Human Gene GCNT4 (ENST00000652361.2_6) from GENCODE V47lift37
  Description: glucosaminyl (N-acetyl) transferase 4 (from RefSeq NM_001366737.1)
Gencode Transcript: ENST00000652361.2_6
Gencode Gene: ENSG00000176928.7_9
Transcript (Including UTRs)
   Position: hg19 chr5:74,321,171-74,348,383 Size: 27,213 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr5:74,324,501-74,325,862 Size: 1,362 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:74,321,171-74,348,383)mRNA (may differ from genome)Protein (453 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: GCNT4_HUMAN
DESCRIPTION: RecName: Full=Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 4; EC=2.4.1.102; AltName: Full=Core 2-branching enzyme 3; AltName: Full=Core2-GlcNAc-transferase 3; Short=C2GnT3;
FUNCTION: Glycosyltransferase that mediates core 2 O-glycan branching, an important step in mucin-type biosynthesis. Does not have core 4 O-glycan or I-branching enzyme activity.
CATALYTIC ACTIVITY: UDP-N-acetyl-D-glucosamine + beta-D- galactosyl-1,3-N-acetyl-D-galactosaminyl-R = UDP + beta-D- galactosyl-1,3-(N-acetyl-beta-D-glucosaminyl-1,6)-N-acetyl-D- galactosaminyl-R.
PATHWAY: Protein modification; protein glycosylation.
SUBCELLULAR LOCATION: Golgi apparatus membrane; Single-pass type II membrane protein (By similarity).
TISSUE SPECIFICITY: Predominantly expressed in thymus. Weakly expressed in pancreas, peripheral blood leukocytes, placenta, small intestine and stomach. Barely detectable in liver, spleen, lung and lymph node.
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=GCNT4";
WEB RESOURCE: Name=Functional Glycomics Gateway - GTase; Note=Core 2 beta-1,6-N-acetylglucosaminyltransferase 3.; URL="http://www.functionalglycomics.org/glycomics/molecule/jsp/glycoEnzyme/viewGlycoEnzyme.jsp?gbpId=gt_hum_542";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  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 -103.90331-0.314 Picture PostScript Text
3' UTR -804.303330-0.242 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 Q9P109
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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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003829 beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity
GO:0008109 N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity
GO:0008375 acetylglucosaminyltransferase activity
GO:0016740 transferase activity
GO:0016757 transferase activity, transferring glycosyl groups

Biological Process:
GO:0002121 inter-male aggressive behavior
GO:0005975 carbohydrate metabolic process
GO:0006486 protein glycosylation
GO:0006493 protein O-linked glycosylation
GO:0016266 O-glycan processing
GO:0042403 thyroid hormone metabolic process
GO:0048729 tissue morphogenesis
GO:0048872 homeostasis of number of cells
GO:0060993 kidney morphogenesis

Cellular Component:
GO:0000139 Golgi membrane
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AF132035 - Homo sapiens core 2 beta-1,6-N-acetylglucosaminyltransferase 3 (C2GnT3) mRNA, complete cds.
LP896364 - Sequence 1228 from Patent EP3253886.
JD080633 - Sequence 61657 from Patent EP1572962.
JD337108 - Sequence 318132 from Patent EP1572962.
JD310322 - Sequence 291346 from Patent EP1572962.
JD508662 - Sequence 489686 from Patent EP1572962.
JD349162 - Sequence 330186 from Patent EP1572962.
JD155321 - Sequence 136345 from Patent EP1572962.
JD511381 - Sequence 492405 from Patent EP1572962.
JD443852 - Sequence 424876 from Patent EP1572962.
JD345267 - Sequence 326291 from Patent EP1572962.
JD178787 - Sequence 159811 from Patent EP1572962.
JD469202 - Sequence 450226 from Patent EP1572962.
JD304204 - Sequence 285228 from Patent EP1572962.
JD281052 - Sequence 262076 from Patent EP1572962.
JD238685 - Sequence 219709 from Patent EP1572962.
JD320210 - Sequence 301234 from Patent EP1572962.
JD328893 - Sequence 309917 from Patent EP1572962.
JD324760 - Sequence 305784 from Patent EP1572962.
JD409420 - Sequence 390444 from Patent EP1572962.
JD562486 - Sequence 543510 from Patent EP1572962.
JD268188 - Sequence 249212 from Patent EP1572962.
JD530716 - Sequence 511740 from Patent EP1572962.
JD449603 - Sequence 430627 from Patent EP1572962.
BC160070 - Synthetic construct Homo sapiens clone IMAGE:100064006, MGC:193185 glucosaminyl (N-acetyl) transferase 4, core 2 (beta-1,6-N-acetylglucosaminyltransferase) (GCNT4) mRNA, encodes complete protein.
LP896365 - Sequence 1229 from Patent EP3253886.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
PWY-7433 - mucin core 1 and core 2 O-glycosylation

Reactome (by CSHL, EBI, and GO)

Protein Q9P109 (Reactome details) participates in the following event(s):

R-HSA-914012 GCNTs transfer GlcNAc from UDP-GlcNAc to Core 1 mucins
R-HSA-913709 O-linked glycosylation of mucins
R-HSA-5173105 O-linked glycosylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000652361.1, GCNT4_HUMAN, NM_001366737, Q9P109, uc328ufk.1, uc328ufk.2
UCSC ID: ENST00000652361.2_6
RefSeq Accession: NM_001366737.1
Protein: Q9P109 (aka GCNT4_HUMAN)

-  Gene Model Information
  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.