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    DSE dermatan sulfate epimerase [ Homo sapiens (human) ]

    Gene ID: 29940, updated on 10-Dec-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
    mouse all
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    Genomic context

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    See DSE in Genome Data Viewer
    Location:
    6q22.1
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (116254171..116444861)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (117438152..117628566)
    RS_2024_09 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. 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
    2. 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
    3. In vitro induction of specific CD8+ T lymphocytes by tumor-associated antigenic peptides in patients with oral squamous cell carcinoma. Toyoshima T, et al. Cancer Lett, 2012 Sep 1. PMID 22366580
    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. Dermatan sulfate is involved in the tumorigenic properties of esophagus squamous cell carcinoma. Thelin MA, et al. Cancer Res, 2012 Apr 15. PMID 22350411, Free PMC Article

    See all (36) 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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    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
    		Compare labs

    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)

    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_2024_08

    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

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

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