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CHST9 carbohydrate sulfotransferase 9 [ Homo sapiens (human) ]

Gene ID: 83539, updated on 11-Sep-2019

Summary

Official Symbol
CHST9provided by HGNC
Official Full Name
carbohydrate sulfotransferase 9provided by HGNC
Primary source
HGNC:HGNC:19898
See related
Ensembl:ENSG00000154080 MIM:610191
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
GalNAc4ST2; GALNAC4ST-2
Summary
The protein encoded by this gene belongs to the sulfotransferase 2 family. It is localized to the golgi membrane, and catalyzes the transfer of sulfate to position 4 of non-reducing N-acetylgalactosamine (GalNAc) residues in both N-glycans and O-glycans. Sulfate groups on carbohydrates confer highly specific functions to glycoproteins, glycolipids, and proteoglycans, and are critical for cell-cell interaction, signal transduction, and embryonic development. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Aug 2011]
Expression
Biased expression in spleen (RPKM 1.3), testis (RPKM 1.2) and 13 other tissues See more
Orthologs

Genomic context

See CHST9 in Genome Data Viewer
Location:
18q11.2
Exon count:
9
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 18 NC_000018.10 (26906481..27185364, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (24494554..24765302, complement)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene ubiquitin recognition factor in ER associated degradation 1 pseudogene Neighboring gene AQP4 antisense RNA 1 Neighboring gene aquaporin 4 Neighboring gene ATPase H+ transporting V1 subunit E1 pseudogene 2 Neighboring gene uncharacterized LOC105372036 Neighboring gene uncharacterized LOC107985143 Neighboring gene long intergenic non-protein coding RNA 1908 Neighboring gene uncharacterized LOC105372038

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

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide association study (GWAS) for bronchopulmonary dysplasia.
NHGRI GWA Catalog
Genome-wide association scan of dental caries in the permanent dentition.
NHGRI GWA Catalog
Genome-wide association study of peripheral neuropathy with D-drug-containing regimens in AIDS Clinical Trials Group protocol 384.
NHGRI GWA Catalog
Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp160, precursor env Sulfate is linked to the carbohydrate chains of HIV-1 glycoproteins gp160, gp120, and gp41 during the endoplasmic reticulum to Golgi transport of the glycoproteins PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Chondroitin sulfate biosynthesis, organism-specific biosystem (from REACTOME)
    Chondroitin sulfate biosynthesis, organism-specific biosystemChondroitin sulfate (CS) glycosaminoglycan consists of N-acetylgalactosamine (GalNAc) residues alternating in glycosidic linkages with glucuronic acid (GlcA). GalNAc residues are sulfated to varying ...
  • Chondroitin sulfate/dermatan sulfate metabolism, organism-specific biosystem (from REACTOME)
    Chondroitin sulfate/dermatan sulfate metabolism, organism-specific biosystemChondroitin sulfate (CS) is a sulfated glycosaminoglycan (GAG). CS chains are unbranched polysaccharides of varying length containing two alternating monosaccharides: D-glucuronic acid (GlcA) and N-a...
  • Glycosaminoglycan metabolism, organism-specific biosystem (from REACTOME)
    Glycosaminoglycan metabolism, organism-specific biosystemGlycosaminoglycans (GAGs) are long, unbranched polysaccharides containing a repeating disaccharide unit composed of a hexosamine (either N-acetylgalactosamine (GalNAc) or N-acetylglucosamine (GlcNAc)...
  • Metabolic pathways, organism-specific biosystem (from KEGG)
    Metabolic pathways, organism-specific biosystem
    Metabolic pathways
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of carbohydrates, organism-specific biosystem (from REACTOME)
    Metabolism of carbohydrates, organism-specific biosystemThese pathways together are responsible for: 1) the extraction of energy and carbon skeletons for biosyntheses from dietary sugars and related molecules; 2) the short-term storage of glucose in the b...
  • Metapathway biotransformation, organism-specific biosystem (from WikiPathways)
    Metapathway biotransformation, organism-specific biosystem
    Metapathway biotransformation

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ42328

Gene Ontology Provided by GOA

Function Evidence Code Pubs
N-acetylgalactosamine 4-O-sulfotransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
N-acetylgalactosamine 4-O-sulfotransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
sulfotransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
carbohydrate biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
chondroitin sulfate biosynthetic process TAS
Traceable Author Statement
more info
 
glycosaminoglycan metabolic process NAS
Non-traceable Author Statement
more info
PubMed 
hormone biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
 
proteoglycan biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
proteoglycan biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
 
sulfur compound metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
Golgi membrane TAS
Traceable Author Statement
more info
 
extracellular region IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane NAS
Non-traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
carbohydrate sulfotransferase 9
Names
GalNAc-4-sulfotransferase 2
N-acetylgalactosamine 4-O-sulfotransferase 2
carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9
galNAc-4-O-sulfotransferase 2
NP_001243245.1
NP_113610.2
XP_005258419.1
XP_006722618.1
XP_016881522.1
XP_016881523.1

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.

Genomic

  1. NG_029856.1 RefSeqGene

    Range
    4988..274695
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001256316.2NP_001243245.1  carbohydrate sulfotransferase 9 isoform 2

    See identical proteins and their annotated locations for NP_001243245.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (2) has a distinct and significantly shorter C-terminus, compared to isoform 1.
    Source sequence(s)
    AC010854, AF239821, BI710997, BM919514, KF456359
    Consensus CDS
    CCDS58618.1
    UniProtKB/Swiss-Prot
    Q7L1S5
    Related
    ENSP00000464655.1, ENST00000580774.2
  2. NM_031422.6NP_113610.2  carbohydrate sulfotransferase 9 isoform 1

    See identical proteins and their annotated locations for NP_113610.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC010854, AF239821, AY358488, KF456359
    Consensus CDS
    CCDS42422.1
    UniProtKB/Swiss-Prot
    Q7L1S5
    UniProtKB/TrEMBL
    A0A024RC28
    Related
    ENSP00000480991.1, ENST00000618847.5
    Conserved Domains (1) summary
    pfam03567
    Location:209438
    Sulfotransfer_2; Sulfotransferase family

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_000018.10 Reference GRCh38.p13 Primary Assembly

    Range
    26906481..27185364 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017026034.1XP_016881523.1  carbohydrate sulfotransferase 9 isoform X2

    Conserved Domains (1) summary
    pfam03567
    Location:152381
    Sulfotransfer_2; Sulfotransferase family
  2. XM_017026033.1XP_016881522.1  carbohydrate sulfotransferase 9 isoform X1

    UniProtKB/Swiss-Prot
    Q7L1S5
    UniProtKB/TrEMBL
    A0A024RC28
    Related
    ENSP00000462852.1, ENST00000581714.5
    Conserved Domains (1) summary
    pfam03567
    Location:209438
    Sulfotransfer_2; Sulfotransferase family
  3. XM_005258362.4XP_005258419.1  carbohydrate sulfotransferase 9 isoform X3

    See identical proteins and their annotated locations for XP_005258419.1

    Conserved Domains (1) summary
    pfam03567
    Location:124353
    Sulfotransfer_2; Sulfotransferase family
  4. XM_006722555.4XP_006722618.1  carbohydrate sulfotransferase 9 isoform X4

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001243848.1: Suppressed sequence

    Description
    NM_001243848.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript, which appears to retain intronic sequence at its 5' end.
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