Human Gene GCNT2 (uc003mze.3) Description and Page Index
  Description: Homo sapiens glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group) (GCNT2), transcript variant 3, mRNA.
RefSeq Summary (NM_145655): This gene encodes the enzyme responsible for formation of the blood group I antigen. The i and I antigens are distinguished by linear and branched poly-N-acetyllactosaminoglycans, respectively. The encoded protein is the I-branching enzyme, a beta-1,6-N-acetylglucosaminyltransferase responsible for the conversion of fetal i antigen to adult I antigen in erythrocytes during embryonic development. Mutations in this gene have been associated with adult i blood group phenotype. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr6:10,585,993-10,629,601 Size: 43,609 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr6:10,586,223-10,626,840 Size: 40,618 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:10,585,993-10,629,601)mRNA (may differ from genome)Protein (402 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIneXtProt
OMIMPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: GNT2C_HUMAN
DESCRIPTION: RecName: Full=N-acetyllactosaminide beta-1,6-N-acetylglucosaminyl-transferase, isoform C; Short=N-acetylglucosaminyltransferase; EC=2.4.1.150; AltName: Full=I-branching enzyme; AltName: Full=IGNT;
FUNCTION: Branching enzyme that converts linear into branched poly-N-acetyllactosaminoglycans. Introduces the blood group I antigen during embryonic development. It is closely associated with the development and maturation of erythroid cells. The expression of the blood group I antigen in erythrocytes is determined by isoform C.
CATALYTIC ACTIVITY: UDP-N-acetyl-D-glucosamine + beta-D- galactosyl-1,4-N-acetyl-D-glucosaminyl-R = UDP + N-acetyl-beta-D- glucosaminyl-1,6-beta-D-galactosyl-1,4-N-acetyl-D-glucosaminyl-R.
PATHWAY: Protein modification; protein glycosylation.
SUBCELLULAR LOCATION: Golgi apparatus membrane; Single-pass type II membrane protein (By similarity).
POLYMORPHISM: GCNT2 is involved in determining the blood group I system (Ii) [MIM:110800]. The i (fetal) and I (adult) antigens are determined by linear and branched poly-N-acetyllactosaminoglycans, respectively. A replacement during development of i by I is dependent on the appearance of a beta-1,6-N- acetylglucosaminyltransferase, the I-branching enzyme. The expression of the blood group I antigen in erythrocytes is determined by isoform C of GCNT2.
SIMILARITY: Belongs to the glycosyltransferase 14 family.
WEB RESOURCE: Name=GGDB; Note=GlycoGene database; URL="http://riodb.ibase.aist.go.jp/rcmg/ggdb/Homolog?cat=symbol&symbol=GCNT2";
WEB RESOURCE: Name=Functional Glycomics Gateway - GTase; Note=N- acetyllactosaminide beta-1,6-N-acetylglucosaminyl-transferase; URL="http://www.functionalglycomics.org/glycomics/molecule/jsp/glycoEnzyme/viewGlycoEnzyme.jsp?gbpId=gt_hum_548";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): GCNT2
CDC HuGE Published Literature: GCNT2
Positive Disease Associations: Alkaline Phosphatase , Brain , Central Nervous System , Cholesterol , congenital cataracts , prostate cancer
Related Studies:
  1. Alkaline Phosphatase
    Emelia J Benjamin et al. BMC medical genetics 2007, Genome-wide association with select biomarker traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903293]
    The Framingham GWAS represents a resource to describe potentially novel genetic influences on systemic biomarker variability. The newly described associations will need to be replicated in other studies.
  2. Brain
    Sudha Seshadri et al. BMC medical genetics 2007, Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study., BMC medical genetics. [PubMed 17903297]
    Our results suggest that genes associated with clinical neurological disease also have detectable effects on subclinical phenotypes. These hypothesis generating data illustrate the use of an unbiased approach to discover novel pathways that may be involved in brain aging, and could be used to replicate observations made in other studies.
  3. Central Nervous System
    Sudha Seshadri et al. BMC medical genetics 2007, Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study., BMC medical genetics. [PubMed 17903297]
    Our results suggest that genes associated with clinical neurological disease also have detectable effects on subclinical phenotypes. These hypothesis generating data illustrate the use of an unbiased approach to discover novel pathways that may be involved in brain aging, and could be used to replicate observations made in other studies.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: GCNT2
Diseases sorted by gene-association score: cataract 13 with adult i phenotype* (930), adult i phenotype without cataract* (900), cataract 9, multiple types* (139), cataract 44* (124), adult i blood group with or without congenital cataract* (100), ophthalmia neonatorum (16), bacterial conjunctivitis (15), mast cell neoplasm (5), muscle eye brain disease (4)
* = Manually curated disease association

-  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: 4.77 RPKM in Prostate
Total median expression: 58.85 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 -59.10230-0.257 Picture PostScript Text
3' UTR -830.222761-0.301 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
IPR003406 - Glyco_trans_14

Pfam Domains:
PF02485 - Core-2/I-Branching enzyme

ModBase Predicted Comparative 3D Structure on Q8NFS9
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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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  AK307337 - Homo sapiens cDNA, FLJ97285.
AK307329 - Homo sapiens cDNA, FLJ97277.
AK307373 - Homo sapiens cDNA, FLJ97321.
AK291767 - Homo sapiens cDNA FLJ76719 complete cds, highly similar to Homo sapiens glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (GCNT2), transcript variant 1, mRNA.
AL832714 - Homo sapiens mRNA; cDNA DKFZp313K0735 (from clone DKFZp313K0735).
AK090483 - Homo sapiens mRNA for FLJ00405 protein.
AB385263 - Synthetic construct DNA, clone: pF1KF0405, Homo sapiens GCNT2 gene for N-acetyllactosaminide beta-1,6-N-acetylglucosaminyl-transferase, complete cds, without stop codon, in Flexi system.
AF458024 - Homo sapiens I beta-1,6-N-acetylglucosaminyltransferase A form mRNA, complete cds.
AY435145 - Homo sapiens I-branching beta-1,6-acetylglucosaminyltransferase family polypeptide 1 mRNA, complete cds.
AB078432 - Homo sapiens IGnT2 mRNA for beta-1,6-N-acetylglucosaminyltransferase 2, complete cds.
AK098105 - Homo sapiens cDNA FLJ40786 fis, clone TRACH2006762, highly similar to N-ACETYLLACTOSAMINIDE BETA-1,6-N-ACETYLGLUCOSAMINYLTRANSFERASE (EC 2.4.1.150).
AK313903 - Homo sapiens cDNA, FLJ94540, Homo sapiens glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (GCNT2), mRNA.
AK291195 - Homo sapiens cDNA FLJ76191 complete cds, highly similar to Homo sapiens glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (GCNT2), transcript variant 2, mRNA.
L19659 - Human I beta 1-6 N-acetylglucosaminyltransferase mRNA, complete cds.
Z19550 - H.sapiens mRNA for I beta 1-6 N-acetylglucosaminyltransferase.
AF401652 - Homo sapiens N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase mRNA, complete cds.
AF401653 - Homo sapiens N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase mRNA, complete cds.
BC074801 - Homo sapiens glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group), transcript variant 2, mRNA (cDNA clone MGC:104075 IMAGE:30915526), complete cds.
BC074802 - Homo sapiens glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group), mRNA (cDNA clone MGC:103921 IMAGE:30915312), complete cds.
AF458025 - Homo sapiens I beta-1,6-N-acetylglucosaminyltransferase B form mRNA, complete cds.
AY435146 - Homo sapiens I-branching beta-1,6-acetylglucosaminyltransferase family polypeptide 2 mRNA, complete cds.
AK313426 - Homo sapiens cDNA, FLJ93965, Homo sapiens I beta-1,6-N-acetylglucosaminyltransferase C form (CIGnT), mRNA.
BX647668 - Homo sapiens mRNA; cDNA DKFZp313I036 (from clone DKFZp313I036).
BX647576 - Homo sapiens mRNA; cDNA DKFZp313I032 (from clone DKFZp313I032).
AL832719 - Homo sapiens mRNA; cDNA DKFZp313C049 (from clone DKFZp313C049).
BC130524 - Homo sapiens glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group), mRNA (cDNA clone MGC:163396 IMAGE:40146555), complete cds.
AB078433 - Homo sapiens IGnT3 mRNA for beta-1,6-N-acetylglucosaminyltransferase 3, complete cds.
AF458026 - Homo sapiens I beta-1,6-N-acetylglucosaminyltransferase C form mRNA, complete cds.
AF458027 - Homo sapiens mutant I beta-1,6-N-acetylglucosaminyltransferase C form mRNA, complete cds.
AF458028 - Homo sapiens mutant I beta-1,6-N-acetylglucosaminyltransferase C form mRNA, complete cds.
AF458029 - Homo sapiens mutant I beta-1,6-N-acetylglucosaminyltransferase C form mRNA, complete cds.
AF458030 - Homo sapiens mutant I beta-1,6-N-acetylglucosaminyltransferase C form mRNA, complete cds.
AY435147 - Homo sapiens I-branching beta-1,6-acetylglucosaminyltransferase family polypeptide 3 mRNA, complete cds.
HQ258240 - Synthetic construct Homo sapiens clone IMAGE:100072549 glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group) (GCNT2), transcript variant 3 (GCNT2) gene, encodes complete protein.
KJ896873 - Synthetic construct Homo sapiens clone ccsbBroadEn_06267 GCNT2 gene, encodes complete protein.
KR711686 - Synthetic construct Homo sapiens clone CCSBHm_00028472 GCNT2 (GCNT2) mRNA, encodes complete protein.
KR711687 - Synthetic construct Homo sapiens clone CCSBHm_00028473 GCNT2 (GCNT2) mRNA, encodes complete protein.
KR711688 - Synthetic construct Homo sapiens clone CCSBHm_00028474 GCNT2 (GCNT2) mRNA, encodes complete protein.
JD441060 - Sequence 422084 from Patent EP1572962.
JD437748 - Sequence 418772 from Patent EP1572962.
JD061424 - Sequence 42448 from Patent EP1572962.
JD466638 - Sequence 447662 from Patent EP1572962.
JD431362 - Sequence 412386 from Patent EP1572962.
JD100010 - Sequence 81034 from Patent EP1572962.
JD137202 - Sequence 118226 from Patent EP1572962.
JD364713 - Sequence 345737 from Patent EP1572962.
DQ601939 - Homo sapiens piRNA piR-40005, complete sequence.
JD342084 - Sequence 323108 from Patent EP1572962.
JD418405 - Sequence 399429 from Patent EP1572962.
JD505062 - Sequence 486086 from Patent EP1572962.
JD491589 - Sequence 472613 from Patent EP1572962.
JD313396 - Sequence 294420 from Patent EP1572962.
JD377612 - Sequence 358636 from Patent EP1572962.
JD239574 - Sequence 220598 from Patent EP1572962.
JD246115 - Sequence 227139 from Patent EP1572962.
JD445503 - Sequence 426527 from Patent EP1572962.
JD524925 - Sequence 505949 from Patent EP1572962.
JD348150 - Sequence 329174 from Patent EP1572962.
JD490711 - Sequence 471735 from Patent EP1572962.
JD242056 - Sequence 223080 from Patent EP1572962.
JD090269 - Sequence 71293 from Patent EP1572962.
JD079729 - Sequence 60753 from Patent EP1572962.
JD361926 - Sequence 342950 from Patent EP1572962.
JD486472 - Sequence 467496 from Patent EP1572962.
JD431356 - Sequence 412380 from Patent EP1572962.
JD554063 - Sequence 535087 from Patent EP1572962.
JD107964 - Sequence 88988 from Patent EP1572962.
JD143272 - Sequence 124296 from Patent EP1572962.
JD159358 - Sequence 140382 from Patent EP1572962.
JD159359 - Sequence 140383 from Patent EP1572962.
JD395854 - Sequence 376878 from Patent EP1572962.
JD135908 - Sequence 116932 from Patent EP1572962.
JD238456 - Sequence 219480 from Patent EP1572962.
JD499048 - Sequence 480072 from Patent EP1572962.
JD531358 - Sequence 512382 from Patent EP1572962.
JD175423 - Sequence 156447 from Patent EP1572962.
JD066571 - Sequence 47595 from Patent EP1572962.
JD180981 - Sequence 162005 from Patent EP1572962.
JD316001 - Sequence 297025 from Patent EP1572962.
JD068924 - Sequence 49948 from Patent EP1572962.
JD468155 - Sequence 449179 from Patent EP1572962.
JD551125 - Sequence 532149 from Patent EP1572962.
JD335590 - Sequence 316614 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00601 - Glycosphingolipid biosynthesis - lacto and neolacto series
hsa01100 - Metabolic pathways

BioCyc Knowledge Library
PWY-6558 - heparan sulfate biosynthesis (late stages)
PWY-6564 - heparan sulfate biosynthesis

-  Other Names for This Gene
  Alternate Gene Symbols: GCNT5, GNT2C_HUMAN, II, NACGT1, NM_145655, NP_663630, Q5T4J1, Q6T5E5, Q8NFS9
UCSC ID: uc003mze.3
RefSeq Accession: NM_145655
Protein: Q8NFS9 (aka GNT2C_HUMAN)
CCDS: CCDS4513.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_145655.3
exon count: 3CDS single in 3' UTR: no RNA size: 4219
ORF size: 1209CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2579.00frame shift in genome: no % Coverage: 99.55
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
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.