Endonuclease which cleaves flap structures at the junction between single-stranded DNA and double-stranded DNA. Specific for 5'-overhanging flap structures in which the 5'-upstream of the flap is completely double-stranded. Prefers the blocked-flap structures similar to those occurring at replication forks, in which the 5' single-strand overhang of the flap is double-stranded. Also possesses weak 5'- to 3'-exonuclease activity on nicked but not gapped double-stranded DNA. Does not cleave bubble-like or Holliday junction substrates. Binds 2 magnesium ions per subunit. They probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding. Optimum pH is 8. Present in stage 1-4 embryos (at protein level). Belongs to the XPG/RAD2 endonuclease family. GEN subfamily. 3' to 5' exonuclease activity reported in PubMed:15576351 is probably artifactual, due to the presence of other nucleases in the preparation.