gria1a notes (Danio rerio, glutamate receptor, ionotropic, AMPA 1a; UniProt Q71E65)

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 in Europe PMC ((gria1a OR gria1b) AND zebrafish,
"gria1b", "gria1a" AND (mutant OR knockout OR morpholino), AUTH:"Hoppmann V" AMPA,
TITLE:"AMPA" AND TITLE:zebrafish, zebrafish AND ("GluR1" OR "GluA1")) and by following ZFIN
expression publications. Pair analysis in gria1a-bioinformatics/RESULTS.md; paralog notes in
../gria1b/gria1b-notes.md.

Accession Q71E65 (TrEMBL, EMBL AAQ08954 "AMPA receptor subunit GluR1A", 914 aa),
ZFIN:ZDB-GENE-020125-1, Ensembl ENSDARG00000021352, chr14. 15 GOA rows (IBA and IEA only), identical
term by term to gria1b.

Origin

• PANTHER TGD_tree (Neopterygii|Teleostei), 1:1, one gar co-ortholog, two medaka co-orthologs.
  Ensembl Compara duplication node Osteoglossocephalai; one gar ortholog for both copies; one-to-one
  medaka orthologs for each copy (so medaka kept both).
• PMID:18224707
• Synteny (RESULTS.md): no teleost-level paralogue pair within 1.5 Mb of both copies; several
  chromosome-level links (chr14 <-> chr21).

Protein (RESULTS.md)

• gria1a vs gria1b 82.5% identical; gria1a 88.3% identical to gar GRIA1 and gria1b 81.7%.
• Glutamate-binding residues, the pore loop and M2-M3 segment (FGIFNSLWFSLGAFMQQGCDISPRSLSG,
  identical to human and gar) and both palmitoylation cysteines kept in both copies.
• Relative rate vs gar: gria1b has significantly more unique changes (86 vs 34).
• C-terminal tail: gria1a keeps the serines at human S849/S863 (mature S831/S845); gria1b has I at
  S849 and no aligned serine at S863. Mammalian background:
  PMID:20716669
• PDZ-binding C-terminus: human ATGL; gar ATGM; gria1a ASGM; gria1b TTGM. The L->M change predates
  the TGD (present in gar).
• PMID:16887104

Mammalian GRIA1 background

• PMID:2166337
• PMID:10364547

Expression

• Hoppmann et al. 2008 (abstract only in cache; ZFIN curated the in situ data):
  PMID:18224707
  ZFIN terms from this paper (24-72 hpf): gria1a-only telencephalon (dorsal and ventral), dorsal
  thalamus, spinal cord, rhombomeres, retinal ganglion cells; gria1b-only otic vesicle; 18 terms
  shared (olfactory bulb, habenula, hypothalamus, thalamus, tegmentum, optic tectum, medulla,
  retinal layers, motor and sensory neurons, spinal interneurons, early clusters).
• Maternal transcripts of all AMPAR genes by RT-PCR:
  PMID:16887104
• E-ERAD-475: gria1a 12-14 TPM and gria1b 5-6 TPM in larvae (gria1a about 2-3 times higher).
• Bgee: shared brain and retina; gria1b adds ovarian follicle, spleen, gill, testis; gar GRIA1 brain,
  eye, larva, ovary, bone, embryo.
• Forebrain: PMID:30929901
• Tectum: PMID:35221915
• Sinoatrial ring: PMID:34600492

Function

• Only mutant data: the schizophrenia-gene screen (Thyme et al. 2019) mutated both copies:
  PMID:30929901
  and gria1 mutants had a pallium activity phenotype:
  PMID:30929901
  The text does not say which copy (or the double) produced it; the per-ortholog data are in a
  supplementary heatmap that I could not read. No other loss-of-function data for either copy.

Annotation decisions

• MF (AMPA receptor activity, transmitter-gated channel involved in postsynaptic potential,
  ligand-gated channel, transmitter-gated channel): ACCEPT. Complex, PSD membrane, postsynaptic
  membrane, plasma membrane, membrane: ACCEPT. Glutamatergic transmission, iGluR signalling,
  regulation of postsynaptic membrane potential, ion transmembrane transport: ACCEPT.
• Dendritic spine (IBA): KEEP_AS_NON_CORE (mammalian donors; no zebrafish data).
• Modulation of chemical synaptic transmission (IBA): KEEP_AS_NON_CORE (mammalian GluA1 plasticity
  role; untested in fish).
• No NEW annotations.