sox9b (Q9DFH1) curation notes

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

Identity and protein

• TGD co-ortholog of SOX9 with sox9a; 407 aa, HMG box 91-159. HMG box 98.6% identical to Sox9a/human SOX9; whole protein 56.8% identical to human SOX9 (see file genes/DANRE/sox9a/sox9a-bioinformatics/RESULTS.md). Sox9b is the more diverged copy, with divergence concentrated C-terminal to the HMG box.
• PMID:11180959
• Nuclear protein: PMID:27565026

Alleles (important for interpreting annotations)

• b971 is a multi-gene deletion: PMID:19210963; PMID:22719264
• fh313 nonsense allele (K68 stop, before the HMG box) used by Delous 2012, Manfroid 2012, Huang 2016.
• Lin et al. 2021 (no PMID; via sox9b-deep-research-falcon.md): CRISPR sox9b frameshift alleles reported grossly normal cartilage. Unverified here; possible genetic compensation.

Copy-specific functions (sox9a not expressed / not required)

• Ducts: PMID:22719264
• Retina: PMID:19210963
• Heart: PMID:23775563; cardiomyocyte requirement PMID:30224706
• Endocrine progenitors: PMID:27565026
• Liver regeneration: PMID:24315993
• Oocytes: PMID:15939378
• Dosage sensitivity: PMID:18784347

Annotation decisions

• regeneration (IMP, PMID:24315993): MODIFY -> GO:0097421 liver regeneration.
• melanocyte and iridophore differentiation (IMP, PMID:15689370): UNDECIDED (abstract-only; b971 deletion caveat).
• hepaticobiliary system development and pancreas development: ACCEPT (copy-specific core).
• heart valve, proepicardium, epicardium, retina, endocrine pancreas, beta-cell differentiation, otic, fin, palate: KEEP_AS_NON_CORE.
• oligodendrocyte differentiation IBA: KEEP_AS_NON_CORE (expressed in glial progenitor domains; not tested directly).
• NEW GO:0001228 (as for sox9a).
• Deep research file arrived during the review and was used (Lin 2021 caveat, Gawdzik 2018 lead).