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    CHST9 carbohydrate sulfotransferase 9 [ Homo sapiens (human) ]

    Gene ID: 83539, updated on 3-Apr-2024

    Summary

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    Official Symbol
    CHST9provided by HGNC
    Official Full Name
    carbohydrate sulfotransferase 9provided by HGNC
    Primary source
    HGNC:HGNC:19898
    See related
    Ensembl:ENSG00000154080 MIM:610191; AllianceGenome:HGNC:19898
    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
    mouse all
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    Genomic context

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    Location:
    18q11.2
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (26906481..27185308, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (27100538..27379358, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (24486445..24765272, complement)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene ubiquitin recognition factor in ER associated degradation 1 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:24442920-24443420 Neighboring gene AQP4 antisense RNA 1 Neighboring gene aquaporin 4 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:24507672-24508283 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:24536524-24537111 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:24537112-24537698 Neighboring gene ATPase H+ transporting V1 subunit E1 pseudogene 2 Neighboring gene uncharacterized LOC124904275 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13194 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13195 Neighboring gene uncharacterized LOC105372036 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr18:24743020-24744219 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:24803365-24803888 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:24812317-24813029 Neighboring gene long intergenic non-protein coding RNA 1908 Neighboring gene uncharacterized LOC105372038

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. A Frameshift Variant in the CHST9 Gene Identified by Family-Based Whole Genome Sequencing Is Associated with Schizophrenia in Chinese Population. Chen J, et al. Sci Rep, 2019 Sep 3. PMID 31481703, Free PMC Article
    2. CHST9 rs1436904 genetic variant contributes to prognosis of triple-negative breast cancer. Yuan J, et al. Sci Rep, 2017 Sep 18. PMID 28924212, Free PMC Article
    3. Examination of copy number variations of CHST9 in multiple types of hematologic malignancies. Zhao X, et al. Cancer Genet Cytogenet, 2010 Dec. PMID 21156230
    4. Molecular cloning and expression of an N-acetylgalactosamine-4-O-sulfotransferase that transfers sulfate to terminal and non-terminal beta 1,4-linked N-acetylgalactosamine. Kang HG, et al. J Biol Chem, 2001 Apr 6. PMID 11139592
    5. Molecular cloning and expression of two distinct human N-acetylgalactosamine 4-O-sulfotransferases that transfer sulfate to GalNAc beta 1-->4GlcNAc beta 1-->R in both N- and O-glycans. Hiraoka N, et al. Glycobiology, 2001 Jun. PMID 11445554

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A Frameshift Variant in the CHST9 Gene Identified by Family-Based Whole Genome Sequencing Is Associated with Schizophrenia in Chinese Population.
      Title: A Frameshift Variant in the CHST9 Gene Identified by Family-Based Whole Genome Sequencing Is Associated with Schizophrenia in Chinese Population.
    2. CHST9 rs1436904 polymorphism significantly contributes to prognosis of early-stage TNBC, suggesting its clinical potential in the screening of high-risk TNBC patients for recurrence and the possibility of patient-tailored therapeutic decisions.
      Title: CHST9 rs1436904 genetic variant contributes to prognosis of triple-negative breast cancer.
    3. the copy number variations of CHST9 have been shown to associate with hematologic malignancies
      Title: Examination of copy number variations of CHST9 in multiple types of hematologic malignancies.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    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 PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ42328

    Gene Ontology Provided by GOA

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

    General protein information

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    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_001385422.1
    NP_113610.2
    XP_005258419.1
    XP_006722618.1
    XP_047293837.1
    XP_054175228.1
    XP_054175229.1

    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.

    Genomic

    1. NG_029856.2 RefSeqGene

      Range
      5000..283827
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001256316.2 → NP_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/TrEMBL
      A0A0S2Z5U9
      Related
      ENSP00000464655.1, ENST00000580774.2

    2. NM_001398493.1 → NP_001385422.1  carbohydrate sulfotransferase 9 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC010854, AC023575, AC116017, KF456359
      Consensus CDS
      CCDS42422.1
      UniProtKB/Swiss-Prot
      Q6UX69, Q7L1S5, Q9BXH3, Q9BXH4, Q9BZW9
      Related
      ENSP00000462852.1, ENST00000581714.5
      Conserved Domains (1) summary
      pfam03567
      Location:209 → 438
      Sulfotransfer_2; Sulfotransferase family

    3. NM_031422.6 → NP_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
      Q6UX69, Q7L1S5, Q9BXH3, Q9BXH4, Q9BZW9
      UniProtKB/TrEMBL
      A0A0S2Z5P0
      Related
      ENSP00000480991.1, ENST00000618847.5
      Conserved Domains (1) summary
      pfam03567
      Location:209 → 438
      Sulfotransfer_2; Sulfotransferase family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      26906481..27185308 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047437881.1 → XP_047293837.1  carbohydrate sulfotransferase 9 isoform X1

    2. XM_005258362.5 → XP_005258419.1  carbohydrate sulfotransferase 9 isoform X2

      See identical proteins and their annotated locations for XP_005258419.1

      UniProtKB/TrEMBL
      A0A0S2Z5P0
      Conserved Domains (1) summary
      pfam03567
      Location:124 → 353
      Sulfotransfer_2; Sulfotransferase family

    3. XM_006722555.5 → XP_006722618.1  carbohydrate sulfotransferase 9 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      27100538..27379358 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054319253.1 → XP_054175228.1  carbohydrate sulfotransferase 9 isoform X1

    2. XM_054319254.1 → XP_054175229.1  carbohydrate sulfotransferase 9 isoform X2

    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.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7L1S5.2 GenPept UniProtKB/Swiss-Prot:Q7L1S5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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