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Aliases for B3GNT6 Gene

Aliases for B3GNT6 Gene

  • UDP-GlcNAc:BetaGal Beta-1,3-N-Acetylglucosaminyltransferase 6 2 3 4 5
  • Core 3 Synthase 2 3 4
  • Beta-1,3-N-Acetylglucosaminyltransferase 6 3 4
  • Beta-1,3-Gn-T6 3 4
  • Beta3Gn-T6 3 4
  • BGnT-6 3 4
  • Acetylgalactosaminyl-O-Glycosyl-Glycoprotein Beta-1,3-N-Acetylglucosaminyltransferase 3
  • Beta-1,3-N-Acetylglucosaminyltransferase Protein 3
  • EC 4
  • B3Gn-T6 3

External Ids for B3GNT6 Gene

Previous GeneCards Identifiers for B3GNT6 Gene

  • GC11M068646
  • GC11M067794
  • GC11M066362
  • GC11M065889
  • GC11M065890
  • GC11M065869
  • GC11P076425
  • GC11P076745
  • GC11P073043

Summaries for B3GNT6 Gene

Entrez Gene Summary for B3GNT6 Gene

  • The protein encoded by this gene is a beta-1,3-N-acetylglucosaminyltransferase that adds an N-acetylglucosamine moiety to N-acetylgalactosamine-modified serine or threonine. The encoded enzyme is responsible for creating the core 3 structure of O-glycans, which are important components of mucin-type glycoproteins. [provided by RefSeq, Dec 2016]

GeneCards Summary for B3GNT6 Gene

B3GNT6 (UDP-GlcNAc:BetaGal Beta-1,3-N-Acetylglucosaminyltransferase 6) is a Protein Coding gene. Among its related pathways are Metabolism of proteins and O-linked glycosylation. Gene Ontology (GO) annotations related to this gene include galactosyltransferase activity and beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity. An important paralog of this gene is B3GNT3.

UniProtKB/Swiss-Prot for B3GNT6 Gene

  • Beta-1,3-N-acetylglucosaminyltransferase that synthesizes the core 3 structure of the O-glycan, an important precursor in the biosynthesis of mucin-type glycoproteins. Plays an important role in the synthesis of mucin-type O-glycans in digestive organs.

Additional gene information for B3GNT6 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for B3GNT6 Gene

Genomics for B3GNT6 Gene

GeneHancer (GH) Regulatory Elements for B3GNT6 Gene

Promoters and enhancers for B3GNT6 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
GH11I077034 Promoter/Enhancer 1.6 EPDnew ENCODE dbSUPER 550.8 +1.4 1427 3.2 PKNOX1 FOXA2 MLX NFIB ZFP64 NEUROD1 RARA SCRT2 FOS RCOR1 B3GNT6 OMP MYO7A ACER3 CAPN5 LOC105369399
GH11I076823 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 5.2 -209.6 -209551 3.1 HDGF PKNOX1 ATF1 ARNT TCF12 ZNF766 GATA2 ZNF548 FOS ATF7 EMSY ACER3 B3GNT6 GDPD4 ENSG00000261578
GH11I077019 Enhancer 1 ENCODE dbSUPER 8.1 -13.9 -13868 1.7 ELF3 PKNOX1 FOXA2 EGR1 FOS EGR2 REST GATAD2B ELF1 SP1 MYO7A ENSG00000254632 GDPD4 B3GNT6 ACER3 ENSG00000254988
GH11I076806 Enhancer 1.2 Ensembl ENCODE dbSUPER 5.8 -226.8 -226789 1.1 HDGF YBX3 ATF1 RB1 NFRKB SIN3A YBX1 NFXL1 ZNF48 RAD21 ACER3 LOC101928837 TSKU ENSG00000255363 EMSY B3GNT6 ENSG00000261578
GH11I077029 Enhancer 0.7 ENCODE dbSUPER 9.3 -4.3 -4253 1.2 ZNF217 CTBP1 DPF2 FOS B3GNT6 ENSG00000254988
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around B3GNT6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the B3GNT6 gene promoter:

Genomic Locations for B3GNT6 Gene

Genomic Locations for B3GNT6 Gene
7,633 bases
Plus strand

Genomic View for B3GNT6 Gene

Genes around B3GNT6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
B3GNT6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for B3GNT6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for B3GNT6 Gene

Proteins for B3GNT6 Gene

  • Protein details for B3GNT6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase
    Protein Accession:
    Secondary Accessions:
    • E9PKS1
    • Q6ZSC5
    • Q8TAZ4
    • Q8TDX1

    Protein attributes for B3GNT6 Gene

    384 amino acids
    Molecular mass:
    42748 Da
    Quaternary structure:
    No Data Available
    • Injection into nude mice significantly suppress lung metastasis, indicating that the core structures of O-glycans are profoundly involved in the metastatic capacity of cancer cells.

    Alternative splice isoforms for B3GNT6 Gene


neXtProt entry for B3GNT6 Gene

Post-translational modifications for B3GNT6 Gene

  • Glycosylation at Asn73, posLast=7777, and posLast=196196
  • Modification sites at PhosphoSitePlus

Other Protein References for B3GNT6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for B3GNT6 Gene

Domains & Families for B3GNT6 Gene

Gene Families for B3GNT6 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted secreted proteins

Protein Domains for B3GNT6 Gene

Suggested Antigen Peptide Sequences for B3GNT6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the glycosyltransferase 31 family.
  • Belongs to the glycosyltransferase 31 family.
genes like me logo Genes that share domains with B3GNT6: view

Function for B3GNT6 Gene

Molecular function for B3GNT6 Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=3.3 mM for GalNAc-alpha-Bn {ECO:0000269 PubMed:7655172}; Vmax=4.5 nmol/h/mg enzyme with GalNAc-alpha-Bn as substrate {ECO:0000269 PubMed:7655172};
UniProtKB/Swiss-Prot CatalyticActivity:
UDP-N-acetyl-alpha-D-glucosamine + O(3)-(N-acetyl-alpha-D-galactosaminyl)-L-threonyl/L-seryl-[protein] = UDP + O(3)-(N-acetyl-beta-D-glucosaminyl-(1->3)-N-acetyl-alpha-D-galactosaminyl)-L-threonyl/L-seryl-[protein].
UniProtKB/Swiss-Prot Function:
Beta-1,3-N-acetylglucosaminyltransferase that synthesizes the core 3 structure of the O-glycan, an important precursor in the biosynthesis of mucin-type glycoproteins. Plays an important role in the synthesis of mucin-type O-glycans in digestive organs.
UniProtKB/Swiss-Prot Induction:
Down-regulated in gastric and colorectal carcinomas, suggesting that it may be used as a marker for distinguishing between benign adenomas and premalignant lesions (at protein level).

Enzyme Numbers (IUBMB) for B3GNT6 Gene

Gene Ontology (GO) - Molecular Function for B3GNT6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008378 galactosyltransferase activity IDA 11821425
GO:0008499 UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity TAS --
GO:0016740 transferase activity IEA --
GO:0016757 transferase activity, transferring glycosyl groups IEA --
GO:0047223 beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity NAS 11821425
genes like me logo Genes that share ontologies with B3GNT6: view
genes like me logo Genes that share phenotypes with B3GNT6: view

Animal Models for B3GNT6 Gene

MGI Knock Outs for B3GNT6:

Clone Products

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for B3GNT6 Gene

Localization for B3GNT6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for B3GNT6 Gene

Golgi apparatus 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 B3GNT6 gene
Compartment Confidence
golgi apparatus 5
extracellular 2
peroxisome 1
endoplasmic reticulum 1
lysosome 1

Gene Ontology (GO) - Cellular Components for B3GNT6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane TAS --
GO:0005794 Golgi apparatus IEA --
GO:0016020 membrane NAS 11821425
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with B3GNT6: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for B3GNT6 Gene

Pathways & Interactions for B3GNT6 Gene

genes like me logo Genes that share pathways with B3GNT6: view

Pathways by source for B3GNT6 Gene

UniProtKB/Swiss-Prot Q6ZMB0-B3GN6_HUMAN

  • Pathway: Protein modification; protein glycosylation.

Interacting Proteins for B3GNT6 Gene

Gene Ontology (GO) - Biological Process for B3GNT6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006486 protein glycosylation IEA --
GO:0009101 glycoprotein biosynthetic process NAS 11821425
GO:0016266 O-glycan processing TAS --
GO:0016269 O-glycan processing, core 3 NAS 11821425
genes like me logo Genes that share ontologies with B3GNT6: view

No data available for SIGNOR curated interactions for B3GNT6 Gene

Drugs & Compounds for B3GNT6 Gene

No Compound Related Data Available

Transcripts for B3GNT6 Gene

mRNA/cDNA for B3GNT6 Gene

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

Unigene Clusters for B3GNT6 Gene

UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for B3GNT6 Gene

No ASD Table

Relevant External Links for B3GNT6 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for B3GNT6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for B3GNT6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for B3GNT6 Gene

This gene is overexpressed in Colon - Transverse (x22.1), Stomach (x11.4), Small Intestine - Terminal Ileum (x7.0), and Esophagus - Mucosa (x6.8).

Protein differential expression in normal tissues from HIPED for B3GNT6 Gene

This gene is overexpressed in Colon (50.4) and Testis (18.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for B3GNT6 Gene

Protein tissue co-expression partners for B3GNT6 Gene

NURSA nuclear receptor signaling pathways regulating expression of B3GNT6 Gene:


SOURCE GeneReport for Unigene cluster for B3GNT6 Gene:


mRNA Expression by UniProt/SwissProt for B3GNT6 Gene:

Tissue specificity: Present in stomach and colon (at protein level). Restricted in the stomach, colon and small intestine, where core 3 structure is present.

Evidence on tissue expression from TISSUES for B3GNT6 Gene

  • Intestine(4.2)
  • Pancreas(4)
  • Nervous system(2.4)
genes like me logo Genes that share expression patterns with B3GNT6: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for B3GNT6 Gene

Orthologs for B3GNT6 Gene

This gene was present in the common ancestor of animals.

Orthologs for B3GNT6 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia B3GNT6 33 34
  • 98.96 (n)
(Canis familiaris)
Mammalia B3GNT6 33 34
  • 86.39 (n)
(Bos Taurus)
Mammalia B3GNT6 33 34
  • 85.22 (n)
(Rattus norvegicus)
Mammalia B3gnt6 33
  • 78.8 (n)
(Mus musculus)
Mammalia B3gnt6 33 16 34
  • 78.41 (n)
(Monodelphis domestica)
Mammalia -- 34
  • 37 (a)
(Gallus gallus)
Aves B3GNT6 33
  • 63.58 (n)
-- 34
  • 47 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia b3gnt3 33
  • 51.42 (n)
(Danio rerio)
Actinopterygii b3gnt3 34
  • 39 (a)
si:ch211-126g16.10 34
  • 38 (a)
si:ch211-126g16.11 34
  • 38 (a)
zgc:86586 34
  • 38 (a)
fruit fly
(Drosophila melanogaster)
Insecta BEST:GH04269 35
  • 31 (a)
Species where no ortholog for B3GNT6 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for B3GNT6 Gene

Gene Tree for B3GNT6 (if available)
Gene Tree for B3GNT6 (if available)

Paralogs for B3GNT6 Gene

(9) SIMAP similar genes for B3GNT6 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with B3GNT6: view

Variants for B3GNT6 Gene

Sequence variations from dbSNP and Humsavar for B3GNT6 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs781821239 likely-pathogenic, Childhood-Onset Schizophrenia 77,040,103(+) C/G/T coding_sequence_variant, missense_variant, synonymous_variant
rs1000965618 -- 77,040,762(+) A/G 3_prime_UTR_variant
rs1000981132 -- 77,035,139(+) C/T intron_variant
rs1000996913 -- 77,040,992(+) A/G 3_prime_UTR_variant
rs1001329034 -- 77,042,079(+) C/T downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for B3GNT6 Gene

Variant ID Type Subtype PubMed ID
nsv1040996 CNV gain 25217958
nsv1138053 CNV deletion 24896259
nsv397 CNV insertion 18451855

Variation tolerance for B3GNT6 Gene

Residual Variation Intolerance Score: 93.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.05; 92.15% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for B3GNT6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for B3GNT6 Gene

Disorders for B3GNT6 Gene

Additional Disease Information for B3GNT6

No disorders were found for B3GNT6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for B3GNT6 Gene

Publications for B3GNT6 Gene

  1. Molecular cloning and characterization of a novel UDP-GlcNAc:GalNAc-peptide beta1,3-N-acetylglucosaminyltransferase (beta 3Gn-T6), an enzyme synthesizing the core 3 structure of O-glycans. (PMID: 11821425) Iwai T … Narimatsu H (The Journal of biological chemistry 2002) 2 3 4 58
  2. Core 3 synthase is down-regulated in colon carcinoma and profoundly suppresses the metastatic potential of carcinoma cells. (PMID: 15755813) Iwai T … Narimatsu H (Proceedings of the National Academy of Sciences of the United States of America 2005) 3 4 58
  3. A Panel of Recombinant Mucins Carrying a Repertoire of Sialylated O-Glycans Based on Different Core Chains for Studies of Glycan Binding Proteins. (PMID: 26274979) Cherian RM … Holgersson J (Biomolecules 2015) 3 58
  4. An integrative framework identifies alternative splicing events in colorectal cancer development. (PMID: 24189147) Bisognin A … Mandruzzato S (Molecular oncology 2014) 3 58
  5. Core3 O-glycan synthase suppresses tumor formation and metastasis of prostate carcinoma PC3 and LNCaP cells through down-regulation of alpha2beta1 integrin complex. (PMID: 19395705) Lee SH … Fukuda M (The Journal of biological chemistry 2009) 3 58

Products for B3GNT6 Gene

Sources for B3GNT6 Gene

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