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A3GALT2 alpha 1,3-galactosyltransferase 2 [ Homo sapiens (human) ]

Gene ID: 127550, updated on 30-Mar-2024

Summary

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Official Symbol
A3GALT2provided by HGNC
Official Full Name
alpha 1,3-galactosyltransferase 2provided by HGNC
Primary source
HGNC:HGNC:30005
See related
Ensembl:ENSG00000184389 MIM:619850; AllianceGenome:HGNC:30005
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
IGB3S; IGBS3S; A3GALT2P
Summary
Predicted to enable N-acetyllactosaminide 3-alpha-galactosyltransferase activity and alpha-1,3-galactosyltransferase activity. Predicted to be involved in lipid glycosylation. Predicted to act upstream of or within glycosphingolipid biosynthetic process. Predicted to be located in Golgi cisterna membrane. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus and vesicle. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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See A3GALT2 in Genome Data Viewer
Location:
1p35.1
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (33306766..33321098, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (33168388..33182706, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (33772367..33786699, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378635 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 615 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33549697-33550196 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33557899-33558556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 706 Neighboring gene antizyme inhibitor 2 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:33592415-33593614 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33605527-33606126 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:33606727-33607326 Neighboring gene zinc finger protein 362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33628780-33629512 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33629513-33630245 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7027 Neighboring gene tripartite motif containing 62 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7034 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7044 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 617 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 618 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 619 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7054 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7061 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 620 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33685009-33685609 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33685744-33686528 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33709758-33710342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 621 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 622 Neighboring gene Sharpr-MPRA regulatory region 4113 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33729134-33729634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33734235-33734736 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33760897-33761407 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:33764372-33764552 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33764984-33765933 Neighboring gene MPRA-validated peak168 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33795184-33795684 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33795685-33796185 Neighboring gene RN7SK pseudogene 16 Neighboring gene microRNA 3605 Neighboring gene polyhomeotic homolog 2

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. Lack of iGb3 and Isoglobo-Series Glycosphingolipids in Pig Organs Used for Xenotransplantation: Implications for Natural Killer T-Cell Biology. Tahiri F, et al. J Carbohydr Chem, 2013 Jan 1. PMID 23378701, Free PMC Article
  2. Humans lack iGb3 due to the absence of functional iGb3-synthase: implications for NKT cell development and transplantation. Christiansen D, et al. PLoS Biol, 2008 Jul 15. PMID 18630988, Free PMC Article
  3. PLK4 deubiquitination by Spata2-CYLD suppresses NEK7-mediated NLRP3 inflammasome activation at the centrosome. Yang XD, et al. EMBO J, 2020 Jan 15. PMID 31762063, Free PMC Article
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

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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Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables N-acetyllactosaminide 3-alpha-galactosyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
NOT enables alpha-1,3-galactosyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables glycosyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in carbohydrate metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in glycosphingolipid biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in lipid glycosylation IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in Golgi cisterna membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in vesicle IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
alpha-1,3-galactosyltransferase 2
Names
alpha 1,3-galactosyltransferase 2, pseudogene
iGb3 synthase
isoglobotriaosylceramide synthase
NP_001073907.1

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_001080438.1 → NP_001073907.1  alpha-1,3-galactosyltransferase 2

    Status: VALIDATED

    Source sequence(s)
    AL513327
    Consensus CDS
    CCDS60080.1
    UniProtKB/Swiss-Prot
    U3KPV4
    Related
    ENSP00000475261.1, ENST00000442999.3
    Conserved Domains (1) summary
    cd02515
    Location:68 → 339
    Glyco_transf_6; Glycosyltransferase family 6 comprises enzymes responsible for the production of the human ABO blood group antigens

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    33306766..33321098 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    33168388..33182706 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NG_012483.1: Suppressed sequence

    Description
    NG_012483.1: This RefSeq was permanently suppressed because it is now thought that this gene does encode a protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
U3KPV4.1 GenPept UniProtKB/Swiss-Prot:U3KPV4

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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