain-containing protein 4 isoform X2

    Conserved Domains (1) summary
    pfam07686
    Location:24 → 114
    V-set; Immunoglobulin V-set domain
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6U7R4.2 GenPept UniProtKB/Swiss-Prot:Q6U7R4

Gene LinkOut

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

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