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    IDI1 isopentenyl-diphosphate delta isomerase 1 [ Homo sapiens (human) ]

    Gene ID: 3422, updated on 27-Nov-2024

    Summary

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    Official Symbol
    IDI1provided by HGNC
    Official Full Name
    isopentenyl-diphosphate delta isomerase 1provided by HGNC
    Primary source
    HGNC:HGNC:5387
    See related
    Ensembl:ENSG00000067064 MIM:604055; AllianceGenome:HGNC:5387
    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
    IPP1; IPPI1
    Summary
    IDI1 encodes a peroxisomally-localized enzyme that catalyzes the interconversion of isopentenyl diphosphate (IPP) to its highly electrophilic isomer, dimethylallyl diphosphate (DMAPP), which are the substrates for the successive reaction that results in the synthesis of farnesyl diphosphate and, ultimately, cholesterol. It has been shown in peroxisomal deficiency diseases such as Zellweger syndrome and neonatal adrenoleukodystrophy that there is reduction in IPP isomerase activity. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in bone marrow (RPKM 23.9), brain (RPKM 23.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See IDI1 in Genome Data Viewer
    Location:
    10p15.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (1039152..1056704, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (1036296..1053319, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (1085092..1102644, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene La ribonucleoprotein 4B Neighboring gene keratinocyte proline-rich protein-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:989167-989668 Neighboring gene LARP4B divergent transcript Neighboring gene Sharpr-MPRA regulatory region 2332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1036121-1037016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1050745-1051244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1054558-1055058 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1055059-1055559 Neighboring gene GTP binding protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2893 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2894 Neighboring gene IDI2 antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:1088961-1090160 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr10:1094306-1094836 and GRCh37_chr10:1094837-1095366 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:1095367-1095896 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2897 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2067 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2898 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2899 Neighboring gene isopentenyl-diphosphate delta isomerase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1130525-1131024 Neighboring gene WD repeat domain 37 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:1141578-1142777 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:1148139-1148671 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:1155609-1156808 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1163429-1163930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1166460-1167101 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:1167102-1167742 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1196487-1196986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1199503-1200004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1200005-1200504 Neighboring gene uncharacterized LOC105376344 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:1201744-1202634 Neighboring gene long intergenic non-protein coding RNA 200

    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. A human promyelocyte mRNA transiently induced by TPA is homologous to yeast IPP isomerase. Xuan JW, et al. Genomics, 1994 Mar 1. PMID 8020941
    2. Isopentenyl diphosphate isomerase, a cholesterol synthesizing enzyme, is localized in Lewy bodies. Nakamura K, et al. Neuropathology, 2015 Oct. PMID 25950736
    3. Copper induces the expression of cholesterogenic genes in human macrophages. Svensson PA, et al. Atherosclerosis, 2003 Jul. PMID 12860252
    4. Idi1 and Hmgcs2 Are Affected by Stretch in HL-1 Atrial Myocytes. Fang CY, et al. Int J Mol Sci, 2018 Dec 18. PMID 30567295, Free PMC Article
    5. The crystal structure of human isopentenyl diphosphate isomerase at 1.7 A resolution reveals its catalytic mechanism in isoprenoid biosynthesis. Zheng W, et al. J Mol Biol, 2007 Mar 9. PMID 17250851

    See all (52) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Canonical pathway analysis, using Ingenuity Pathway Analysis software, revealed that the only genes in the "superpathway of cholesterol biosynthesis" were Idi1 (upregulated) and Hmgcs2 (downregulated). The Idi1 and Hmgcs2 genes have regulatory roles in atrial lipotoxic myopathy associated with atrial enlargement
      Title: Idi1 and Hmgcs2 Are Affected by Stretch in HL-1 Atrial Myocytes.
    2. The present findings suggest that IDI1 and IDI2 may be associated with the production of cholesterol metabolites in neurons, leading to alpha-synuclein aggregation during the process of Lewy body formation.
      Title: Isopentenyl diphosphate isomerase, a cholesterol synthesizing enzyme, is localized in Lewy bodies.
    3. Within the 40-kb region on 10p15.3 subtelomere, which harbours two genes encoding isopentenyl diphosphate isomerase 1 (IDI1) and IDI2, there was found a segmental copy-number gain in a large proportion of sporadic amyotrophic lateral sclerosis patients.
      Title: Segmental copy-number gain within the region of isopentenyl diphosphate isomerase genes in sporadic amyotrophic lateral sclerosis.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    5. only one of the two isoforms (IDI1) is highly conserved, ubiquitously expressed and most likely responsible for housekeeping isomerase activity
      Title: Isopentenyl-diphosphate isomerases in human and mouse: evolutionary analysis of a mammalian gene duplication.
    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)

    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 isopentenyl-diphosphate delta-isomerase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables isopentenyl-diphosphate delta-isomerase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables magnesium ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables manganese ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cholesterol biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in dimethylallyl diphosphate biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in isopentenyl diphosphate biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in isoprenoid biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in peroxisome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    isopentenyl-diphosphate Delta-isomerase 1
    Names
    IPP isomerase 1
    isopentenyl diphosphate dimethylallyl diphosphate isomerase 1
    isopentenyl pyrophosphate isomerase 1
    NP_001304884.1
    NP_001304885.1
    NP_001304886.1
    NP_004499.2
    XP_016871680.1
    XP_024303747.1
    XP_024303748.1
    XP_047281132.1
    XP_054221728.1
    XP_054221729.1
    XP_054221730.1
    XP_054221731.1

    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_001317955.2 → NP_001304884.1  isopentenyl-diphosphate Delta-isomerase 1 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains alternate 5' exon structure, and it thus differs in the 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a. Both variants 2 and 3 encode isoform b.
      Source sequence(s)
      AC022536, AI305202, BC006999, BC057827, BX110963, DB479813, HY182673
      Consensus CDS
      CCDS91201.1
      UniProtKB/Swiss-Prot
      B4E155, Q13907, Q32Q13, Q53GQ6, Q86U81, Q8WUX8, Q96IZ4, Q9BQ74
      UniProtKB/TrEMBL
      A0A8Q3WKR8
      Conserved Domains (1) summary
      cl00447
      Location:22 → 228
      Nudix_Hydrolase; Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ ...

    2. NM_001317956.2 → NP_001304885.1  isopentenyl-diphosphate Delta-isomerase 1 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains an alternate 5' terminal exon, and it thus differs in the 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a. Both variants 2 and 3 encode isoform b.
      Source sequence(s)
      AC022536, AI305202, BC006999, BC057827, BI600349, BX110963, CD251816, DA185312
      Consensus CDS
      CCDS91201.1
      UniProtKB/Swiss-Prot
      B4E155, Q13907, Q32Q13, Q53GQ6, Q86U81, Q8WUX8, Q96IZ4, Q9BQ74
      UniProtKB/TrEMBL
      A0A8Q3WKR8
      Related
      ENSP00000401879.2, ENST00000429642.2
      Conserved Domains (1) summary
      cl00447
      Location:22 → 228
      Nudix_Hydrolase; Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ ...

    3. NM_001317957.2 → NP_001304886.1  isopentenyl-diphosphate Delta-isomerase 1 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains an alternate 5' terminal exon and lacks an exon in the 5' coding region, and it thus differs in the 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (c) has a distinct N-terminus and is shorter than isoform a.
      Source sequence(s)
      AC022536, AI305202, BC006999, BC057827, BI600349, BX110963, DA185312, DA792902
      UniProtKB/Swiss-Prot
      Q13907
      Conserved Domains (1) summary
      cl00447
      Location:18 → 198
      Nudix_Hydrolase; Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ ...

    4. NM_004508.4 → NP_004499.2  isopentenyl-diphosphate Delta-isomerase 1 isoform a

      See identical proteins and their annotated locations for NP_004499.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AC022536
      Consensus CDS
      CCDS7056.1
      UniProtKB/Swiss-Prot
      Q13907
      Related
      ENSP00000370748.3, ENST00000381344.8
      Conserved Domains (2) summary
      COG1443
      Location:76 → 265
      Idi; Isopentenyldiphosphate isomerase [Lipid transport and metabolism]
      cl00447
      Location:78 → 284
      Nudix_Hydrolase; Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ ...

    RNA

    1. NR_134300.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) contains alternate 5' exon structure and lacks an internal exon, compared to variant 1. This variant is represented as non-coding because it lacks an ORF that is in-frame with the supported coding region.
      Source sequence(s)
      AC022536, AI305202, BC006999, BX110963, DA842794, DB479813, HY182673

    2. NR_134301.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) 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)
      AI305202, AK311110, BC006999, BX110963, CN481934, DA289206

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      1039152..1056704 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047425176.1 → XP_047281132.1  isopentenyl-diphosphate Delta-isomerase 1 isoform X1

      UniProtKB/TrEMBL
      A0A8Q3WKR8

    2. XM_024447979.2 → XP_024303747.1  isopentenyl-diphosphate Delta-isomerase 1 isoform X3

      Conserved Domains (1) summary
      cl00447
      Location:13 → 191
      Nudix_Hydrolase; Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ ...

    3. XM_017016191.3 → XP_016871680.1  isopentenyl-diphosphate Delta-isomerase 1 isoform X2

      UniProtKB/Swiss-Prot
      B4E155, Q13907, Q32Q13, Q53GQ6, Q86U81, Q8WUX8, Q96IZ4, Q9BQ74

    4. XM_024447980.2 → XP_024303748.1  isopentenyl-diphosphate Delta-isomerase 1 isoform X4

      Conserved Domains (1) summary
      cl00447
      Location:1 → 187
      Nudix_Hydrolase; Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      1036296..1053319 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054365753.1 → XP_054221728.1  isopentenyl-diphosphate Delta-isomerase 1 isoform X1

      UniProtKB/TrEMBL
      A0A8Q3WKR8

    2. XM_054365755.1 → XP_054221730.1  isopentenyl-diphosphate Delta-isomerase 1 isoform X3

    3. XM_054365754.1 → XP_054221729.1  isopentenyl-diphosphate Delta-isomerase 1 isoform X2

    4. XM_054365756.1 → XP_054221731.1  isopentenyl-diphosphate Delta-isomerase 1 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q13907.2 GenPept UniProtKB/Swiss-Prot:Q13907

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