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    UXS1 UDP-glucuronate decarboxylase 1 [ Homo sapiens (human) ]

    Gene ID: 80146, updated on 3-Apr-2024

    Summary

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    Official Symbol
    UXS1provided by HGNC
    Official Full Name
    UDP-glucuronate decarboxylase 1provided by HGNC
    Primary source
    HGNC:HGNC:17729
    See related
    Ensembl:ENSG00000115652 MIM:609749; AllianceGenome:HGNC:17729
    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
    UGD; hUXS; hUXS1; SDR6E1
    Summary
    This gene encodes an enzyme found in the perinuclear Golgi which catalyzes the synthesis of UDP-xylose used in glycosaminoglycan (GAG) synthesis on proteoglycans. The GAG chains are covalently attached to proteoglycans which participate in signaling pathways during development. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2014]
    Expression
    Ubiquitous expression in kidney (RPKM 16.4), placenta (RPKM 15.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    2q12.2
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (106093311..106194301, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (106554193..106655255, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (106709767..106810757, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373531 Neighboring gene uncharacterized LOC124906055 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:106669310-106670509 Neighboring gene ECRG4 augurin precursor Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:106713148-106713820 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:106713821-106714492 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:106746920-106747434 Neighboring gene Sharpr-MPRA regulatory region 936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16337 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16338 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:106781527-106782046 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11845 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16339 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11846 Neighboring gene ribosomal protein L22 pseudogene 10 Neighboring gene SRSF3 pseudogene 4

    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. Man o' war mutation in UDP-α-D-xylose synthase favors the abortive catalytic cycle and uncovers a latent potential for hexamer formation. Walsh RM Jr, et al. Biochemistry, 2015 Jan 27. PMID 25521717
    2. Functional UDP-xylose transport across the endoplasmic reticulum/Golgi membrane in a Chinese hamster ovary cell mutant defective in UDP-xylose Synthase. Bakker H, et al. J Biol Chem, 2009 Jan 23. PMID 19028698, Free PMC Article
    3. Human UDP-α-d-xylose synthase forms a catalytically important tetramer that has not been observed in crystal structures. Polizzi SJ, et al. Biochemistry, 2013 Jun 4. PMID 23656592
    4. Structure and mechanism of human UDP-xylose synthase: evidence for a promoting role of sugar ring distortion in a three-step catalytic conversion of UDP-glucuronic acid. Eixelsberger T, et al. J Biol Chem, 2012 Sep 7. PMID 22810237, Free PMC Article
    5. Human UDP-α-D-xylose synthase and Escherichia coli ArnA conserve a conformational shunt that controls whether xylose or 4-keto-xylose is produced. Polizzi SJ, et al. Biochemistry, 2012 Nov 6. PMID 23072385, Free PMC Article

    See all (40) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. UXS1: a sweet spot for cell death.
      Title: UXS1: a sweet spot for cell death.
    2. The persistence of a latent hexamer-building interface in the human enzyme suggests that the ancestral UXS may have been a hexamer.
      Title: Man o' war mutation in UDP-α-D-xylose synthase favors the abortive catalytic cycle and uncovers a latent potential for hexamer formation.
    3. hUXS forms a tetramer in solution that is important for activity. The higher activity of the tetramer coupled with the relative instability of the dimeric complex suggests that an association-dissociation mechanism may regulate hUXS activity.
      Title: Human UDP-α-d-xylose synthase forms a catalytically important tetramer that has not been observed in crystal structures.
    4. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    7. Complementation was achieved by expression of a cytoplasmic variant of UDP-xylose Synthase, which proves the existence of a functional Golgi UDP-xylose transporter[UDP-xylose Synthase]
      Title: Functional UDP-xylose transport across the endoplasmic reticulum/Golgi membrane in a Chinese hamster ovary cell mutant defective in UDP-xylose Synthase.
    8. UDP-glucuronate decarboxylase, a key enzyme in proteoglycan synthesis: cloning, characterization, and localization.
      Title: UDP-glucuronate decarboxylase, a key enzyme in proteoglycan synthesis: cloning, characterization, and localization.
    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

    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

    Clone Names

    • FLJ23591

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables NAD+ binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables NAD+ binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables UDP-glucuronate decarboxylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables UDP-glucuronate decarboxylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in D-xylose metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in UDP-D-xylose biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in UDP-D-xylose biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi cisterna membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of catalytic complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular exosome HDA PubMed 

    General protein information

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    Preferred Names
    UDP-glucuronic acid decarboxylase 1
    Names
    UXS-1
    short chain dehydrogenase/reductase family 6E, member 12
    NP_001240804.1
    NP_001240805.1
    NP_001364433.1
    NP_001364434.1
    NP_001364435.1
    NP_001364436.1
    NP_001364437.1
    NP_001364438.1
    NP_079352.2
    XP_011510204.2
    XP_011510205.2
    XP_024308925.1
    XP_047301874.1
    XP_054200010.1
    XP_054200011.1
    XP_054200012.1
    XP_054200013.1
    XP_054200014.1
    XP_054200015.1

    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_001253875.2 → NP_001240804.1  UDP-glucuronic acid decarboxylase 1 isoform 1

      See identical proteins and their annotated locations for NP_001240804.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest protein (isoform 1).
      Source sequence(s)
      AC018878
      Consensus CDS
      CCDS58721.1
      UniProtKB/TrEMBL
      A8K3Q3
      Related
      ENSP00000283148.7, ENST00000283148.12
      Conserved Domains (3) summary
      cd05230
      Location:94 → 397
      UGD_SDR_e; UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs
      COG0451
      Location:94 → 401
      WcaG; Nucleoside-diphosphate-sugar epimerase [Cell wall/membrane/envelope biogenesis]
      pfam11803
      Location:4 → 83
      UXS1_N; UDP-glucuronate decarboxylase N-terminal

    2. NM_001253876.2 → NP_001240805.1  UDP-glucuronic acid decarboxylase 1 isoform 3

      See identical proteins and their annotated locations for NP_001240805.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks several exons in the 5' coding region, and uses a downstream AUG compared to variant 1. The resulting protein (isoform 3) is shorter and has a distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC018878
      Consensus CDS
      CCDS58720.1
      UniProtKB/Swiss-Prot
      Q8NBZ7
      Related
      ENSP00000387096.1, ENST00000409032.5
      Conserved Domains (1) summary
      cl25409
      Location:1 → 224
      SDR; Short-chain dehydrogenases/reductases (SDR)

    3. NM_001377504.1 → NP_001364433.1  UDP-glucuronic acid decarboxylase 1 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC018878
      UniProtKB/TrEMBL
      A8K3Q3
      Conserved Domains (2) summary
      cd05230
      Location:94 → 343
      UGD_SDR_e; UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs
      pfam11803
      Location:4 → 83
      UXS1_N; UDP-glucuronate decarboxylase N-terminal

    4. NM_001377505.1 → NP_001364434.1  UDP-glucuronic acid decarboxylase 1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC018878
      UniProtKB/TrEMBL
      A8K3Q3
      Conserved Domains (2) summary
      cd05230
      Location:89 → 338
      UGD_SDR_e; UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs
      pfam11803
      Location:4 → 78
      UXS1_N; UDP-glucuronate decarboxylase N-terminal

    5. NM_001377506.1 → NP_001364435.1  UDP-glucuronic acid decarboxylase 1 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC018878
      UniProtKB/TrEMBL
      A8K3Q3
      Conserved Domains (1) summary
      cd05230
      Location:34 → 337
      UGD_SDR_e; UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs

    6. NM_001377507.1 → NP_001364436.1  UDP-glucuronic acid decarboxylase 1 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC018878
      UniProtKB/TrEMBL
      A8K3Q3
      Conserved Domains (2) summary
      cd05230
      Location:94 → 350
      UGD_SDR_e; UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs
      pfam11803
      Location:4 → 83
      UXS1_N; UDP-glucuronate decarboxylase N-terminal

    7. NM_001377508.1 → NP_001364437.1  UDP-glucuronic acid decarboxylase 1 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC018878
      UniProtKB/TrEMBL
      A8K3Q3
      Conserved Domains (2) summary
      cd05230
      Location:89 → 345
      UGD_SDR_e; UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs
      pfam11803
      Location:4 → 78
      UXS1_N; UDP-glucuronate decarboxylase N-terminal

    8. NM_001377509.1 → NP_001364438.1  UDP-glucuronic acid decarboxylase 1 isoform 9

      Status: VALIDATED

      Source sequence(s)
      AC018878
      Conserved Domains (1) summary
      cd05230
      Location:1 → 284
      UGD_SDR_e; UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs

    9. NM_025076.5 → NP_079352.2  UDP-glucuronic acid decarboxylase 1 isoform 2

      See identical proteins and their annotated locations for NP_079352.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.
      Source sequence(s)
      AC018878
      Consensus CDS
      CCDS46378.1
      UniProtKB/Swiss-Prot
      Q8NBX3, Q8NBZ7, Q9H5C2
      UniProtKB/TrEMBL
      A8K3Q3
      Related
      ENSP00000387019.3, ENST00000409501.7
      Conserved Domains (2) summary
      cd05230
      Location:89 → 392
      UGD_SDR_e; UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs
      pfam11803
      Location:4 → 78
      UXS1_N; UDP-glucuronate decarboxylase N-terminal

    RNA

    1. NR_045607.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an alternate internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC018878

    2. NR_165308.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC018878

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      106093311..106194301 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011511903.3 → XP_011510205.2  UDP-glucuronic acid decarboxylase 1 isoform X2

      UniProtKB/TrEMBL
      A8K3Q3

    2. XM_011511902.3 → XP_011510204.2  UDP-glucuronic acid decarboxylase 1 isoform X1

      UniProtKB/TrEMBL
      A8K3Q3

    3. XM_047445918.1 → XP_047301874.1  UDP-glucuronic acid decarboxylase 1 isoform X3

    4. XM_024453157.2 → XP_024308925.1  UDP-glucuronic acid decarboxylase 1 isoform X4

      Conserved Domains (1) summary
      cl25409
      Location:1 → 224
      SDR; Short-chain dehydrogenases/reductases (SDR)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      106554193..106655255 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054344036.1 → XP_054200011.1  UDP-glucuronic acid decarboxylase 1 isoform X2

    2. XM_054344035.1 → XP_054200010.1  UDP-glucuronic acid decarboxylase 1 isoform X1

    3. XM_054344039.1 → XP_054200014.1  UDP-glucuronic acid decarboxylase 1 isoform X3

    4. XM_054344038.1 → XP_054200013.1  UDP-glucuronic acid decarboxylase 1 isoform X6

      UniProtKB/TrEMBL
      B3KV61

    5. XM_054344037.1 → XP_054200012.1  UDP-glucuronic acid decarboxylase 1 isoform X5

    6. XM_054344040.1 → XP_054200015.1  UDP-glucuronic acid decarboxylase 1 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NBZ7.1 GenPept UniProtKB/Swiss-Prot:Q8NBZ7

    Gene LinkOut

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