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CSGALNACT2 chondroitin sulfate N-acetylgalactosaminyltransferase 2 [ Homo sapiens (human) ]

Gene ID: 55454, updated on 11-Sep-2019

Summary

Official Symbol
CSGALNACT2provided by HGNC
Official Full Name
chondroitin sulfate N-acetylgalactosaminyltransferase 2provided by HGNC
Primary source
HGNC:HGNC:24292
See related
Ensembl:ENSG00000169826 MIM:616616
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
CHGN2; ChGn-2; PRO0082; GALNACT2; GALNACT-2; beta4GalNAcT
Summary
This gene encodes a member of the chondroitin N-acetylgalactosaminyltransferase family. The encoded protein is involved in elongation during chondroitin sulfate synthesis. Alternative splicing of this gene results in multiple transcript variants. Two related pseudogenes have been identified on chromosome X. [provided by RefSeq, Feb 2016]
Expression
Broad expression in bone marrow (RPKM 48.3), gall bladder (RPKM 16.8) and 23 other tissues See more
Orthologs

Genomic context

See CSGALNACT2 in Genome Data Viewer
Location:
10q11.21
Exon count:
11
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 10 NC_000010.11 (43138445..43185308)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (43633893..43680756)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene RET 5' regulatory region Neighboring gene VISTA enhancer hs2326 Neighboring gene RET intron 1 enhancer Neighboring gene ret proto-oncogene Neighboring gene RasGEF domain family member 1A Neighboring gene uncharacterized LOC107984225 Neighboring gene uncharacterized LOC105378271 Neighboring gene long intergenic non-protein coding RNA 2633

Genomic regions, transcripts, and products

Expression

  • Project title: 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

NHGRI GWAS Catalog

Description
A genome-wide association study identifies potential susceptibility Loci for hirschsprung disease.
NHGRI GWA Catalog
Genome-wide association study identifies NRG1 as a susceptibility locus for Hirschsprung's disease.
NHGRI GWA Catalog

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ43310, MGC40204, DKFZp686H13226

General protein information

Preferred Names
chondroitin sulfate N-acetylgalactosaminyltransferase 2
Names
beta 4 GalNAcT-2
chondroitin beta1,4 N-acetylgalactosaminyltransferase 2
glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase 2
NP_001306583.1
NP_001306585.1
NP_061060.3
XP_011538240.1
XP_016871877.1
XP_016871878.1
XP_016871880.1

NCBI Reference Sequences (RefSeq)

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_001319654.1NP_001306583.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon, which results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (2) has a distinct and shorter C-terminus, compared to isoform 1. The 5' UTR is incomplete because no 5'-complete transcripts exist for this variant, and there is splice pattern ambiguity further upstream.
    Source sequence(s)
    AA721408, AK074474, AK125300, KU178705
    UniProtKB/Swiss-Prot
    Q8N6G5
    UniProtKB/TrEMBL
    A0A0S2Z5K4
    Conserved Domains (1) summary
    cl11394
    Location:140389
    Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold
  2. NM_001319656.1NP_001306585.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks two alternate exons, which results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (3) has a distinct and shorter C-terminus, compared to isoform 1. The 5' UTR is incomplete because no 5'-complete transcripts exist for this variant, and there is splice pattern ambiguity further upstream.
    Source sequence(s)
    AA721408, AK074474, AK125300, KU178706
    UniProtKB/Swiss-Prot
    Q8N6G5
    UniProtKB/TrEMBL
    A0A0S2Z5F9
    Conserved Domains (1) summary
    cl11394
    Location:140327
    Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold
  3. NM_018590.5NP_061060.3  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform 1

    See identical proteins and their annotated locations for NP_061060.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    BC030268, BX102005, DA674683, DB291068
    Consensus CDS
    CCDS7201.1
    UniProtKB/Swiss-Prot
    Q8N6G5
    UniProtKB/TrEMBL
    A0A0S2Z5F5
    Related
    ENSP00000363590.3, ENST00000374466.4
    Conserved Domains (1) summary
    cl11394
    Location:140516
    Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold

RNA

  1. NR_135077.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) includes an additional exon in the central region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AA721408, BX640967, CT003455, DB291068

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p13 Primary Assembly

    Range
    43138445..43185308
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017016388.2XP_016871877.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X2

    UniProtKB/TrEMBL
    A0A0S2Z5K4
    Conserved Domains (1) summary
    cl11394
    Location:140389
    Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold
  2. XM_017016389.2XP_016871878.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X3

    UniProtKB/TrEMBL
    A0A0S2Z5F9
    Conserved Domains (1) summary
    cl11394
    Location:140327
    Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold
  3. XM_011539938.2XP_011538240.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X1

    Conserved Domains (1) summary
    cl11394
    Location:140414
    Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold
  4. XM_017016391.2XP_016871880.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X4

RNA

  1. XR_002956986.1 RNA Sequence

  2. XR_945783.3 RNA Sequence

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