Human Gene APEX1 (ENST00000216714.8_4) from GENCODE V47lift37
  Description: apurinic/apyrimidinic endodeoxyribonuclease 1, transcript variant 1 (from RefSeq NM_001641.4)
Gencode Transcript: ENST00000216714.8_4
Gencode Gene: ENSG00000100823.12_9
Transcript (Including UTRs)
   Position: hg19 chr14:20,923,385-20,925,926 Size: 2,542 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr14:20,923,805-20,925,667 Size: 1,863 Coding Exon Count: 4 

Page IndexSequence and LinksPrimersMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:20,923,385-20,925,926)mRNA (may differ from genome)Protein (318 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid 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


-  MalaCards Disease Associations
  MalaCards Gene Search: APEX1
Diseases sorted by gene-association score: attenuated familial adenomatous polyposis (10), bardet-biedl syndrome 19 (7), pituitary-dependent cushing's disease (7), exanthema subitum (6), intraocular retinoblastoma (5), xeroderma pigmentosum, group d (5), lung cancer (2), cystic fibrosis (2), colorectal cancer (1), amyotrophic lateral sclerosis 1 (1)

-  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: 87.16 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1670.12 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 -77.00237-0.325 Picture PostScript Text
3' UTR -48.50259-0.187 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
  InterPro Domains: Graphical view of domain structure
IPR020847 - AP_endonuclease_F1_BS
IPR020848 - AP_endonuclease_F1_CS
IPR005135 - Endo/exonuclease/phosphatase
IPR004808 - ExoDNase_III

Pfam Domains:
PF03372 - Endonuclease/Exonuclease/phosphatase family

SCOP Domains:
56219 - DNase I-like

ModBase Predicted Comparative 3D Structure on Q5TZP7
FrontTopSide
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0004518 nuclease activity
GO:0004519 endonuclease activity
GO:0004521 endoribonuclease activity
GO:0016787 hydrolase activity
GO:0016829 lyase activity
GO:0044877 macromolecular complex binding
GO:0046872 metal ion binding
GO:0051059 NF-kappaB binding

Biological Process:
GO:0006281 DNA repair
GO:0006974 cellular response to DNA damage stimulus
GO:0007568 aging
GO:0010243 response to organonitrogen compound
GO:0014912 negative regulation of smooth muscle cell migration
GO:0042493 response to drug
GO:0045454 cell redox homeostasis
GO:0070301 cellular response to hydrogen peroxide
GO:0071320 cellular response to cAMP
GO:0071375 cellular response to peptide hormone stimulus
GO:0071417 cellular response to organonitrogen compound
GO:0090305 nucleic acid phosphodiester bond hydrolysis
GO:0090502 RNA phosphodiester bond hydrolysis, endonucleolytic
GO:1900087 positive regulation of G1/S transition of mitotic cell cycle

Cellular Component:
GO:0005622 intracellular
GO:0005634 nucleus
GO:0005667 transcription factor complex
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005813 centrosome


-  Descriptions from all associated GenBank mRNAs
  AK098588 - Homo sapiens cDNA FLJ25722 fis, clone TST05409, highly similar to DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE (EC 4.2.99.18).
AK291100 - Homo sapiens cDNA FLJ76713 complete cds, highly similar to Homo sapiens APEX nuclease (multifunctional DNA repair enzyme) 1 (APEX1), transcript variant 2, mRNA.
BC095428 - Homo sapiens APEX nuclease (multifunctional DNA repair enzyme) 1, mRNA (cDNA clone MGC:110965 IMAGE:30709297), complete cds.
AK311548 - Homo sapiens cDNA, FLJ18590.
BX161454 - human full-length cDNA clone CS0DI036YP02 of Placenta of Homo sapiens (human).
S43127 - ref-1=redox factor [human, mRNA, 1441 nt].
BC002338 - Homo sapiens APEX nuclease (multifunctional DNA repair enzyme) 1, mRNA (cDNA clone MGC:8338 IMAGE:2819505), complete cds.
BC019291 - Homo sapiens APEX nuclease (multifunctional DNA repair enzyme) 1, mRNA (cDNA clone MGC:4057 IMAGE:2823545), complete cds.
BC008145 - Homo sapiens APEX nuclease (multifunctional DNA repair enzyme) 1, mRNA (cDNA clone MGC:17277 IMAGE:4180383), complete cds.
M81955 - Human apurinic/apyrimidinic endonuclease (HAP1h) mRNA, complete cds.
X59764 - Human HAP1 mRNA.
D90373 - Homo sapiens mRNA for apurinic/apyrimidinic endonuclease, complete cds.
BC004979 - Homo sapiens APEX nuclease (multifunctional DNA repair enzyme) 1, mRNA (cDNA clone MGC:3855 IMAGE:2905681), complete cds.
M80261 - Human apurinic endonuclease (APE) mRNA, complete cds.
U79268 - Human apurinic/apyrimidinic endonuclease mRNA, complete cds.
JD475387 - Sequence 456411 from Patent EP1572962.
JD540970 - Sequence 521994 from Patent EP1572962.
JD057389 - Sequence 38413 from Patent EP1572962.
KJ890683 - Synthetic construct Homo sapiens clone ccsbBroadEn_00077 APEX1 gene, encodes complete protein.
KJ896440 - Synthetic construct Homo sapiens clone ccsbBroadEn_05834 APEX1 gene, encodes complete protein.
KR709886 - Synthetic construct Homo sapiens clone CCSBHm_00007076 APEX1 (APEX1) mRNA, encodes complete protein.
KR709887 - Synthetic construct Homo sapiens clone CCSBHm_00007077 APEX1 (APEX1) mRNA, encodes complete protein.
KR709888 - Synthetic construct Homo sapiens clone CCSBHm_00007078 APEX1 (APEX1) mRNA, encodes complete protein.
KR709889 - Synthetic construct Homo sapiens clone CCSBHm_00007081 APEX1 (APEX1) mRNA, encodes complete protein.
AB463413 - Synthetic construct DNA, clone: pF1KB6453, Homo sapiens APEX1 gene for APEX nuclease (multifunctional DNA repair enzyme) 1, without stop codon, in Flexi system.
BT007236 - Homo sapiens APEX nuclease (multifunctional DNA repair enzyme) 1 mRNA, complete cds.
BT020133 - Homo sapiens APEX nuclease (multifunctional DNA repair enzyme) 1 mRNA, complete cds.
DQ891814 - Synthetic construct clone IMAGE:100004444; FLH180185.01X; RZPDo839H02132D APEX nuclease (multifunctional DNA repair enzyme) 1 (APEX1) gene, encodes complete protein.
DQ894998 - Synthetic construct Homo sapiens clone IMAGE:100009458; FLH180181.01L; RZPDo839H02131D APEX nuclease (multifunctional DNA repair enzyme) 1 (APEX1) gene, encodes complete protein.
JD126296 - Sequence 107320 from Patent EP1572962.
JD410363 - Sequence 391387 from Patent EP1572962.
JD039771 - Sequence 20795 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_setPathway - Granzyme A mediated Apoptosis Pathway

-  Other Names for This Gene
  Alternate Gene Symbols: APEX1 , ENST00000216714.1, ENST00000216714.2, ENST00000216714.3, ENST00000216714.4, ENST00000216714.5, ENST00000216714.6, ENST00000216714.7, hCG_40473 , NM_001641, Q5TZP7, Q5TZP7_HUMAN, uc317crt.1, uc317crt.2
UCSC ID: ENST00000216714.8_4
RefSeq Accession: NM_001641.4
Protein: Q5TZP7

-  Gene Model Information
  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.