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Aliases for CHSY3 Gene

Aliases for CHSY3 Gene

  • Chondroitin Sulfate Synthase 3 2 3 5
  • Glucuronosyl-N-Acetylgalactosaminyl-Proteoglycan 4-Beta-N-Acetylgalactosaminyltransferase II 3 4
  • N-Acetylgalactosaminyl-Proteoglycan 3-Beta-Glucuronosyltransferase 3 3 4
  • Chondroitin Glucuronyltransferase 3 3 4
  • N-Acetylgalactosaminyltransferase 3 3 4
  • Carbohydrate Synthase 2 3 4
  • ChSy-2 3 4
  • CHSY2 3 4
  • CSS3 3 4
  • Chondroitin Synthase-2 3
  • Chondroitin Synthase 2 4
  • EC 4
  • EC 4

External Ids for CHSY3 Gene

Previous GeneCards Identifiers for CHSY3 Gene

  • GC05P129273
  • GC05P124432

Summaries for CHSY3 Gene

Entrez Gene Summary for CHSY3 Gene

  • CSS3 is a glycosyltransferase that has both glucuronyltransferase and N-acetylgalactosaminyltransferase activities (Yada et al., 2003 [PubMed 12907687]).[supplied by OMIM, Mar 2008]

GeneCards Summary for CHSY3 Gene

CHSY3 (Chondroitin Sulfate Synthase 3) is a Protein Coding gene. Among its related pathways are Glycosaminoglycan metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include transferase activity, transferring glycosyl groups and glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity. An important paralog of this gene is CHSY1.

UniProtKB/Swiss-Prot for CHSY3 Gene

  • Has both beta-1,3-glucuronic acid and beta-1,4-N-acetylgalactosamine transferase activity. Transfers glucuronic acid (GlcUA) from UDP-GlcUA and N-acetylgalactosamine (GalNAc) from UDP-GalNAc to the non-reducing end of the elongating chondroitin polymer. Specific activity is much reduced compared to CHSY1.

Additional gene information for CHSY3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CHSY3 Gene

Genomics for CHSY3 Gene

GeneHancer (GH) Regulatory Elements for CHSY3 Gene

Promoters and enhancers for CHSY3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05I129903 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 565.3 +1.1 1082 2.2 KLF17 SIN3A ZNF76 FEZF1 ZNF2 ETS1 ZNF335 ZNF121 GLIS2 ZNF366 CHSY3 ENSG00000251680
GH05I129906 Promoter 1 Ensembl 9.9 +3.4 3392 0.4 CTCF TAF1 ARID4B MAX RAD21 YY1 TEAD3 HNF4G EZH2 STAT1 ENSG00000251680 CHSY3 GC05P129975
GH05I129716 Enhancer 0.4 ENCODE 13.1 -185.1 -185140 3.5 ATF4 ATF7 CHSY3 ENSG00000251680 KIAA1024L PIR62990 ADAMTS19
GH05I129723 Enhancer 0.3 ENCODE 10.3 -178.8 -178834 3 FOXA2 CHSY3 HSPA8P4 ENSG00000251680 KIAA1024L PIR62990 ADAMTS19
GH05I129944 Enhancer 0.2 ENCODE 12.5 +41.9 41926 0.7 CHSY3 GC05P129975 ENSG00000251680
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CHSY3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CHSY3 gene promoter:

Genomic Locations for CHSY3 Gene

Genomic Locations for CHSY3 Gene
283,271 bases
Plus strand

Genomic View for CHSY3 Gene

Genes around CHSY3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CHSY3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CHSY3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CHSY3 Gene

Proteins for CHSY3 Gene

  • Protein details for CHSY3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Chondroitin sulfate synthase 3
    Protein Accession:
    Secondary Accessions:
    • B2RP97
    • Q76L22
    • Q86Y52

    Protein attributes for CHSY3 Gene

    882 amino acids
    Molecular mass:
    100284 Da
    Name=Co(2+); Xref=ChEBI:CHEBI:48828; Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Name=Cd(2+); Xref=ChEBI:CHEBI:48775;
    Quaternary structure:
    No Data Available
    • Sequence=CAD43233.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for CHSY3 Gene

Post-translational modifications for CHSY3 Gene

  • Glycosylation at posLast=100100, Asn155, posLast=279279, posLast=710710, and posLast=878878

Other Protein References for CHSY3 Gene

No data available for DME Specific Peptides for CHSY3 Gene

Domains & Families for CHSY3 Gene

Gene Families for CHSY3 Gene

Protein Domains for CHSY3 Gene

Suggested Antigen Peptide Sequences for CHSY3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the chondroitin N-acetylgalactosaminyltransferase family.
  • Belongs to the chondroitin N-acetylgalactosaminyltransferase family.
genes like me logo Genes that share domains with CHSY3: view

Function for CHSY3 Gene

Molecular function for CHSY3 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
UDP-N-acetyl-alpha-D-galactosamine + beta-D-glucuronosyl-(1->3)-N-acetyl-beta-D-galactosaminyl-proteoglycan = UDP + N-acetyl-beta-D-galactosaminyl-(1->4)-beta-D-glucuronosyl-(1->3)-N-acetyl-beta-D-galactosaminyl-proteoglycan.
UniProtKB/Swiss-Prot CatalyticActivity:
UDP-alpha-D-glucuronate + N-acetyl-beta-D-galactosaminyl-(1->4)-beta-D-glucuronosyl-proteoglycan = UDP + beta-D-glucuronosyl-(1->3)-N-acetyl-beta-D-galactosaminyl-(1->4)-beta-D-glucuronosyl-proteoglycan.
UniProtKB/Swiss-Prot Function:
Has both beta-1,3-glucuronic acid and beta-1,4-N-acetylgalactosamine transferase activity. Transfers glucuronic acid (GlcUA) from UDP-GlcUA and N-acetylgalactosamine (GalNAc) from UDP-GalNAc to the non-reducing end of the elongating chondroitin polymer. Specific activity is much reduced compared to CHSY1.

Enzyme Numbers (IUBMB) for CHSY3 Gene

Phenotypes From GWAS Catalog for CHSY3 Gene

Gene Ontology (GO) - Molecular Function for CHSY3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008376 acetylgalactosaminyltransferase activity IEA --
GO:0016740 transferase activity IEA --
GO:0046872 metal ion binding IEA --
GO:0047238 glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity TAS --
GO:0050510 N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity TAS --
genes like me logo Genes that share ontologies with CHSY3: view
genes like me logo Genes that share phenotypes with CHSY3: view

Animal Model Products

CRISPR Products

miRNA for CHSY3 Gene

Inhibitory RNA Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CHSY3 Gene

Localization for CHSY3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CHSY3 Gene

Golgi apparatus, Golgi stack membrane; Single-pass type II membrane protein.

Subcellular locations from

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 CHSY3 gene
Compartment Confidence
golgi apparatus 5
extracellular 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
lysosome 1

Gene Ontology (GO) - Cellular Components for CHSY3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane TAS --
GO:0005794 Golgi apparatus IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0032580 Golgi cisterna membrane IEA --
genes like me logo Genes that share ontologies with CHSY3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CHSY3 Gene

Pathways & Interactions for CHSY3 Gene

genes like me logo Genes that share pathways with CHSY3: view

Gene Ontology (GO) - Biological Process for CHSY3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030206 chondroitin sulfate biosynthetic process TAS --
genes like me logo Genes that share ontologies with CHSY3: view

No data available for SIGNOR curated interactions for CHSY3 Gene

Drugs & Compounds for CHSY3 Gene

(4) Drugs for CHSY3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Manganese Approved Nutra 37
UDP-alpha-D-glucuronic acid Experimental Pharma 0
Uridine-5'-Diphosphate Experimental Pharma 0
Cobalt Pharma 174

(4) Additional Compounds for CHSY3 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • Cadmium atom
  • Cadmium elemental
  • Cadmium metallicum
  • Cd
  • Colloidal cadmium
  • 2-Amino-2-deoxy-4-O-beta-D-galactopyranosyl-D-glucose
  • 2-Amino-2-deoxy-4-O-beta-delta-galactopyranosyl-delta-glucose
  • beta-D-Galactopyranosyl-(1->4)-2-amino-2-deoxy-D-glucose
  • beta-D-Galactopyranosyl-(1->4)-D-glucosamine
  • beta-delta-Galactopyranosyl-(1->4)-2-amino-2-deoxy-delta-glucose
Uridine diphosphate-N-acetylgalactosamine
  • UDP-N-Acetyl-D-galactosamine
  • UDP-N-Acetyl-delta-galactosamine
  • UDP-N-Acetylgalactosamine
  • Uridine 5'-diphospho-N-acetylgalactosamine
  • Uridine diphosphate-N-acetyl-D-galactosamine
genes like me logo Genes that share compounds with CHSY3: view

Transcripts for CHSY3 Gene

mRNA/cDNA for CHSY3 Gene

(8) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(9) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CHSY3 Gene

Chondroitin sulfate synthase 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for CHSY3 Gene

No ASD Table

Relevant External Links for CHSY3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CHSY3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CHSY3 Gene

mRNA differential expression in normal tissues according to GTEx for CHSY3 Gene

This gene is overexpressed in Artery - Tibial (x6.5) and Artery - Aorta (x6.1).

Protein differential expression in normal tissues from HIPED for CHSY3 Gene

This gene is overexpressed in Breast (24.1), Heart (21.9), Esophagus (12.2), and Peripheral blood mononuclear cells (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CHSY3 Gene

Protein tissue co-expression partners for CHSY3 Gene

NURSA nuclear receptor signaling pathways regulating expression of CHSY3 Gene:


SOURCE GeneReport for Unigene cluster for CHSY3 Gene:


mRNA Expression by UniProt/SwissProt for CHSY3 Gene:

Tissue specificity: Detected at low levels in brain, cerebral cortex, uterus and small intestine.

Evidence on tissue expression from TISSUES for CHSY3 Gene

  • Pancreas(4.1)
genes like me logo Genes that share expression patterns with CHSY3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for CHSY3 Gene

Orthologs for CHSY3 Gene

This gene was present in the common ancestor of animals.

Orthologs for CHSY3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CHSY3 33 34
  • 99.58 (n)
(Canis familiaris)
Mammalia CHSY3 33 34
  • 91.8 (n)
(Bos Taurus)
Mammalia CHSY3 33 34
  • 91.78 (n)
(Mus musculus)
Mammalia Chsy3 33 16 34
  • 86.85 (n)
(Rattus norvegicus)
Mammalia Chsy3 33
  • 86.58 (n)
(Gallus gallus)
Aves CHSY3 33 34
  • 76.99 (n)
(Anolis carolinensis)
Reptilia CHSY3 34
  • 77 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia chsy3 33
  • 71.82 (n)
(Danio rerio)
Actinopterygii chsy3 34
  • 70 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.984 33
fruit fly
(Drosophila melanogaster)
Insecta CG9220 34
  • 38 (a)
(Caenorhabditis elegans)
Secernentea sqv-5 33 34
  • 49.28 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 45 (a)
Species where no ortholog for CHSY3 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)
  • 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • 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 CHSY3 Gene

Gene Tree for CHSY3 (if available)
Gene Tree for CHSY3 (if available)

Paralogs for CHSY3 Gene

Paralogs for CHSY3 Gene

(3) SIMAP similar genes for CHSY3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with CHSY3: view

Variants for CHSY3 Gene

Sequence variations from dbSNP and Humsavar for CHSY3 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1000000041 -- 130,132,535(+) C/T genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant
rs1000017732 -- 130,096,326(+) C/G genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant
rs1000029362 -- 129,923,938(+) T/C genic_upstream_transcript_variant, intron_variant
rs1000030013 -- 129,952,595(+) T/C genic_upstream_transcript_variant, intron_variant
rs1000036900 -- 130,174,826(+) A/T genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CHSY3 Gene

Variant ID Type Subtype PubMed ID
nsv980724 CNV duplication 23825009
nsv950389 CNV deletion 24416366
nsv830488 CNV gain 17160897
nsv599706 CNV loss 21841781
nsv599704 CNV gain 21841781
nsv477664 CNV novel sequence insertion 20440878
nsv472757 CNV novel sequence insertion 20440878
nsv471046 CNV loss 18288195
nsv462445 CNV loss 19166990
nsv327235 CNV deletion 16902084
nsv1028296 CNV gain 25217958
esv3890736 CNV gain 25118596
esv3606773 CNV loss 21293372
esv3606771 CNV gain 21293372
esv3606769 CNV loss 21293372
esv3606768 CNV loss 21293372
esv3606767 CNV loss 21293372
esv2763498 CNV gain 21179565
esv2730772 CNV deletion 23290073
esv2671963 CNV deletion 23128226
esv2668447 CNV deletion 23128226
esv2663844 CNV deletion 23128226
dgv1136e214 CNV loss 21293372

Variation tolerance for CHSY3 Gene

Residual Variation Intolerance Score: 13.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.19; 61.89% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CHSY3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CHSY3 Gene

Disorders for CHSY3 Gene

Additional Disease Information for CHSY3

No disorders were found for CHSY3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CHSY3 Gene

Publications for CHSY3 Gene

  1. Chondroitin sulfate synthase-3. Molecular cloning and characterization. (PMID: 12907687) Yada T … Kimata K (The Journal of biological chemistry 2003) 2 3 4 22 58
  2. Involvement of chondroitin sulfate synthase-3 (chondroitin synthase-2) in chondroitin polymerization through its interaction with chondroitin synthase-1 or chondroitin-polymerizing factor. (PMID: 17253960) Izumikawa T … Kitagawa H (The Biochemical journal 2007) 3 22 58
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  4. Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. (PMID: 25609649) Li X … Chen J (Molecular systems biology 2015) 3 58
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 58

Products for CHSY3 Gene

  • Addgene plasmids for CHSY3

Sources for CHSY3 Gene

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