Protein localization to ER exit site obsoletion

GO:0070973 → five destinations, chosen per annotation

AI Gene Review · projects/ER_EXIT_SITE_LOCALIZATION_OBSOLETION · 2026

Bottom line

  • GO obsoleted GO:0070973 because curators used it for four different roles; there is no single replacement.
  • The 10 curated annotations each get their own term: COPII coat assembly, ER→Golgi transport, its regulation, ER stress, or deletion.
  • In this repo, BCAP31 is already aligned and yeast YET2 only has the same IBA in its cached UniProt record; LRRK2's two ACCEPT rows now MODIFY to GO:0060628, fixed in #3241 (merged).

Why the term went

  • The name says where a protein ends up, not what process it takes part in.
  • It was applied to COPII scaffolds, cargo receptors, a kinase regulator and ER quality-control chaperones.
  • OLS obsoletion note: replacements "depend on the specific biological context".
  • One UniRule mapping (UR001349783) propagated it to ~14,414 annotations, mostly IEA and IBA.

Four roles at the ER exit site

One term, five destinations

Curated rows to move

Gene Organism Evidence Destination
SEC16A · sec-16A.1 · SEC16 human · worm · yeast IMP GO:0048208
MIA3 · GBF1 human IMP GO:0006888 / vesicle transport
LRRK2 human IMP (PMID:25201882) GO:0060628
Bcap29 · Bcap31 mouse IGI GO:0034976 or child
Lrrk2 · Tb03.28C22.610 mouse · T. brucei IMP delete (redundant)

From QuickGO (2026-05-29) and the go-ontology#19122 plan.

Repo impact

Review GO:0070973 rows Current action Needed
genes/human/LRRK2 IEA (GO_REF:0000120), IMP (PMID:25201882) ACCEPT → MODIFY ×2 → GO:0060628, fixed in #3241 (merged)
genes/human/BCAP31 IBA (GO_REF:0000033) MARK_AS_OVER_ANNOTATED none
genes/yeast/YET2 IBA, cached UniProt record only (not in GOA file) not reviewed none; same PTN000294723 node
  • SEC16A, MIA3 and GBF1 have no review here yet.

Next steps

  1. ✅ #3241 merged: both LRRK2 GO:0070973 rows already MODIFY to GO:0060628.
  2. Optional: review SEC16A, MIA3, GBF1 as clean cases for the three main replacement terms.
  3. Flag UniRule UR001349783 for retargeting so the IEA tail does not re-propagate.

Upstream: go-annotation#6434 · go-ontology#19122 · go-annotation#6172
Read more: projects/ER_EXIT_SITE_LOCALIZATION_OBSOLETION.md