abi1a notes

Setup and provenance

• Fetched with just fetch-gene on A0A8M3AND6 (TrEMBL, RefSeq XP_009295502.1, "isoform X1",
  522 aa); 8 GOA rows (5 IBA, 3 IEA), none with a PMID. ZFIN ZDB-GENE-040426-1701,
  Ensembl ENSDARG00000010155, chromosome 24.
• Deep research unavailable: Edison returned 402 Payment Required and the OpenAI key is
  invalid, so no -deep-research-*.md was generated. Literature searched by hand via Europe PMC
  (queries: abi1a zebrafish, abi1b zebrafish, (abi1 OR "abl interactor 1") AND zebrafish,
  title searches for ABI1, ABI2, WAVE regulatory complex).
• Part of DANRE_DUPLICATION batch 3 (random draw 7 of seed 20260928); paralog abi1b.

What the zebrafish literature says

Essentially nothing on function. The only experiment found:

• F0 CRISPR knockdown of "abi1" in a congenital-heart-disease follow-up gave no cardiac
  phenotype (1/72 embryos with reversed looping) PMID:32368696.
  The authors speculate compensation by the paralog, without testing it
  PMID:32368696.
  F0 embryos are mosaic PMID:32368696.
• Other hits (inner-ear transcriptomes, spinal-cord microarrays, mutagenesis screens) only list the
  gene in datasets.

Mammalian ABI1 (the ancestral function)

• Discovered as an SH3 protein binding the Abl C-terminus PMID:7590237
  and widely expressed PMID:7590237.
• Core subunit of the WAVE regulatory complex (WRC = SCAR complex)
  PMID:15048123;
  needed for Rac-dependent lamellipodia PMID:15048123
  and relocalizes to the leading edge PMID:15048123.
• Structure: Abi forms a four-helix bundle with WAVE and HSPC300 in the WRC
  PMID:21107423;
  the Abi subunit forms part of the WIRS receptor-binding surface
  PMID:24439376.
• Also activates N-WASP PMID:16155590.
• Mouse knockouts: Abi1 is essential mid-gestation, heart and brain affected
  PMID:21482783;
  PMID:21173240.
  Abi2 cannot compensate PMID:21482783.
• Neuron migration donor for the IBA is mouse Abi2 (MGI:106913)
  PMID:15572692.

Own analyses

abi1a-bioinformatics/pair_analysis.py (results in RESULTS.md, raw output.txt):
protein identity, conserved regions, gar relative-rate test, E-ERAD-475 time course, Bgee
calls for both copies and gar, local synteny. Key points:
- abi1a 81.6% identical to human ABI1; abi1b 77.5%; abi1a vs abi1b 79.2%.
- WAVE-binding N-terminus, coiled coil and SH3 conserved in both; Y213 (ABL site) kept.
- Relative-rate test vs gar not significant (17 vs 28 unique changes).
- Temporal reciprocity: abi1b is the maternal/cleavage-stage transcript (26-28 TPM at 128- to
1k-cell) while abi1a takes over from mid-gastrula (26-36 TPM from 75% epiboly onward; abi1b
3-7 TPM).
- Synteny: no conserved microsynteny within 1.5 Mb; 3 teleost-level paralogue pairs from the
abi1a neighbourhood have partners elsewhere on chr2 (kmt2c, agtr1). Ensembl Compara places the
duplication at Clupeocephala, agreeing with PANTHER.
- Bgee: abi1a called in many adult tissues (gill, intestine, skin, spleen, liver, muscle,
kidney, testis, eye); abi1b only in embryo, retina, brain, ovary, bone. Gar ABI1 is broadly
expressed, like abi1a.

Curation decisions (summary)

All 8 rows are family-level (IBA, SubCell IEA). WRC membership, lamellipodium location and
adaptor MF are accepted; neuron migration (Abi2-seeded IBA) and filopodium kept as non-core.
No NEW terms: nothing zebrafish-specific supports one.