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

Summary

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. Predicted to be integral component of membrane. Is expressed in brain; dorsal aorta; liver; lung; and reproductive system. Used to study systemic lupus erythematosus. Orthologous to human TIMD4 (T cell immunoglobulin and mucin domain containing 4). [provided by Alliance of Genome Resources, Apr 2022]
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

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_000077.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Tim4 deficiency reduces CD301b[+] macrophage and aggravates periodontitis bone loss.
Title: Tim4 deficiency reduces CD301b(+) macrophage and aggravates periodontitis bone loss.
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.
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.
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.
Tim4 recognizes carbon nanotubes and mediates phagocytosis leading to granuloma formation.
Title: Tim4 recognizes carbon nanotubes and mediates phagocytosis leading to granuloma formation.
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.
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.
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.
TIM4 expression by dendritic cells mediates uptake of tumor-associated antigens and anti-tumor responses.
Title: TIM4 expression by dendritic cells mediates uptake of tumor-associated antigens and anti-tumor responses.

Submit: New GeneRIF Correction See all GeneRIFs (53)

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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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)

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

NC_000077.7 Reference GRCm39 C57BL/6J

Range

46701613..46735160

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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