APEX1 (apurinic/apyrimidinic endodeoxyribonuclease 1)

Gene

• Entrez ID: 328
• Gene name: Apurinic/apyrimidinic endodeoxyribonuclease 1
• Gene symbol: APEX1
• Synonyms: APE, APE1, APEN, APEX, APX, HAP1, REF1
• Chromosome: 14
• Chromosome location: 14q11.2
• Summary: The APEX gene encodes the major AP endonuclease in human cells. It encodes the APEX endonuclease, a DNA repair enzyme with apurinic/apyrimidinic (AP) activity. Such AP activity sites occur frequently in DNA molecules by spontaneous hydrolysis, by DNA dama

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT050830	hsa-miR-17-5p	CLASH	23622248
MIRT048610	hsa-miR-99a-5p	CLASH	23622248
MIRT048405	hsa-miR-100-5p	CLASH	23622248
MIRT045386	hsa-miR-185-5p	CLASH	23622248
MIRT036701	hsa-miR-935	CLASH	23622248
MIRT481806	hsa-miR-3681-3p	PAR-CLIP	20371350
MIRT481805	hsa-miR-216a-3p	PAR-CLIP	20371350
MIRT481804	hsa-miR-128-3p	PAR-CLIP	20371350
MIRT481803	hsa-miR-27a-3p	PAR-CLIP	20371350
MIRT481802	hsa-miR-27b-3p	PAR-CLIP	20371350
MIRT481799	hsa-miR-1197	PAR-CLIP	20371350
MIRT481796	hsa-miR-4678	PAR-CLIP	20371350
MIRT481792	hsa-miR-135a-3p	PAR-CLIP	20371350
MIRT481774	hsa-miR-597-5p	PAR-CLIP	20371350
MIRT481770	hsa-miR-331-5p	PAR-CLIP	20371350
MIRT481806	hsa-miR-3681-3p	PAR-CLIP	23592263
MIRT481805	hsa-miR-216a-3p	PAR-CLIP	23592263
MIRT481804	hsa-miR-128-3p	PAR-CLIP	23592263
MIRT481803	hsa-miR-27a-3p	PAR-CLIP	23592263
MIRT481802	hsa-miR-27b-3p	PAR-CLIP	23592263
MIRT481801	hsa-miR-3609	PAR-CLIP	23592263
MIRT481800	hsa-miR-548ah-5p	PAR-CLIP	23592263
MIRT481799	hsa-miR-1197	PAR-CLIP	23592263
MIRT481798	hsa-miR-6805-5p	PAR-CLIP	23592263
MIRT481797	hsa-miR-6782-5p	PAR-CLIP	23592263
MIRT481796	hsa-miR-4678	PAR-CLIP	23592263
MIRT481795	hsa-miR-1245a	PAR-CLIP	23592263
MIRT481794	hsa-miR-8079	PAR-CLIP	23592263
MIRT481793	hsa-miR-8062	PAR-CLIP	23592263
MIRT481792	hsa-miR-135a-3p	PAR-CLIP	23592263
MIRT481791	hsa-miR-3973	PAR-CLIP	23592263
MIRT481790	hsa-miR-520g-3p	PAR-CLIP	23592263
MIRT481789	hsa-miR-520h	PAR-CLIP	23592263
MIRT481788	hsa-miR-6890-3p	PAR-CLIP	23592263
MIRT481787	hsa-miR-3155a	PAR-CLIP	23592263
MIRT481786	hsa-miR-3155b	PAR-CLIP	23592263
MIRT481785	hsa-miR-484	PAR-CLIP	23592263
MIRT481784	hsa-miR-6840-3p	PAR-CLIP	23592263
MIRT481783	hsa-miR-1915-3p	PAR-CLIP	23592263
MIRT481782	hsa-miR-6764-5p	PAR-CLIP	23592263
MIRT481781	hsa-miR-4726-3p	PAR-CLIP	23592263
MIRT341107	hsa-miR-27a-5p	PAR-CLIP	23592263
MIRT481780	hsa-miR-6846-5p	PAR-CLIP	23592263
MIRT481779	hsa-miR-6848-5p	PAR-CLIP	23592263
MIRT481778	hsa-miR-4651	PAR-CLIP	23592263
MIRT481777	hsa-miR-608	PAR-CLIP	23592263
MIRT481776	hsa-miR-1293	PAR-CLIP	23592263
MIRT481775	hsa-miR-4483	PAR-CLIP	23592263
MIRT481774	hsa-miR-597-5p	PAR-CLIP	23592263
MIRT481773	hsa-miR-6824-5p	PAR-CLIP	23592263
MIRT481772	hsa-miR-6789-5p	PAR-CLIP	23592263
MIRT481771	hsa-miR-4278	PAR-CLIP	23592263
MIRT481770	hsa-miR-331-5p	PAR-CLIP	23592263
MIRT481769	hsa-miR-7977	PAR-CLIP	23592263
MIRT481768	hsa-miR-2909	PAR-CLIP	23592263
MIRT481803	hsa-miR-27a-3p	HITS-CLIP	22473208
MIRT481802	hsa-miR-27b-3p	HITS-CLIP	22473208
MIRT481783	hsa-miR-1915-3p	PAR-CLIP	26701625
MIRT481783	hsa-miR-1915-3p	PAR-CLIP	26701625
MIRT341107	hsa-miR-27a-5p	PAR-CLIP	26701625
MIRT341107	hsa-miR-27a-5p	PAR-CLIP	26701625
MIRT481787	hsa-miR-3155a	PAR-CLIP	26701625
MIRT481787	hsa-miR-3155a	PAR-CLIP	26701625
MIRT481786	hsa-miR-3155b	PAR-CLIP	26701625
MIRT481786	hsa-miR-3155b	PAR-CLIP	26701625
MIRT481801	hsa-miR-3609	PAR-CLIP	26701625
MIRT481801	hsa-miR-3609	PAR-CLIP	26701625
MIRT481791	hsa-miR-3973	PAR-CLIP	26701625
MIRT481791	hsa-miR-3973	PAR-CLIP	26701625
MIRT481781	hsa-miR-4726-3p	PAR-CLIP	26701625
MIRT481781	hsa-miR-4726-3p	PAR-CLIP	26701625
MIRT481785	hsa-miR-484	PAR-CLIP	26701625
MIRT481785	hsa-miR-484	PAR-CLIP	26701625
MIRT481790	hsa-miR-520g-3p	PAR-CLIP	26701625
MIRT481790	hsa-miR-520g-3p	PAR-CLIP	26701625
MIRT481789	hsa-miR-520h	PAR-CLIP	26701625
MIRT481789	hsa-miR-520h	PAR-CLIP	26701625
MIRT481800	hsa-miR-548ah-5p	PAR-CLIP	26701625
MIRT481800	hsa-miR-548ah-5p	PAR-CLIP	26701625
MIRT481782	hsa-miR-6764-5p	PAR-CLIP	26701625
MIRT481782	hsa-miR-6764-5p	PAR-CLIP	26701625
MIRT481798	hsa-miR-6805-5p	PAR-CLIP	26701625
MIRT481798	hsa-miR-6805-5p	PAR-CLIP	26701625
MIRT481784	hsa-miR-6840-3p	PAR-CLIP	26701625
MIRT481784	hsa-miR-6840-3p	PAR-CLIP	26701625
MIRT481780	hsa-miR-6846-5p	PAR-CLIP	26701625
MIRT481780	hsa-miR-6846-5p	PAR-CLIP	26701625
MIRT481779	hsa-miR-6848-5p	PAR-CLIP	26701625
MIRT481779	hsa-miR-6848-5p	PAR-CLIP	26701625
MIRT481769	hsa-miR-7977	PAR-CLIP	26701625
MIRT481769	hsa-miR-7977	PAR-CLIP	26701625
MIRT481776	hsa-miR-1293	Luciferase reporter assay, Western blotting, Microarray, Immunohistochemistry (IHC), Immunofluorescence, qRT-PCR, In situ hybridization	32320642
MIRT481806	hsa-miR-3681-3p	PAR-CLIP	20371350
MIRT481805	hsa-miR-216a-3p	PAR-CLIP	20371350
MIRT481804	hsa-miR-128-3p	PAR-CLIP	20371350
MIRT481803	hsa-miR-27a-3p	PAR-CLIP	20371350
MIRT481802	hsa-miR-27b-3p	PAR-CLIP	20371350
MIRT481799	hsa-miR-1197	PAR-CLIP	20371350
MIRT481796	hsa-miR-4678	PAR-CLIP	20371350
MIRT481792	hsa-miR-135a-3p	PAR-CLIP	20371350
MIRT481774	hsa-miR-597-5p	PAR-CLIP	20371350
MIRT481770	hsa-miR-331-5p	PAR-CLIP	20371350
MIRT481806	hsa-miR-3681-3p	PAR-CLIP	23592263
MIRT481805	hsa-miR-216a-3p	PAR-CLIP	23592263
MIRT481804	hsa-miR-128-3p	PAR-CLIP	23592263
MIRT481803	hsa-miR-27a-3p	PAR-CLIP	23592263
MIRT481802	hsa-miR-27b-3p	PAR-CLIP	23592263
MIRT481801	hsa-miR-3609	PAR-CLIP	23592263
MIRT481800	hsa-miR-548ah-5p	PAR-CLIP	23592263
MIRT481799	hsa-miR-1197	PAR-CLIP	23592263
MIRT481798	hsa-miR-6805-5p	PAR-CLIP	23592263
MIRT481797	hsa-miR-6782-5p	PAR-CLIP	23592263
MIRT481796	hsa-miR-4678	PAR-CLIP	23592263
MIRT481795	hsa-miR-1245a	PAR-CLIP	23592263
MIRT481794	hsa-miR-8079	PAR-CLIP	23592263
MIRT481793	hsa-miR-8062	PAR-CLIP	23592263
MIRT481792	hsa-miR-135a-3p	PAR-CLIP	23592263
MIRT481791	hsa-miR-3973	PAR-CLIP	23592263
MIRT481790	hsa-miR-520g-3p	PAR-CLIP	23592263
MIRT481789	hsa-miR-520h	PAR-CLIP	23592263
MIRT481788	hsa-miR-6890-3p	PAR-CLIP	23592263
MIRT481787	hsa-miR-3155a	PAR-CLIP	23592263
MIRT481786	hsa-miR-3155b	PAR-CLIP	23592263
MIRT481785	hsa-miR-484	PAR-CLIP	23592263
MIRT481784	hsa-miR-6840-3p	PAR-CLIP	23592263
MIRT481783	hsa-miR-1915-3p	PAR-CLIP	23592263
MIRT481782	hsa-miR-6764-5p	PAR-CLIP	23592263
MIRT481781	hsa-miR-4726-3p	PAR-CLIP	23592263
MIRT341107	hsa-miR-27a-5p	PAR-CLIP	23592263
MIRT481780	hsa-miR-6846-5p	PAR-CLIP	23592263
MIRT481779	hsa-miR-6848-5p	PAR-CLIP	23592263
MIRT481778	hsa-miR-4651	PAR-CLIP	23592263
MIRT481777	hsa-miR-608	PAR-CLIP	23592263
MIRT481776	hsa-miR-1293	PAR-CLIP	23592263
MIRT481775	hsa-miR-4483	PAR-CLIP	23592263
MIRT481774	hsa-miR-597-5p	PAR-CLIP	23592263
MIRT481773	hsa-miR-6824-5p	PAR-CLIP	23592263
MIRT481772	hsa-miR-6789-5p	PAR-CLIP	23592263
MIRT481771	hsa-miR-4278	PAR-CLIP	23592263
MIRT481770	hsa-miR-331-5p	PAR-CLIP	23592263
MIRT481769	hsa-miR-7977	PAR-CLIP	23592263
MIRT481768	hsa-miR-2909	PAR-CLIP	23592263
MIRT789085	hsa-miR-1252	CLIP-seq
MIRT789086	hsa-miR-186	CLIP-seq
MIRT789087	hsa-miR-1915	CLIP-seq
MIRT789088	hsa-miR-3133	CLIP-seq
MIRT789089	hsa-miR-3155	CLIP-seq
MIRT789090	hsa-miR-3184	CLIP-seq
MIRT789091	hsa-miR-3613-3p	CLIP-seq
MIRT789092	hsa-miR-3659	CLIP-seq
MIRT789093	hsa-miR-3671	CLIP-seq
MIRT789094	hsa-miR-3921	CLIP-seq
MIRT789095	hsa-miR-4653-5p	CLIP-seq
MIRT789096	hsa-miR-4703-3p	CLIP-seq
MIRT789097	hsa-miR-4709-3p	CLIP-seq
MIRT789098	hsa-miR-4790-3p	CLIP-seq
MIRT789099	hsa-miR-520g	CLIP-seq
MIRT789100	hsa-miR-548ac	CLIP-seq
MIRT789101	hsa-miR-548c-3p	CLIP-seq
MIRT789102	hsa-miR-548d-3p	CLIP-seq
MIRT789103	hsa-miR-548z	CLIP-seq
MIRT789091	hsa-miR-3613-3p	CLIP-seq
MIRT789093	hsa-miR-3671	CLIP-seq
MIRT789104	hsa-miR-4443	CLIP-seq
MIRT789105	hsa-miR-513a-5p	CLIP-seq
MIRT789100	hsa-miR-548ac	CLIP-seq
MIRT789102	hsa-miR-548d-3p	CLIP-seq
MIRT789103	hsa-miR-548z	CLIP-seq
MIRT789106	hsa-miR-765	CLIP-seq
MIRT1932775	hsa-miR-1261	CLIP-seq
MIRT1932776	hsa-miR-384	CLIP-seq
MIRT789104	hsa-miR-4443	CLIP-seq
MIRT1932777	hsa-miR-4760-3p	CLIP-seq
MIRT789105	hsa-miR-513a-5p	CLIP-seq
MIRT789106	hsa-miR-765	CLIP-seq
MIRT2476159	hsa-miR-1244	CLIP-seq
MIRT1932775	hsa-miR-1261	CLIP-seq
MIRT2476160	hsa-miR-135a	CLIP-seq
MIRT2476161	hsa-miR-135b	CLIP-seq
MIRT2476162	hsa-miR-3607-5p	CLIP-seq
MIRT2476163	hsa-miR-3691-5p	CLIP-seq
MIRT2476164	hsa-miR-375	CLIP-seq
MIRT2476165	hsa-miR-4491	CLIP-seq
MIRT2476166	hsa-miR-4657	CLIP-seq
MIRT2476167	hsa-miR-4738-3p	CLIP-seq
MIRT2476168	hsa-miR-4752	CLIP-seq
MIRT1932777	hsa-miR-4760-3p	CLIP-seq
MIRT2476169	hsa-miR-760	CLIP-seq
MIRT2476159	hsa-miR-1244	CLIP-seq
MIRT1932775	hsa-miR-1261	CLIP-seq
MIRT2476160	hsa-miR-135a	CLIP-seq
MIRT2476161	hsa-miR-135b	CLIP-seq
MIRT2476162	hsa-miR-3607-5p	CLIP-seq
MIRT2476163	hsa-miR-3691-5p	CLIP-seq
MIRT2476164	hsa-miR-375	CLIP-seq
MIRT2476165	hsa-miR-4491	CLIP-seq
MIRT2476166	hsa-miR-4657	CLIP-seq
MIRT2476167	hsa-miR-4738-3p	CLIP-seq
MIRT2476168	hsa-miR-4752	CLIP-seq
MIRT1932777	hsa-miR-4760-3p	CLIP-seq
MIRT2476169	hsa-miR-760	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
HIF1A	Repression	19524065
SP1	Repression	18208837
SP1	Unknown	7534297
USF1	Unknown	7534297

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000723	Process	Telomere maintenance	IDA	24703901
GO:0000781	Component	Chromosome, telomeric region	IC	24703901
GO:0003677	Function	DNA binding	IDA	11286553
GO:0003684	Function	Damaged DNA binding	IDA	12524539, 14706345, 24703901
GO:0003691	Function	Double-stranded telomeric DNA binding	IDA	24703901
GO:0003713	Function	Transcription coactivator activity	IDA	9119221, 18809583
GO:0003714	Function	Transcription corepressor activity	TAS	7961715
GO:0003723	Function	RNA binding	HDA	22681889
GO:0003906	Function	DNA-(apurinic or apyrimidinic site) endonuclease activity	IBA	21873635
GO:0003906	Function	DNA-(apurinic or apyrimidinic site) endonuclease activity	IDA	8932386, 15707971, 18973764, 19188445, 24703901
GO:0003906	Function	DNA-(apurinic or apyrimidinic site) endonuclease activity	TAS	9119221
GO:0004519	Function	Endonuclease activity	IDA	11478795
GO:0004520	Function	Endodeoxyribonuclease activity	TAS
GO:0004523	Function	RNA-DNA hybrid ribonuclease activity	TAS	11286553
GO:0004528	Function	Phosphodiesterase I activity	IBA	21873635
GO:0004528	Function	Phosphodiesterase I activity	TAS	9119221
GO:0004844	Function	Uracil DNA N-glycosylase activity	TAS
GO:0005515	Function	Protein binding	IPI	8621488, 9108029, 9207062, 11118054, 11809897, 12524539, 15518571, 15942031, 18809583, 19188445, 19465398, 19505873, 19934257, 20231292, 20696907, 20808282, 20856196, 32911434
GO:0005634	Component	Nucleus	IBA	21873635
GO:0005634	Component	Nucleus	IDA	9119221, 15942031, 19934257, 28404743
GO:0005654	Component	Nucleoplasm	IDA	17148573
GO:0005654	Component	Nucleoplasm	TAS
GO:0005667	Component	Transcription regulator complex	IEA
GO:0005730	Component	Nucleolus	IDA	17148573, 19188445
GO:0005737	Component	Cytoplasm	IDA	9560228
GO:0005739	Component	Mitochondrion	IDA	20231292
GO:0005783	Component	Endoplasmic reticulum	TAS	12524539
GO:0005813	Component	Centrosome	IDA
GO:0005840	Component	Ribosome	TAS	12524539
GO:0006281	Process	DNA repair	IDA	9560228
GO:0006284	Process	Base-excision repair	IBA	21873635
GO:0006284	Process	Base-excision repair	IDA	8932386
GO:0006284	Process	Base-excision repair	TAS
GO:0006286	Process	Base-excision repair, base-free sugar-phosphate removal	TAS
GO:0006310	Process	DNA recombination	IEA
GO:0007568	Process	Aging	IEA
GO:0008081	Function	Phosphoric diester hydrolase activity	IDA	11478795, 18973764
GO:0008309	Function	Double-stranded DNA exodeoxyribonuclease activity	IDA	24703901
GO:0008311	Function	Double-stranded DNA 3'-5' exodeoxyribonuclease activity	IBA	21873635
GO:0008408	Function	3'-5' exonuclease activity	IDA	11832948
GO:0008408	Function	3'-5' exonuclease activity	TAS	11286553
GO:0014912	Process	Negative regulation of smooth muscle cell migration	IEA
GO:0016491	Function	Oxidoreductase activity	IDA	9119221, 12524539
GO:0016607	Component	Nuclear speck	IDA	17148573
GO:0016890	Function	Site-specific endodeoxyribonuclease activity, specific for altered base	IDA	19188445, 24703901
GO:0031490	Function	Chromatin DNA binding	IDA	11809897
GO:0042493	Process	Response to drug	IEA
GO:0042981	Process	Regulation of apoptotic process	IDA	19934257
GO:0043488	Process	Regulation of mRNA stability	IMP	19401441
GO:0044877	Function	Protein-containing complex binding	IEA
GO:0045454	Process	Cell redox homeostasis	IEA
GO:0045892	Process	Negative regulation of transcription, DNA-templated	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	18809583
GO:0046872	Function	Metal ion binding	IDA	11286553
GO:0048471	Component	Perinuclear region of cytoplasm	IDA	12524539
GO:0051059	Function	NF-kappaB binding	IEA
GO:0070301	Process	Cellular response to hydrogen peroxide	IEA
GO:0071320	Process	Cellular response to cAMP	IEA
GO:0071375	Process	Cellular response to peptide hormone stimulus	IEA
GO:0080111	Process	DNA demethylation	IDA	21496894
GO:0090502	Process	RNA phosphodiester bond hydrolysis, endonucleolytic	IEA
GO:0097698	Process	Telomere maintenance via base-excision repair	IDA	24703901
GO:1900087	Process	Positive regulation of G1/S transition of mitotic cell cycle	IEA

Other IDs

• MIM: 107748
• HGNC: 587
• e!Ensembl: ENSG00000100823

Protein

• UniProt ID: P27695
• Protein name: DNA repair nuclease/redox regulator APEX1 (EC 3.1.11.2) (EC 3.1.21.-) (APEX nuclease) (APEN) (Apurinic-apyrimidinic endonuclease 1) (AP endonuclease 1) (APE-1) (DNA-(apurinic or apyrimidinic site) endonuclease) (Redox factor-1) (REF-1) [Cleaved into: DNA
• Protein function: Multifunctional protein that plays a central role in the cellular response to oxidative stress. The two major activities of APEX1 are DNA repair and redox regulation of transcriptional factors (PubMed:11118054, PubMed:11452037, PubMed:15831793,
• PDB: 1BIX, 1CQG, 1CQH, 1DE8, 1DE9, 1DEW, 1E9N, 1HD7, 2ISI, 2O3H, 3U8U, 4IEM, 4LND, 4QH9, 4QHD, 4QHE, 5CFG, 5DFF, 5DFH, 5DFI, 5DFJ, 5DG0, 5WN0, 5WN1, 5WN2, 5WN3, 5WN4, 5WN5, 6BOQ, 6BOR, 6BOS, 6BOT, 6BOU, 6BOV, 6BOW, 6MK3, 6MKK, 6MKM, 6MKO, 6P93, 6P94, 6W0Q, 6W2P, 6W3L, 6W3N, 6W3Q, 6W3U, 6W43, 6W4I, 6W4T, 7LPG
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF03372	Exo_endo_phos	65 → 309	Endonuclease/Exonuclease/phosphatase family	Domain

• Sequence:

  MPKRGKKGAVAEDGDELRTEPEAKKSKTAAKKNDKEAAGEGPALYEDPPDQKTSPSGKPA
  TLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWS
  APSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLV
  RLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGF
  GELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKI
  RSKALGSDHCPITLYLAL

• Sequence length: 318