mapre3a notes

Setup and provenance

• Fetched with just fetch-gene on A0A8M2B5B2 (TrEMBL, RefSeq XP_005158903.1, 273 aa), the
  mapre3a accession with the most GOA rows (10: 8 IBA, 2 IEA, none with a PMID). Other
  accessions for the gene (Q4V903 and A0ACM8Q7J9, RefSeq NP_001025298.1, 259 aa) carry only 2
  GOA rows each and no experimental rows (checked with
  projects/DANRE_DUPLICATION/scripts/accession_audit.py, printed to the terminal only).
  ZFIN ZDB-GENE-050913-88; Ensembl ENSDARG00000020231, chromosome 17.
• Deep research unavailable: Edison returned 402 Payment Required and the OpenAI key is
  invalid, so no -deep-research-*.md file exists. Literature was searched by hand in Europe
  PMC (mapre3a, mapre3b, mapre3 AND zebrafish, zebrafish AND (EB3 OR mapre3), and
  EB3/MAPRE3 mammalian searches).
• DANRE_DUPLICATION batch 4 (random draw, seed 20260928); paralog mapre3b. Compara duplication
  node Clupeocephala; PANTHER call TGD_tree.

Zebrafish literature

• No functional study of mapre3a (or mapre3b). Most zebrafish "EB3" hits use tagged mammalian
  EB3 (EB3-GFP) as a reporter of microtubule growth, which says nothing about the zebrafish genes.
• mapre3a appears only in a list of genes near hypermethylated CpGs after developmental
  glucocorticoid exposure
  PMID:38989456.
  This is an expression/methylation observation, not function.
• ZFIN has no curated wild-type expression for mapre3a (ZFIN download checked by
  mapre3a-bioinformatics/pair_analysis.py).

Mammalian EB3 (MAPRE3)

• Identified as an APCL-binding EB1 homolog, brain enriched
  PMID:10644998;
  on the cytoplasmic microtubule network
  PMID:10644998.
• Endogenous EB3 is enriched in brain extracts and marks growing microtubule ends in neurons
  PMID:12684451.
• EB1 and EB3 (not EB2) promote persistent microtubule growth by suppressing catastrophes;
  plus-end tracking depends on the CH domain, anti-catastrophe activity needs dimerization
  PMID:19255245
  PMID:19255245
  PMID:19255245.

IBA sources

• All 8 IBA rows come from PANTHER node PTN000065701 (the RP/EB family); donors include
  human MAPRE1 (Q15691) and MAPRE3 (Q9UPY8), yeast Bim1 (SGD:S000000818), fission yeast Mal3
  (PomBase:SPAC18G6.15), Arabidopsis EB1 genes, worm, fly and Dictyostelium EBs. This is a
  deep, very conserved node; both zebrafish copies are inside it.

Pair analysis

See mapre3a-bioinformatics/RESULTS.md (protein identity, domain conservation, relative rate
with gar, expression from E-ERAD-475, Bgee and ZFIN, and synteny).