Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.




P43138 - APEX1_RAT

(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)


DNA-(apurinic or apyrimidinic site) lyase



Rattus norvegicus (Rat)
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli


Multifunctional protein that plays a central role in the cellular response to oxidative stress. The two major activities of APEX1 in DNA repair and redox regulation of transcriptional factors. Functions as a apurinic/apyrimidinic (AP) endodeoxyribonuclease in the DNA base excision repair (BER) pathway of DNA lesions induced by oxidative and alkylating agents. Initiates repair of AP sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone immediately adjacent to the damage, generating a single-strand break with 5'-deoxyribose phosphate and 3'-hydroxyl ends. Does also incise at AP sites in the DNA strand of DNA/RNA hybrids, single-stranded DNA regions of R-loop structures, and single-stranded RNA molecules. Has a 3'-5' exoribonuclease activity on mismatched deoxyribonucleotides at the 3' termini of nicked or gapped DNA molecules during short-patch BER. Possesses a DNA 3' phosphodiesterase activity capable of removing lesions (such as phosphoglycolate) blocking the 3' side of DNA strand breaks. May also play a role in the epigenetic regulation of gene expression by participating in DNA demethylation. Acts as a loading factor for POLB onto non-incised AP sites in DNA and stimulates the 5'-terminal deoxyribose 5'-phosphate (dRp) excision activity of POLB. Plays a role in the protection from granzymes-mediated cellular repair leading to cell death. Also involved in the DNA cleavage step of class switch recombination (CSR). On the other hand, APEX1 also exerts reversible nuclear redox activity to regulate DNA binding affinity and transcriptional activity of transcriptional factors by controlling the redox status of their DNA-binding domain, such as the FOS/JUN AP-1 complex after exposure to IR. Involved in calcium-dependent down-regulation of parathyroid hormone (PTH) expression by binding to negative calcium response elements (nCaREs). Together with HNRNPL or the dimer XRCC5/XRCC6, associates with nCaRE, acting as an activator of transcriptional repression. Stimulates the YBX1-mediated MDR1 promoter activity, when acetylated at Lys-6, leading to drug resistance. Acts also as an endoribonuclease involved in the control of single-stranded RNA metabolism. Plays a role in regulating MYC mRNA turnover by preferentially cleaving in between UA and CA dinucleotides of the MYC coding region determinant (CRD). In association with NMD1, plays a role in the rRNA quality control process during cell cycle progression. Associates, together with YBX1, on the MDR1 promoter. Together with NPM1, associates with rRNA. Binds DNA and RNA.1 Publication

Catalytic activityi

The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.PROSITE-ProRule annotation


Mg2+By similarity, Mn2+By similarityNote: Probably binds two magnesium or manganese ions per subunit.By similarity

Enzyme regulationi

NPM1 stimulates endodeoxyribonuclease activity on double-stranded DNA with AP sites, but inhibits endoribonuclease activity on single-stranded RNA containing AP sites.By similarity


Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei30 – 312Cleavage; by granzyme ABy similarity
Metal bindingi69 – 691Magnesium 1By similarity
Metal bindingi95 – 951Magnesium 1By similarity
Active sitei170 – 1701By similarity
Active sitei209 – 2091Proton donor/acceptorBy similarity
Metal bindingi209 – 2091Magnesium 2By similarity
Metal bindingi211 – 2111Magnesium 2By similarity
Sitei211 – 2111Transition state stabilizerBy similarity
Sitei282 – 2821Important for catalytic activityBy similarity
Metal bindingi307 – 3071Magnesium 1By similarity
Sitei308 – 3081Interaction with DNA substrateBy similarity

GO - Molecular functioni

  1. 3'-5' exonuclease activity Source: UniProtKB
  2. chromatin DNA binding Source: UniProtKB
  3. damaged DNA binding Source: UniProtKB
  4. DNA-(apurinic or apyrimidinic site) lyase activity Source: UniProtKB
  5. DNA binding Source: UniProtKB
  6. double-stranded DNA 3'-5' exodeoxyribonuclease activity Source: RefGenome
  7. endoribonuclease activity Source: RGD
  8. metal ion binding Source: UniProtKB
  9. NF-kappaB binding Source: RGD
  10. oxidoreductase activity Source: UniProtKB
  11. phosphoric diester hydrolase activity Source: Ensembl
  12. poly(A) RNA binding Source: Ensembl
  13. protein complex binding Source: RGD
  14. site-specific endodeoxyribonuclease activity, specific for altered base Source: UniProtKB
  15. transcription coactivator activity Source: UniProtKB

GO - Biological processi

  1. aging Source: RGD
  2. base-excision repair Source: RefGenome
  3. cell redox homeostasis Source: Ensembl
  4. cellular response to cAMP Source: RGD
  5. cellular response to hydrogen peroxide Source: RGD
  6. cellular response to organonitrogen compound Source: RGD
  7. cellular response to peptide hormone stimulus Source: RGD
  8. DNA catabolic process, endonucleolytic Source: GOC
  9. DNA catabolic process, exonucleolytic Source: GOC
  10. DNA demethylation Source: UniProtKB
  11. DNA recombination Source: UniProtKB-KW
  12. DNA repair Source: UniProtKB
  13. negative regulation of smooth muscle cell migration Source: RGD
  14. nucleic acid phosphodiester bond hydrolysis Source: GOC
  15. positive regulation of DNA repair Source: UniProtKB
  16. positive regulation of G1/S transition of mitotic cell cycle Source: RGD
  17. regulation of mRNA stability Source: UniProtKB
  18. regulation of transcription, DNA-templated Source: UniProtKB-KW
  19. response to drug Source: RGD
  20. response to organonitrogen compound Source: RGD
  21. RNA phosphodiester bond hydrolysis, endonucleolytic Source: GOC
  22. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Activator, Endonuclease, Exonuclease, Hydrolase, Lyase, Nuclease, Repressor

Keywords - Biological processi

DNA damage, DNA recombination, DNA repair, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, RNA-binding

Enzyme and pathway databases

ReactomeiREACT_211792. Processive synthesis on the lagging strand.
REACT_235056. Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta).
REACT_235984. Gap-filling DNA repair synthesis and ligation in TC-NER.
REACT_238907. Displacement of DNA glycosylase by APE1.
REACT_253309. Resolution of AP sites via the multiple-nucleotide patch replacement pathway.
REACT_253725. Resolution of D-loop structures through Holliday junction intermediates.
REACT_256001. Base-free sugar-phosphate removal via the single-nucleotide replacement pathway.
REACT_256392. Removal of DNA patch containing abasic residue.
REACT_260603. Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha).
REACT_262454. Gap-filling DNA repair synthesis and ligation in GG-NER.
REACT_263291. Processive synthesis on the C-strand of the telomere.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-(apurinic or apyrimidinic site) lyase (EC:3.1.-.-, EC:
Alternative name(s):
APEX nuclease
Short name:
Apurinic-apyrimidinic endonuclease 1
Short name:
AP endonuclease 1
Redox factor-1
Cleaved into the following chain:
Gene namesi
Synonyms:Ape, Apex, Ref1
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
ProteomesiUP000002494: Chromosome 15

Organism-specific databases

RGDi2126. Apex1.

Subcellular locationi

Nucleus 1 PublicationPROSITE-ProRule annotation. Nucleusnucleolus By similarity. Nucleus speckle PROSITE-ProRule annotation. Endoplasmic reticulum By similarity. Cytoplasm PROSITE-ProRule annotation
Note: Colocalized with SIRT1 in the nucleus. Colocalized with YBX1 in nuclear speckles after genotoxic stress. Together with OGG1 is recruited to nuclear speckles in UVA-irradiated cells. Colocalized with nucleolin and NPM1 in the nucleolus. Its nucleolar localization is cell cycle dependent and requires active rRNA transcription. Colocalized with calreticulin in the endoplasmic reticulum. Translocation from the nucleus to the cytoplasm is stimulated in presence of nitric oxide (NO) and function in a CRM1-dependent manner, possibly as a consequence of demasking a nuclear export signal (amino acid position 63-79). S-nitrosylation at Cys-92 and Cys-309 regulates its nuclear-cytosolic shuttling. Detected in the cytoplasm of B cells stimulated to switch. Ubiquitinated form is localized predominantly in the cytoplasm (By similarity).By similarity
Chain DNA-(apurinic or apyrimidinic site) lyase, mitochondrial : Mitochondrion
Note: The cleaved APEX2 is only detected in mitochondria. Translocation from the cytoplasm to the mitochondria is mediated by ROS signaling and cleavage mediated by granzyme A. Tom20-dependent translocated mitochondrial APEX1 level is significantly increased after genotoxic stress (By similarity).By similarity

GO - Cellular componenti

  1. centrosome Source: Ensembl
  2. cytoplasm Source: RGD
  3. endoplasmic reticulum Source: UniProtKB-SubCell
  4. mitochondrion Source: RGD
  5. nuclear speck Source: UniProtKB
  6. nucleolus Source: UniProtKB
  7. nucleus Source: UniProtKB
  8. perinuclear region of cytoplasm Source: UniProtKB
  9. transcription factor complex Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Endoplasmic reticulum, Mitochondrion, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11RemovedBy similarity
Chaini2 – 317316DNA-(apurinic or apyrimidinic site) lyasePRO_0000200012Add
Chaini31 – 317287DNA-(apurinic or apyrimidinic site) lyase, mitochondrialBy similarityPRO_0000402574Add

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei6 – 61N6-acetyllysine; by EP300By similarity
Modified residuei26 – 261N6-acetyllysineBy similarity
Modified residuei30 – 301N6-acetyllysineBy similarity
Modified residuei31 – 311N6-acetyllysineBy similarity
Modified residuei34 – 341N6-acetyllysineBy similarity
Disulfide bondi64 ↔ 92AlternateBy similarity
Modified residuei64 – 641S-nitrosocysteine; alternateBy similarity
Modified residuei92 – 921S-nitrosocysteine; alternateBy similarity
Modified residuei196 – 1961N6-acetyllysineBy similarity
Modified residuei232 – 2321Phosphothreonine; by CDK5By similarity
Modified residuei309 – 3091S-nitrosocysteineBy similarity

Post-translational modificationi

Phosphorylated. Phosphorylation by kinase PKC or casein kinase CK2 results in enhanced redox activity that stimulates binding of the FOS/JUN AP-1 complex to its cognate binding site. AP-endodeoxyribonuclease activity is not affected by CK2-mediated phosphorylation. Phosphorylation of Thr-232 by CDK5 in response to MPP+/MPTP (1-methyl-4-phenylpyridinium) reduces AP-endodeoxyribonuclease activity resulting in accumulation of DNA damage and contributing to neuronal death (By similarity).By similarity
Acetylated on Lys-6. Acetylation is increased by the transcriptional coactivator EP300 acetyltransferase, genotoxic agents like H2O2 and methyl methanesulfonate (MMS). Acetylation increases its binding affinity to the negative calcium response element (nCaRE) DNA promoter. The acetylated form induces a stronger binding of YBX1 to the Y-box sequence in the MDR1 promoter than the unacetylated form. Deacetylated on lysines. Lys-6 is deacetylated by SIRT1 (By similarity).By similarity
Cleaved at Lys-30 by granzyme A to create the mitochondrial form; leading in reduction of binding to DNA, AP endodeoxyribonuclease activity, redox activation of transcription factors and to enhanced cell death. Cleaved by granzyme K; leading to intracellular ROS accumulation and enhanced cell death after oxidative stress (By similarity).By similarity
Cys-64 and Cys-92 are nitrosylated in response to nitric oxide (NO) and lead to the exposure of the nuclear export signal (NES).By similarity
Ubiquitinated by MDM2; leading to translocation to the cytoplasm and proteasomal degradation.By similarity

Keywords - PTMi

Acetylation, Cleavage on pair of basic residues, Disulfide bond, Phosphoprotein, S-nitrosylation, Ubl conjugation

Proteomic databases


PTM databases



Gene expression databases

ExpressionAtlasiP43138. baseline and differential.


Subunit structurei

Monomer. Homodimer; disulfide-linked. Component of the SET complex, composed of at least APEX1, SET, ANP32A, HMGB2, NME1 and TREX1. Associates with the dimer XRCC5/XRCC6 in a DNA-dependent manner. Interacts with SIRT1; the interaction is increased in the context of genotoxic stress. Interacts with HDAC1, HDAC2 and HDAC3; the interactions are not dependent on the APEX1 acetylation status. Interacts with XRCC1; the interaction is induced by SIRT1 and increased with the APEX1 acetylated form. Interacts with NPM1 (via N-terminal domain); the interaction is RNA-dependent and decreases in hydrogen peroxide-damaged cells. Interacts (via N-terminus) with YBX1 (via C-terminus); the interaction is increased in presence of APEX1 acetylated. Interacts with HNRNPL; the interaction is DNA-dependent. Interacts (via N-terminus) with KPNA1 and KPNA2. Interacts with TXN; the interaction stimulates the FOS/JUN AP-1 complex DNA-binding activity in a redox-dependent manner. Interacts with GZMA, KRT8, MDM2, POLB, PRDX6, PRPF19, RPLP0, TOMM20 and WDR77. Binds to CDK5 (By similarity).By similarity


3D structure databases

SMRiP43138. Positions 39-317.

Family & Domainsi


Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni2 – 3231Necessary for interaction with YBX1, binding to RNA, association together with NPM1 to rRNA, endoribonuclease activity on abasic RNA and localization in the nucleoliBy similarityAdd
Regioni8 – 125Nuclear localization signal (NLS)By similarity
Regioni22 – 3211Necessary for interaction with NPM1 and for efficient rRNA bindingBy similarityAdd
Regioni63 – 7917Nuclear export signal (NES)By similarityAdd
Regioni288 – 31730Mitochondrial targeting sequence (MTS)By similarityAdd


The N-terminus contains the redox activity while the C-terminus exerts the DNA AP-endodeoxyribonuclease activity; both function are independent in their actions. An unconventional mitochondrial targeting sequence (MTS) is harbored within the C-terminus, that appears to be masked by the N-terminal sequence containing the nuclear localization signal (NLS), that probably blocks the interaction between the MTS and Tom proteins (By similarity).By similarity

Sequence similaritiesi

Belongs to the DNA repair enzymes AP/ExoA family.Curated

Phylogenomic databases


Family and domain databases

Gene3Di3.60.10.10. 1 hit.
InterProiIPR004808. AP_endonuc_1.
IPR020847. AP_endonuclease_F1_BS.
IPR020848. AP_endonuclease_F1_CS.
IPR005135. Endo/exonuclease/phosphatase.
[Graphical view]
PANTHERiPTHR22748. PTHR22748. 1 hit.
PfamiPF03372. Exo_endo_phos. 1 hit.
[Graphical view]
SUPFAMiSSF56219. SSF56219. 1 hit.
TIGRFAMsiTIGR00633. xth. 1 hit.
PROSITEiPS00726. AP_NUCLEASE_F1_1. 1 hit.
PS00727. AP_NUCLEASE_F1_2. 1 hit.
PS00728. AP_NUCLEASE_F1_3. 1 hit.
PS51435. AP_NUCLEASE_F1_4. 1 hit.
[Graphical view]


Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P43138-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
60 70 80 90 100
110 120 130 140 150
160 170 180 190 200
210 220 230 240 250
260 270 280 290 300
Mass (Da):35,538
Last modified:January 23, 2007 - v2

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti10 – 101Missing in AAA21019. (PubMed:7510394)Curated
Sequence conflicti236 – 2361R → A in AAA21019. (PubMed:7510394)Curated
Sequence conflicti288 – 2881H → Q in AAA21019. (PubMed:7510394)Curated

Sequence databases

Select the link destinations:
Links Updated
L27076 mRNA. Translation: AAA21019.1.
AB023065 Genomic DNA. Translation: BAA82124.1.
D44495 mRNA. Translation: BAA07938.1.
AF309114 mRNA. Translation: AAG40859.1.
BC078816 mRNA. Translation: AAH78816.1.
RefSeqiNP_077062.1. NM_024148.1.
XP_006251975.1. XM_006251913.1.

Genome annotation databases

EnsembliENSRNOT00000013176; ENSRNOP00000013176; ENSRNOG00000009663.
UCSCiRGD:2126. rat.


Sequence databases

Select the link destinations:
Links Updated
L27076 mRNA. Translation: AAA21019.1 .
AB023065 Genomic DNA. Translation: BAA82124.1 .
D44495 mRNA. Translation: BAA07938.1 .
AF309114 mRNA. Translation: AAG40859.1 .
BC078816 mRNA. Translation: AAH78816.1 .
PIRi S42397.
RefSeqi NP_077062.1. NM_024148.1.
XP_006251975.1. XM_006251913.1.
UniGenei Rn.5949.

3D structure databases

ProteinModelPortali P43138.
SMRi P43138. Positions 39-317.
ModBasei Search...
MobiDBi Search...

PTM databases

PhosphoSitei P43138.

Proteomic databases

PaxDbi P43138.
PRIDEi P43138.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSRNOT00000013176 ; ENSRNOP00000013176 ; ENSRNOG00000009663 .
GeneIDi 79116.
KEGGi rno:79116.
UCSCi RGD:2126. rat.

Organism-specific databases

CTDi 328.
RGDi 2126. Apex1.

Phylogenomic databases

eggNOGi COG0708.
GeneTreei ENSGT00530000063540.
HOGENOMi HOG000034586.
InParanoidi P43138.
KOi K10771.
OrthoDBi EOG7C8GJ6.
PhylomeDBi P43138.
TreeFami TF315048.

Enzyme and pathway databases

Reactomei REACT_211792. Processive synthesis on the lagging strand.
REACT_235056. Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta).
REACT_235984. Gap-filling DNA repair synthesis and ligation in TC-NER.
REACT_238907. Displacement of DNA glycosylase by APE1.
REACT_253309. Resolution of AP sites via the multiple-nucleotide patch replacement pathway.
REACT_253725. Resolution of D-loop structures through Holliday junction intermediates.
REACT_256001. Base-free sugar-phosphate removal via the single-nucleotide replacement pathway.
REACT_256392. Removal of DNA patch containing abasic residue.
REACT_260603. Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha).
REACT_262454. Gap-filling DNA repair synthesis and ligation in GG-NER.
REACT_263291. Processive synthesis on the C-strand of the telomere.

Miscellaneous databases

NextBioi 614526.
PROi P43138.

Gene expression databases

ExpressionAtlasi P43138. baseline and differential.
Genevestigatori P43138.

Family and domain databases

Gene3Di 1 hit.
InterProi IPR004808. AP_endonuc_1.
IPR020847. AP_endonuclease_F1_BS.
IPR020848. AP_endonuclease_F1_CS.
IPR005135. Endo/exonuclease/phosphatase.
[Graphical view ]
PANTHERi PTHR22748. PTHR22748. 1 hit.
Pfami PF03372. Exo_endo_phos. 1 hit.
[Graphical view ]
SUPFAMi SSF56219. SSF56219. 1 hit.
TIGRFAMsi TIGR00633. xth. 1 hit.
PROSITEi PS00726. AP_NUCLEASE_F1_1. 1 hit.
PS00727. AP_NUCLEASE_F1_2. 1 hit.
PS00728. AP_NUCLEASE_F1_3. 1 hit.
PS51435. AP_NUCLEASE_F1_4. 1 hit.
[Graphical view ]
ProtoNeti Search...


« Hide 'large scale' publications
  1. "Cloning of the multifunctional rat apurinic/apyrimidinic endonuclease (rAPEN)/redox factor from an immature T cell line."
    Wilson T.M., Carney J.P., Kelley M.R.
    Nucleic Acids Res. 22:530-531(1994) [PubMed] [Europe PMC] [Abstract]
    Strain: Sprague-Dawley.
    Tissue: Testis.
  2. "Genomic structure of the rat major AP endonuclease gene (Apex) with an adjacent putative O-sialoglycoprotease gene (Prsmg1/Gcpl1) and a processed Apex pseudogene (Apexp1)."
    Yao M., Akiyama K., Tan Y., Sarker A.H., Ikeda S., Alam S.S., Tsutsui K., Yoshida M.C., Seki S.
    Acta Med. Okayama 53:245-252(1999) [PubMed] [Europe PMC] [Abstract]
  3. "cDNA and deduced amino acid sequence of rat APEX nuclease."
    Tan Y., Akiyama K., Seki S., Tabayashi T., Taniyama M.
    Submitted (DEC-1994) to the EMBL/GenBank/DDBJ databases
    Strain: Sprague-Dawley.
    Tissue: Brain.
  4. "Cloning of APEX cDNA gene from PC12 cell line."
    Xie Z.H., Liu C.Z., Wang A.M., Ma C.
    Submitted (SEP-2000) to the EMBL/GenBank/DDBJ databases
    Tissue: Pheochromocytoma.
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Tissue: Kidney.
  7. "Identification of apurinic/apyrimidinic endonuclease 1 (APE1) as the endoribonuclease that cleaves c-myc mRNA."
    Barnes T., Kim W.C., Mantha A.K., Kim S.E., Izumi T., Mitra S., Lee C.H.
    Nucleic Acids Res. 37:3946-3958(2009) [PubMed] [Europe PMC] [Abstract]

Entry informationi

Entry nameiAPEX1_RAT
AccessioniPrimary (citable) accession number: P43138
Secondary accession number(s): Q548N9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: January 23, 2007
Last modified: January 7, 2015
This is version 137 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program



The specific activity of the cleaved mitochondrial endodeoxyribonuclease appeared to be about 3-fold higher than of the full-length form. Extract of mitochondria, but not of nuclei or cytosol, cleaves recombinant APEX1 to generate a mitochondrial APEX1-sized product (By similarity).By similarity

Keywords - Technical termi

Complete proteome, Reference proteome


  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.