Havcr1 hepatitis A virus cellular receptor 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Havcr1provided by MGI
Official Full Name: hepatitis A virus cellular receptor 1provided by MGI
Primary source: MGI:MGI:2159680
See related: Ensembl:ENSMUSG00000040405 AllianceGenome:MGI:2159680
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: Tim1; KIM-1; TIM-1; Timd1
Summary: Enables phosphatidylserine binding activity. Acts upstream of or within positive regulation of mast cell activation; response to lipopolysaccharide; and response to wounding. Located in brush border and cell surface. Is expressed in brain; dorsal aorta; liver; lung; and reproductive system. Human ortholog(s) of this gene implicated in atopic dermatitis. Orthologous to human HAVCR1 (hepatitis A virus cellular receptor 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in kidney adult (RPKM 7.2), placenta adult (RPKM 0.8) and 2 other tissues See more
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Genomic context

Location:: 11 B1.1; 11 28.08 cM

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	11	NC_000077.7 (46630644..46670405)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	11	NC_000077.6 (46739822..46779578)

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?

A renal YY1-KIM1-DR5 axis regulates the progression of acute kidney injury.
Title: A renal YY1-KIM1-DR5 axis regulates the progression of acute kidney injury.
KIM-1 augments hypoxia-induced tubulointerstitial inflammation through uptake of small extracellular vesicles by tubular epithelial cells.
Title: KIM-1 augments hypoxia-induced tubulointerstitial inflammation through uptake of small extracellular vesicles by tubular epithelial cells.
T-Cell Immunoglobulin and Mucin Domain 1 (TIM-1) Is a Functional Entry Factor for Tick-Borne Encephalitis Virus.
Title: T-Cell Immunoglobulin and Mucin Domain 1 (TIM-1) Is a Functional Entry Factor for Tick-Borne Encephalitis Virus.
Tim-1 mucin domain-mutant mice display exacerbated atherosclerosis.
Title: Tim-1 mucin domain-mutant mice display exacerbated atherosclerosis.
Acute Kidney Injury Associates with Long-Term Increases in Plasma TNFR1, TNFR2, and KIM-1: Findings from the CRIC Study.
Title: Acute Kidney Injury Associates with Long-Term Increases in Plasma TNFR1, TNFR2, and KIM-1: Findings from the CRIC Study.
Kidney injury molecule-1 inhibits metastasis of renal cell carcinoma.
Title: Kidney injury molecule-1 inhibits metastasis of renal cell carcinoma.
Rutin coated gold nanoparticles prevent rhabdomyolysis-induced kidney injury via down-regulation of NF-kB, iNOS, IL-6 and up-regulation of HO-1 and Kim-1 genes in mice.
Title: Rutin coated gold nanoparticles prevent rhabdomyolysis-induced kidney injury via down-regulation of NF-kB, iNOS, IL-6 and up-regulation of HO-1 and Kim-1 genes in mice.
KIM-1-mediated anti-inflammatory activity is preserved by MUC1 induction in the proximal tubule during ischemia-reperfusion injury.
Title: KIM-1-mediated anti-inflammatory activity is preserved by MUC1 induction in the proximal tubule during ischemia-reperfusion injury.
Mapping and functional characterization of murine kidney injury molecule-1 proteolytic cleavage site.
Title: Mapping and functional characterization of murine kidney injury molecule-1 proteolytic cleavage site.
These studies provide evidence that at late times during Ebola virus glycoprotein/recombinant vesiculovirus infection, TIM-1 increased virus load and associated mortality, consistent with an important role of this receptor in virus entry.
Title: TIM-1 serves as a receptor for Ebola virus in vivo, enhancing viremia and pathogenesis.

Submit: New GeneRIF Correction See all GeneRIFs (62)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (5) 1 citation
Endonuclease-mediated (4) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI503787 (e-PCR)
- UniSTS:160088

Timd1 (e-PCR), detects polymorphism
- UniSTS:239192

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
enables virus receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables virus receptor activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in phagocytosis, engulfment	IBA Inferred from Biological aspect of Ancestor more info
involved_in phagocytosis, engulfment	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of mast cell activation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of mast cell activation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within response to lipopolysaccharide	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within response to wounding	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in apical plasma membrane	ISO Inferred from Sequence Orthology more info
located_in brush border	IDA Inferred from Direct Assay more info	PubMed
is_active_in cell surface	IBA Inferred from Biological aspect of Ancestor more info
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in cell surface	ISO Inferred from Sequence Orthology more info
located_in extracellular space	ISO Inferred from Sequence Orthology more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in motile cilium	ISO Inferred from Sequence Orthology more info
located_in phagocytic vesicle	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: hepatitis A virus cellular receptor 1 homolog

Names: HAVcr-1; T-cell immunoglobulin and mucin domain containing 1; T-cell immunoglobulin mucin receptor 1; TIMD-1; kidney injury molecule 1; t cell immunoglobulin and mucin domain-containing protein 1; t cell membrane protein 1

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_001166631.1 → NP_001160103.1 hepatitis A virus cellular receptor 1 homolog isoform b precursor

See identical proteins and their annotated locations for NP_001160103.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 2 and 3 both encode the same isoform.

Source sequence(s)

AK133466, BC053400

Consensus CDS

CCDS48778.1

UniProtKB/Swiss-Prot

Q5QNS5, Q7TPU2, Q8VIM1, Q8VIM2

UniProtKB/TrEMBL

Q3V033

Related

ENSMUSP00000104846.2, ENSMUST00000109223.8

Conserved Domains (2) summary

smart00410
Location:25 → 127

IG_like; Immunoglobulin like

pfam07686
Location:24 → 110

V-set; Immunoglobulin V-set domain
NM_001166632.1 → NP_001160104.1 hepatitis A virus cellular receptor 1 homolog isoform b precursor

See identical proteins and their annotated locations for NP_001160104.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 2 and 3 both encode the same isoform.

Source sequence(s)

BC053400, CA551363

Consensus CDS

CCDS48778.1

UniProtKB/Swiss-Prot

Q5QNS5, Q7TPU2, Q8VIM1, Q8VIM2

UniProtKB/TrEMBL

Q3V033

Related

ENSMUSP00000080503.5, ENSMUST00000081819.11

Conserved Domains (2) summary

smart00410
Location:25 → 127

IG_like; Immunoglobulin like

pfam07686
Location:24 → 110

V-set; Immunoglobulin V-set domain
NM_134248.2 → NP_599009.2 hepatitis A virus cellular receptor 1 homolog isoform a precursor

See identical proteins and their annotated locations for NP_599009.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (a). The 5' UTR of this transcript has not been determined.

Source sequence(s)

AL669892, BC053400, CA551363

Consensus CDS

CCDS24583.1

UniProtKB/Swiss-Prot

Q5QNS5, Q7TPU2, Q8VIM1, Q8VIM2

UniProtKB/TrEMBL

A0A0A0MQ86

Related

ENSMUSP00000043827.5, ENSMUST00000047568.5

Conserved Domains (1) summary

pfam07686
Location:24 → 122

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

46630644..46670405

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006532393.4 → XP_006532456.1 hepatitis A virus cellular receptor 1 homolog isoform X2

See identical proteins and their annotated locations for XP_006532456.1

UniProtKB/Swiss-Prot

Q5QNS5, Q7TPU2, Q8VIM1, Q8VIM2

UniProtKB/TrEMBL

A0A0A0MQ86

Conserved Domains (1) summary

pfam07686
Location:24 → 122

V-set; Immunoglobulin V-set domain
XM_006532392.4 → XP_006532455.1 hepatitis A virus cellular receptor 1 homolog isoform X1

See identical proteins and their annotated locations for XP_006532455.1

UniProtKB/Swiss-Prot

Q5QNS5, Q7TPU2, Q8VIM1, Q8VIM2

Conserved Domains (1) summary

pfam07686
Location:24 → 122

V-set; Immunoglobulin V-set domain
XM_011248784.3 → XP_011247086.1 hepatitis A virus cellular receptor 1 homolog isoform X3

Conserved Domains (1) summary

pfam07686
Location:24 → 122

V-set; Immunoglobulin V-set domain
XM_030245623.2 → XP_030101483.1 hepatitis A virus cellular receptor 1 homolog isoform X2

UniProtKB/Swiss-Prot

Q5QNS5, Q7TPU2, Q8VIM1, Q8VIM2

UniProtKB/TrEMBL

A0A0A0MQ86

Conserved Domains (1) summary

pfam07686
Location:24 → 122

V-set; Immunoglobulin V-set domain
XM_011248783.2 → XP_011247085.1 hepatitis A virus cellular receptor 1 homolog isoform X1

See identical proteins and their annotated locations for XP_011247085.1

UniProtKB/Swiss-Prot

Q5QNS5, Q7TPU2, Q8VIM1, Q8VIM2

Conserved Domains (1) summary

pfam07686
Location:24 → 122

V-set; Immunoglobulin V-set domain