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B3GNT5 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5 [ Homo sapiens (human) ]

Gene ID: 84002, updated on 11-Apr-2024

Summary

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Official Symbol
B3GNT5provided by HGNC
Official Full Name
UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5provided by HGNC
Primary source
HGNC:HGNC:15684
See related
Ensembl:ENSG00000176597 MIM:615333; AllianceGenome:HGNC:15684
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
B3GN-T5; beta3Gn-T5
Summary
This gene encodes a member of the beta-1,3-N-acetylglucosaminyltransferase family. This enzyme is a type II membrane protein. It exhibits strong activity to transfer GlcNAc to glycolipid substrates and is identified as the most likely candidate for lactotriaosylceramide synthase. This enzyme is essential for the expression of Lewis X epitopes on glycolipids. [provided by RefSeq, Jul 2008]
Expression
Broad expression in bone marrow (RPKM 17.8), small intestine (RPKM 13.8) and 20 other tissues See more
Orthologs
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Genomic context

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See B3GNT5 in Genome Data Viewer
Location:
3q27.1
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (183253253..183273385)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (186060144..186080277)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (182971041..182991173)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14937 Neighboring gene small nucleolar RNA, C/D box 3 pseudogene 4 Neighboring gene MCF.2 cell line derived transforming sequence-like 2 Neighboring gene MPRA-validated peak4957 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr3:182951891-182952104 Neighboring gene uncharacterized LOC124906310 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:182980890-182981594 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:182983517-182984716 Neighboring gene RNA, 5S ribosomal pseudogene 151 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:183003113-183004312 Neighboring gene uncharacterized LOC107986160 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:183014350-183015174 Neighboring gene Sharpr-MPRA regulatory region 12547 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14938 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14939 Neighboring gene NANOG hESC enhancer GRCh37_chr3:183118178-183118679 Neighboring gene Sharpr-MPRA regulatory region 15184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14940 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:183152219-183153159 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:183165063-183165598 Neighboring gene small nucleolar RNA, H/ACA box 63D Neighboring gene small nucleolar RNA host gene 33

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. B3GNT5 is a novel marker correlated with stem-like phenotype and poor clinical outcome in human gliomas. Jeong HY, et al. CNS Neurosci Ther, 2020 Nov. PMID 32677340, Free PMC Article
  2. High expression of lactotriaosylceramide, a differentiation-associated glycosphingolipid, in the bone marrow of acute myeloid leukemia patients. Wang Z, et al. Glycobiology, 2012 Jul. PMID 22411838, Free PMC Article
  3. Helicobacter pylori induces beta3GnT5 in human gastric cell lines, modulating expression of the SabA ligand sialyl-Lewis x. Marcos NT, et al. J Clin Invest, 2008 Jun. PMID 18483624, Free PMC Article
  4. Molecular cloning and characterization of UDP-GlcNAc:lactosylceramide beta 1,3-N-acetylglucosaminyltransferase (beta 3Gn-T5), an essential enzyme for the expression of HNK-1 and Lewis X epitopes on glycolipids. Togayachi A, et al. J Biol Chem, 2001 Jun 22. PMID 11283017
  5. Cloning of a mouse beta 1,3 N-acetylglucosaminyltransferase GlcNAc(beta 1,3)Gal(beta 1,4)Glc-ceramide synthase gene encoding the key regulator of lacto-series glycolipid biosynthesis. Henion TR, et al. J Biol Chem, 2001 Aug 10. PMID 11384981

See all (18) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. B3GNT5 is a novel marker correlated with stem-like phenotype and poor clinical outcome in human gliomas.
    Title: B3GNT5 is a novel marker correlated with stem-like phenotype and poor clinical outcome in human gliomas.
  2. bone marrow samples of acute myeloid leukemia patients had 16-fold higher expression of B3GNT5 than those of healthy donors
    Title: High expression of lactotriaosylceramide, a differentiation-associated glycosphingolipid, in the bone marrow of acute myeloid leukemia patients.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: A large-scale candidate gene association study of age at menarche and age at natural menopause.
  4. Helicobacter pylori induces beta3GnT5 in human gastric cell lines, modulating expression of the SabA ligand sialyl-Lewis x
    Title: Helicobacter pylori induces beta3GnT5 in human gastric cell lines, modulating expression of the SabA ligand sialyl-Lewis x.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity TAS
Traceable Author Statement
more info
  
enables beta-galactosyl-N-acetylglucosaminylgalactosylglucosyl-ceramide beta-1,3-acetylglucosaminyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables beta-galactosyl-N-acetylglucosaminylgalactosylglucosyl-ceramide beta-1,3-acetylglucosaminyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase activity TAS
Traceable Author Statement
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in O-glycan processing TAS
Traceable Author Statement
more info
  
involved_in central nervous system development IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in glycolipid biosynthetic process TAS
Traceable Author Statement
more info
 PubMed 
involved_in glycosphingolipid biosynthetic process TAS
Traceable Author Statement
more info
  
involved_in protein O-linked glycosylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein glycosylation TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
is_active_in Golgi membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in Golgi membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase
Names
BGnT-5
UDP-GlcNAc:beta-Gal beta-1,3-N-acetylglucosaminyltransferase 5
beta 1,3 N-acetyglucosaminyltransferase Lc3 synthase
beta-1,3-Gn-T5
beta-1,3-N-acetylglucosaminyltransferase 5
beta-1,3-N-acetylglucosaminyltransferase bGnT-5
lactotriaosylceramide synthase
lc(3)Cer synthase
lc3 synthase
NP_114436.1
XP_005247880.1
XP_011511529.1
XP_011511530.1
XP_047305013.1
XP_047305014.1
XP_047305015.1
XP_054204045.1
XP_054204046.1

NCBI Reference Sequences (RefSeq)

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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_032047.5 → NP_114436.1  lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase

    See identical proteins and their annotated locations for NP_114436.1

    Status: REVIEWED

    Source sequence(s)
    AK074235, AK074424, BP270576
    Consensus CDS
    CCDS3244.1
    UniProtKB/Swiss-Prot
    D3DNS5, Q59FE3, Q7L9Z5, Q8WWP9, Q9BYG0
    UniProtKB/TrEMBL
    B3KRF8
    Related
    ENSP00000316173.3, ENST00000326505.4
    Conserved Domains (1) summary
    cl21608
    Location:102 → 299
    Galactosyl_T; Galactosyltransferase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    183253253..183273385
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011513228.3 → XP_011511530.1  lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase isoform X1

    See identical proteins and their annotated locations for XP_011511530.1

    UniProtKB/Swiss-Prot
    D3DNS5, Q59FE3, Q7L9Z5, Q8WWP9, Q9BYG0
    UniProtKB/TrEMBL
    B3KRF8
    Conserved Domains (1) summary
    cl21608
    Location:102 → 299
    Galactosyl_T; Galactosyltransferase

  2. XM_047449057.1 → XP_047305013.1  lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase isoform X1

    UniProtKB/Swiss-Prot
    D3DNS5, Q59FE3, Q7L9Z5, Q8WWP9, Q9BYG0

  3. XM_011513227.3 → XP_011511529.1  lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase isoform X1

    See identical proteins and their annotated locations for XP_011511529.1

    UniProtKB/Swiss-Prot
    D3DNS5, Q59FE3, Q7L9Z5, Q8WWP9, Q9BYG0
    UniProtKB/TrEMBL
    B3KRF8
    Conserved Domains (1) summary
    cl21608
    Location:102 → 299
    Galactosyl_T; Galactosyltransferase

  4. XM_047449058.1 → XP_047305014.1  lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase isoform X1

    UniProtKB/Swiss-Prot
    D3DNS5, Q59FE3, Q7L9Z5, Q8WWP9, Q9BYG0

  5. XM_047449059.1 → XP_047305015.1  lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase isoform X1

    UniProtKB/Swiss-Prot
    D3DNS5, Q59FE3, Q7L9Z5, Q8WWP9, Q9BYG0

  6. XM_005247823.6 → XP_005247880.1  lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase isoform X1

    See identical proteins and their annotated locations for XP_005247880.1

    UniProtKB/Swiss-Prot
    D3DNS5, Q59FE3, Q7L9Z5, Q8WWP9, Q9BYG0
    UniProtKB/TrEMBL
    B3KRF8
    Related
    ENSP00000420778.1, ENST00000460419.1
    Conserved Domains (1) summary
    cl21608
    Location:102 → 299
    Galactosyl_T; Galactosyltransferase

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    186060144..186080277
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348070.1 → XP_054204045.1  lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase isoform X1

    UniProtKB/Swiss-Prot
    D3DNS5, Q59FE3, Q7L9Z5, Q8WWP9, Q9BYG0

  2. XM_054348071.1 → XP_054204046.1  lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase isoform X1

    UniProtKB/Swiss-Prot
    D3DNS5, Q59FE3, Q7L9Z5, Q8WWP9, Q9BYG0
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BYG0.1 GenPept UniProtKB/Swiss-Prot:Q9BYG0

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