exoc3l2b notes

Setup and provenance

• Fetched with just fetch-gene on A0A8M9Q5H9 (TrEMBL, RefSeq XP_021328615.1, "Exocyst complex
  component 3-like protein 2 isoform X1", 917 aa); 2 GOA rows (both IEA from InterPro), none with
  a PMID. The PANTHER TGD table lists a different accession for this gene (A0A8M3B147). UniProt
  reports that accession as inactive ("Deleted from sequence source (RefSeq)", checked 2026-09-28),
  and QuickGO returns no annotations for it. This is why the current entry has none of the IBA rows
  that exoc3l2a carries: an accession artefact, not a biological difference. ZFIN ZDB-GENE-100728-5, Ensembl ENSDARG00000030782, chromosome 15.
• Deep research unavailable: Edison returned 402 Payment Required and the OpenAI key is
  invalid, so no -deep-research-*.md file exists. Literature searched by hand via Europe PMC
  (see exoc3l2a notes for the queries). exoc3l2b itself returns no paper.
• DANRE_DUPLICATION random sample, draw 4 (seed 20260928); paralog exoc3l2a.

Orthology

Same as exoc3l2a (see genes/DANRE/exoc3l2a/exoc3l2a-notes.md and
file:DANRE/exoc3l2a/exoc3l2a-bioinformatics/RESULTS.md): 35.9% identical to human EXOC3L2 and
20.6-21.9% to EXOC3, EXOC3L1, EXOC3L4 and TNFAIP2. Ensembl Compara: human EXOC3L2 ortholog
(one-to-many), one gar ortholog shared with exoc3l2a, one-to-one medaka ortholog; paralog
duplication node Osteoglossocephalai. The PANTHER table's EXOC3L4 call is not supported by sequence.

Zebrafish literature

• ZFIN curates four wild-type expression rows for exoc3l2b, all from one paper (ZDB-PUB-100518-8
  = PMID:20463035, Piloto and Schilling 2010): neural crest at 5-9 somites (in situ), dorsal
  hindbrain and pharyngeal arches from prim-5 to protruding-mouth (in situ), whole embryo (RT-PCR).
  The paper calls the gene "sec6"; the assignment to exoc3l2b is ZFIN's curation (the probe
  sequence is in the paper's supplementary primer table, which I have not seen).
  PMID:20463035
  PMID:20463035
  "sec6" was up-regulated in Ovo1 morphants (microarray, qPCR) and after dnTcf3 induction:
  PMID:20463035
  Overexpression phenocopy was shown for rab11fip2, not for sec6.
• No mutant, morphant or protein-level study of exoc3l2b.

Mammalian EXOC3L2

See exoc3l2a notes (PMID:21566143, PMID:36362885, PMID:30327448, PMID:30086153). Of note for the
pair: mouse Exoc3l2 is expressed both in endothelium and in probable cranial neural crest
PMID:36362885.

Own analyses

Shared pair analysis in genes/DANRE/exoc3l2a/exoc3l2a-bioinformatics/ (RESULTS.md). exoc3l2b is
the slower-evolving copy (71 lineage-specific changes vs 138 for exoc3l2a against gar), and is
closer to gar (56.2% vs 47.5%). Whole-embryo time course similar to exoc3l2a (both rise from
segmentation to 8-13 TPM at 3-5 dpf). Bgee adult calls broadly overlap exoc3l2a (intestine,
gill, kidney, heart, liver, skin, bone, muscle, granulocytes).

Annotation decisions

• exocyst (IEA): accepted, as for exoc3l2a.
• exocytosis (IEA): kept as non-core, as for exoc3l2a.
• No NEW rows: the neural-crest in situ data are expression, not function; the Ovo1 paper did not
  test sec6/exoc3l2b function.