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DSE dermatan sulfate epimerase [ Homo sapiens (human) ]

Gene ID: 29940, updated on 5-Mar-2024

Summary

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Official Symbol
DSEprovided by HGNC
Official Full Name
dermatan sulfate epimeraseprovided by HGNC
Primary source
HGNC:HGNC:21144
See related
Ensembl:ENSG00000111817 MIM:605942; AllianceGenome:HGNC:21144
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
DSEP; DSEPI; SART2; EDSMC2; SART-2; DS-epi1
Summary
The protein encoded by this gene is a tumor-rejection antigen. It is localized to the endoplasmic reticulum and functions to convert D-glucuronic acid to L-iduronic acid during the biosynthesis of dermatan sulfate. This antigen possesses tumor epitopes capable of inducing HLA-A24-restricted and tumor-specific cytotoxic T lymphocytes in cancer patients and may be useful for specific immunotherapy. Mutations in this gene cause inmusculocontractural Ehlers-Danlos syndrome. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 9, and a paralogous gene exists on chromosome 18. [provided by RefSeq, Apr 2016]
Expression
Ubiquitous expression in appendix (RPKM 7.0), fat (RPKM 5.7) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
6q22.1
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (116254171..116444861)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (117438152..117628566)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (116575334..116766024)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene 5'-nucleotidase domain containing 1 Neighboring gene collagen type X alpha 1 chain Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_88113 Neighboring gene MPRA-validated peak6050 silencer Neighboring gene NIP7 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24981 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24982 Neighboring gene ribosomal protein S5 pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr6:116592289-116592790 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24983 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24984 Neighboring gene TSPY like 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24985 Neighboring gene RPS5 pseudogene 1 Neighboring gene TSPY like 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_88171 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:116644935-116645502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:116646525-116647026 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24986 Neighboring gene uncharacterized LOC100287467 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24987 Neighboring gene Sharpr-MPRA regulatory region 2122 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:116692481-116692981 Neighboring gene Sharpr-MPRA regulatory region 1381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24989 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24990 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:116720114-116720614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:116720615-116721115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24991 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17494 Neighboring gene keratin 18 pseudogene 22 Neighboring gene CBX3 pseudogene 9

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. Dermatan sulfate epimerase 1 expression and mislocalization may interfere with dermatan sulfate synthesis and breast cancer cell growth. Listik E, et al. Carbohydr Res, 2020 Feb. PMID 31972438
  2. DSE promotes aggressive glioma cell phenotypes by enhancing HB-EGF/ErbB signaling. Liao WC, et al. PLoS One, 2018. PMID 29864158, Free PMC Article
  3. Deciphering the Mode of Action of the Processive Polysaccharide Modifying Enzyme Dermatan Sulfate Epimerase 1 by Hydrogen-Deuterium Exchange Mass Spectrometry. Tykesson E, et al. Chem Sci, 2016 Feb 1. PMID 26900446, Free PMC Article
  4. Genetic heterogeneity and clinical variability in musculocontractural Ehlers-Danlos syndrome caused by impaired dermatan sulfate biosynthesis. Syx D, et al. Hum Mutat, 2015 May. PMID 25703627
  5. Loss of dermatan sulfate epimerase (DSE) function results in musculocontractural Ehlers-Danlos syndrome. Müller T, et al. Hum Mol Genet, 2013 Sep 15. PMID 23704329

See all (35) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Dermatan sulfate epimerase 1 expression and mislocalization may interfere with dermatan sulfate synthesis and breast cancer cell growth.
    Title: Dermatan sulfate epimerase 1 expression and mislocalization may interfere with dermatan sulfate synthesis and breast cancer cell growth.
  2. DS-epi1, DS-epi2, and D4ST1 form homomers and are all part of a hetero-oligomeric complex where D4ST1 directly interacts with DS-epi1, but not with DS-epi2. The cooperation of DS-epi1 with D4ST1 may therefore explain the processive mode of the formation of iduronic acid blocks.
    Title: Dermatan sulfate epimerase 1 and dermatan 4-O-sulfotransferase 1 form complexes that generate long epimerized 4-O-sulfated blocks.
  3. Study showed that DSE is frequently upregulated in human glioma tissue and cell lines and associated with a worse tumor grade and poor overall survival. Its knockdown suppresses malignant phenotypes, whereas DSE overexpression enhances glioma cell malignancy, both in vitro and in vivo. Mechanically, DSE modulates HB-EGF-induced EGFR/ErbB2 activity and downstream signaling.
    Title: DSE promotes aggressive glioma cell phenotypes by enhancing HB-EGF/ErbB signaling.
  4. study identified a homozygous DSE missense mutation (c.803C>T, p.S268L) in a male child with musculocontractural type of Ehlers-Danlos syndrome; data indicate mutation affects the epimerase activity, resulting in reduced dermatan sulfate (DS) biosynthesis and an increased synthesis or an accumulation or reduced conversion of chondroitin sulfate
    Title: Loss of dermatan sulfate epimerase (DSE) function results in musculocontractural Ehlers-Danlos syndrome.
  5. Dermatan sulfate epimerase 1 was highly upregulated in esophagus squamous cell carcinoma
    Title: Dermatan sulfate is involved in the tumorigenic properties of esophagus squamous cell carcinoma.
  6. Identification of the active site of DS-epimerase 1 and requirement of N-glycosylation for enzyme function.
    Title: Identification of the active site of DS-epimerase 1 and requirement of N-glycosylation for enzyme function.
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

Associated conditions

Description Tests
Ehlers-Danlos syndrome, musculocontractural type 2
MedGen: C3809845 OMIM: 615539 GeneReviews: Not available
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EBI GWAS Catalog

Description
A genome-wide search for quantitative trait loci affecting the cortical surface area and thickness of Heschl's gyrus.
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

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chondroitin-glucuronate 5-epimerase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables chondroitin-glucuronate 5-epimerase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables chondroitin-glucuronate 5-epimerase activity TAS
Traceable Author Statement
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in chondroitin sulfate biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in chondroitin sulfate metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in dermatan sulfate biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in dermatan sulfate biosynthetic process TAS
Traceable Author Statement
more info
  
involved_in dermatan sulfate metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in heparan sulfate proteoglycan biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in Golgi membrane TAS
Traceable Author Statement
more info
  
located_in cytoplasmic vesicle membrane IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
dermatan-sulfate epimerase
Names
DS epimerase
chondroitin-glucuronate 5-epimerase
squamous cell carcinoma antigen recognized by T-cells 2
NP_001074445.1
NP_001309866.1
NP_001309867.1
NP_001309868.1
NP_001309869.1
NP_001309870.1
NP_001309872.1
NP_001309873.1
NP_001361449.1
NP_001361450.1
NP_001361451.1
NP_037484.1

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_033266.4 RefSeqGene

    Range
    121777..195691
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1184

mRNA and Protein(s)

  1. NM_001080976.3 → NP_001074445.1  dermatan-sulfate epimerase isoform a precursor

    See identical proteins and their annotated locations for NP_001074445.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 all encode the same isoform (a).
    Source sequence(s)
    AL050331, Z84488
    Consensus CDS
    CCDS5107.1
    UniProtKB/Swiss-Prot
    Q5R3K6, Q9UL01
    Related
    ENSP00000404049.2, ENST00000452085.7

  2. NM_001322937.2 → NP_001309866.1  dermatan-sulfate epimerase isoform a precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 all encode the same isoform (a).
    Source sequence(s)
    AL050331, Z84488
    Consensus CDS
    CCDS5107.1
    UniProtKB/Swiss-Prot
    Q5R3K6, Q9UL01

  3. NM_001322938.2 → NP_001309867.1  dermatan-sulfate epimerase isoform a precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 all encode the same isoform (a).
    Source sequence(s)
    AL050331, Z84488
    Consensus CDS
    CCDS5107.1
    UniProtKB/Swiss-Prot
    Q5R3K6, Q9UL01

  4. NM_001322939.2 → NP_001309868.1  dermatan-sulfate epimerase isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) contains an alternate 5' exon and it thus differs in the 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is longer than isoform a.
    Source sequence(s)
    Z84488
    UniProtKB/TrEMBL
    B7Z765

  5. NM_001322940.2 → NP_001309869.1  dermatan-sulfate epimerase isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) contains alternate 5' exon structure, and it thus differs in the 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) is shorter at the N-terminus, compared to isoform a. Both variants 6 and 7 encode isoform c.
    Source sequence(s)
    AL050331, Z84488
    UniProtKB/Swiss-Prot
    Q9UL01
    UniProtKB/TrEMBL
    B7Z1T3

  6. NM_001322941.2 → NP_001309870.1  dermatan-sulfate epimerase isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) uses an alternate splice site in a 5' exon, and it it thus differs in the 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) is shorter at the N-terminus, compared to isoform a. Both variants 6 and 7 encode isoform c.
    Source sequence(s)
    Z84488
    UniProtKB/Swiss-Prot
    Q9UL01

  7. NM_001322943.2 → NP_001309872.1  dermatan-sulfate epimerase isoform e precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) lacks two alternate exons, resulting in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (e) has a distinct C-terminus and is shorter than isoform a.
    Source sequence(s)
    Z84488
    Consensus CDS
    CCDS87433.1
    UniProtKB/TrEMBL
    A0A2R8YE23
    Related
    ENSP00000495970.1, ENST00000646710.1

  8. NM_001322944.2 → NP_001309873.1  dermatan-sulfate epimerase isoform d precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) lacks an alternate exon, resulting in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (d) has a distinct C-terminus and is shorter than isoform a.
    Source sequence(s)
    Z84488
    Consensus CDS
    CCDS87432.1
    UniProtKB/TrEMBL
    A0A2R8Y6J1, A0A2U3TZJ0
    Related
    ENSP00000352567.3, ENST00000359564.3

  9. NM_001374520.1 → NP_001361449.1  dermatan-sulfate epimerase isoform f

    Status: REVIEWED

    Source sequence(s)
    AL050331, Z84488
    UniProtKB/TrEMBL
    B3KY37

  10. NM_001374521.1 → NP_001361450.1  dermatan-sulfate epimerase isoform g

    Status: REVIEWED

    Source sequence(s)
    AL050331, Z84488

  11. NM_001374522.1 → NP_001361451.1  dermatan-sulfate epimerase isoform h precursor

    Status: REVIEWED

    Source sequence(s)
    AL050331, Z84488
    UniProtKB/TrEMBL
    A0A2R8Y6J1

  12. NM_013352.4 → NP_037484.1  dermatan-sulfate epimerase isoform a precursor

    See identical proteins and their annotated locations for NP_037484.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform a. Variants 1, 2, 3 and 4 all encode the same isoform (a).
    Source sequence(s)
    AF098066, AL832471, AW630671, Z84488
    Consensus CDS
    CCDS5107.1
    UniProtKB/Swiss-Prot
    Q5R3K6, Q9UL01
    Related
    ENSP00000494147.2, ENST00000644252.3

RNA

  1. NR_136520.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) does not share exon structure with variant 1, but it shares its 5' terminal exon with variants 3 and 6 and contains an alternate 3' terminal exon. This variant is represented as non-coding because it lacks the entire ORF found in variant 1.
    Source sequence(s)
    AK093256, AL050331, BX095954, BX489961
    Related
    ENST00000448740.2

  2. NR_136521.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (11) does not share exon structure with variant 1, but it shares its 5' terminal exon with variants 2, 12, 13 and 14, and contains alternate 3' exon structure that is shared with variants 12 and 13. This variant is represented as non-coding because it lacks the entire ORF found in variant 1.
    Source sequence(s)
    AW292369, BC043526, HY050986
    Related
    ENST00000645959.1

  3. NR_136522.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (12) does not share exon structure with variant 1, but it shares its 5' terminal exon with variants 2, 11, 13 and 14, and contains alternate 3' exon structure, some of which is shared with variants 11 and 13. This variant is represented as non-coding because it lacks the entire ORF found in variant 1.
    Source sequence(s)
    AW292369, BC043526, BX110619, DC333659, HY012067

  4. NR_136523.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (13) does not share exon structure with variant 1, but it shares its 5' terminal exon with variants 2, 11, 12 and 14, and contains alternate 3' exon structure, some of which is shared with variants 11 and 12. This variant is represented as non-coding because it lacks the entire ORF found in variant 1.
    Source sequence(s)
    AW292369, BC043526, DC333659
    Related
    ENST00000449314.5

  5. NR_136524.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (14) contains an alternate 5' terminal exon, uses an alternate splice site in an internal exon and lacks an internal exon, 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)
    AL050331, Z84488

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    116254171..116444861
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    117438152..117628566
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UL01.1 GenPept UniProtKB/Swiss-Prot:Q9UL01

Gene LinkOut

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