APEX1 notes

2026-10-20 ORGANELLES batch 1 (mitochondrion rows)

• GO:0005739 rows: IEA (GO_REF:0000044, SL-0173; UniProt line is by similarity), HTP (PMID:34800366, mitochondrial proteome), IDA (PMID:20231292, MTS mapping). All kept ACCEPT; reasons now record that the direct assays resolve only the organelle.
• Sub-mitochondrial evidence (rule 4), from the Tell/Vascotto group:
• IMS: PMID:25956655;
  PMID:25956655;
  PMID:25956655
• Matrix: PMID:25956655;
  matrix-restricted MTS-APE1 rescues mtDNA damage and respiration PMID:33028238
• Outcome: two NEW IC rows, GO:0005758 mitochondrial intermembrane space (main pool) and GO:0005759 mitochondrial matrix (minor pool, where mtBER acts). The earlier fractionation paper behind the "majority in IMS" claim was not read directly, hence IC.
• Note on form: older work proposed an N-terminally truncated (NLS-less) form enters mitochondria; PMID:25956655 states full-length APE1 is present in mitochondria. The IEA row summary keeps the older wording.
• core_functions.locations left at nucleus: the core functions there are written for nuclear BER/redox; mitochondrial BER is real but not yet a separate core function entry.

2026-11-04 ORGANELLES ER batch 1 (endoplasmic reticulum rows)

• Rows: GO:0005783 IEA (GO_REF:0000044, SL-0095) and TAS (PMID:12524539), no qualifier; both kept KEEP_AS_NON_CORE.
• Check: UniProt location line "Endoplasmic reticulum." is untagged, and the note "Colocalized with calreticulin in the endoplasmic reticulum." sits in a note block carrying only {ECO:0000250} [file:human/APEX1/APEX1-uniprot.txt]. The human basis is Fan et al. 2003 (abstract-only cache): Ape1 "is contained in the SET complex, a macromolecular complex of 270-420 kDa that is associated with the endoplasmic reticulum" PMID:12524539. TAS curator had the full text.
• No signal peptide or TM segment; nuclear BER enzyme with a minor ER-associated (SET complex, cytosolic face) pool. Root only, no NEW row.
• Replaced title-only supported_by quotes on both ER rows with the abstract sentence and the UniProt note.