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

    Gene ID: 84002, updated on 28-Oct-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (183253253..183273385)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (186060144..186080277)
    RS_2024_09 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 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 N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity TAS
    Traceable Author Statement
    more info
    		  
    enables lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase 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_2024_08

    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

    Gene LinkOut

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