Havcr2 hepatitis A virus cellular receptor 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Havcr2provided by RGD
Official Full Name: hepatitis A virus cellular receptor 2provided by RGD
Primary source: RGD:1305233
See related: EnsemblRapid:ENSRNOG00000031443 AllianceGenome:RGD:1305233
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: tim3
Summary: Predicted to enable metal ion binding activity. Predicted to be involved in several processes, including regulation of cytokine production; regulation of defense response; and regulation of leukocyte activation. Located in cell surface. Biomarker of transient cerebral ischemia. Human ortholog(s) of this gene implicated in hepatocellular carcinoma and renal cell carcinoma. Orthologous to human HAVCR2 (hepatitis A virus cellular receptor 2). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Thymus (RPKM 13.0), Spleen (RPKM 11.5) and 7 other tissues See more
Orthologs: human mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 10q21

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (31383801..31415334)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (30882484..30914018)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (31561838..31590624)

Chromosome 10 - NC_086028.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Galectin-9 and Tim-3 are upregulated in response to microglial activation induced by the peptide Amyloid-beta (25-35).
Title: Galectin-9 and Tim-3 are upregulated in response to microglial activation induced by the peptide Amyloid-β (25-35).
A newly intervention strategy in preeclampsia: Targeting PD-1/Tim-3 signaling pathways to modulate the polarization of decidual macrophages.
Title: A newly intervention strategy in preeclampsia: Targeting PD-1/Tim-3 signaling pathways to modulate the polarization of decidual macrophages.
Tim-3 deteriorates neuroinflammatory and neurocyte apoptosis after subarachnoid hemorrhage through the Nrf2/HMGB1 signaling pathway in rats.
Title: Tim-3 deteriorates neuroinflammatory and neurocyte apoptosis after subarachnoid hemorrhage through the Nrf2/HMGB1 signaling pathway in rats.
Negative regulation of glial Tim-3 inhibits the secretion of inflammatory factors and modulates microglia to antiinflammatory phenotype after experimental intracerebral hemorrhage in rats.
Title: Negative regulation of glial Tim-3 inhibits the secretion of inflammatory factors and modulates microglia to antiinflammatory phenotype after experimental intracerebral hemorrhage in rats.
we show that the galectin-9/Tim-3 cell signaling pathway is involved in inflammation induced by stroke
Title: Tim-3 cell signaling and iNOS are involved in the protective effects of ischemic postconditioning against focal ischemia in rats.
Osteoclasts and osteoclast precursors express Tim-3, and osteoclast differentiation is negatively regulated by its ligand galectin-9.
Title: Regulation of osteoclastogenesis through Tim-3: possible involvement of the Tim-3/galectin-9 system in the modulation of inflammatory bone destruction.
The study described that enhanced Tim-3 and its ligand Galectin-9 in allografts might play an important role in the pathogenesis of rat lung transplant rejection.
Title: Increased expression of Tim-3 and its ligand Galectin-9 in rat allografts during acute rejection episodes.
Tim3(+) cells might include a distinct macrophage population, which may be involved in anti-inflammatory effect and recovery from experimental autoimmune neuritis
Title: Distinct expression of Tim-3 during different stages of rat experimental autoimmune neuritis.

Submit: New GeneRIF Correction

General gene information

Go to the top of the page Help

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in adaptive immune response	IEA Inferred from Electronic Annotation more info
involved_in biological_process	ND No biological Data available more info
involved_in cellular response to lipopolysaccharide	ISO Inferred from Sequence Orthology more info
involved_in defense response to Gram-positive bacterium	ISO Inferred from Sequence Orthology more info
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in macrophage activation involved in immune response	ISO Inferred from Sequence Orthology more info
involved_in maternal process involved in female pregnancy	ISO Inferred from Sequence Orthology more info
involved_in natural killer cell tolerance induction	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of NF-kappaB transcription factor activity	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of T cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of T-helper 1 type immune response	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of defense response to bacterium	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of granulocyte colony-stimulating factor production	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of immune response to tumor cell	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of immunological synapse formation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of innate immune response	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of interferon-alpha production	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of interleukin-2 production	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of interleukin-3 production	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of interleukin-6 production	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of myeloid dendritic cell activation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of natural killer cell activation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of tumor necrosis factor production	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of type I interferon production	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of type II interferon production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of ERK1 and ERK2 cascade	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of T cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of chemokine production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cytokine production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of defense response to bacterium	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of innate immune response	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interleukin-1 production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interleukin-4 production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of macrophage activation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of non-canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of tumor necrosis factor production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of type II interferon production	ISO Inferred from Sequence Orthology more info
involved_in regulation of tolerance induction dependent upon immune response	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in toll-like receptor 3 signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in toll-like receptor 7 signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in toll-like receptor 9 signaling pathway	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in anchoring junction	IEA Inferred from Electronic Annotation 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 early endosome	ISO Inferred from Sequence Orthology more info
located_in immunological synapse	ISO Inferred from Sequence Orthology more info
part_of mediator complex	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IEA Inferred from Electronic Annotation more info

General protein information

Go to the top of the page Help

Preferred Names: hepatitis A virus cellular receptor 2 homolog

Names: HAVcr-2; T cell immunoglobulin mucin-3; T-cell immunoglobulin and mucin domain-containing protein 3; T-cell immunoglobulin mucin receptor 3; T-cell membrane protein 3; TIM-3; TIMD-3

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_001100762.1 → NP_001094232.1 hepatitis A virus cellular receptor 2 homolog precursor

See identical proteins and their annotated locations for NP_001094232.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/Swiss-Prot

G3V9I4, P0C0K5

Related

ENSRNOP00000048351.2, ENSRNOT00000048485.4

Conserved Domains (2) summary

smart00410
Location:26 → 112

IG_like; Immunoglobulin like

pfam07686
Location:27 → 131

V-set; Immunoglobulin V-set domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086028.1 Reference GRCr8

Range

31383801..31415334

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039086455.2 → XP_038942383.1 hepatitis A virus cellular receptor 2 homolog isoform X2

Conserved Domains (1) summary

cd20982
Location:24 → 130

IgV_TIM-3_like; Immunoglobulin Variable (IgV) domain of T cell Immunoglobulin Domain and Mucin Domain 3 (Tim-3), and similar domains
XM_063269494.1 → XP_063125564.1 hepatitis A virus cellular receptor 2 homolog isoform X4
XM_039086454.2 → XP_038942382.1 hepatitis A virus cellular receptor 2 homolog isoform X1

Related

ENSRNOP00000107631.1, ENSRNOT00000121601.1

Conserved Domains (1) summary

cd20982
Location:24 → 130

IgV_TIM-3_like; Immunoglobulin Variable (IgV) domain of T cell Immunoglobulin Domain and Mucin Domain 3 (Tim-3), and similar domains
XM_063269493.1 → XP_063125563.1 hepatitis A virus cellular receptor 2 homolog isoform X3

UniProtKB/TrEMBL

A0A8I5ZXZ2

Related

ENSRNOP00000084467.1, ENSRNOT00000108848.2
XM_063269495.1 → XP_063125565.1 hepatitis A virus cellular receptor 2 homolog isoform X5