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HAVCR1 Gene

protein-coding   GIFtS: 65

GC05M156389
hepatitis A virus cellular receptor 1
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
HAVCR 1, 2, 5
HAVCR-1 1, 2
HAVcr-1 3
KIM-1 2
KIM1 2
TIM 3
TIM-1 1, 2, 3
TIM1 1, 2, 3
TIMD-1 3
TIMD1 1, 2, 3
Descriptions
T cell immunoglobin domain and mucin domain protein 1 2
T-cell immunoglobulin and mucin domain-containing protein 1 3
T-cell membrane protein 1 3
hepatitis A virus cellular receptor 1 2
kidney injury molecule 1 2
External Ids
HGNC: 178661
Entrez Gene: 267622
UniProtKB: Q96D423
Ensembl: ENSG000001132497
Search outside databases for aliases for HAVCR1 gene

Previous GC identifers: GC05M157007 GC05M156391 GC05M156437

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: TIMD1_HUMAN, Q96D42
Function: May play a role in T-helper cell development and the regulation of asthma and allergic
diseases. Receptor for TIMD4 (By similarity). In case of human hepatitis A virus (HHAV) infection,
functions as a cell-surface receptor for the virus

Gene Wiki entry for HAVCR1

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the HAVCR1 gene  

Entrez Gene cytogenetic band: 5q33.2   Ensembl cytogenetic band:  5q33.3   HGNC cytogenetic band: 5q33.2

HAVCR1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05M156389:     (about GC identifiers)

Start:
156,389,109 bp from pter
End:
156,418,065 bp from pter
Size:
28,957 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000005.8  NT_023133.12  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

UniProtKB/Swiss-Prot: TIMD1_HUMAN, Q96D42 (See protein sequence)
Recommended Name: Hepatitis A virus cellular receptor 1 precursor  
Size: 359 amino acids; 38720 Da
Subcellular location: Membrane; Single-pass type I membrane protein (Probable)
Secondary accessions: O43656

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins (2 alternative transcripts): 
    NP_001092884.1  NP_036338.2  


    ENSEMBL proteins: 
    ENSP00000344844 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
    Browse Human Recombinant Proteins at Sigma-Aldrich  
    R&D Systems Recombinant & Natural Proteins for HAVCR1 (TIM-1/KIM-1/HAVCR)
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Recombinant Proteins from Abcam (TIM 1)
    Human Recombinant Proteins from Abnova (HAVCR1)
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    2 Gene Ontology (GO) cellular component terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016020 membrane IEA--
    GO:0016021 integral to membrane IEA--
    About this table

    Antibodies for HAVCR1: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Sigma-Aldrich Antibodies for HAVCR1
    R&D Systems Antibodies for HAVCR1 (TIM-1/KIM-1/HAVCR)
    Antibodies from Abcam (TIM 1), each with their AbpromiseSM
    Browse Abnova for Monoclonal and Polyclonal Antibodies
    Novus Biologicals Antibodies for HAVCR1

    Assays for HAVCR1: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    R&D Systems ELISAs for HAVCR1 (TIM-1/KIM-1/HAVCR)         (see all)
    Browse biochemical assays available from Enzo Life Sciences

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    5 InterPro domains/families:
     IPR007110 Ig-like
     IPR003006 Ig/MHC_CS
     IPR003599 Ig_sub
     IPR013783 Ig-like_fold
     IPR013106 Ig_V-set


       GeneDecks  HAVCR1 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q96D42

    ProtoNet protein and cluster: Q96D42

    1 Blocks protein family: IPB013106 Immunoglobulin V-set

    UniProtKB/Swiss-Prot: TIMD1_HUMAN, Q96D42
    Similarity: Belongs to the immunoglobulin superfamily. TIM family
    Similarity: Contains 1 Ig-like V-type (immunoglobulin-like) domain

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (HAVCR1)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (HAVCR1)
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 3): NM_012206

                  Applied Biosystems Silencer® siRNAs for HAVCR1

                  Sigma-Aldrich siRNA and siRNA Panels for HAVCR1  
                         Sigma-Aldrich shRNA Panels and shRNA for HAVCR1  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Invitrogen Clones for HAVCR1
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                   OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_001099414
                                     Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_001099414
                                     untagged cDNA clones in CMV expression vector (see all 4): BC013325 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_012206

    UniProtKB/Swiss-Prot: TIMD1_HUMAN, Q96D42
    Function: May play a role in T-helper cell development and the regulation of asthma and allergic
    diseases. Receptor for TIMD4 (By similarity). In case of human hepatitis A virus (HHAV) infection,
    functions as a cell-surface receptor for the virus

    1 Gene Ontology (GO) molecular function term (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004872 receptor activity IEA--
    About this table

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section


     Gene Network CentralTM Interacting Genes and Proteins Network for  HAVCR1 


    5/8 Interacting proteins for HAVCR1 (ENSP000003448443 Q96D422) via UniProtKB, MINT, and/or STRING (see all 8 )
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UBQLN4Q9NRR52MINT-2872068
    LGALS9ENSP000003182143STRING (score=.834)
    PHF11ENSP000003675703STRING (score=.774)
    ADAM33ENSP000003489123STRING (score=.757)
    TGM4ENSP000002961253STRING (score=.734)
    About this table

    1 Gene Ontology (GO) biological process term (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0044419 interspecies interaction between organisms IEA--
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for HAVCR1
    1 Novoseek chemical compound relationship for HAVCR1 gene
    Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    tyrosine 0.00 4 16284246 (1)
    About this table


    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (HAVCR1)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (HAVCR1)
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 3): NM_012206

                  Sigma-Aldrich siRNA and siRNA Panels for HAVCR1  
                         Sigma-Aldrich shRNA Panels and shRNA for HAVCR1  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_001099414  NM_012206  

    REFSEQ mRNAs for HAVCR1 gene (2 alternative transcripts): 

    NM_001099414.1   NM_012206.2   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_001099414  NM_012206  

                   OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_001099414
                                     Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_001099414
                                     untagged cDNA clones in CMV expression vector (see all 4): BC013325 

    Additional cDNA sequence: 

    AK298259.1 BC013325.1 CR457114.1 

    5 DOTS entries:

    DT.91905981  DT.40127952  DT.95266388  DT.91653394  DT.40262844 

    23 AceView cDNA sequences:

    AW849281 BX283851 AW849356 AI218437 AA912911 CR457114 BV188647 BE739579 
    BC013325 AW439507 BU148837 BG168159 AW849406 BG326440 AW849403 AF043724 
    BE273684 NM_012206 BG752287 BX957193 BE739332 AW604191 BE811431 

    highest scoring ESTs for HAVCR1:

    AF043724 AW604297 BC013325 BE739332 BG168159 BG752287 BU148837 BX283851 CR457114 AW377044 

    Unigene Cluster for HAVCR1:

    Hepatitis A virus cellular receptor 1
    Hs.129711  [show with all ESTs]
    Unigene Representative Sequence: NM_012206


    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for HAVCR1

    ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10
    SP1:                                                                                          
    SP2:              -     -                                                                     
    SP3:        -     -                                                                           
    SP4:                                                                                -         

    About this scheme

    ECgene alternative splicing isoforms for HAVCR1

    1 Ensembl transcript including schematic representation:
    ENST00000339252  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    HAVCR1 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for HAVCR1

    1 / 2 / 3

    3 probe-sets matching HAVCR1 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

    33000_at2, 3 U95-A 1 1.00 1.00 1.00 1.00 AF043724 1.00 1.00 1.00 1

    207052_at2, 3 U133-A 1 1.00 1.00 -- -- NM_012206 0.60 1.00 0.82 1

    207052_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    About this table
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: AAAATCACCG

    SOURCE GeneReport for Unigene cluster: Hs.129711

    Expression variation in blood from EXPOLDB for HAVCR1

    UniProtKB/Swiss-Prot: TIMD1_HUMAN, Q96D42
    Tissue specificity: Widely expressed, with highest levels in kidney and testis. Expressed by
    activated CD4+ T-cells during the development of helper T-cells responses

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for HAVCR1 gene from 5 species
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    HAVCR11   -- hepatitis A virus cellular receptor 1 73.51(n)
    61.16(a)
    612069  XM_849795.1  XP_854888.1 
    chimpanzee
    (Pan troglodytes)
    HAVCR11   -- hepatitis A virus cellular receptor 1 98.53(n)
    97.8(a)
    462218  XM_518058.2  XP_518058.2 
    rat
    (Rattus norvegicus)
    Havcr11   -- hepatitis A virus cellular receptor 1 57.7(n)
    48.97(a)
    286934  NM_173149.1  NP_775172.1 
    mouse
    (Mus musculus)
    Havcr11, 5 115
    hepatitis A virus cellular receptor 11, 5 58.79(n)1
    48.63(a)1
    1712831  NM_134248.11  NP_599009.11 
     AA6454265  AF3998295  (see all 13)
    zebrafish
    (Danio rerio)
    zgc:926471   -- zgc:92647 44.04(n)
    37.96(a)
    436707  NM_001002434.1  NP_001002434.1 
    About this table        Species with no ortholog for HAVCR1

    ENSEMBL Gene Tree for HAVCR1
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for HAVCR1 gene
    HAVCR22  TIMD42  

    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section

    UniProtKB/Swiss-Prot: TIMD1_HUMAN, Q96D42
    Polymorphism: HHAV seropositivity protects against atopy in individuals with the variants
    Met-Thr-Thr-Val-Pro-157 ins and Met-Thr-Thr-Thr-Val-Pro-157 ins. Modernisation has led to a
    reduction in HAV seroprevalence and thus, may be, to an increase of expression of atopy, such as
    asthma, allergic rhinitis and atopic dermatitis. Allelic variation does not affect HAV-infection
    rates in Caucasians, Asians and African Americans


    10/297 NCBI SNPs in HAVCR1 are shown (see all 297 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 68)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 5 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    --
    rs125222481,2
    A,C,F,H156412004(+) GACCGT/CTGTTG 2 A/T mis14Minor allele frequency- C:0.16EU EA WA 414
    rs15533161,2
    A,C,F,H156412087(-) TGTTCC/TGACGA 2 L/P mis1 ese315Minor allele frequency- T:0.07EU EA WA NA 1394
    rs64200751,2
    C,F,H156418698(+) ATGCAC/GTAATA 2 -- ng3116Minor allele frequency- G:0.11EU EA WA NA 1472
    rs125162701,2
    C,F,H156420050(+) ATCCCG/AGCTTA 2 -- ng31 tfbs316Minor allele frequency- A:0.13EU EA WA NA 1418
    --
    rs93134221,2
    A,C156417948(+) gagatC/Ggagac 2 -- ut510--------
    --
    rs22709221,2
    F156415017(-) AGGCTC/TATGTT 2 S/L mis11Minor allele frequency- T:0.01EA 1502
    --
    rs77029191,2
    C156419169(+) TGAGGC/TAGAAG 2 -- ng310--------
    --
    rs15533171,2
    A,C,F,H156412002(-) ACAACG/TGTCTC 2 T/T syn1 ese37Minor allele frequency- T:0.12MN EA WA NA 622
    rs18099411,2
    A,C,O156415037(-) ACATCA/CATGTG 2 S/S syn10--------
    rs9535691,2
    A,C,F,H,O156409978(-) ACTCCA/CGGGAA 2 -- int118Minor allele frequency- N:0.00NS EA NA EU WA 1354
    About this table

    HapMap Linkage Disequilibrium images for HAVCR1 (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 606518   disorders: 147050  

    9 Novoseek disease relationships for HAVCR1 gene

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    hepatitis 60.81 20 17229699 (2), 9658108 (2), 12618867 (1), 12901378 (1) (see all 10)
    atopy 51.31 6 14637143 (1), 16159638 (1), 16481347 (1), 17229699 (1)
    asthma allergic 47.95 5 15300647 (3), 16284246 (1)
    autoimmunity 45.35 2 17069754 (1), 16938542 (1)
    asthma 43.78 19 17570927 (4), 17117951 (4), 15867855 (3), 12618867 (1) (see all 6)
    allergic rhinitis 41.72 2 17460580 (1), 19159567 (1)
    dermatitis atopic 24.49 3 16940744 (2), 14637143 (1)
    autoimmune diseases 20.06 2 15565336 (1), 17729033 (1)
    rheumatoid arthritis 1.01 4 15565336 (2), 14985107 (2)
    About this table

    Human Gene Mutation Database: HAVCR1
    Genetic Association Database: HAVCR1
    Human Genome Epidemiology Navigator: HAVCR1 (10 documents)

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/64 PubMed articles for HAVCR1 gene (see all 64 ):
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)
    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
    About This Section

    Entrez Gene: 26762 HGNC: 17866 AceView: HAVCR1 Ensembl:ENSG00000113249 euGenes: HUgn26762
    ECgene: HAVCR1 H-InvDB: HAVCR1
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

    NameDescription
    ATLAS Chromosomes in Cancer entry for HAVCR1 Genetics and Cytogenetics in Oncology and Haematology
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for HAVCR1:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Predesigned and custom siRNAs for HAVCR1 Antibodies for HAVCR1
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for HAVCR1 Browse small molecules at Sigma-Aldrich
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