tbx5b (E3W6T6) notes

Setup and provenance

• Gene fetched earlier with just fetch-gene on E3W6T6 (TrEMBL). That accession holds the 31 GOA rows,
  experimental and IBA. The genes were not re-fetched.
• Deep research failed. Edison returned 402 Payment Required and the OpenAI key is invalid. It was not
  retried. The literature below was researched by hand from the cached publications and from Europe PMC
  searches.

Identity and origin

• 422 aa. T-box domain at residues 57-237 (PROSITE). UniProt caution: "Lacks conserved residue(s) required
  for the propagation of feature annotation". ZFIN ZDB-GENE-060601-2.
• TGD paralog of tbx5a:
  PMID:19925885
  PMID:23441045
  The 23441045 abstract also states a phylogenetic TGD origin; that sentence contains a "~" character, so it
  is not quoted here.
• 49.2% identical to tbx5a overall (compare_pair.py) and 83% in the T-box
  PMID:39079985.
  PMID:30532148

Expression

• PMID:19925885
• The fin result is disputed:
  PMID:24759614
• Later onset and ventricle restriction:
  PMID:30532148
  PMID:30532148
  PMID:29382818

Alleles

• A CRISPR allele: 4-bp insertion in intron 1, which causes a splicing defect, a frameshift and a PTC. It may
  be subject to NMD and so could trigger transcriptional adaptation; this was not tested.
  PMID:30532148
  PMID:30532148
• Morpholinos: translation-blocking and splice-blocking, both used in PMID:24759614, and two morpholinos in
  PMID:23441045 (ZFIN MRPHLNO-130123-3 and 130702-2).

Function

• Heart: PMID:30532148
  PMID:30532148
  The two copies are not redundant:
  PMID:23441045
  PMID:23441045
• Jogging (morpholino-only): PMID:24759614
• Fin: PMID:24759614
  PMID:34756968
• Beyond the lateral plate mesoderm: PMID:30532148
  This is morpholino/RNA-seq only and was not proposed as NEW.
• Swim bladder: PMID:30532148
  This concerns inflation, not formation, so the NOT swim bladder development annotation from PMID:30352852
  stands.

Annotation decisions (summary)

• ACCEPT:
• MF (IBA/IEA). There is no direct assay of Tbx5b, but there is a conserved T-box, rescue by its own mRNA,
  and a mutant phenocopy.
• nucleus, chromatin, regulation of transcription.
• heart looping, heart morphogenesis, heart development.
• pectoral fin development (copy-specific late role).
• NOT swim bladder development.
• KEEP_AS_NON_CORE:
• heart jogging (morpholino-only, but no contradicting mutant; tbx5a jogging rows are UNDECIDED).
• optic nerve and retina (double morphants), cytoplasm, cell fate and pattern specification.
• MARK_AS_OVER_ANNOTATED: cardiac left ventricle formation (IBA, with a propagation_review), epithelium
  development (ARBA).
• No NEW terms. The vasculature and somite effects are morpholino-only, and possibly indirect.