prom1a notes (Danio rerio, prominin 1a; UniProt Q9W735)

2026-09-28 — session log (DANRE_DUPLICATION batch 4, random TGD_tree sample)

Deep research: not available (Edison 402 Payment Required; OpenAI key invalid). Not attempted, per
instructions. Literature found by hand through Europe PMC; pair analysis in prom1a-bioinformatics/RESULTS.md.

Accession Q9W735 (Swiss-Prot, 826 aa; alias proml1), ZFIN:ZDB-GENE-030131-1577, Ensembl ENSDARG00000039966,
chr14. Paralog prom1b (chr1). PANTHER TGD_tree pair (PTHR22730, PROM1 co-orthologs); Ensembl Compara places
the duplication at Osteoglossocephalai with one gar ortholog (ENSLOCG00000003057, LG4) for both copies. prom2 is a
separate, older paralog (Vertebrata level).

Nomenclature: PMID:21407811

Expression

• Embryo: PMID:20503380
• Adult retina, both in the ONL: PMID:21407811
  INL split: PMID:21407811
  PMID:21407811
  Authors' reading: PMID:21407811
• Adult brain: PMID:23723983
• Bulk data (my scripts): prom1a maternal (11-12 TPM cleavage-blastula) and broad in adult organs, like gar PROM1;
  prom1b zygotic only, restricted to retina/brain. Photoreceptor scRNA: both in rods and cones, prom1b 3-4x higher.

Function

• PMID:31362982
• Full text (PMC6755801, read on the web; not in the publications cache, so not quoted here): TALEN alleles for both
  copies (prom1a c.138_141delTACT, p.Asp46Glufs*15); prom1a mutants had normal ONL and outer-segment thickness up
  to 11 months; no double mutant; prom1a mRNA not significantly changed in its mutant at 2 mpf.
• Corbeil, Fargeas & Jaszai letter (PMID:31704774; text not cached) questioned the conclusion, citing prom1a splice
  variants and prom1a expression in the retina; authors replied (PMID:31704775).

Annotation decisions

• ER and ERGIC (IEA + ISS): MARK_AS_OVER_ANNOTATED (transit compartments).
• Plasma membrane, apical PM, microvillus, microvillus membrane, cilium, membrane: ACCEPT.
• Microvillus organization, prominosome (IBA): KEEP_AS_NON_CORE (no zebrafish data).
• Camera-type eye photoreceptor cell differentiation (IBA): MARK_AS_OVER_ANNOTATED with propagation review
  (the photoreceptor role went to prom1b).