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Aliases for CYP39A1 Gene

Aliases for CYP39A1 Gene

  • Cytochrome P450 Family 39 Subfamily A Member 1 2 3 5
  • Cytochrome P450, Subfamily XXXIX (Oxysterol 7 Alpha-Hydroxylase), Polypeptide 1 2 3
  • Cytochrome P450, Family 39, Subfamily A, Polypeptide 1 2 3
  • 24-Hydroxycholesterol 7-Alpha-Hydroxylase 3
  • Oxysterol 7-Alpha-Hydroxylase 4
  • Cytochrome P450 39A1 4
  • EC 4
  • HCYP39A1 4

External Ids for CYP39A1 Gene

Previous GeneCards Identifiers for CYP39A1 Gene

  • GC06M046519
  • GC06M046564
  • GC06M046625
  • GC06M046240

Summaries for CYP39A1 Gene

Entrez Gene Summary for CYP39A1 Gene

  • This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This endoplasmic reticulum protein is involved in the conversion of cholesterol to bile acids. Its substrates include the oxysterols 25-hydroxycholesterol, 27-hydroxycholesterol and 24-hydroxycholesterol. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

GeneCards Summary for CYP39A1 Gene

CYP39A1 (Cytochrome P450 Family 39 Subfamily A Member 1) is a Protein Coding gene. Among its related pathways are Cytochrome P450 - arranged by substrate type and Metabolism. Gene Ontology (GO) annotations related to this gene include iron ion binding and oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen. An important paralog of this gene is CYP8B1.

UniProtKB/Swiss-Prot for CYP39A1 Gene

  • Involved in the bile acid metabolism. Has a preference for 24-hydroxycholesterol, and converts it into a 7-alpha-hydroxylated product.

Gene Wiki entry for CYP39A1 Gene

Additional gene information for CYP39A1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CYP39A1 Gene

Genomics for CYP39A1 Gene

GeneHancer (GH) Regulatory Elements for CYP39A1 Gene

Promoters and enhancers for CYP39A1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J046651 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.7 +0.3 316 2.6 PKNOX1 ATF1 FOXA2 ARID4B SIN3A DMAP1 ZNF2 ZNF48 YY1 ETS1 SLC25A27 CYP39A1 TDRD6 PLA2G7 RCAN2
GH06J046734 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 21 -82.1 -82056 1.8 ZSCAN4 KLF17 ZNF2 RAD21 ZNF335 ZNF121 GLIS2 ZNF366 EGR2 SP3 PLA2G7 SLC25A27 TDRD6 CYP39A1 CD2AP GC06P046731
GH06J046325 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 9.9 +327.0 326996 0.9 INSM2 KLF17 FEZF1 ZNF2 ZNF366 ZSCAN5C ATF7 ZNF280D ZNF362 TSHZ1 RCAN2 CYP39A1 LOC101926915 RPL36P10
GH06J047403 Enhancer 0.8 ENCODE 12.7 -752.9 -752937 4.8 FOXA2 NFIB FEZF1 KLF14 ZNF366 FOS EGR2 RXRA CEBPB REST CD2AP ADGRF2 CYP39A1 LOC105375082 ENSG00000270761
GH06J045922 Enhancer 0.8 Ensembl 10.4 +729.9 729946 0.2 FOXA2 RB1 RAD21 ZNF366 ZNF143 RUNX3 EGR2 ZNF654 RXRA REST CLIC5 CYP39A1 LOC105375078 GC06M045521
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CYP39A1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CYP39A1 gene promoter:
  • PPAR-alpha
  • Sox5
  • MIF-1
  • CUTL1
  • HOXA3
  • LyF-1
  • Cart-1
  • STAT5A
  • FAC1
  • Pax-4a

Genomic Locations for CYP39A1 Gene

Genomic Locations for CYP39A1 Gene
103,268 bases
Minus strand
103,079 bases
Minus strand

Genomic View for CYP39A1 Gene

Genes around CYP39A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CYP39A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CYP39A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CYP39A1 Gene

Proteins for CYP39A1 Gene

  • Protein details for CYP39A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    24-hydroxycholesterol 7-alpha-hydroxylase
    Protein Accession:
    Secondary Accessions:
    • Q5VTT0
    • Q96FW5

    Protein attributes for CYP39A1 Gene

    469 amino acids
    Molecular mass:
    54116 Da
    Name=heme; Xref=ChEBI:CHEBI:30413;
    Quaternary structure:
    No Data Available

neXtProt entry for CYP39A1 Gene

Post-translational modifications for CYP39A1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CYP39A1 Gene

Domains & Families for CYP39A1 Gene

Gene Families for CYP39A1 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted membrane proteins

Protein Domains for CYP39A1 Gene

Suggested Antigen Peptide Sequences for CYP39A1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the cytochrome P450 family.
  • Belongs to the cytochrome P450 family.
genes like me logo Genes that share domains with CYP39A1: view

Function for CYP39A1 Gene

Molecular function for CYP39A1 Gene

UniProtKB/Swiss-Prot Function:
Involved in the bile acid metabolism. Has a preference for 24-hydroxycholesterol, and converts it into a 7-alpha-hydroxylated product.
UniProtKB/Swiss-Prot CatalyticActivity:
(24S)-cholest-5-ene-3-beta,24-diol + [reduced NADPH--hemoprotein reductase] + O(2) = (24S)-cholest-5-ene-3-beta,7-alpha,24-triol + [oxidized NADPH--hemoprotein reductase] + H(2)O.

Enzyme Numbers (IUBMB) for CYP39A1 Gene

Gene Ontology (GO) - Molecular Function for CYP39A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005506 iron ion binding IEA --
GO:0008387 steroid 7-alpha-hydroxylase activity IEA --
GO:0008395 steroid hydroxylase activity IBA --
GO:0008396 oxysterol 7-alpha-hydroxylase activity IEA,TAS --
GO:0016491 oxidoreductase activity IEA --
genes like me logo Genes that share ontologies with CYP39A1: view
genes like me logo Genes that share phenotypes with CYP39A1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for CYP39A1

miRNA for CYP39A1 Gene

miRTarBase miRNAs that target CYP39A1

Clone Products

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CYP39A1 Gene

Localization for CYP39A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CYP39A1 Gene

Endoplasmic reticulum membrane; Peripheral membrane protein. Microsome membrane; Peripheral membrane protein.

Subcellular locations from

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 CYP39A1 gene
Compartment Confidence
endoplasmic reticulum 5
golgi apparatus 2
peroxisome 1

Gene Ontology (GO) - Cellular Components for CYP39A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0016020 membrane IEA --
GO:0031090 organelle membrane IEA --
GO:0043231 intracellular membrane-bounded organelle TAS 10748047
genes like me logo Genes that share ontologies with CYP39A1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CYP39A1 Gene

Pathways & Interactions for CYP39A1 Gene

genes like me logo Genes that share pathways with CYP39A1: view

Pathways by source for CYP39A1 Gene

Gene Ontology (GO) - Biological Process for CYP39A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006699 bile acid biosynthetic process TAS,IEA --
GO:0006707 cholesterol catabolic process IEA --
GO:0007586 digestion TAS 10748047
GO:0008202 steroid metabolic process IEA --
genes like me logo Genes that share ontologies with CYP39A1: view

No data available for SIGNOR curated interactions for CYP39A1 Gene

Drugs & Compounds for CYP39A1 Gene

(3) Drugs for CYP39A1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Oxygen Approved, Vet_approved Pharma 0
Water Approved Pharma 0
heme Pharma Agonist 0

(4) Additional Compounds for CYP39A1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (24R)-24-Hydroxycholesterol
  • 24(R)-Hydoxycholesterol
  • 5-Cholesten-3-beta,24(R)-diol
  • Cholest-5-ene-3,24-diol
  • Cholest-5-ene-3-beta,24-diol
  • (24R)-Cholest-5-ene 3-b,7-a,24-triol
  • (24R)-Cholest-5-ene-3beta,7alpha,24-triol
  • 5a-Cholesta-7,24-dien-3-b-ol
  • 5a-Cholesta-7,24-dien-3-beta-ol
  • beta-Nicotinamide adenine dinucleotide phosphate
  • NADP+
  • Nicotinamide adenine dinucleotide phosphate
  • Oxidized nicotinamide-adenine dinucleotide phosphate
  • TPN
  • 2'-(Dihydrogen phosphate) 5'-(trihydrogen pyrophosphate) adenosine 5'-ester with 1,4-dihydro-1-b-D-ribofuranosylnicotinamide
  • 2'-(Dihydrogen phosphate) 5'-(trihydrogen pyrophosphate) adenosine 5'-ester with 1,4-dihydro-1-beta-delta-ribofuranosylnicotinamide
  • Adenosine 5'-(trihydrogen diphosphate) 2'-(dihydrogen phosphate) p'-5'-ester with 1,4-dihydro-1-beta-D-ribofuranosyl-3-pyridinecarboxamide
  • Adenosine 5'-(trihydrogen diphosphate) 2'-(dihydrogen phosphate) p'-5'-ester with 1,4-dihydro-1-beta-delta-ribofuranosyl-3-pyridinecarboxamide
  • b-NADPH
genes like me logo Genes that share compounds with CYP39A1: view

Transcripts for CYP39A1 Gene

Unigene Clusters for CYP39A1 Gene

Cytochrome P450, family 39, subfamily A, polypeptide 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CYP39A1 Gene

No ASD Table

Relevant External Links for CYP39A1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CYP39A1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CYP39A1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CYP39A1 Gene

This gene is overexpressed in Liver (x9.0).

Protein differential expression in normal tissues from HIPED for CYP39A1 Gene

This gene is overexpressed in Kidney (60.5) and Heart (6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CYP39A1 Gene

Protein tissue co-expression partners for CYP39A1 Gene

NURSA nuclear receptor signaling pathways regulating expression of CYP39A1 Gene:


SOURCE GeneReport for Unigene cluster for CYP39A1 Gene:


mRNA Expression by UniProt/SwissProt for CYP39A1 Gene:

Tissue specificity: Liver specific.

Evidence on tissue expression from TISSUES for CYP39A1 Gene

  • Liver(4.5)
  • Skin(4.2)
genes like me logo Genes that share expression patterns with CYP39A1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CYP39A1 Gene

Orthologs for CYP39A1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CYP39A1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CYP39A1 34 33
  • 99.64 (n)
(Canis familiaris)
Mammalia CYP39A1 34 33
  • 88.89 (n)
(Bos Taurus)
Mammalia CYP39A1 34 33
  • 85.61 (n)
(Mus musculus)
Mammalia Cyp39a1 16 34 33
  • 80.69 (n)
(Rattus norvegicus)
Mammalia Cyp39a1 33
  • 78.75 (n)
(Ornithorhynchus anatinus)
Mammalia CYP39A1 34
  • 69 (a)
(Monodelphis domestica)
Mammalia CYP39A1 34
  • 57 (a)
(Gallus gallus)
Aves CYP39A1 34 33
  • 63.69 (n)
(Anolis carolinensis)
Reptilia CYP39A1 34
  • 53 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100486848 33
  • 59.71 (n)
(Danio rerio)
Actinopterygii cyp39a1 34 33
  • 58.56 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5434 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 21 (a)
-- 34
  • 19 (a)
Species where no ortholog for CYP39A1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CYP39A1 Gene

Gene Tree for CYP39A1 (if available)
Gene Tree for CYP39A1 (if available)
Evolutionary constrained regions (ECRs) for CYP39A1: view image

Paralogs for CYP39A1 Gene

Paralogs for CYP39A1 Gene

(1) SIMAP similar genes for CYP39A1 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with CYP39A1: view

Variants for CYP39A1 Gene

Sequence variations from dbSNP and Humsavar for CYP39A1 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000036463 -- 46,632,950(-) T/C intron_variant
rs1000055341 -- 46,609,913(-) T/C intron_variant
rs1000058560 -- 46,618,170(-) T/A intron_variant
rs1000121095 -- 46,608,802(-) C/T intron_variant
rs1000168292 -- 46,567,927(-) G/A genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CYP39A1 Gene

Variant ID Type Subtype PubMed ID
esv2662881 CNV deletion 23128226
esv3608885 CNV loss 21293372
nsv1109774 CNV deletion 24896259
nsv348640 CNV deletion 16902084

Variation tolerance for CYP39A1 Gene

Residual Variation Intolerance Score: 68.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.32; 85.26% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CYP39A1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CYP39A1 Gene

Disorders for CYP39A1 Gene

Additional Disease Information for CYP39A1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for CYP39A1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CYP39A1 Gene

Publications for CYP39A1 Gene

  1. Expression cloning of an oxysterol 7alpha-hydroxylase selective for 24-hydroxycholesterol. (PMID: 10748047) Li-Hawkins J … Russell DW (The Journal of biological chemistry 2000) 2 3 4 58
  2. A Large-scale genetic association study of esophageal adenocarcinoma risk. (PMID: 20453000) Liu CY … Christiani DC (Carcinogenesis 2010) 3 44 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. CYP39A1 polymorphism is associated with toxicity during intensive induction chemotherapy in patients with advanced head and neck cancer. (PMID: 26475344) Melchardt T … Egle A (BMC cancer 2015) 3 58

Products for CYP39A1 Gene

Sources for CYP39A1 Gene

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