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LGALS9 galectin 9 [ Homo sapiens (human) ]

Gene ID: 3965, updated on 23-Dec-2018

Summary

Official Symbol
LGALS9provided by HGNC
Official Full Name
galectin 9provided by HGNC
Primary source
HGNC:HGNC:6570
See related
Ensembl:ENSG00000168961 MIM:601879
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
HUAT; LGALS9A
Summary
The galectins are a family of beta-galactoside-binding proteins implicated in modulating cell-cell and cell-matrix interactions. The protein encoded by this gene is an S-type lectin. It is overexpressed in Hodgkin's disease tissue and might participate in the interaction between the H&RS cells with their surrounding cells and might thus play a role in the pathogenesis of this disease and/or its associated immunodeficiency. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Broad expression in spleen (RPKM 33.5), stomach (RPKM 28.4) and 23 other tissues See more
Orthologs

Genomic context

See LGALS9 in Genome Data Viewer
Location:
17q11.2
Exon count:
12
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 17 NC_000017.11 (27631148..27649560)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (25958174..25976586)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene kinase suppressor of ras 1 Neighboring gene Myb/SANT DNA binding domain containing 3 pseudogene Neighboring gene integral membrane protein 2B pseudogene 1 Neighboring gene TBC1 domain family member 29, pseudogene pseudogene Neighboring gene nitric oxide synthase 2 pseudogene 1

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
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
NHGRI GWA Catalog

Pathways from BioSystems

  • Cytokine Signaling in Immune system, organism-specific biosystem (from REACTOME)
    Cytokine Signaling in Immune system, organism-specific biosystemCytokines are small proteins that regulate and mediate immunity, inflammation, and hematopoiesis. They are secreted in response to immune stimuli, and usually act briefly, locally, at very low concen...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Interleukin-2 signaling, organism-specific biosystem (from REACTOME)
    Interleukin-2 signaling, organism-specific biosystemInterleukin-2 (IL-2) is a cytokine that is produced by T cells in response to antigen stimulation. Originally, IL-2 was discovered because of its potent growth factor activity on activated T cells in...
  • Signaling by Interleukins, organism-specific biosystem (from REACTOME)
    Signaling by Interleukins, organism-specific biosystemInterleukins are low molecular weight proteins that bind to cell surface receptors and act in an autocrine and/or paracrine fashion. They were first identified as factors produced by leukocytes but a...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC117375, MGC125973, MGC125974

Gene Ontology Provided by GOA

Function Evidence Code Pubs
carbohydrate binding IDA
Inferred from Direct Assay
more info
PubMed 
disaccharide binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
galactose binding TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
ERK1 and ERK2 cascade IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to interferon-gamma IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to virus IMP
Inferred from Mutant Phenotype
more info
PubMed 
chemotaxis IEA
Inferred from Electronic Annotation
more info
 
female pregnancy IDA
Inferred from Direct Assay
more info
PubMed 
inflammatory response IDA
Inferred from Direct Assay
more info
PubMed 
maternal process involved in female pregnancy IDA
Inferred from Direct Assay
more info
PubMed 
NOT mature conventional dendritic cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
natural killer cell tolerance induction IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of CD4-positive, alpha-beta T cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of activated T cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of chemokine production IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of gene expression IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of interferon-gamma production IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of mast cell degranulation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of natural killer cell mediated cytotoxicity IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of tumor necrosis factor production IMP
Inferred from Mutant Phenotype
more info
PubMed 
p38MAPK cascade IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of CD4-positive, alpha-beta T cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of ERK1 and ERK2 cascade IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of I-kappaB kinase/NF-kappaB signaling HMP PubMed 
positive regulation of NF-kappaB transcription factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of NIK/NF-kappaB signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of activated T cell autonomous cell death IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of dendritic cell apoptotic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of dendritic cell chemotaxis IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of dendritic cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of gene expression IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interferon-gamma secretion IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interleukin-1 beta secretion IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interleukin-10 secretion IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interleukin-12 secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of interleukin-13 secretion IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interleukin-4 production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interleukin-4 production IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of interleukin-6 secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of interleukin-8 secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of monocyte chemotactic protein-1 production IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transforming growth factor beta production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of tumor necrosis factor secretion IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of viral entry into host cell IDA
Inferred from Direct Assay
more info
PubMed 
NOT regulation of interleukin-4 production IDA
Inferred from Direct Assay
more info
PubMed 
NOT regulation of interleukin-5 production IDA
Inferred from Direct Assay
more info
PubMed 
NOT regulation of p38MAPK cascade IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to interleukin-1 IDA
Inferred from Direct Assay
more info
PubMed 
response to lipopolysaccharide IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT toll-like receptor 2 signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
NOT toll-like receptor 4 signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
galectin-9
Names
ecalectin
gal-9
lectin, galactoside-binding, soluble, 9
tumor antigen HOM-HD-21
urate transporter/channel protein

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.

mRNA and Protein(s)

  1. NM_001330163.1NP_001317092.1  galectin-9 isoform 3

    Status: REVIEWED

    Source sequence(s)
    BC110340, BX400388, DA999005
    Consensus CDS
    CCDS82093.1
    UniProtKB/Swiss-Prot
    O00182
    Related
    ENSP00000318214.6, ENST00000313648.10
    Conserved Domains (2) summary
    cd00070
    Location:16146
    GLECT; Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may ...
    pfam12380
    Location:149182
    Peptidase_C62; Gill-associated viral 3C-like peptidase
  2. NM_002308.3NP_002299.2  galectin-9 isoform short

    See identical proteins and their annotated locations for NP_002299.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) is lacking an internal, in-frame coding exon compared to variant 1, resulting in a shorter isoform (short) missing a 32 aa protein segment compared to isoform long.
    Source sequence(s)
    AC015688, BC110340
    Consensus CDS
    CCDS32592.1
    UniProtKB/Swiss-Prot
    O00182
    UniProtKB/TrEMBL
    A0A024QZ02
    Related
    ENSP00000306228.5, ENST00000302228.9
    Conserved Domains (2) summary
    smart00908
    Location:201322
    Gal-bind_lectin; Galactoside-binding lectin
    cd00070
    Location:16146
    GLECT; Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may ...
  3. NM_009587.3NP_033665.1  galectin-9 isoform long

    See identical proteins and their annotated locations for NP_033665.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (long).
    Source sequence(s)
    AB006782, BC110340
    Consensus CDS
    CCDS11222.1
    UniProtKB/Swiss-Prot
    O00182
    UniProtKB/TrEMBL
    A0A024QZ55
    Related
    ENSP00000378856.2, ENST00000395473.6
    Conserved Domains (3) summary
    smart00908
    Location:233354
    Gal-bind_lectin; Galactoside-binding lectin
    cd00070
    Location:16146
    GLECT; Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may ...
    pfam12380
    Location:154214
    Peptidase_C62; Gill-associated viral 3C-like peptidase

RNA

  1. NR_024043.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate acceptor splice site at one of the coding exons, and is also lacking an internal coding exon compared to variant 1. This results in a frame-shift and premature translation termination rendering this transcript susceptible to NMD. This variant has transcript support, but is not expected to encode a viable protein product.
    Source sequence(s)
    AC015688, BC110340
    Related
    ENST00000467111.5

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.p12 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p12 Primary Assembly

    Range
    27631148..27649560
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006721892.3XP_006721955.1  galectin-9 isoform X2

    See identical proteins and their annotated locations for XP_006721955.1

    UniProtKB/Swiss-Prot
    O00182
    Conserved Domains (2) summary
    smart00908
    Location:189310
    Gal-bind_lectin; Galactoside-binding lectin
    cd00070
    Location:16146
    GLECT; Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may ...
  2. XM_006721895.4XP_006721958.1  galectin-9 isoform X4

    UniProtKB/Swiss-Prot
    O00182
    Conserved Domains (1) summary
    cd00070
    Location:16146
    GLECT; Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may ...
  3. XM_017024623.2XP_016880112.1  galectin-9 isoform X1

    UniProtKB/Swiss-Prot
    O00182
    Conserved Domains (2) summary
    smart00908
    Location:221342
    Gal-bind_lectin; Galactoside-binding lectin
    cd00070
    Location:16146
    GLECT; Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may ...
  4. XM_006721893.3XP_006721956.1  galectin-9 isoform X3

    Conserved Domains (2) summary
    cd00070
    Location:16146
    GLECT; Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may ...
    pfam12380
    Location:154214
    Peptidase_C62; Gill-associated viral 3C-like peptidase
  5. XM_011524796.2XP_011523098.1  galectin-9 isoform X5

    Conserved Domains (1) summary
    cd00070
    Location:16146
    GLECT; Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may ...
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