gria1b notes (Danio rerio, glutamate receptor, ionotropic, AMPA 1b; UniProt E7F1V8)

2026-09-28 — session log (DANRE_DUPLICATION batch 4, random TGD_tree sample)

Deep research: not available (Edison/Falcon 402 Payment Required; OpenAI key invalid). Not
attempted, per instructions. Literature searched by hand (queries listed in ../gria1a/gria1a-notes.md).
Pair analysis in ../gria1a/gria1a-bioinformatics/RESULTS.md.

Accession E7F1V8 (TrEMBL, RefSeq XP_005161396 "isoform X1", 917 aa), ZFIN:ZDB-GENE-020125-2,
Ensembl ENSDARG00000032714, chr21. 15 GOA rows (IBA and IEA only), identical to gria1a.

Literature

• No study of gria1b alone. It appears in the survey of all eight AMPA receptor genes:
  PMID:18224707
  ZFIN curation of that paper gives gria1b 17 anatomy terms, all shared with gria1a except otic
  vesicle (long-pec and protruding-mouth stages).
• Maternal transcript: PMID:16887104
• The Thyme et al. 2019 screen mutated both copies of duplicated genes
  PMID:30929901;
  which copy (or the double) gave the gria1 pallium phenotype is not stated in the text.

Protein (RESULTS.md)

• 82.5% identical to gria1a, 81.7% to gar GRIA1 (gria1a 88.3%). gria1b has significantly more
  changes than gria1a relative to gar (86 vs 34, chi2 = 22.5).
• Ligand-binding residues, pore loop, M2-M3 segment and palmitoylation cysteines unchanged.
• The C-terminal tail is the most diverged part: I at the position of human S849 (mature S831,
  CaMKII/PKC site) and no aligned serine at S863 (mature S845, PKA site); C-terminus TTGM.
  PMID:20716669
  All Ensembl gria1b translations carry the same changes (not an isoform artefact). The medaka
  gria1b ortholog has L at S849 (so this change is shared by the teleost b lineage) but keeps S at
  S863, and is itself strongly diverged from gar (71.6% vs 87.4% for medaka gria1a).

Expression (RESULTS.md)

• E-ERAD-475 whole embryo: 5-6 TPM in larvae vs 12-14 for gria1a.
• Bgee: brain, retina, testis (both copies; testis score higher for gria1b) plus mature ovarian follicle, spleen, gill (gria1b only).

Annotation decisions

• Same as gria1a (see gria1a notes): MF, complex, membrane locations and glutamatergic transmission
  terms accepted; dendritic spine and modulation of chemical synaptic transmission kept as non-core.
• The C-terminal changes do not touch any existing GO term, so no copy-specific change is made;
  they are recorded as a question.