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CHPF2 chondroitin polymerizing factor 2 [ Homo sapiens (human) ]

Gene ID: 54480, updated on 2-Nov-2024

Summary

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Official Symbol
CHPF2provided by HGNC
Official Full Name
chondroitin polymerizing factor 2provided by HGNC
Primary source
HGNC:HGNC:29270
See related
Ensembl:ENSG00000033100 MIM:608037; AllianceGenome:HGNC:29270
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ChSy-3; chPF-2; CSGlcAT; CSGLCA-T
Summary
Predicted to enable glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity. Predicted to be involved in chondroitin sulfate biosynthetic process. Located in membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in spleen (RPKM 11.8), placenta (RPKM 11.6) and 25 other tissues See more
Orthologs
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Genomic context

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See CHPF2 in Genome Data Viewer
Location:
7q36.1
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (151232483..151238822)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (152405601..152411942)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (150929569..150935908)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ABCF2-H2BK1 readthrough Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:150910975-150912174 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:150916273-150916470 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18805 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26853 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26854 Neighboring gene H2B.K variant histone 1 Neighboring gene ATP binding cassette subfamily F member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26855 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18806 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150930441-150931006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150932437-150932937 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:150936637-150937836 Neighboring gene uncharacterized LOC124901779 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150938593-150939094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150941724-150942298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150942299-150942872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150942873-150943447 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150943448-150944021 Neighboring gene Sharpr-MPRA regulatory region 13648 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18809 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150949301-150950210 Neighboring gene SWI/SNF related BAF chromatin remodeling complex subunit D3 Neighboring gene microRNA 671 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150953220-150953720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150953721-150954221 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150971756-150972555 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150974709-150975418 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:151000420-151001278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26856 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26857 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26858 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:151038519-151039020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26859 Neighboring gene negative regulator of ubiquitin like proteins 1 Neighboring gene WD repeat domain 86

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 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. MEK-mediated CHPF2 phosphorylation promotes colorectal cancer cell proliferation and metastasis by activating NF-κB signaling. Wen X, et al. Cancer Lett, 2024 Mar 1. PMID 38253217
  2. Molecular cloning and characterization of a novel chondroitin sulfate glucuronyltransferase that transfers glucuronic acid to N-acetylgalactosamine. Gotoh M, et al. J Biol Chem, 2002 Oct 11. PMID 12145278
  3. Exosomal lncRNA DUXAP8 affecting CHPF2 in the pathogenesis of intracranial aneurysms. Han L, et al. Gene, 2024 May 25. PMID 38341004
  4. Identification of chondroitin sulfate glucuronyltransferase as chondroitin synthase-3 involved in chondroitin polymerization: chondroitin polymerization is achieved by multiple enzyme complexes consisting of chondroitin synthase family members. Izumikawa T, et al. J Biol Chem, 2008 Apr 25. PMID 18316376
  5. Chondroitin synthases I, II, III and chondroitin sulfate glucuronyltransferase expression in colorectal cancer. Kalathas D, et al. Mol Med Rep, 2011 Mar-Apr. PMID 21468578

See all (32) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Exosomal lncRNA DUXAP8 affecting CHPF2 in the pathogenesis of intracranial aneurysms.
    Title: Exosomal lncRNA DUXAP8 affecting CHPF2 in the pathogenesis of intracranial aneurysms.
  2. MEK-mediated CHPF2 phosphorylation promotes colorectal cancer cell proliferation and metastasis by activating NF-kappaB signaling.
    Title: MEK-mediated CHPF2 phosphorylation promotes colorectal cancer cell proliferation and metastasis by activating NF-κB signaling.
  3. The present study focused on the expression of chondroitin-synthesizing enzymes in colorectal cancer.
    Title: Chondroitin synthases I, II, III and chondroitin sulfate glucuronyltransferase expression in colorectal cancer.
  4. chondroitin polymerization is achieved by multiple combinations of ChSy-1, ChSy-2, CSGlcA-T, and ChPF and each combination may play a unique role in the biosynthesis of CS; CSGlcA-T is identified as chondroitin synthase-3 (ChSy-3)
    Title: Identification of chondroitin sulfate glucuronyltransferase as chondroitin synthase-3 involved in chondroitin polymerization: chondroitin polymerization is achieved by multiple enzyme complexes consisting of chondroitin synthase family members.
  5. Results describe a novel human gene that possesses homology with chondroitin synthase.
    Title: Molecular cloning and characterization of a novel chondroitin sulfate glucuronyltransferase that transfers glucuronic acid to N-acetylgalactosamine.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 interacts with CHPF2; predicted interaction to be within the Golgi PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1402

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity TAS
Traceable Author Statement
more info
  
enables glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in chondroitin sulfate biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in chondroitin sulfate biosynthetic process TAS
Traceable Author Statement
more info
  
Component Evidence Code Pubs
located_in Golgi cisterna membrane IEA
Inferred from Electronic Annotation
more info
  
located_in Golgi membrane TAS
Traceable Author Statement
more info
  
located_in membrane HDA PubMed 

General protein information

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Preferred Names
chondroitin sulfate glucuronyltransferase
Names
N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase
chondroitin synthase-3
NP_001271224.1
NP_001376580.1
NP_001376581.1
NP_001376582.1
NP_061888.1

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_001284295.2 → NP_001271224.1  chondroitin sulfate glucuronyltransferase isoform 2

    See identical proteins and their annotated locations for NP_001271224.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks a segment in the 5' UTR and 5' coding region which results in the use of an alternate start codon, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC021097, AI191668, AK056331
    Consensus CDS
    CCDS64803.1
    UniProtKB/TrEMBL
    B3KPG6, G5E9W2
    Related
    ENSP00000418914.1, ENST00000495645.5
    Conserved Domains (2) summary
    pfam05679
    Location:234 → 751
    CHGN; Chondroitin N-acetylgalactosaminyltransferase
    cl21608
    Location:169 → 261
    Galactosyl_T; Galactosyltransferase

  2. NM_001389651.1 → NP_001376580.1  chondroitin sulfate glucuronyltransferase isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC021097
    Consensus CDS
    CCDS94234.1
    UniProtKB/TrEMBL
    A0A8I5KRN5, B3KPG6
    Related
    ENSP00000509142.1, ENST00000692651.1
    Conserved Domains (2) summary
    pfam05679
    Location:242 → 698
    CHGN; Chondroitin N-acetylgalactosaminyltransferase
    cl21608
    Location:177 → 269
    Galactosyl_T; Galactosyltransferase

  3. NM_001389652.1 → NP_001376581.1  chondroitin sulfate glucuronyltransferase isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC021097
    Consensus CDS
    CCDS94233.1
    UniProtKB/TrEMBL
    B3KPG6, C9JZF7
    Related
    ENSP00000419769.2, ENST00000482173.6
    Conserved Domains (2) summary
    pfam05679
    Location:171 → 688
    CHGN; Chondroitin N-acetylgalactosaminyltransferase
    cl21608
    Location:106 → 198
    Galactosyl_T; Galactosyltransferase

  4. NM_001389653.1 → NP_001376582.1  chondroitin sulfate glucuronyltransferase isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC021097
    UniProtKB/TrEMBL
    B3KPG6
    Conserved Domains (2) summary
    pfam05679
    Location:171 → 627
    CHGN; Chondroitin N-acetylgalactosaminyltransferase
    cl21608
    Location:106 → 198
    Galactosyl_T; Galactosyltransferase

  5. NM_019015.3 → NP_061888.1  chondroitin sulfate glucuronyltransferase isoform 1

    See identical proteins and their annotated locations for NP_061888.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC021097
    Consensus CDS
    CCDS34779.1
    UniProtKB/Swiss-Prot
    B2DBD8, Q6P2I4, Q6UXD2, Q9P2E5
    UniProtKB/TrEMBL
    B3KPG6
    Related
    ENSP00000035307.2, ENST00000035307.7
    Conserved Domains (2) summary
    pfam05679
    Location:242 → 759
    CHGN; Chondroitin N-acetylgalactosaminyltransferase
    cl21608
    Location:177 → 269
    Galactosyl_T; Galactosyltransferase

RNA

  1. NR_171547.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC021097

  2. NR_171548.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC021097

  3. NR_171549.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC021097

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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    151232483..151238822
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    152405601..152411942
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9P2E5.2 GenPept UniProtKB/Swiss-Prot:Q9P2E5

Gene LinkOut

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

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