col1a1a notes

2026-09-28 (claude-opus-5-5, DANRE_DUPLICATION pair review col1a1a/col1a1b)

• Deep research failed. Edison returned 402 Payment Required and the OpenAI key is invalid. It was not retried. The literature research below was done by hand (Europe PMC REST search plus cached publications).
• Accession Q6U1J5 (1447 aa, TrEMBL, EMBL AAR24536 "Chihuahua", RefSeq NP_954684). It holds all GOA rows (27).
• Identity: PMID:26876635.
• TGD origin: PANTHER TGD_tree (Neopterygii|Teleostei, 1 gar co-ortholog, 2 medaka). Literature: PMID:26876635.
• Expression: co-expressed with col1a1b and col1a2 PMID:26876635, except in the fin fold PMID:26876635.
• Loss of function (PMID:30082390, full text): the col1a1a sa1748 null is lethal PMID:30082390. It lacks actinotrichia PMID:30082390. The heterozygote is normal; the double heterozygote with col1a1b is fragile.
• Dominant alleles: chihuahua dc124 PMID:14623232; dmh13 and dmh14 PMID:28835471.
• ZFIN genotype check (zfin.org pages fetched 2026-09-28):
• 180503-6 = col1a1a^dmh13/+
• 180504-3 = col1a1a^dmh14/+
• 110630-21 = col1a1a^dc124/+
• 180503-7 = col1a1b^dmh29/+
• 180503-8 = col1a2^dmh15/+
• 190402-1 = col1a1a^sa1748/+; col1a1b^sa12931/+
• 221115-1 = col1a1a^dc124/+
• 011017-1 = col1a1a^dc124
• 111013-8 = col1a1a^tt281/tt281
• MRPHLNO-110630-1 = MO2-col1a1a

Two col1a1a skeletal system development IMP rows (PMID:30082390) therefore rest on genotypes with no col1a1a lesion. Those two rows are marked REMOVE; the term is kept through the other rows.
- Cytoplasm IDA (PMID:19757382). The full text was read. col1a1 is only an mRNA FISH marker PMID:19757382. The IDA row is MARK_AS_OVER_ANNOTATED. The IBA cytoplasm row (PTN002771199, sole source col1a1a) is REMOVE, and the same is done on col1a1b.
- Decisions:
- skeletal system development: IMP ACCEPT (col1a1a alleles); 2 mis-attached rows REMOVE.
- regulation of ossification: MODIFY to ossification (GO:0001503). Structural, not regulatory.
- fin development and fin morphogenesis: ACCEPT (copy-specific actinotrichia role). Pectoral fin development (morphant) and fin regeneration: non-core.
- bone mineralization, bone mineralization involved in bone maturation, and bone remodeling: non-core (downstream or indirect).
- collagen fibril organization (IBA and IMP), ECM structural constituent conferring tensile strength, ECM, extracellular region, ECM structural constituent: ACCEPT.
- skin development and skeletal system morphogenesis (IBA): non-core.
- NEW GO:0005584 collagen type I trimer (IDA, PMID:26876635). Comparator: human COL1A1 carries it by IDA/IPI/IMP (QuickGO, 2026-09-28).
- Pair page: projects/DANRE_DUPLICATION/pairs/col1a1a_col1a1b/col1a1a_col1a1b.md