This gene was initially thought to represent a pseudogene of galectin 9; however, this transcript has good exon-intron structure and encodes a predicted protein of the same size as and highly similar to galectin 9. This gene is one of two similar loci on chromosome 17p similar to galectin 9 and now thought to be protein-encoding. This gene is the more telomeric gene. [provided ... See more...

Aliases for LGALS9C Gene

Aliases for LGALS9C Gene

  • Galectin 9C 2 3 5
  • Lectin, Galactoside-Binding, Soluble, 9C 2 3
  • Galectin-9-Like Protein B 3 4
  • Galectin-9C 3 4
  • Gal-9C 3 4
  • Lectin, Galactoside-Binding, Soluble, 9 (Galectin 9) Pseudogene 3
  • Galectin-9-Like Protein A 3
  • Galectin 9 Like 3
  • Galectin-9B 3
  • LGALS9B 3
  • Gal-9B 3

External Ids for LGALS9C Gene

Previous GeneCards Identifiers for LGALS9C Gene

  • GC17P018322
  • GC17P018380
  • GC17P018478
  • GC17P018617
  • GC17P018638
  • GC17P018479
  • GC17P018500
  • GC17P018525
  • GC17P018556
  • GC17P018575
  • GC17P018604

Summaries for LGALS9C Gene

Entrez Gene Summary for LGALS9C Gene

  • This gene was initially thought to represent a pseudogene of galectin 9; however, this transcript has good exon-intron structure and encodes a predicted protein of the same size as and highly similar to galectin 9. This gene is one of two similar loci on chromosome 17p similar to galectin 9 and now thought to be protein-encoding. This gene is the more telomeric gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for LGALS9C Gene

LGALS9C (Galectin 9C) is a Protein Coding gene. Diseases associated with LGALS9C include Shwachman-Diamond Syndrome 1. Gene Ontology (GO) annotations related to this gene include carbohydrate binding. An important paralog of this gene is LGALS9B.

UniProtKB/Swiss-Prot Summary for LGALS9C Gene

Additional gene information for LGALS9C Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LGALS9C Gene

Genomics for LGALS9C Gene

GeneHancer (GH) Regulatory Elements for LGALS9C Gene

Promoters and enhancers for LGALS9C Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J018476 Promoter/Enhancer 1.1 EPDnew Ensembl ENCODE 755.1 +0.4 370 1.4 IKZF1 ZIC2 IKZF2 DPF2 ATF7 LGALS9C KRT17P2 piR-52378-001
GH17J018478 Promoter 0.4 Ensembl 750.6 +2.0 1964 0.2 ZIC2 LGALS9C piR-52378-001
GH17J018489 Promoter 0.3 EPDnew 750.4 +12.7 12693 0.1 LGALS9C piR-52378-001
GH17J018402 Enhancer 0.4 Ensembl 5.6 -73.6 -73636 1.4 NFIB ZNF544 NFIC ZNF624 piR-36649-001 piR-37000-001 piR-40708-001 piR-43246-001 piR-40874-002 piR-32001 piR-38288-001 piR-43615-001 piR-44009-001 piR-35135-001
GH17J018485 Enhancer 0.2 Ensembl 0.4 +9.7 9664 1.2 LGALS9C piR-52378-001
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LGALS9C on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LGALS9C gene promoter:
  • AML1a
  • CUTL1
  • FOXJ2
  • FOXJ2 (long isoform)
  • NF-AT
  • NF-AT1
  • NF-AT2
  • NF-AT3
  • PPAR-alpha
  • Sox5

Genomic Locations for LGALS9C Gene

Genomic Locations for LGALS9C Gene
chr17:18,476,737-18,494,945
(GRCh38/hg38)
Size:
18,209 bases
Orientation:
Plus strand
chr17:18,380,051-18,398,259
(GRCh37/hg19)
Size:
18,209 bases
Orientation:
Plus strand

Genomic View for LGALS9C Gene

Genes around LGALS9C on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LGALS9C Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LGALS9C Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LGALS9C Gene

Proteins for LGALS9C Gene

  • Protein details for LGALS9C Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6DKI2-LEG9C_HUMAN
    Recommended name:
    Galectin-9C
    Protein Accession:
    Q6DKI2
    Secondary Accessions:
    • B0AZM7

    Protein attributes for LGALS9C Gene

    Size:
    356 amino acids
    Molecular mass:
    39607 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • The LGALS9-like proteins are encoded by a duplicated regions on chromosome 17; there are at least 3 genes coding for galectin-9-like proteins.

neXtProt entry for LGALS9C Gene

Post-translational modifications for LGALS9C Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LGALS9C Gene

Domains & Families for LGALS9C Gene

Gene Families for LGALS9C Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for LGALS9C Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LGALS9C Gene

GenScript: Design optimal peptide antigens:
  • Galectin-9-like protein B (LEG9C_HUMAN)
genes like me logo Genes that share domains with LGALS9C: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LGALS9C Gene

Function for LGALS9C Gene

Molecular function for LGALS9C Gene

UniProtKB/Swiss-Prot Function:
Binds galactosides.

Gene Ontology (GO) - Molecular Function for LGALS9C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0016936 galactoside binding IBA 21873635
GO:0030246 carbohydrate binding IBA,IEA 21873635
genes like me logo Genes that share ontologies with LGALS9C: view

Phenotypes for LGALS9C Gene

genes like me logo Genes that share phenotypes with LGALS9C: view

Animal Model Products

CRISPR Products

miRNA for LGALS9C Gene

miRTarBase miRNAs that target LGALS9C

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LGALS9C

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LGALS9C Gene

Localization for LGALS9C Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LGALS9C gene
Compartment Confidence
nucleus 4
cytosol 4
extracellular 1
endoplasmic reticulum 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for LGALS9C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with LGALS9C: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for LGALS9C Gene

Pathways & Interactions for LGALS9C Gene

PathCards logo

SuperPathways for LGALS9C Gene

No Data Available

Gene Ontology (GO) - Biological Process for LGALS9C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010628 positive regulation of gene expression IBA 21873635
GO:0010629 negative regulation of gene expression IBA 21873635
GO:0032689 negative regulation of interferon-gamma production IBA 21873635
GO:2000562 negative regulation of CD4-positive, alpha-beta T cell proliferation IBA 21873635
GO:2000778 positive regulation of interleukin-6 secretion IBA 21873635
genes like me logo Genes that share ontologies with LGALS9C: view

No data available for Pathways by source and SIGNOR curated interactions for LGALS9C Gene

Drugs & Compounds for LGALS9C Gene

No Compound Related Data Available

Transcripts for LGALS9C Gene

mRNA/cDNA for LGALS9C Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(15) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LGALS9C

Alternative Splicing Database (ASD) splice patterns (SP) for LGALS9C Gene

No ASD Table

Relevant External Links for LGALS9C Gene

GeneLoc Exon Structure for
LGALS9C
ECgene alternative splicing isoforms for
LGALS9C

Expression for LGALS9C Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LGALS9C Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LGALS9C Gene

This gene is overexpressed in Colon - Transverse (x12.2), Stomach (x10.7), Whole Blood (x8.5), and Esophagus - Mucosa (x7.5).

Protein differential expression in normal tissues from HIPED for LGALS9C Gene

This gene is overexpressed in Urine (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LGALS9C Gene



Protein tissue co-expression partners for LGALS9C Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LGALS9C Gene:

LGALS9C

SOURCE GeneReport for Unigene cluster for LGALS9C Gene:

Hs.462402

Evidence on tissue expression from TISSUES for LGALS9C Gene

  • Intestine(4.2)
  • Pancreas(4.1)
genes like me logo Genes that share expression patterns with LGALS9C: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LGALS9C Gene

Orthologs for LGALS9C Gene

This gene was present in the common ancestor of animals.

Orthologs for LGALS9C Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LGALS9C 32
  • 99.53 (n)
-- 33
  • 99 (a)
OneToMany
dog
(Canis familiaris)
Mammalia LGALS9 33
  • 74 (a)
OneToMany
cow
(Bos Taurus)
Mammalia LGALS9 33
  • 73 (a)
ManyToMany
-- 33
  • 58 (a)
ManyToMany
mouse
(Mus musculus)
Mammalia Lgals9 33
  • 69 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia -- 33
  • 60 (a)
ManyToMany
-- 33
  • 56 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 33
  • 59 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 33
  • 44 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia lgals9b 32
  • 50.83 (n)
zebrafish
(Danio rerio)
Actinopterygii zgc:92326 33
  • 47 (a)
ManyToMany
lgals9l1 33
  • 45 (a)
ManyToMany
zgc:171951 33
  • 43 (a)
ManyToMany
zgc:136924 33
  • 42 (a)
ManyToMany
si:ch211-209m20.9 33
  • 42 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta CG11374 33
  • 17 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea lec-12 33
  • 27 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 33
  • 32 (a)
ManyToMany
CSA.123 33
  • 29 (a)
ManyToMany
Species where no ortholog for LGALS9C was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for LGALS9C Gene

ENSEMBL:
Gene Tree for LGALS9C (if available)
TreeFam:
Gene Tree for LGALS9C (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LGALS9C: view image

Paralogs for LGALS9C Gene

(15) SIMAP similar genes for LGALS9C Gene using alignment to 9 proteins:

  • LEG9C_HUMAN
  • C9JHN9_HUMAN
  • J3KRF0_HUMAN
  • J3KSV0_HUMAN
  • J3KSY2_HUMAN
  • J3KT17_HUMAN
  • J3QKS2_HUMAN
  • J3QR96_HUMAN
  • J3QSH0_HUMAN
genes like me logo Genes that share paralogs with LGALS9C: view

Variants for LGALS9C Gene

Sequence variations from dbSNP and Humsavar for LGALS9C Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1001084561 -- 18,489,256(+) A/C intron_variant
rs1001470721 -- 18,491,740(+) G/A intron_variant
rs1001523080 -- 18,492,323(+) T/A intron_variant
rs1001807907 -- 18,486,906(+) A/G 5_prime_UTR_variant, intron_variant
rs1001858659 -- 18,488,415(+) A/AA intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LGALS9C Gene

Variant ID Type Subtype PubMed ID
dgv27e213 CNV loss 24956385
dgv3110n100 CNV gain 25217958
dgv3111n100 CNV gain 25217958
dgv3112n100 CNV gain+loss 25217958
dgv3113n100 CNV loss 25217958
dgv3114n100 CNV gain+loss 25217958
dgv3115n100 CNV gain 25217958
dgv5484n54 CNV gain 21841781
dgv5485n54 CNV gain 21841781
dgv5486n54 CNV gain 21841781
dgv5487n54 CNV loss 21841781
dgv5488n54 CNV loss 21841781
dgv5489n54 CNV loss 21841781
dgv5490n54 CNV loss 21841781
dgv55e203 CNV gain+loss 21179565
esv2670394 CNV deletion 23128226
esv2758677 CNV gain+loss 17122850
esv29257 CNV gain+loss 19812545
esv3332213 CNV duplication 20981092
esv3374502 CNV duplication 20981092
esv3385951 CNV duplication 20981092
esv3394763 CNV duplication 20981092
esv3414138 CNV duplication 20981092
nsv1066489 CNV gain 25217958
nsv1121932 CNV deletion 24896259
nsv1146382 CNV duplication 26484159
nsv1160459 CNV duplication 26073780
nsv1160460 OTHER complex 26073780
nsv1160461 CNV deletion 26073780
nsv428333 CNV gain 18775914
nsv442738 CNV gain+loss 18776908
nsv469661 CNV gain 16826518
nsv511052 OTHER complex 20534489
nsv511593 CNV loss 21212237
nsv514828 CNV gain+loss 21397061
nsv574542 CNV gain+loss 21841781
nsv574548 CNV gain 21841781
nsv821444 CNV deletion 20802225
nsv827913 CNV gain 20364138
nsv827914 CNV gain 20364138
nsv833388 CNV loss 17160897
nsv9504 CNV gain+loss 18304495
nsv953840 CNV deletion 24416366
nsv962275 CNV duplication 23825009

Variation tolerance for LGALS9C Gene

Residual Variation Intolerance Score: 85.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.80; 58.30% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LGALS9C Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LGALS9C

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LGALS9C Gene

Disorders for LGALS9C Gene

MalaCards: The human disease database

(1) MalaCards diseases for LGALS9C Gene - From: DISEASES

Disorder Aliases PubMed IDs
shwachman-diamond syndrome 1
  • sds1
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for LGALS9C

genes like me logo Genes that share disorders with LGALS9C: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LGALS9C Gene

Publications for LGALS9C Gene

  1. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 56
  2. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 56
  3. Phospho-tyrosine dependent protein-protein interaction network. (PMID: 25814554) Grossmann A … Stelzl U (Molecular systems biology 2015) 3 56
  4. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T … Vidal M (Cell 2014) 3 56
  5. The palmitoyl acyltransferase HIP14 shares a high proportion of interactors with huntingtin: implications for a role in the pathogenesis of Huntington's disease. (PMID: 24705354) Butland SL … Hayden MR (Human molecular genetics 2014) 3 56

Products for LGALS9C Gene

Sources for LGALS9C Gene