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A3GALT2 Gene

protein-coding   GIFtS: 25
GCID: GC01M033772          (predicted)

Alpha 1,3-Galactosyltransferase 2

(Previous names: alpha 1,3-galactosyltransferase 2, pseudogene)
(Previous symbol: A3GALT2P)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Alpha 1,3-Galactosyltransferase 21 2
A3GALT2P1 2
Alpha 1,3-Galactosyltransferase 2, Pseudogene1 2
IGb3 Synthase1 2
Isoglobotriaosylceramide Synthase1 2
IGBS3S2

External Ids:    HGNC: 300051   Entrez Gene: 1275502   Ensembl: ENSG000001843897   UniProtKB: U3KPV44   UniProtKB: U3KQ184   

Export aliases for A3GALT2 gene to outside databases

Previous GC identifers: GC01M033442 GC01M033544


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for A3GALT2 Gene:
A3GALT2 (alpha 1,3-galactosyltransferase 2) is a protein-coding gene. An important paralog of this gene is GBGT1.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the A3GALT2 gene promoter:
         ER-alpha   STAT1   STAT1beta   NF-kappaB   STAT1alpha   POU2F1   POU2F1a   COMP1   NF-kappaB1   En-1   
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat A3GALT2


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1p35.1   Ensembl cytogenetic band:  1p35.1   HGNC cytogenetic band: 1p35.1

A3GALT2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
A3GALT2 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M033772:  view genomic region     (about GC identifiers)

Start:
33,772,367 bp from pter      End:
33,786,699 bp from pter
Size:
14,333 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/TrEMBL: U3KPV4 (See protein sequence)
Recommended Name: Protein A3GALT2  
Size: 340 amino acids; 38754 Da
Caution: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered
as preliminary data

UniProtKB/TrEMBL: U3KQ18 (See protein sequence)

Recommended Name: Protein A3GALT2  
Size: 285 amino acids; 32381 Da
Caution: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered
as preliminary data

Explore proteomics data for A3GALT2 at MOPED


See A3GALT2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001073907.1  
ENSEMBL proteins: 
 ENSP00000475261   ENSP00000475462  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
GLT6: Glycosyltransferase family 6 domain containing

1 InterPro protein domain:
 IPR005076 Glyco_trans_6

Graphical View of Domain Structure for InterPro Entry U3KPV4
Graphical View of Domain Structure for InterPro Entry U3KQ18

ProtoNet protein and cluster: U3KPV4


Find genes that share domains with A3GALT2           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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     Gene Ontology (GO): 2 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0016757transferase activity, transferring glycosyl groups ----
GO:0016758transferase activity, transferring hexosyl groups ----
     
Find genes that share ontologies with A3GALT2           About GenesLikeMe


Phenotypes:
     2 MGI mutant phenotypes (inferred from 1 allele(MGI details for A3galt2):
 immune system  normal 

Find genes that share phenotypes with A3GALT2           About GenesLikeMe

Animal Models:
     MGI mouse knock-out A3galt2tm1.1Hjg for A3GALT2

   genOway: Develop your customized and physiologically relevant rodent model for A3GALT2

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
golgi apparatus3
extracellular2
endoplasmic reticulum1

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0016020membrane ----

Find genes that share ontologies with A3GALT2           About GenesLikeMe


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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SuperPaths for A3GALT2 About    
See pathways by source

SuperPathContained pathways About
1Glycosphingolipid biosynthesis - ganglio series
Ganglio Sphingolipid Metabolism0.53


1 BioSystems Pathway for A3GALT2
    Ganglio Sphingolipid Metabolism


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Interactions:

    Search GeneGlobe Interaction Network for A3GALT2

Gene Ontology (GO): 2 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005975carbohydrate metabolic process ----
GO:0006688glycosphingolipid biosynthetic process ----

Find genes that share ontologies with A3GALT2           About GenesLikeMe



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Tocris compounds for A3GALT2



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for A3GALT2 gene: 
NM_001080438.1  

2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000442999 ENST00000330379
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GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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See probesets specificity/sensitivity at GeneAnnot
CGAP TAG: --

A3GALT2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

A3GALT2 Protein Expression
    Custom PCR Arrays for A3GALT2
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for A3GALT2

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of human and mouse.

Orthologs for A3GALT2 gene from Selected species (see all 7)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia A3galt21 , 5 alpha 1,3-galactosyltransferase 2 (isoglobotriaosylceramide more1, 5 77.38(n)1
69.07(a)1
  4 (62.23 cM)5
2154931  NM_001009819.21  NP_001009819.11 
 1287553645 


ENSEMBL Gene Tree for A3GALT2 (if available)
TreeFam Gene Tree for A3GALT2 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for A3GALT2 gene
GBGT12  GLT6D12  
4 SIMAP similar genes for A3GALT2 using alignment to 2 protein entries:     U3KPV4_HUMAN (see all proteins):
ABO-B    GLT6D1    GBGT1    ABO

Find genes that share paralogs with A3GALT2           About GenesLikeMe



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for A3GALT2 (see all 375)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 1 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1906993221,2
--33772107(+) GAGCTA/CCCCAA 1 -- ds50010--------
rs1506105381,2
--33772282(+) CTTCCC/TGGGGC 1 -- ds50010--------
rs776753881,2
C--33772740(+) GCGCCA/CCCGAC 2 G V mis10--------
rs1132186771,2
C--33772792(+) GTCCAC/TGTCCA 2 M V mis10--------
rs118120521,2
C,H--33772799(+) TCCATG/TCAGAA 2 * C stg1 ese30--------
rs1449467901,2
--33772876(+) CGACAC/GGTCTT 2 L V mis10--------
rs2017119671,2
C,F--33772924(+) CCGGCG/CTCCCG 2 /R /G mis11Minor allele frequency- C:0.01EU 457
rs2000619241,2
C,F--33773009(+) AAGTGC/ATGCTC 2 /Q /H mis11Minor allele frequency- A:0.01EU 569
rs1815692691,2
C--33773016(+) GCTCCA/GCCGTC 2 A V mis10--------
rs1858430661,2
--33773386(+) ACCCAA/CCCCAA 1 -- int10--------

HapMap Linkage Disequilibrium report for A3GALT2 (33772367 - 33786699 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for A3GALT2: --
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing A3GALT2
DNA2.0 Custom Variant and Variant Library Synthesis for A3GALT2

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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  --

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for A3GALT2 gene integrated from 10 sources:
(articles sorted by number of sources associating them with A3GALT2)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Humans lack iGb3 due to the absence of functional iGb3-synthase: implications for NKT cell development and transplantation. (PubMed id 18630988)1, 3 Christiansen D....Sandrin M.S. (PLoS Biol. 2008)
  2. Lack of iGb3 and Isoglobo-Series Glycosphingolipids in Pig Organs Used for Xenotransplantation: Implications for Natural Killer T-Cell Biology. (PubMed id 23378701)1 Tahiri F....Zhou D. (J Carbohydr Chem 2013)
  3. Expression cloning of a new member of the ABO blood group glycosyltransferases, iGb3 synthase, that directs the synthesis of isoglobo-glycosphingolipids. (PubMed id 10854427)3 Keusch J.J....Baenziger J.U. (J. Biol. Chem. 2000)
  4. Structural basis of UDP-galactose binding by alpha-1,3-galactosyltransferase (alpha3GT): role of negative charge on aspartic acid 316 in structure and activity. (PubMed id 18651752)9 Tumbale P....Acharya K.R. (Biochemistry 2008)
  5. Sensitive detection of isoglobo and globo series tetraglycosylceramides in human thymus by ion trap mass spectrometry. (PubMed id 18056651)9 Li Y....Zhou D. (Glycobiology 2008)
  6. Carbohydrate residues downstream of the terminal Galalpha(1,3)Gal epitope modulate the specificity of xenoreactive antibodies. (PubMed id 17724458)9 Milland J....Sandrin M.S. (Immunol. Cell Biol. 2007)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 127550 HGNC: 30005 Ensembl:ENSG00000184389 euGenes: HUgn127550 ECgene: A3GALT2
H-InvDB: A3GALT2

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for A3GALT2 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for A3GALT2 gene:
Search GeneIP for patents involving A3GALT2

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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