olfm3a notes

Setup and provenance

• Fetched with just fetch-gene on A8KB73 (TrEMBL, ZGC cDNA AAI53994.1, 457 aa); 6 GOA rows
  (2 IBA, 2 IEA, 2 ND root-term placeholders), none with a PMID. ZFIN ZDB-GENE-080219-11,
  Ensembl ENSDARG00000071493, chromosome 24 (an alternate-contig copy ENSDARG00000110039 also
  exists).
• Deep research unavailable: Edison returned 402 Payment Required and the OpenAI key is
  invalid. Literature searched by hand via Europe PMC (olfm3a, olfm3b,
  (olfm3 OR noelin-3 OR optimedin) AND zebrafish, olfm3 OR optimedin OR "olfactomedin 3").
• DANRE_DUPLICATION batch 3 (random draw 10 of seed 20260928); paralog olfm3b.

Zebrafish literature

No functional study of either copy. The only specific mention is a single-cell atlas of larval
brain, where olfm3a is one of the effector genes shared by glutamatergic clusters
PMID:34895465.
ZFIN has no curated wild-type expression for olfm3a or olfm3b (checked in the ZFIN
wildtype-expression download, 2026-09-28).

Mammalian OLFM3 (optimedin, noelin-3)

• Secreted olfactomedin-domain glycoprotein of retina, brain and anterior eye
  PMID:12019210;
  PMID:12019210;
  binds myocilin via the OLF domain and homodimerizes via the N-terminus
  PMID:12019210.
• Pax6 target with two promoters PMID:16115881.
• Overexpression in PC12 cells changes adhesion PMID:17054946.
• Forms heteromers with Olfm1/Olfm2 PMID:21228389.
• Noelins 1-3 are extracellular AMPA-receptor complex constituents; triple KO reduces synaptic
  AMPARs PMID:37591201.
  Olfm3 single KO is mild PMID:37591201;
  Noe3 transcripts are sparse and interneuron-biased in hippocampus.
• OLFM3 co-immunoprecipitates with GluA1/GluA2 and raises seizure susceptibility in mouse
  PMID:32850838.
• IBA donors for "signal transduction" are myocilin (mouse, human) and mouse Olfm1; no OLFM3
  member donates.

Own analyses

olfm3a-bioinformatics/pair_analysis.py (RESULTS.md, output.txt). Key points:
- olfm3a vs olfm3b 83.2% identity; to human OLFM3 isoform Q96PB7-3 (458 aa) 83.8% / 81.0%.
Both zebrafish entries have the N-terminus of Q96PB7-3, not of the 478-aa canonical isoform.
- OLF domain 86.6% / 85.0% identical to human; all 6 human cysteines kept in both; the two
calcium-site residues described for Olfm1 kept in both; N-glycosylation sequons at identical
positions in the two copies.
- Relative-rate test vs gar not significant (21 vs 32).
- E-ERAD-475: olfm3a rises from prim-25 to 9-11 TPM in larvae; olfm3b stays at 0-1 TPM
through day 5.
- Synteny: abca4a is ~125 kb from olfm3a (chr24) and its teleost paralogue abca4b ~140 kb from
olfm3b (chr2); several other chr24/chr2 teleost paralogue pairs (hs6st1, plppr4, agl, hccs).
Ensembl Compara nonetheless places the olfm3a/olfm3b node at Gnathostomata (PANTHER: TGD_tree).
- Bgee: olfm3a brain, retina, larva, bone; olfm3b brain, intestine, early embryo/blastula,
ovary, tail, bone (low scores). Gar OLFM3 highest in brain, ovary, eye.

Curation decisions

Location rows (extracellular region, synapse) accepted; signal transduction IBA marked
over-annotated (donors are myocilin/Olfm1; no OLFM3 evidence). ND rows accepted as accurate
records of absent curated data. No NEW terms.