Human Gene CYP1A2 (uc002ayr.1)
  Description: Homo sapiens cytochrome P450, family 1, subfamily A, polypeptide 2 (CYP1A2), mRNA.
RefSeq Summary (NM_000761): 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. The protein encoded by this gene localizes to the endoplasmic reticulum and its expression is induced by some polycyclic aromatic hydrocarbons (PAHs), some of which are found in cigarette smoke. The enzyme's endogenous substrate is unknown; however, it is able to metabolize some PAHs to carcinogenic intermediates. Other xenobiotic substrates for this enzyme include caffeine, aflatoxin B1, and acetaminophen. The transcript from this gene contains four Alu sequences flanked by direct repeats in the 3' untranslated region. [provided by RefSeq, Jul 2008]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments.
Transcript (Including UTRs)
   Position: hg19 chr15:75,041,184-75,048,941 Size: 7,758 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr15:75,042,080-75,047,429 Size: 5,350 Coding Exon Count: 6 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:75,041,184-75,048,941)mRNA (may differ from genome)Protein (516 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMalacardsMGI
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CYP1A2
CDC HuGE Published Literature: CYP1A2
Positive Disease Associations: 2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine , breast cancer , Caffeine , cholesterol glucose insulin triglycerides , colorectal cancer , Diastolic blood pressure , liver cancer , liver cancer; liver disease , lung cancer , myocardial infarct , Neural Tube Defects , ovarian cancer , Plasma caffeine metabolite ratio , QT intervals , schizophrenia , urinary mutagenicity
Related Studies:
  1. 2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine
    Moonen, H. J. et al. 2004, CYP1A2 and NAT2 genotype/phenotype relations and urinary excretion of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) in a human dietary intervention study., Food and chemical toxicology. 2004 Jun;42(6):869-78. [PubMed 15110095]
    Although the found correlations are driven primarily by a small number of subjects possessing the homozygous variant constellation, the strong influence of this genotype indicates that the CYP1A2*1F polymorphism could play an important role in human cancer risk susceptibility.
  2. breast cancer
    Kotsopoulos, J. et al. 2007, The CYP1A2 Genotype Modifies the Association Between Coffee Consumption and Breast Cancer Risk Among BRCA1 Mutation Carriers, Cancer Epidemiol Biomarkers Prev 2007 16(5) 912-6. [PubMed 17507615]
  3. Caffeine
    Marilyn C Cornelis et al. PLoS genetics 2011, Genome-wide meta-analysis identifies regions on 7p21 (AHR) and 15q24 (CYP1A2) as determinants of habitual caffeine consumption., PLoS genetics. [PubMed 21490707]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: CYP1A2
Diseases sorted by gene-association score: cyp1a2-related altered drug metabolism* (100), toxicity or absent response to clozapine* (25), porphyria cutanea tarda (12), hepatocellular adenoma (9), cytochrome p450 oxidoreductase deficiency (9), extraskeletal mesenchymal chondrosarcoma (9), headache (8), hypoadrenalism (7), autoimmune hepatitis (7), porphyria (7), tardive dyskinesia (7), female stress incontinence (6), amelogenesis imperfecta, type ib (6), kleptomania (5), clopidogrel resistance (5), asthma (2), colorectal cancer (1), schizophrenia (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 35.18 RPKM in Liver
Total median expression: 36.48 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -7.2064-0.112 Picture PostScript Text
3' UTR -517.271512-0.342 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF00067 - Cytochrome P450

SCOP Domains:
48264 - Cytochrome P450

ModBase Predicted Comparative 3D Structure on P05177-2
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  BC067424 - Homo sapiens cytochrome P450, family 1, subfamily A, polypeptide 2, mRNA (cDNA clone MGC:79250 IMAGE:7002123), complete cds.
BC067425 - Homo sapiens cytochrome P450, family 1, subfamily A, polypeptide 2, mRNA (cDNA clone MGC:79251 IMAGE:7002124), complete cds.
BC067426 - Homo sapiens cytochrome P450, family 1, subfamily A, polypeptide 2, mRNA (cDNA clone MGC:79252 IMAGE:7002125), complete cds.
BC067427 - Homo sapiens cytochrome P450, family 1, subfamily A, polypeptide 2, mRNA (cDNA clone MGC:79253 IMAGE:7002126), complete cds.
BC067428 - Homo sapiens cytochrome P450, family 1, subfamily A, polypeptide 2, mRNA (cDNA clone MGC:79254 IMAGE:7002128), complete cds.
BC067429 - Homo sapiens cytochrome P450, family 1, subfamily A, polypeptide 2, mRNA (cDNA clone MGC:79255 IMAGE:7002129), complete cds.
JD348683 - Sequence 329707 from Patent EP1572962.
KJ891013 - Synthetic construct Homo sapiens clone ccsbBroadEn_00407 CYP1A2 gene, encodes complete protein.
KR711984 - Synthetic construct Homo sapiens clone CCSBHm_00034488 CYP1A2 (CYP1A2) mRNA, encodes complete protein.
KR711985 - Synthetic construct Homo sapiens clone CCSBHm_00034489 CYP1A2 (CYP1A2) mRNA, encodes complete protein.
KR711986 - Synthetic construct Homo sapiens clone CCSBHm_00034490 CYP1A2 (CYP1A2) mRNA, encodes complete protein.
AF182274 - Homo sapiens cytochrome P450-1A2 (CYP1A2) mRNA, complete cds.
M55053 - Human cytochrome P-3-450 mRNA, complete cds.
Z00036 - Human mRNA for cytochrome P-3-450.
JD317141 - Sequence 298165 from Patent EP1572962.
E10852 - cDNA encoding human cytochrome P450.
E11498 - cDNA encoding human cytochrome P-4501A2.
M12078 - Human cytochrome P-450 4 mRNA, partial cds.
JD174048 - Sequence 155072 from Patent EP1572962.
JD081183 - Sequence 62207 from Patent EP1572962.
JD409104 - Sequence 390128 from Patent EP1572962.
JD564622 - Sequence 545646 from Patent EP1572962.
JD442903 - Sequence 423927 from Patent EP1572962.
JD092576 - Sequence 73600 from Patent EP1572962.
JD559820 - Sequence 540844 from Patent EP1572962.
JD539036 - Sequence 520060 from Patent EP1572962.
JD434841 - Sequence 415865 from Patent EP1572962.
JD269295 - Sequence 250319 from Patent EP1572962.
JD188731 - Sequence 169755 from Patent EP1572962.
JD265833 - Sequence 246857 from Patent EP1572962.
JD375487 - Sequence 356511 from Patent EP1572962.
JD080485 - Sequence 61509 from Patent EP1572962.
JD494198 - Sequence 475222 from Patent EP1572962.
JD514424 - Sequence 495448 from Patent EP1572962.
JD371262 - Sequence 352286 from Patent EP1572962.
JD337553 - Sequence 318577 from Patent EP1572962.
JD463079 - Sequence 444103 from Patent EP1572962.
JD059590 - Sequence 40614 from Patent EP1572962.
JD533808 - Sequence 514832 from Patent EP1572962.
JD095255 - Sequence 76279 from Patent EP1572962.
JD514007 - Sequence 495031 from Patent EP1572962.
JD120918 - Sequence 101942 from Patent EP1572962.
JD452111 - Sequence 433135 from Patent EP1572962.
JD101224 - Sequence 82248 from Patent EP1572962.
JD342662 - Sequence 323686 from Patent EP1572962.
JD435406 - Sequence 416430 from Patent EP1572962.
JD308108 - Sequence 289132 from Patent EP1572962.
JD165355 - Sequence 146379 from Patent EP1572962.
JD561125 - Sequence 542149 from Patent EP1572962.
JD213646 - Sequence 194670 from Patent EP1572962.
JD554450 - Sequence 535474 from Patent EP1572962.
JD356574 - Sequence 337598 from Patent EP1572962.
JD506279 - Sequence 487303 from Patent EP1572962.
JD374339 - Sequence 355363 from Patent EP1572962.
JD223650 - Sequence 204674 from Patent EP1572962.
JD177625 - Sequence 158649 from Patent EP1572962.
JD514399 - Sequence 495423 from Patent EP1572962.
JD321924 - Sequence 302948 from Patent EP1572962.
JD323930 - Sequence 304954 from Patent EP1572962.
JD189363 - Sequence 170387 from Patent EP1572962.
JD365105 - Sequence 346129 from Patent EP1572962.
JD242687 - Sequence 223711 from Patent EP1572962.
JD330957 - Sequence 311981 from Patent EP1572962.
JD550518 - Sequence 531542 from Patent EP1572962.
JD513927 - Sequence 494951 from Patent EP1572962.
JD069745 - Sequence 50769 from Patent EP1572962.
JD397056 - Sequence 378080 from Patent EP1572962.
JD414851 - Sequence 395875 from Patent EP1572962.
JD379697 - Sequence 360721 from Patent EP1572962.
JD311828 - Sequence 292852 from Patent EP1572962.
JD081630 - Sequence 62654 from Patent EP1572962.
JD040242 - Sequence 21266 from Patent EP1572962.
JD078434 - Sequence 59458 from Patent EP1572962.
JD265907 - Sequence 246931 from Patent EP1572962.
JD438034 - Sequence 419058 from Patent EP1572962.
JD369127 - Sequence 350151 from Patent EP1572962.
JD254408 - Sequence 235432 from Patent EP1572962.
JD133304 - Sequence 114328 from Patent EP1572962.
JD153399 - Sequence 134423 from Patent EP1572962.
JD161872 - Sequence 142896 from Patent EP1572962.
JD161873 - Sequence 142897 from Patent EP1572962.
JD547991 - Sequence 529015 from Patent EP1572962.
JD547992 - Sequence 529016 from Patent EP1572962.
JD547993 - Sequence 529017 from Patent EP1572962.
JD228484 - Sequence 209508 from Patent EP1572962.
JD541263 - Sequence 522287 from Patent EP1572962.
JD275390 - Sequence 256414 from Patent EP1572962.
JD374564 - Sequence 355588 from Patent EP1572962.
JD489238 - Sequence 470262 from Patent EP1572962.
JD081033 - Sequence 62057 from Patent EP1572962.
JD379672 - Sequence 360696 from Patent EP1572962.
JD311796 - Sequence 292820 from Patent EP1572962.
JD313747 - Sequence 294771 from Patent EP1572962.
JD356645 - Sequence 337669 from Patent EP1572962.
JD238889 - Sequence 219913 from Patent EP1572962.
JD125305 - Sequence 106329 from Patent EP1572962.
JD253310 - Sequence 234334 from Patent EP1572962.
JD126500 - Sequence 107524 from Patent EP1572962.
JD536738 - Sequence 517762 from Patent EP1572962.
JD397687 - Sequence 378711 from Patent EP1572962.
JD364786 - Sequence 345810 from Patent EP1572962.
JD417384 - Sequence 398408 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00232 - Caffeine metabolism
hsa00380 - Tryptophan metabolism
hsa00591 - Linoleic acid metabolism
hsa00830 - Retinol metabolism
hsa00980 - Metabolism of xenobiotics by cytochrome P450
hsa00982 - Drug metabolism - cytochrome P450
hsa01100 - Metabolic pathways

BioCyc Knowledge Library
PWY66-201 - nicotine degradation II
PWY66-221 - nicotine degradation III
PWY66-241 - bupropion degradation

BioCarta from NCI Cancer Genome Anatomy Project
h_nuclearRsPathway - Nuclear Receptors in Lipid Metabolism and Toxicity
h_AcetaminophenPathway - Mechanism of Acetaminophen Activity and Toxicity

Reactome (by CSHL, EBI, and GO)

Protein P05177 (Reactome details) participates in the following event(s):

R-HSA-76373 N-hydroxylation of 4-aminobiphenyl
R-HSA-76386 CYP1A2 S-demethylates 6MMP
R-HSA-76426 N-atom dealkylation of caffeine
R-HSA-5423678 CYP1A2 hydroxylates AFB1 to AFM1
R-HSA-2161814 Arachidonic acid is hydroxylated to 19-HETE by CYP(2)
R-HSA-2161890 Arachidonic acid is epoxidated to 5,6-EET by CYP(4)
R-HSA-2161940 Arachidonic acid is hydroxylated to 20-HETE by CYP(3)
R-HSA-2161899 Arachidonic acid is epoxidated to 8,9/11,12/14,15-EET by CYP(5)
R-HSA-2161795 Arachidonic acid is hydroxylated to 16/17/18-HETE by CYP(1)
R-HSA-156526 CYP1A2,3A4,3A5,2A13 oxidise AFB1 to AFXBO
R-HSA-5423672 CYP1A2, 3A4 oxidise AFB1 to AFNBO
R-HSA-9027043 CYPs hydroxylate DHA to 14(R)-HDHA
R-HSA-9037761 CYP1, CYP2 hydroxylate (N)PD1 to 22-OH-(N)PD1
R-HSA-211957 Aromatic amines can be N-hydroxylated or N-dealkylated by CYP1A2
R-HSA-156581 Methylation
R-HSA-5423646 Aflatoxin activation and detoxification
R-HSA-2142816 Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE)
R-HSA-2142670 Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET)
R-HSA-9027307 Biosynthesis of maresin-like SPMs
R-HSA-9018681 Biosynthesis of protectins
R-HSA-211981 Xenobiotics
R-HSA-156580 Phase II - Conjugation of compounds
R-HSA-211859 Biological oxidations
R-HSA-2142753 Arachidonic acid metabolism
R-HSA-9018682 Biosynthesis of maresins
R-HSA-9018677 Biosynthesis of DHA-derived SPMs
R-HSA-211897 Cytochrome P450 - arranged by substrate type
R-HSA-1430728 Metabolism
R-HSA-8978868 Fatty acid metabolism
R-HSA-9018678 Biosynthesis of specialized proresolving mediators (SPMs)
R-HSA-211945 Phase I - Functionalization of compounds
R-HSA-556833 Metabolism of lipids

-  Other Names for This Gene
  Alternate Gene Symbols: NM_000761, NP_000752, P05177-2
UCSC ID: uc002ayr.1
RefSeq Accession: NM_000761
Protein: P05177-2, splice isoform of P05177 CCDS: CCDS32293.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_000761.3
exon count: 7CDS single in 3' UTR: no RNA size: 3127
ORF size: 1551CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2819.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.