sox9a (Q9DFH2) curation notes

2026-09-27 — initial review (DANRE_DUPLICATION project, pair sox9a/sox9b)

One of two zebrafish co-orthologs of tetrapod SOX9; alias jellyfish (jef).
PMID:12397114
Duplicated chromosome segments: PMID:11180959
PANTHER v19 calls the pair TGD_or_lineage (duplication on Teleostei|DANRE, one gar co-ortholog, one medaka co-ortholog), see projects/DANRE_DUPLICATION/panther_tgd_pairs.tsv.

HMG box 107-175 (UniProt). Region identity script: sox9a-bioinformatics/ (HMG box 98.6% identical to Sox9b and human SOX9; whole protein 61.3% vs Sox9b, 70.2% vs human SOX9). Sox9a is the less diverged copy relative to human SOX9.
Both proteins bind DNA and transactivate: PMID:11180959
ChIP of tagged Sox9a: PMID:25568117

Cartilage: PMID:12397114
Stacking vs number: PMID:15689370
Glia: PMID:20023158
Otic: redundancy with sox9b / dlx3b / dlx4b PMID:12668634
Heart: not required PMID:23775563
Gonad: PMID:15939378
Deep research (sox9a-deep-research-falcon.md, arrived during review) cites Lin et al. 2021 (Aquaculture and Fisheries, doi:10.1016/j.aaf.2019.12.009, no PMID found in Europe PMC) with CRISPR sox9a frameshift alleles that lose neurocranial and most arch cartilage; not independently verified here.

REMOVE protein binding (IPI, Ewsa co-IP): uninformative; also the anti-SOX9 antibody was commercial, so the copy detected is unclear.
cytoplasm (IMP, PMID:12397114) x2: MARK_AS_OVER_ANNOTATED. The paper's observation is about nuclear retention of unspliced sox9a transcript after splice-blocking MO, not protein. Sun et al. 2013 (PMID:24263104) reports a cytoplasmic Sox9a protein pool in juvenile gonad, so not removed outright.
heart development (IBA): MARK_AS_OVER_ANNOTATED for sox9a (paralog-partitioned function; donor is sox9b; sox9a MO had no cardiac effect). Added propagation_review.
NEW GO:0001228 (transcription activator activity) on both copies, from PMID:11180959.
Otic, fin, glial, placode terms: KEEP_AS_NON_CORE. Cartilage/chondrocyte: ACCEPT (core).