Human Gene HAVCR2 (ENST00000307851.9) from GENCODE V44
  Description: Homo sapiens hepatitis A virus cellular receptor 2 (HAVCR2), mRNA. (from RefSeq NM_032782)
RefSeq Summary (NM_032782): The protein encoded by this gene belongs to the immunoglobulin superfamily, and TIM family of proteins. CD4-positive T helper lymphocytes can be divided into types 1 (Th1) and 2 (Th2) on the basis of their cytokine secretion patterns. Th1 cells are involved in cell-mediated immunity to intracellular pathogens and delayed-type hypersensitivity reactions, whereas, Th2 cells are involved in the control of extracellular helminthic infections and the promotion of atopic and allergic diseases. This protein is a Th1-specific cell surface protein that regulates macrophage activation, and inhibits Th1-mediated auto- and alloimmune responses, and promotes immunological tolerance. [provided by RefSeq, Sep 2011].
Gencode Transcript: ENST00000307851.9
Gencode Gene: ENSG00000135077.10
Transcript (Including UTRs)
   Position: hg38 chr5:157,085,832-157,109,044 Size: 23,213 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg38 chr5:157,087,102-157,108,983 Size: 21,882 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:157,085,832-157,109,044)mRNA (may differ from genome)Protein (301 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGImyGene2
neXtProtOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: HAVR2_HUMAN
DESCRIPTION: RecName: Full=Hepatitis A virus cellular receptor 2; Short=HAVcr-2; AltName: Full=T-cell immunoglobulin and mucin domain-containing protein 3; Short=TIMD-3; AltName: Full=T-cell membrane protein 3; AltName: Full=TIM-3; Flags: Precursor;
FUNCTION: Regulates macrophage activation. Inhibits T-helper type 1 lymphocyte (Th1)-mediated auto- and alloimmune responses and promotes immunological tolerance. May be also involved in T-cell homing. Receptor for LGALS9.
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein (Potential).
TISSUE SPECIFICITY: T-helper type 1 lymphocyte (Th1)-specific.
PTM: O-glycosylated with core 1 or possibly core 8 glycans.
SIMILARITY: Belongs to the immunoglobulin superfamily. TIM family.
SIMILARITY: Contains 1 Ig-like V-type (immunoglobulin-like) domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: HAVCR2
Diseases sorted by gene-association score: hepatitis a (34), hepatitis (30), far eastern spotted fever (11), histiocytic sarcoma (8), vulvar intraepithelial neoplasia (5), hepatitis c virus (3), malaria (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 12.78 RPKM in Spleen
Total median expression: 123.95 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -10.9061-0.179 Picture PostScript Text
3' UTR -391.501270-0.308 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR003599 - Ig_sub
IPR013106 - Ig_V-set

Pfam Domains:
PF07686 - Immunoglobulin V-set domain

ModBase Predicted Comparative 3D Structure on Q8TDQ0
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0001819 positive regulation of cytokine production
GO:0002250 adaptive immune response
GO:0002281 macrophage activation involved in immune response
GO:0002376 immune system process
GO:0002519 natural killer cell tolerance induction
GO:0002652 regulation of tolerance induction dependent upon immune response
GO:0002826 negative regulation of T-helper 1 type immune response
GO:0002838 negative regulation of immune response to tumor cell
GO:0002859 negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target
GO:0006954 inflammatory response
GO:0010629 negative regulation of gene expression
GO:0030886 negative regulation of myeloid dendritic cell activation
GO:0032088 negative regulation of NF-kappaB transcription factor activity
GO:0032480 negative regulation of type I interferon production
GO:0032687 negative regulation of interferon-alpha production
GO:0032689 negative regulation of interferon-gamma production
GO:0032703 negative regulation of interleukin-2 production
GO:0032712 negative regulation of interleukin-3 production
GO:0032715 negative regulation of interleukin-6 production
GO:0032720 negative regulation of tumor necrosis factor production
GO:0032722 positive regulation of chemokine production
GO:0032729 positive regulation of interferon-gamma production
GO:0032732 positive regulation of interleukin-1 production
GO:0032753 positive regulation of interleukin-4 production
GO:0032815 negative regulation of natural killer cell activation
GO:0034138 toll-like receptor 3 signaling pathway
GO:0034154 toll-like receptor 7 signaling pathway
GO:0034162 toll-like receptor 9 signaling pathway
GO:0042102 positive regulation of T cell proliferation
GO:0042130 negative regulation of T cell proliferation
GO:0043032 positive regulation of macrophage activation
GO:0045087 innate immune response
GO:0045089 positive regulation of innate immune response
GO:0045824 negative regulation of innate immune response
GO:0050830 defense response to Gram-positive bacterium
GO:0060135 maternal process involved in female pregnancy
GO:0070374 positive regulation of ERK1 and ERK2 cascade
GO:0071222 cellular response to lipopolysaccharide
GO:0071656 negative regulation of granulocyte colony-stimulating factor production
GO:1900425 negative regulation of defense response to bacterium
GO:1900426 positive regulation of defense response to bacterium
GO:1901224 positive regulation of NIK/NF-kappaB signaling
GO:1904469 positive regulation of tumor necrosis factor secretion
GO:2000521 negative regulation of immunological synapse formation
GO:2001189 negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell

Cellular Component:
GO:0001772 immunological synapse
GO:0005769 early endosome
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction


-  Descriptions from all associated GenBank mRNAs
  AK027334 - Homo sapiens cDNA FLJ14428 fis, clone HEMBA1006293.
AF251707 - Homo sapiens hepatitis A virus cellular receptor 2 mRNA, complete cds.
BC063431 - Homo sapiens hepatitis A virus cellular receptor 2, mRNA (cDNA clone MGC:74657 IMAGE:5229539), complete cds.
AK130144 - Homo sapiens cDNA FLJ26634 fis, clone MPC07695.
JD465955 - Sequence 446979 from Patent EP1572962.
JD483737 - Sequence 464761 from Patent EP1572962.
JD102561 - Sequence 83585 from Patent EP1572962.
JD184101 - Sequence 165125 from Patent EP1572962.
JD076907 - Sequence 57931 from Patent EP1572962.
JD107486 - Sequence 88510 from Patent EP1572962.
JD476667 - Sequence 457691 from Patent EP1572962.
JD256510 - Sequence 237534 from Patent EP1572962.
JD476665 - Sequence 457689 from Patent EP1572962.
JD560658 - Sequence 541682 from Patent EP1572962.
JD256509 - Sequence 237533 from Patent EP1572962.
JD414693 - Sequence 395717 from Patent EP1572962.
JD037352 - Sequence 18376 from Patent EP1572962.
JD435452 - Sequence 416476 from Patent EP1572962.
JD398825 - Sequence 379849 from Patent EP1572962.
JD070597 - Sequence 51621 from Patent EP1572962.
JD070598 - Sequence 51622 from Patent EP1572962.
JD484566 - Sequence 465590 from Patent EP1572962.
JD482919 - Sequence 463943 from Patent EP1572962.
JD152567 - Sequence 133591 from Patent EP1572962.
JD047343 - Sequence 28367 from Patent EP1572962.
JD214814 - Sequence 195838 from Patent EP1572962.
AF450242 - Homo sapiens clone 1 T cell immunoglobulin mucin-3 (TIM3) mRNA, complete cds.
AF450243 - Homo sapiens clone 2 T cell immunoglobulin mucin-3 (TIM3) mRNA, complete cds.
JD378960 - Sequence 359984 from Patent EP1572962.
JD322418 - Sequence 303442 from Patent EP1572962.
JD532755 - Sequence 513779 from Patent EP1572962.
JD102301 - Sequence 83325 from Patent EP1572962.
JD444862 - Sequence 425886 from Patent EP1572962.
JD116389 - Sequence 97413 from Patent EP1572962.
JD202215 - Sequence 183239 from Patent EP1572962.
AY069944 - Homo sapiens putative kidney injury molecule-3 mRNA, complete cds.
JX049979 - Homo sapiens T-cell immunoglobulin and mucin domain-containing protein 3 mRNA, complete cds.
AK314406 - Homo sapiens cDNA, FLJ95186, highly similar to Homo sapiens hepatitis A virus cellular receptor 2 (HAVCR2), mRNA.
KJ899836 - Synthetic construct Homo sapiens clone ccsbBroadEn_09230 HAVCR2 gene, encodes complete protein.
HQ448118 - Synthetic construct Homo sapiens clone IMAGE:100071500; CCSB012144_01 hepatitis A virus cellular receptor 2 (HAVCR2) gene, encodes complete protein.
CU687712 - Synthetic construct Homo sapiens gateway clone IMAGE:100021671 5' read HAVCR2 mRNA.
AB924452 - Homo sapiens Tim-3 mRNA for T-cell immunoglobulin mucin receptor 3, partial cds.
BC020843 - Homo sapiens hepatitis A virus cellular receptor 2, mRNA (cDNA clone IMAGE:4701288), complete cds.
KJ903472 - Synthetic construct Homo sapiens clone ccsbBroadEn_12866 HAVCR2 gene, encodes complete protein.
DL492581 - Novel nucleic acids.
JD300437 - Sequence 281461 from Patent EP1572962.
JD162427 - Sequence 143451 from Patent EP1572962.
JD230557 - Sequence 211581 from Patent EP1572962.
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-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8TDQ0 (Reactome details) participates in the following event(s):

R-HSA-5340385 HAVCR2 binds LGALS9
R-HSA-451927 Interleukin-2 family signaling
R-HSA-449147 Signaling by Interleukins
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: B2RAY2, ENST00000307851.1, ENST00000307851.2, ENST00000307851.3, ENST00000307851.4, ENST00000307851.5, ENST00000307851.6, ENST00000307851.7, ENST00000307851.8, HAVR2_HUMAN, NM_032782, Q8TDQ0, Q8WW60, Q96K94, TIM3, TIMD3, uc003lwk.1, uc003lwk.2, uc003lwk.3, uc003lwk.4
UCSC ID: ENST00000307851.9
RefSeq Accession: NM_032782
Protein: Q8TDQ0 (aka HAVR2_HUMAN)
CCDS: CCDS4333.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.