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HAVCR1 hepatitis A virus cellular receptor 1 [ Homo sapiens (human) ]

Gene ID: 26762, updated on 17-Jun-2019

Summary

Official Symbol
HAVCR1provided by HGNC
Official Full Name
hepatitis A virus cellular receptor 1provided by HGNC
Primary source
HGNC:HGNC:17866
See related
Ensembl:ENSG00000113249 MIM:606518
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TIM; KIM1; TIM1; CD365; HAVCR; KIM-1; TIM-1; TIMD1; TIMD-1; HAVCR-1
Summary
The protein encoded by this gene is a membrane receptor for both human hepatitis A virus (HHAV) and TIMD4. The encoded protein may be involved in the moderation of asthma and allergic diseases. The reference genome represents an allele that retains a MTTVP amino acid segment that confers protection against atopy in HHAV seropositive individuals. Alternative splicing of this gene results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 4, 12 and 19. [provided by RefSeq, Apr 2015]
Expression
Biased expression in kidney (RPKM 1.3), colon (RPKM 1.2) and 6 other tissues See more
Orthologs

Genomic context

See HAVCR1 in Genome Data Viewer
Location:
5q33.3
Exon count:
11
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (157028383..157069633, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (156455989..156486130, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene PPP1R2 family member B Neighboring gene T cell immunoglobulin and mucin domain containing 4 Neighboring gene apolipoprotein O pseudogene 1 Neighboring gene hepatitis A virus cellular receptor 2 Neighboring gene mediator complex subunit 7

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Biological, clinical and population relevance of 95 loci for blood lipids.
NHGRI GWA Catalog
Common variants at 30 loci contribute to polygenic dyslipidemia.
NHGRI GWA Catalog
Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope transmembrane glycoprotein gp41 env Immunoprecipitation using an antibody against TIM-1 can pull down HIV-1 gp41 in cells, indicating that TIM-1 interacts with gp41 in vivo PubMed
Pr55(Gag) gag TIM-1 induces accumulation of HIV-1 Gag-GFP at the plasma membrane of 293 T cells and inhibits release of HIV-1 Gag-GFP virus-like particles PubMed
capsid gag TIM-1 mutants N114A, D115A, and ND114/115AA exhibit a significantly decreased ability to inhibit HIV-1 release in terms of CA levels compared with wild-type TIM-1 in 293T cells PubMed
gag TIM-1 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-1 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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
virus receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
viral entry into host cell IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
motile cilium IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
hepatitis A virus cellular receptor 1
Names
T cell immunoglobin domain and mucin domain protein 1
T-cell immunoglobulin mucin family member 1
T-cell immunoglobulin mucin receptor 1
T-cell membrane protein 1
kidney injury molecule 1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_017001.1 RefSeqGene

    Range
    4841..34547
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001173393.3NP_001166864.1  hepatitis A virus cellular receptor 1 isoform a precursor

    See identical proteins and their annotated locations for NP_001166864.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Both variants 1 and 3 encode isoform a.
    Source sequence(s)
    AC026777, AF043724, AK298259, BC013325
    Consensus CDS
    CCDS43392.1
    UniProtKB/Swiss-Prot
    Q96D42
    UniProtKB/TrEMBL
    B4DPB1
    Related
    ENSP00000427898.1, ENST00000523175.5
    Conserved Domains (1) summary
    pfam07686
    Location:21120
    V-set; Immunoglobulin V-set domain
  2. NM_001308156.2NP_001295085.1  hepatitis A virus cellular receptor 1 isoform b precursor

    See identical proteins and their annotated locations for NP_001295085.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, and lacks an alternate exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (b) has a distinct C-terminus and is longer than isoform a.
    Source sequence(s)
    AC026777, AK298259, BC013325
    Consensus CDS
    CCDS78076.1
    UniProtKB/Swiss-Prot
    Q96D42
    UniProtKB/TrEMBL
    B4DPB1, E9PFX0
    Related
    ENSP00000428524.1, ENST00000522693.5
    Conserved Domains (1) summary
    pfam07686
    Location:21120
    V-set; Immunoglobulin V-set domain
  3. NM_012206.3NP_036338.2  hepatitis A virus cellular receptor 1 isoform a precursor

    See identical proteins and their annotated locations for NP_036338.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the shorter isoform (a). Both variants 1 and 3 encode isoform a.
    Source sequence(s)
    AK298259, AW604297, BC013325, BG752287
    Consensus CDS
    CCDS43392.1
    UniProtKB/Swiss-Prot
    Q96D42
    UniProtKB/TrEMBL
    B4DPB1
    Related
    ENSP00000344844.3, ENST00000339252.7
    Conserved Domains (1) summary
    pfam07686
    Location:21120
    V-set; Immunoglobulin V-set domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    157028383..157069633 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024446023.1XP_024301791.1  hepatitis A virus cellular receptor 1 isoform X1

    Conserved Domains (1) summary
    pfam07686
    Location:21120
    V-set; Immunoglobulin V-set domain
  2. XM_024446021.1XP_024301789.1  hepatitis A virus cellular receptor 1 isoform X1

    Conserved Domains (1) summary
    pfam07686
    Location:21120
    V-set; Immunoglobulin V-set domain
  3. XM_024446020.1XP_024301788.1  hepatitis A virus cellular receptor 1 isoform X1

    Conserved Domains (1) summary
    pfam07686
    Location:21120
    V-set; Immunoglobulin V-set domain
  4. XM_017009339.2XP_016864828.1  hepatitis A virus cellular receptor 1 isoform X2

  5. XM_024446022.1XP_024301790.1  hepatitis A virus cellular receptor 1 isoform X1

    Conserved Domains (1) summary
    pfam07686
    Location:21120
    V-set; Immunoglobulin V-set domain
  6. XM_024446019.1XP_024301787.1  hepatitis A virus cellular receptor 1 isoform X1

    Conserved Domains (1) summary
    pfam07686
    Location:21120
    V-set; Immunoglobulin V-set domain
  7. XM_011534515.2XP_011532817.1  hepatitis A virus cellular receptor 1 isoform X4

  8. XM_024446024.1XP_024301792.1  hepatitis A virus cellular receptor 1 isoform X3

    Conserved Domains (1) summary
    pfam07686
    Location:21120
    V-set; Immunoglobulin V-set domain

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001099414.1: Suppressed sequence

    Description
    NM_001099414.1: This RefSeq was removed because currently there is insufficient support for the transcript.
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