Human Gene GALNT2 (uc010pwa.1) Description and Page Index
  Description: Homo sapiens UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2) (GALNT2), mRNA.
RefSeq Summary (NM_004481): This gene encodes a member of the glycosyltransferase 2 protein family. Members of this family initiate mucin-type O-glycoslation of peptides in the Golgi apparatus. The encoded protein may be involved in O-linked glycosylation of the immunoglobulin A1 hinge region. This gene may influence triglyceride levels, and may be involved Type 2 diabetes, as well as several types of cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014].
Transcript (Including UTRs)
   Position: hg19 chr1:230,202,956-230,417,875 Size: 214,920 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr1:230,203,028-230,415,204 Size: 212,177 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:230,202,956-230,417,875)mRNA (may differ from genome)Protein (571 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: GALT2_HUMAN
DESCRIPTION: RecName: Full=Polypeptide N-acetylgalactosaminyltransferase 2; EC=2.4.1.41; AltName: Full=Polypeptide GalNAc transferase 2; Short=GalNAc-T2; Short=pp-GaNTase 2; AltName: Full=Protein-UDP acetylgalactosaminyltransferase 2; AltName: Full=UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 2; Contains: RecName: Full=Polypeptide N-acetylgalactosaminyltransferase 2 soluble form;
FUNCTION: Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D- galactosamine residue to a serine or threonine residue on the protein receptor. Has a broad spectrum of substrates for peptides such as EA2, Muc5AC, Muc1a, Muc1b. Probably involved in O-linked glycosylation of the immunoglobulin A1 (IgA1) hinge region.
CATALYTIC ACTIVITY: UDP-N-acetyl-D-galactosamine + polypeptide = UDP + N-acetyl-D-galactosaminyl-polypeptide.
COFACTOR: Manganese (By similarity).
COFACTOR: Calcium (By similarity).
PATHWAY: Protein modification; protein glycosylation.
SUBCELLULAR LOCATION: Golgi apparatus, Golgi stack membrane; Single-pass type II membrane protein. Secreted. Note=Resides preferentially in the trans and medial parts of the Golgi stack. A secreted form also exists.
TISSUE SPECIFICITY: Widely expressed.
DOMAIN: There are two conserved domains in the glycosyltransferase region: the N-terminal domain (domain A, also called GT1 motif), which is probably involved in manganese coordination and substrate binding and the C-terminal domain (domain B, also called Gal/GalNAc-T motif), which is probably involved in catalytic reaction and UDP-Gal binding (By similarity).
DOMAIN: The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity (By similarity).
SIMILARITY: Belongs to the glycosyltransferase 2 family. GalNAc-T subfamily.
SIMILARITY: Contains 1 ricin B-type lectin domain.
WEB RESOURCE: Name=GGDB; Note=GlycoGene database; URL="http://riodb.ibase.aist.go.jp/rcmg/ggdb/";
WEB RESOURCE: Name=Functional Glycomics Gateway - GTase; Note=Polypeptide N-acetylgalactosaminyltransferase 2; URL="http://www.functionalglycomics.org/glycomics/molecule/jsp/glycoEnzyme/viewGlycoEnzyme.jsp?gbpId=gt_hum_484";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): GALNT2
CDC HuGE Published Literature: GALNT2
Positive Disease Associations: Cholesterol, HDL , HDL cholesterol , Lipoproteins, HDL , Metabolic Syndrome X , triglycerides
Related Studies:
  1. Cholesterol, HDL
    Cristen J Willer et al. Nature genetics 2008, Newly identified loci that influence lipid concentrations and risk of coronary artery disease., Nature genetics. [PubMed 18193043]
  2. Cholesterol, HDL
    Sekar Kathiresan et al. Nature genetics 2008, Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans., Nature genetics. [PubMed 18193044]
  3. Cholesterol, HDL
    Sekar Kathiresan et al. Nature genetics 2009, Common variants at 30 loci contribute to polygenic dyslipidemia., Nature genetics. [PubMed 19060906]
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 37.58 RPKM in Artery - Aorta
Total median expression: 677.98 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -32.1072-0.446 Picture PostScript Text
3' UTR -1053.092671-0.394 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001173 - Glyco_trans_2
IPR000772 - Ricin_B_lectin

Pfam Domains:
PF00535 - Glycosyl transferase family 2
PF00652 - Ricin-type beta-trefoil lectin domain

SCOP Domains:
50370 - Ricin B-like lectins
53448 - Nucleotide-diphospho-sugar transferases

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2FFU
- X-ray MuPIT

2FFV
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q10471
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
  EnsemblFlyBaseWormBase 
  Protein SequenceProtein SequenceProtein Sequence 
  AlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004653 polypeptide N-acetylgalactosaminyltransferase activity
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0016757 transferase activity, transferring glycosyl groups
GO:0030145 manganese ion binding
GO:0030246 carbohydrate binding
GO:0046872 metal ion binding

Biological Process:
GO:0002378 immunoglobulin biosynthetic process
GO:0006486 protein glycosylation
GO:0006493 protein O-linked glycosylation
GO:0016266 O-glycan processing
GO:0018242 protein O-linked glycosylation via serine
GO:0018243 protein O-linked glycosylation via threonine

Cellular Component:
GO:0000139 Golgi membrane
GO:0005576 extracellular region
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005795 Golgi stack
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030173 integral component of Golgi membrane
GO:0032580 Golgi cisterna membrane
GO:0048471 perinuclear region of cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AK300453 - Homo sapiens cDNA FLJ58625 complete cds, highly similar to Polypeptide N-acetylgalactosaminyltransferase 2 (EC 2.4.1.41).
LC043140 - Homo sapiens GALNT2 mRNA for polypeptide N-acetylgalactosaminyltransferase 2, complete cds.
LC043141 - Homo sapiens GALNT2 mRNA for polypeptide N-acetylgalactosaminyltransferase 2, contains SNP, complete cds.
BC041120 - Homo sapiens UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2), mRNA (cDNA clone MGC:47616 IMAGE:5553465), complete cds.
LF384498 - JP 2014500723-A/192001: Polycomb-Associated Non-Coding RNAs.
AK296886 - Homo sapiens cDNA FLJ58016 complete cds, highly similar to Polypeptide N-acetylgalactosaminyltransferase2 (EC 2.4.1.41).
AK290048 - Homo sapiens cDNA FLJ75604 complete cds, highly similar to Homo sapiens UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2) (GALNT2), mRNA.
AK304029 - Homo sapiens cDNA FLJ58226 complete cds, highly similar to Polypeptide N-acetylgalactosaminyltransferase 2 (EC 2.4.1.41).
KJ896858 - Synthetic construct Homo sapiens clone ccsbBroadEn_06252 GALNT2 gene, encodes complete protein.
AB591001 - Synthetic construct DNA, clone: pFN21AE1992, Homo sapiens GALNT2 gene for UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2, without stop codon, in Flexi system.
X85019 - H.sapiens mRNA for UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase (T2).
MA620075 - JP 2018138019-A/192001: Polycomb-Associated Non-Coding RNAs.
LF375261 - JP 2014500723-A/182764: Polycomb-Associated Non-Coding RNAs.
LF208354 - JP 2014500723-A/15857: Polycomb-Associated Non-Coding RNAs.
LF375263 - JP 2014500723-A/182766: Polycomb-Associated Non-Coding RNAs.
LF375267 - JP 2014500723-A/182770: Polycomb-Associated Non-Coding RNAs.
LF375270 - JP 2014500723-A/182773: Polycomb-Associated Non-Coding RNAs.
LF375271 - JP 2014500723-A/182774: Polycomb-Associated Non-Coding RNAs.
LF375272 - JP 2014500723-A/182775: Polycomb-Associated Non-Coding RNAs.
BC050583 - Homo sapiens UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2), mRNA (cDNA clone IMAGE:6068693).
AK097996 - Homo sapiens cDNA FLJ40677 fis, clone THYMU2022289.
LF375273 - JP 2014500723-A/182776: Polycomb-Associated Non-Coding RNAs.
LF375276 - JP 2014500723-A/182779: Polycomb-Associated Non-Coding RNAs.
JD137962 - Sequence 118986 from Patent EP1572962.
AK056187 - Homo sapiens cDNA FLJ31625 fis, clone NT2RI2003304.
JD408403 - Sequence 389427 from Patent EP1572962.
AF130059 - Homo sapiens clone FLB5634 PRO1477 mRNA, complete cds.
JD340366 - Sequence 321390 from Patent EP1572962.
JD363779 - Sequence 344803 from Patent EP1572962.
JD046689 - Sequence 27713 from Patent EP1572962.
JD506574 - Sequence 487598 from Patent EP1572962.
AK098468 - Homo sapiens cDNA FLJ25602 fis, clone JTH13990.
JD072927 - Sequence 53951 from Patent EP1572962.
LF375277 - JP 2014500723-A/182780: Polycomb-Associated Non-Coding RNAs.
LF375278 - JP 2014500723-A/182781: Polycomb-Associated Non-Coding RNAs.
AK025845 - Homo sapiens cDNA: FLJ22192 fis, clone HRC01106.
LF375279 - JP 2014500723-A/182782: Polycomb-Associated Non-Coding RNAs.
JD421128 - Sequence 402152 from Patent EP1572962.
JD278213 - Sequence 259237 from Patent EP1572962.
JD336106 - Sequence 317130 from Patent EP1572962.
JD097649 - Sequence 78673 from Patent EP1572962.
JD051207 - Sequence 32231 from Patent EP1572962.
JD216013 - Sequence 197037 from Patent EP1572962.
JD191224 - Sequence 172248 from Patent EP1572962.
JD097562 - Sequence 78586 from Patent EP1572962.
JD432678 - Sequence 413702 from Patent EP1572962.
JD053420 - Sequence 34444 from Patent EP1572962.
JD303321 - Sequence 284345 from Patent EP1572962.
JD071473 - Sequence 52497 from Patent EP1572962.
JD205142 - Sequence 186166 from Patent EP1572962.
JD283227 - Sequence 264251 from Patent EP1572962.
JD192752 - Sequence 173776 from Patent EP1572962.
JD292614 - Sequence 273638 from Patent EP1572962.
LF375280 - JP 2014500723-A/182783: Polycomb-Associated Non-Coding RNAs.
JD444682 - Sequence 425706 from Patent EP1572962.
JD467328 - Sequence 448352 from Patent EP1572962.
JD162608 - Sequence 143632 from Patent EP1572962.
JD521937 - Sequence 502961 from Patent EP1572962.
JD101327 - Sequence 82351 from Patent EP1572962.
MA610838 - JP 2018138019-A/182764: Polycomb-Associated Non-Coding RNAs.
MA443931 - JP 2018138019-A/15857: Polycomb-Associated Non-Coding RNAs.
MA610840 - JP 2018138019-A/182766: Polycomb-Associated Non-Coding RNAs.
MA610844 - JP 2018138019-A/182770: Polycomb-Associated Non-Coding RNAs.
MA610847 - JP 2018138019-A/182773: Polycomb-Associated Non-Coding RNAs.
MA610848 - JP 2018138019-A/182774: Polycomb-Associated Non-Coding RNAs.
MA610849 - JP 2018138019-A/182775: Polycomb-Associated Non-Coding RNAs.
MA610850 - JP 2018138019-A/182776: Polycomb-Associated Non-Coding RNAs.
MA610853 - JP 2018138019-A/182779: Polycomb-Associated Non-Coding RNAs.
MA610854 - JP 2018138019-A/182780: Polycomb-Associated Non-Coding RNAs.
MA610855 - JP 2018138019-A/182781: Polycomb-Associated Non-Coding RNAs.
MA610856 - JP 2018138019-A/182782: Polycomb-Associated Non-Coding RNAs.
MA610857 - JP 2018138019-A/182783: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00512 - O-Glycan biosynthesis
hsa01100 - Metabolic pathways

Reactome (by CSHL, EBI, and GO)

Protein Q10471 (Reactome details) participates in the following event(s):

R-HSA-8849348 RAB6:GTP and BICD homodimers bind COPI-independent Golgi-to-ER retrograde cargo
R-HSA-913675 GALNTs transfer GalNAc from UDP-GalNAc to mucins to form Tn antigens
R-HSA-8849350 RAB6:GTP displaces PAFAH1B1 from dynein:dynactin complex
R-HSA-6811436 COPI-independent Golgi-to-ER retrograde traffic
R-HSA-913709 O-linked glycosylation of mucins
R-HSA-8856688 Golgi-to-ER retrograde transport
R-HSA-5173105 O-linked glycosylation
R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-597592 Post-translational protein modification
R-HSA-199991 Membrane Trafficking
R-HSA-392499 Metabolism of proteins
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: A8K1Y3, C5HU00, GALT2_HUMAN, NM_004481, NP_004472, Q10471, Q9NPY4
UCSC ID: uc010pwa.1
RefSeq Accession: NM_004481
Protein: Q10471 (aka GALT2_HUMAN or GLT2_HUMAN)
CCDS: CCDS1582.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_004481.3
exon count: 16CDS single in 3' UTR: no RNA size: 4463
ORF size: 1716CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3632.00frame shift in genome: no % Coverage: 99.91
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.