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    PDSS2 decaprenyl diphosphate synthase subunit 2 [ Homo sapiens (human) ]

    Gene ID: 57107, updated on 6-Jun-2024

    Summary

    Official Symbol
    PDSS2provided by HGNC
    Official Full Name
    decaprenyl diphosphate synthase subunit 2provided by HGNC
    Primary source
    HGNC:HGNC:23041
    See related
    Ensembl:ENSG00000164494 MIM:610564; AllianceGenome:HGNC:23041
    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
    DLP1; COQ1B; hDLP1; COQ10D3; C6orf210; bA59I9.3
    Summary
    The protein encoded by this gene is an enzyme that synthesizes the prenyl side-chain of coenzyme Q, or ubiquinone, one of the key elements in the respiratory chain. The gene product catalyzes the formation of all trans-polyprenyl pyrophosphates from isopentyl diphosphate in the assembly of polyisoprenoid side chains, the first step in coenzyme Q biosynthesis. Defects in this gene are a cause of coenzyme Q10 deficiency.[provided by RefSeq, Oct 2009]
    Expression
    Ubiquitous expression in kidney (RPKM 6.5), adrenal (RPKM 5.0) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PDSS2 in Genome Data Viewer
    Location:
    6q21
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (107152562..107459564, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (108331503..108638499, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (107473766..107780768, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr6:107414410-107414593 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:107426683-107427338 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17437 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17438 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17439 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:107437205-107437968 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:107437969-107438734 Neighboring gene BEN domain containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24901 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24902 Neighboring gene RNA, U6 small nuclear 1299, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107470292-107470792 Neighboring gene ribosomal protein S24 pseudogene 12 Neighboring gene uncharacterized LOC124901366 Neighboring gene MPRA-validated peak6006 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:107780809-107781730 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17440 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17441 Neighboring gene sine oculis binding protein homolog Neighboring gene NANOG hESC enhancer GRCh37_chr6:107906855-107907747 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107925473-107925974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107925975-107926474 Neighboring gene Sharpr-MPRA regulatory region 6907 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107978733-107979310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107979311-107979887 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107989710-107990210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107990211-107990711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24906 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107994533-107995032 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:107995930-107996511 Neighboring gene uncharacterized LOC124901367 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:107996512-107997092

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Coenzyme Q10 deficiency, primary, 3 Compare labs

    EBI GWAS Catalog

    Description
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    contributes_to all-trans-decaprenyl-diphosphate synthase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables all-trans-nonaprenyl-diphosphate synthase (geranyl-diphosphate specific) activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables prenyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein heterodimerization activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in cerebellum development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in isoprenoid biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in isoprenoid biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of body fluid levels IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ubiquinone biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in ubiquinone biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in ubiquinone biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    part_of heterotetrameric polyprenyl diphosphate synthase complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
     
    part_of transferase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    all trans-polyprenyl-diphosphate synthase PDSS2
    Names
    all-trans-decaprenyl-diphosphate synthase subunit 2
    decaprenyl pyrophosphate synthase subunit 2
    decaprenyl pyrophosphate synthetase subunit 2
    prenyl (decaprenyl) diphosphate synthase, subunit 2
    solanesyl-diphosphate synthase subunit 2
    subunit 2 of decaprenyl diphosphate synthase
    NP_065114.3
    XP_011534258.1
    XP_011534259.1
    XP_011534260.1
    XP_011534261.1
    XP_011534262.1
    XP_011534263.1
    XP_011534265.1
    XP_016866571.1
    XP_047275052.1
    XP_047275053.1
    XP_047275054.1
    XP_047275055.1
    XP_047275056.1
    XP_047275057.1
    XP_054211939.1
    XP_054211940.1
    XP_054211941.1
    XP_054211942.1
    XP_054211943.1
    XP_054211944.1
    XP_054211945.1
    XP_054211946.1
    XP_054211947.1
    XP_054211948.1
    XP_054211949.1
    XP_054211950.1
    XP_054211951.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_013033.1 RefSeqGene

      Range
      5012..312014
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_020381.4NP_065114.3  all trans-polyprenyl-diphosphate synthase PDSS2

      See identical proteins and their annotated locations for NP_065114.3

      Status: REVIEWED

      Source sequence(s)
      AL832290, BC039906, DC341808
      Consensus CDS
      CCDS5059.1
      UniProtKB/Swiss-Prot
      Q33DR4, Q4G158, Q5VU38, Q5VU39, Q86YH6, Q9NR58
      UniProtKB/TrEMBL
      B2RE48
      Related
      ENSP00000358033.4, ENST00000369037.9
      Conserved Domains (1) summary
      cl00210
      Location:68399
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

    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
      107152562..107459564 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011535960.4XP_011534262.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X8

      Conserved Domains (1) summary
      cl00210
      Location:5329
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1
    2. XM_047419100.1XP_047275056.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X12

    3. XM_047419098.1XP_047275054.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X9

      UniProtKB/TrEMBL
      B4DWD3
    4. XM_047419101.1XP_047275057.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X13

    5. XM_047419099.1XP_047275055.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X10

    6. XM_047419097.1XP_047275053.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X7

      UniProtKB/TrEMBL
      B2RE48
    7. XM_011535958.4XP_011534260.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X3

      UniProtKB/TrEMBL
      B2RE48
      Conserved Domains (1) summary
      cl00210
      Location:64420
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1
    8. XM_011535961.4XP_011534263.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X11

      See identical proteins and their annotated locations for XP_011534263.1

      UniProtKB/TrEMBL
      B4DKU5
      Conserved Domains (1) summary
      cl00210
      Location:64225
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1
    9. XM_047419096.1XP_047275052.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X4

    10. XM_011535959.4XP_011534261.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X6

      UniProtKB/TrEMBL
      B2RE48
      Conserved Domains (1) summary
      cl00210
      Location:68355
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1
    11. XM_011535957.4XP_011534259.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X2

      Conserved Domains (1) summary
      cl00210
      Location:68421
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1
    12. XM_011535956.4XP_011534258.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X1

      UniProtKB/TrEMBL
      B2RE48
      Conserved Domains (1) summary
      cl00210
      Location:68465
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1
    13. XM_017011082.3XP_016866571.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X5

      UniProtKB/TrEMBL
      B2RE48
    14. XM_011535963.4XP_011534265.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X14

      UniProtKB/Swiss-Prot
      Q86YH6
      Related
      ENSP00000358027.4, ENST00000369031.4
      Conserved Domains (1) summary
      cl00210
      Location:68208
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      108331503..108638499 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355971.1XP_054211946.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X8

    2. XM_054355972.1XP_054211947.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X9

      UniProtKB/TrEMBL
      B4DWD3
    3. XM_054355975.1XP_054211950.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X13

    4. XM_054355973.1XP_054211948.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X10

    5. XM_054355970.1XP_054211945.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X7

      UniProtKB/TrEMBL
      B2RE48
    6. XM_054355966.1XP_054211941.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X3

      UniProtKB/TrEMBL
      B2RE48
    7. XM_054355974.1XP_054211949.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X11

      UniProtKB/TrEMBL
      B4DKU5
    8. XM_054355967.1XP_054211942.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X4

    9. XM_054355969.1XP_054211944.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X6

      UniProtKB/TrEMBL
      B2RE48
    10. XM_054355965.1XP_054211940.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X2

    11. XM_054355964.1XP_054211939.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X1

      UniProtKB/TrEMBL
      B2RE48
    12. XM_054355968.1XP_054211943.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X5

      UniProtKB/TrEMBL
      B2RE48
    13. XM_054355976.1XP_054211951.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X14