Endonuclease which cleaves flap structures at the junction between single-stranded DNA and double-stranded DNA with a specific cleavage site in the 5' overhang strand exactly one nucleotide 3' of the branch point (PubMed:25037209). Structure- and sequence-specific nuclease that resolves holliday junctions (HJs) by symmetrically oriented incisions in two opposing strands near the junction point, thus leading to ligatable products; HJs are physical links between homologous DNA molecules that arise as central intermediary structures during homologous recombination and repair in meiotic and somatic cells (PubMed:25037209). Structure-specific nuclease with 5'-flap endonuclease activity, preferentially cleaving static flaps 5' overhang strand exactly one nucleotide in the 3' direction of the branch point and, to lower extent, on the two neighboring positions (PubMed:25037209). Also able to cleave double-stranded flap strand 1 one nucleotide in the 3' direction of the branch point (PubMed:25037209). Together with MUS81, essential for the resolution of toxic replication structures to ensure genome stability, and to maintain telomere integrity and replication (PubMed:26704385). 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. Normal sensitivity to DNA damaging agents (PubMed:26704385). Mild UV sensitivity in the gen1 send1 double mutant (PubMed:26704385). The double mutant mus81 send1 exhibits severe developmental defects (e.g. strong growth retardation and impaired leaf and shoot development), increased endoreduplication, slower cell cycle progression, spontaneous cell death and genome instability associated with a dramatic loss of telomeric repeats (PubMed:26704385). May be due to an intron retention. Belongs to the XPG/RAD2 endonuclease family. GEN subfamily. Was originally thought to correspond to two different genes At3g48900 and At3g48910. Was originally thought to correspond to two different genes At3g48900 and At3g48910.