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GCNT1 glucosaminyl (N-acetyl) transferase 1 [ Homo sapiens (human) ]

Gene ID: 2650, updated on 17-Sep-2024

Summary

Official Symbol
GCNT1provided by HGNC
Official Full Name
glucosaminyl (N-acetyl) transferase 1provided by HGNC
Primary source
HGNC:HGNC:4203
See related
Ensembl:ENSG00000187210 MIM:600391; AllianceGenome:HGNC:4203
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
G6NT; C2GNT; C2GNT1; NACGT2; NAGCT2; C2GNT-L; C2GlcNAcT
Summary
This gene is a member of the beta-1,6-N-acetylglucosaminyltransferase gene family. It is essential to the formation of Gal beta 1-3(GlcNAc beta 1-6)GalNAc structures and the core 2 O-glycan branch. The gene coding this enzyme was originally mapped to 9q21, but was later localized to 9q13. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]
Expression
Biased expression in duodenum (RPKM 20.0), stomach (RPKM 13.9) and 13 other tissues See more
Orthologs
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Genomic context

See GCNT1 in Genome Data Viewer
Location:
9q21.13
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (76393869..76507416)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (88550440..88663979)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (79008785..79122332)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene proprotein convertase subtilisin/kexin type 5 Neighboring gene uncharacterized LOC124902183 Neighboring gene RNA binding motif protein 22 pseudogene 5 Neighboring gene Sharpr-MPRA regulatory region 15008 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:78992236-78992496 Neighboring gene Sharpr-MPRA regulatory region 15545 Neighboring gene Sharpr-MPRA regulatory region 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28471 Neighboring gene Sharpr-MPRA regulatory region 2310 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28472 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:79032201-79032782 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28473 Neighboring gene ribosomal protein SA pseudogene 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28474 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19961 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19962 Neighboring gene riboflavin kinase Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:79085403-79086064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28476 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28477 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28478 Neighboring gene H3 histone pseudogene 32 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:79126066-79126566 Neighboring gene uncharacterized LOC124902184 Neighboring gene peptidylprolyl isomerase A pseudogene 87

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC126335, MGC126336

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in O-glycan processing TAS
Traceable Author Statement
more info
 
involved_in O-glycan processing, core 2 IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cell adhesion molecule production IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in glycoprotein biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in kidney morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in leukocyte tethering or rolling IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of leukocyte tethering or rolling IEA
Inferred from Electronic Annotation
more info
 
involved_in response to insulin IEA
Inferred from Electronic Annotation
more info
 
involved_in tissue morphogenesis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in Golgi cisterna IDA
Inferred from Direct Assay
more info
PubMed 
located_in Golgi membrane TAS
Traceable Author Statement
more info
 
located_in extracellular space IEA
Inferred from Electronic Annotation
more info
 
located_in membrane TAS
Traceable Author Statement
more info
PubMed 
located_in trans-Golgi network IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase
Names
beta-1,6-N-acetylglucosaminyltransferase
core 2 GnT
core 2 beta-1,6-N-acetylglucosaminyltransferase I
core 2 beta1,6 N-acetylglucosaminyltransferase-I
core 2 branching enzyme
core2-GlcNAc-transferase
glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetylglucosaminyltransferase)
leukocyte type core 2 beta-1,6-N-acetylglucosaminyltransferase
NP_001091102.1
NP_001091103.1
NP_001091104.1
NP_001091105.1
NP_001394110.1
NP_001394111.1
NP_001394112.1
NP_001394113.1
NP_001481.2
XP_047279183.1
XP_047279184.1
XP_047279185.1
XP_054218707.1
XP_054218708.1
XP_054218709.1

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_001097633.2NP_001091102.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase

    See identical proteins and their annotated locations for NP_001091102.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1, and uses the P2 promoter.
    Source sequence(s)
    AI445628, AL161626, AL832647, BC109101, DA479942
    Consensus CDS
    CCDS6653.1
    UniProtKB/Swiss-Prot
    Q02742, Q6DJZ4
    UniProtKB/TrEMBL
    Q86T81
    Related
    ENSP00000390703.2, ENST00000444201.6
    Conserved Domains (1) summary
    pfam02485
    Location:123391
    Branch; Core-2/I-Branching enzyme
  2. NM_001097634.1NP_001091103.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase

    See identical proteins and their annotated locations for NP_001091103.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript, and uses the P1 promoter.
    Source sequence(s)
    AI445628, AL161626, AL832647, AY196293, BC109101
    Consensus CDS
    CCDS6653.1
    UniProtKB/Swiss-Prot
    Q02742, Q6DJZ4
    UniProtKB/TrEMBL
    Q86T81
    Related
    ENSP00000415454.1, ENST00000442371.5
    Conserved Domains (1) summary
    pfam02485
    Location:123391
    Branch; Core-2/I-Branching enzyme
  3. NM_001097635.2NP_001091104.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase

    See identical proteins and their annotated locations for NP_001091104.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1, and uses the P3 promoter.
    Source sequence(s)
    AI445628, AL161626, AL832647, AY196296, BC109101
    Consensus CDS
    CCDS6653.1
    UniProtKB/Swiss-Prot
    Q02742, Q6DJZ4
    UniProtKB/TrEMBL
    Q86T81
    Conserved Domains (1) summary
    pfam02485
    Location:123391
    Branch; Core-2/I-Branching enzyme
  4. NM_001097636.2NP_001091105.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase

    See identical proteins and their annotated locations for NP_001091105.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1, and uses the P4 promoter.
    Source sequence(s)
    AI445628, AL161626, AL832647, AY196297, BC109101
    Consensus CDS
    CCDS6653.1
    UniProtKB/Swiss-Prot
    Q02742, Q6DJZ4
    UniProtKB/TrEMBL
    Q86T81
    Conserved Domains (1) summary
    pfam02485
    Location:123391
    Branch; Core-2/I-Branching enzyme
  5. NM_001407181.1NP_001394110.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase

    Status: REVIEWED

    Source sequence(s)
    AL161626, AL391868, AL590664
    UniProtKB/Swiss-Prot
    Q02742, Q6DJZ4
    UniProtKB/TrEMBL
    Q86T81
  6. NM_001407182.1NP_001394111.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase

    Status: REVIEWED

    Source sequence(s)
    AL161626, AL391868
    UniProtKB/Swiss-Prot
    Q02742, Q6DJZ4
    UniProtKB/TrEMBL
    Q86T81
  7. NM_001407183.1NP_001394112.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase

    Status: REVIEWED

    Source sequence(s)
    AL161626, AL391868
    UniProtKB/Swiss-Prot
    Q02742, Q6DJZ4
    UniProtKB/TrEMBL
    Q86T81
  8. NM_001407184.1NP_001394113.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase

    Status: REVIEWED

    Source sequence(s)
    AL161626, AL391868
    UniProtKB/Swiss-Prot
    Q02742, Q6DJZ4
    UniProtKB/TrEMBL
    Q86T81
  9. NM_001490.5NP_001481.2  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase

    See identical proteins and their annotated locations for NP_001481.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1, and uses the P2 promoter.
    Source sequence(s)
    AI445628, AL161626, AL832647, BC109101, BP359964
    Consensus CDS
    CCDS6653.1
    UniProtKB/Swiss-Prot
    Q02742, Q6DJZ4
    UniProtKB/TrEMBL
    Q86T81
    Related
    ENSP00000365920.4, ENST00000376730.5
    Conserved Domains (1) summary
    pfam02485
    Location:123391
    Branch; Core-2/I-Branching enzyme

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    76393869..76507416
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047423227.1XP_047279183.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase isoform X1

    UniProtKB/Swiss-Prot
    Q02742, Q6DJZ4
    UniProtKB/TrEMBL
    Q86T81
  2. XM_047423228.1XP_047279184.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase isoform X1

    UniProtKB/Swiss-Prot
    Q02742, Q6DJZ4
    UniProtKB/TrEMBL
    Q86T81
  3. XM_047423229.1XP_047279185.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase isoform X1

    UniProtKB/Swiss-Prot
    Q02742, Q6DJZ4
    UniProtKB/TrEMBL
    Q86T81

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    88550440..88663979
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054362732.1XP_054218707.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase isoform X1

    UniProtKB/Swiss-Prot
    Q02742, Q6DJZ4
    UniProtKB/TrEMBL
    Q86T81
  2. XM_054362733.1XP_054218708.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase isoform X1

    UniProtKB/Swiss-Prot
    Q02742, Q6DJZ4
    UniProtKB/TrEMBL
    Q86T81
  3. XM_054362734.1XP_054218709.1  beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase isoform X1

    UniProtKB/Swiss-Prot
    Q02742, Q6DJZ4
    UniProtKB/TrEMBL
    Q86T81