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... See more...

Aliases for IDI1 Gene

Aliases for IDI1 Gene

  • Isopentenyl-Diphosphate Delta Isomerase 1 2 3 5
  • Isopentenyl-Diphosphate Delta-Isomerase 1 3 4
  • Isopentenyl Pyrophosphate Isomerase 1 3 4
  • IPP Isomerase 1 3 4
  • EC 5.3.3.2 4 52
  • IPPI1 3 4
  • Isopentenyl Diphosphate Dimethylallyl Diphosphate Isomerase 1 3
  • Isopentenyl-Diphosphate Delta Isomerase 2
  • IPP Isomerase 2
  • IPP1 3

External Ids for IDI1 Gene

Previous GeneCards Identifiers for IDI1 Gene

  • GC10M001056
  • GC10M001075

Summaries for IDI1 Gene

Entrez Gene Summary for IDI1 Gene

  • 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]

GeneCards Summary for IDI1 Gene

IDI1 (Isopentenyl-Diphosphate Delta Isomerase 1) is a Protein Coding gene. Diseases associated with IDI1 include Zellweger Syndrome and Neonatal Adrenoleukodystrophy. Among its related pathways are Terpenoid backbone biosynthesis and Regulation of cholesterol biosynthesis by SREBP (SREBF). Gene Ontology (GO) annotations related to this gene include hydrolase activity and manganese ion binding. An important paralog of this gene is IDI2.

UniProtKB/Swiss-Prot Summary for IDI1 Gene

  • Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP).

Additional gene information for IDI1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for IDI1 Gene

Genomics for IDI1 Gene

GeneHancer (GH) Regulatory Elements for IDI1 Gene

Promoters and enhancers for IDI1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10J001054 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 500.7 +0.1 141 4.4 HNRNPK ZBTB40 ZNF217 EP300 NRF1 TCF12 POLR2G PHF8 JUND FOS WDR37 IDI1 lnc-IDI1-2 IDI2 IDI2-AS1
GH10J001042 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 500.4 +9.7 9653 8.9 FOXK2 ZBTB40 ZNF217 EP300 SIN3A TCF12 NRF1 POLR2G SP1 GTF2E2 WDR37 lnc-IDI2-1 IDI1 IDI2 IDI2-AS1 ENSG00000205740 GTPBP4 LARP4B lnc-IDI1-2 piR-50437-033
GH10J000546 Enhancer 1.4 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 4.9 +509.3 509298 2.8 ZNF217 ZIC2 CUX1 GATAD2B CTBP1 MXI1 ZNF341 SIN3A ESRRA ELK1 DIP2C IDI1 TUBB8 piR-49402 HSALNG0075491
GH10J000554 Enhancer 1 Ensembl ENCODE dbSUPER 4.9 +498.5 498498 8.4 NRF1 USF1 ZNF10 ZIC2 FOS JUND SCRT1 PRDM6 ZNF18 GLIS1 DIP2C ENSG00000225140 IDI1 piR-49402 HSALNG0075491
GH10J000575 Enhancer 0.5 Ensembl dbSUPER 5.1 +480.9 480899 3.2 SCRT1 SCRT2 ENSG00000225140 IDI1 piR-49402 HSALNG0075491 DIP2C
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around IDI1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for IDI1

Top Transcription factor binding sites by QIAGEN in the IDI1 gene promoter:
  • aMEF-2
  • CUTL1
  • Elk-1
  • Hlf
  • Lhx3a
  • LHX3b
  • NF-kappaB
  • NF-kappaB1
  • NF-kappaB2

Genomic Locations for IDI1 Gene

Genomic Locations for IDI1 Gene
chr10:1,039,152-1,056,699
(GRCh38/hg38)
Size:
17,548 bases
Orientation:
Minus strand
chr10:1,085,848-1,095,110
(GRCh37/hg19)
Size:
9,263 bases
Orientation:
Minus strand

Genomic View for IDI1 Gene

Genes around IDI1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
IDI1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for IDI1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for IDI1 Gene

Proteins for IDI1 Gene

  • Protein details for IDI1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13907-IDI1_HUMAN
    Recommended name:
    Isopentenyl-diphosphate Delta-isomerase 1
    Protein Accession:
    Q13907
    Secondary Accessions:
    • B4E155
    • Q32Q13
    • Q53GQ6
    • Q86U81
    • Q8WUX8
    • Q96IZ4
    • Q9BQ74

    Protein attributes for IDI1 Gene

    Size:
    227 amino acids
    Molecular mass:
    26319 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Monomer.
    SequenceCaution:
    • Sequence=AAH57827.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAK29357.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAK49434.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAK49435.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAP35407.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAA34890.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for IDI1 Gene

    Alternative splice isoforms for IDI1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for IDI1 Gene

Selected DME Specific Peptides for IDI1 Gene

Q13907:
  • FLFKWWD
  • LLLQQRS
  • IGAETKKNCHLNENIE
  • NTCCSHP
  • KNVTLNPDPNEIKSYCYV
  • EEVPPEEINYLTRIHYKAQSD

Post-translational modifications for IDI1 Gene

  • Ubiquitination at Lys113, Lys169, Lys180, Lys192, and Lys223
  • Modification sites at PhosphoSitePlus

Domains & Families for IDI1 Gene

Gene Families for IDI1 Gene

IUPHAR :
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for IDI1 Gene

Blocks:
  • NUDIX hydrolase
  • Isopentenyl-diphosphate delta-isomerase
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for IDI1 Gene

GenScript: Design optimal peptide antigens:
  • Isopentenyl pyrophosphate isomerase 1 (IDI1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q13907

UniProtKB/Swiss-Prot:

IDI1_HUMAN :
  • Belongs to the IPP isomerase type 1 family.
Family:
  • Belongs to the IPP isomerase type 1 family.
genes like me logo Genes that share domains with IDI1: view

Function for IDI1 Gene

Molecular function for IDI1 Gene

UniProtKB/Swiss-Prot Function:
Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=isopentenyl diphosphate = dimethylallyl diphosphate; Xref=Rhea:RHEA:23284, ChEBI:CHEBI:57623, ChEBI:CHEBI:128769; EC=5.3.3.2; Evidence=. ;.

Enzyme Numbers (IUBMB) for IDI1 Gene

Gene Ontology (GO) - Molecular Function for IDI1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004452 isopentenyl-diphosphate delta-isomerase activity IBA 21873635
GO:0016787 hydrolase activity IEA --
GO:0016853 isomerase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with IDI1: view
genes like me logo Genes that share phenotypes with IDI1: view

Animal Models for IDI1 Gene

MGI Knock Outs for IDI1:
  • Idi1 Idi1<tm1b(EUCOMM)Hmgu>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for IDI1

Clone Products

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for IDI1 Gene

Localization for IDI1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for IDI1 Gene

Peroxisome.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for IDI1 gene
Compartment Confidence
peroxisome 5
cytosol 5
mitochondrion 3
nucleus 3
extracellular 2
plasma membrane 1
cytoskeleton 1
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for IDI1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005777 peroxisome IEA,IDA 17180682
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with IDI1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for IDI1 Gene

Pathways & Interactions for IDI1 Gene

genes like me logo Genes that share pathways with IDI1: view

UniProtKB/Swiss-Prot Q13907-IDI1_HUMAN

  • Pathway: Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from isopentenyl diphosphate: step 1/1.

Gene Ontology (GO) - Biological Process for IDI1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006694 steroid biosynthetic process IEA --
GO:0006695 cholesterol biosynthetic process TAS --
GO:0008202 steroid metabolic process IEA --
GO:0008203 cholesterol metabolic process IEA --
genes like me logo Genes that share ontologies with IDI1: view

No data available for SIGNOR curated interactions for IDI1 Gene

Drugs & Compounds for IDI1 Gene

(6) Drugs for IDI1 Gene - From: DrugBank, DGIdb, IUPHAR, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Magnesium Approved, Experimental, Investigational Pharma 0
DIMETHYLALLYL DIPHOSPHATE Experimental Pharma Competitive, Inhibitor, Target 0
Isopentenyl pyrophosphate Experimental Pharma 0
NE21650 Pharma Inhibition, Inhibitor 0

(1) Additional Compounds for IDI1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with IDI1: view

Transcripts for IDI1 Gene

mRNA/cDNA for IDI1 Gene

4 REFSEQ mRNAs :
28 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for IDI1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for IDI1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b
SP1: -
SP2: - - -
SP3: - -
SP4:

Relevant External Links for IDI1 Gene

GeneLoc Exon Structure for
IDI1

Expression for IDI1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for IDI1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for IDI1 Gene

This gene is overexpressed in Fetal testis (21.1) and Fetal Liver (18.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for IDI1 Gene



Protein tissue co-expression partners for IDI1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for IDI1

SOURCE GeneReport for Unigene cluster for IDI1 Gene:

Hs.283652

Evidence on tissue expression from TISSUES for IDI1 Gene

  • Nervous system(4.8)
  • Liver(4.7)
  • Skin(4.5)
  • Bone marrow(4.4)
  • Kidney(4.3)
  • Blood(2.9)
  • Lung(2.9)
genes like me logo Genes that share expression patterns with IDI1: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for IDI1 Gene

Orthologs for IDI1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for IDI1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia IDI1 31 30
  • 99.06 (n)
OneToOne
dog
(Canis familiaris)
Mammalia IDI1 31 30
  • 87.2 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia IDI1 31
  • 85 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Idi1 17 31 30
  • 80.68 (n)
rat
(Rattus norvegicus)
Mammalia Idi1 30
  • 79.95 (n)
oppossum
(Monodelphis domestica)
Mammalia IDI1 31
  • 79 (a)
OneToOne
cow
(Bos Taurus)
Mammalia IDI1 31 30
  • 76.88 (n)
OneToOne
chicken
(Gallus gallus)
Aves -- 31
  • 81 (a)
OneToMany
IDI1 30
  • 69.63 (n)
lizard
(Anolis carolinensis)
Reptilia -- 31
  • 81 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia idi1 30
  • 71.51 (n)
Str.12004 30
zebrafish
(Danio rerio)
Actinopterygii idi1 31 30
  • 69.46 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001704 30
  • 55.3 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG5919 31 32 30
  • 51.32 (n)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea K06H7.9 32
  • 38 (a)
idi-1 31
  • 37 (a)
OneToMany
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F00924g 30
  • 60 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes IDI1 33 31 30
  • 55.97 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ADL268C 30
  • 52.12 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons IPP2 30
  • 57.86 (n)
rice
(Oryza sativa)
Liliopsida Os07g0546000 30
  • 55.09 (n)
Os.18877 30
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes idi1 30
  • 57.34 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU07719 30
  • 55.11 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9971 31
  • 50 (a)
OneToMany
Cin.3020 30
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3020 30
Species where no ortholog for IDI1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for IDI1 Gene

ENSEMBL:
Gene Tree for IDI1 (if available)
TreeFam:
Gene Tree for IDI1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for IDI1: view image

Paralogs for IDI1 Gene

Paralogs for IDI1 Gene

(1) SIMAP similar genes for IDI1 Gene using alignment to 3 proteins:

  • IDI1_HUMAN
  • C9JD53_HUMAN
  • C9JKM8_HUMAN

Pseudogenes.org Pseudogenes for IDI1 Gene

genes like me logo Genes that share paralogs with IDI1: view

Variants for IDI1 Gene

Additional dbSNP identifiers (rs#s) for IDI1 Gene

Structural Variations from Database of Genomic Variants (DGV) for IDI1 Gene

Variant ID Type Subtype PubMed ID
esv2156728 CNV deletion 18987734
esv2483699 CNV deletion 19546169
esv2660097 CNV deletion 23128226
esv2729373 CNV deletion 23290073
esv2729384 CNV deletion 23290073
esv2729395 CNV deletion 23290073
esv3891735 CNV gain 25118596
esv990965 CNV deletion 20482838
nsv1046220 CNV gain 25217958
nsv1068263 CNV deletion 25765185
nsv512136 CNV loss 21212237
nsv549765 CNV gain 21841781
nsv5532 CNV deletion 18451855
nsv951231 CNV duplication 24416366

Variation tolerance for IDI1 Gene

Residual Variation Intolerance Score: 38.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.07; 37.91% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for IDI1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
IDI1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for IDI1 Gene

Disorders for IDI1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for IDI1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
zellweger syndrome
  • zs
neonatal adrenoleukodystrophy
  • adrenoleukodystrophy autosomal neonatal form
pelizaeus-merzbacher disease
  • pmd
- elite association - COSMIC cancer census association via MalaCards
Search IDI1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for IDI1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with IDI1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for IDI1 Gene

Publications for IDI1 Gene

  1. The crystal structure of human isopentenyl diphosphate isomerase at 1.7 A resolution reveals its catalytic mechanism in isoprenoid biosynthesis. (PMID: 17250851) Zheng W … Rao Z (Journal of molecular biology 2007) 3 4 23 54
  2. Human isopentenyl diphosphate: dimethylallyl diphosphate isomerase: overproduction, purification, and characterization. (PMID: 8806705) Hahn FM … Poulter CD (Archives of biochemistry and biophysics 1996) 3 4 23 54
  3. A human promyelocyte mRNA transiently induced by TPA is homologous to yeast IPP isomerase. (PMID: 8020941) Xuan JW … Denhardt DT (Genomics 1994) 2 3 4 54
  4. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 41 54
  5. Multiple genetic variants along candidate pathways influence plasma high-density lipoprotein cholesterol concentrations. (PMID: 18660489) Lu Y … Boer JM (Journal of lipid research 2008) 3 41 54

Products for IDI1 Gene

Sources for IDI1 Gene