gad1b notes (Danio rerio, glutamate decarboxylase 1b, GAD67; UniProt Q7ZUS3)

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 (see ../gad1a/gad1a-notes.md
for the queries). Pair analysis in ../gad1a/gad1a-bioinformatics/RESULTS.md; paralog notes in
../gad1a/gad1a-notes.md.

Accession Q7ZUS3 (TrEMBL, RefSeq NP_919400, 587 aa), ZFIN:ZDB-GENE-030909-3 (formerly gad1 /
gad67), Ensembl ENSDARG00000027419, chr6. 8 GOA rows: IBA/IEA plus one ZFIN IEP for GABA
biosynthetic process from PMID:9634146.

Nomenclature

• Older zebrafish papers use "GAD67", "gad67" or "gad1" for this gene. The sequenced Martin et al.
  1998 GAD67 cDNA (AF017266) is 99.6% identical to Gad1b vs 90.9% to Gad1a (probe_identity.py in
  gad1a-bioinformatics). Mueller & Guo used a probe from AF017266:
  PMID:19673006
  (AF017266 is only 696 nt, so the coordinates quoted cannot be right as written, but the accession
  is clear).
• The old probe names map to gad1b:
  PMID:26896392

Expression

• Martin et al. 1998 (abstract): PMID:9634146
  PMID:9634146
• Pan-GABAergic marker of choice: PMID:42466317
• Locus coeruleus: PMID:24374659
  (Filippi et al. compared gad1b with gad2, not with gad1a.)
• Lateral-line efferent neurons: PMID:41950195
• Public data (RESULTS.md): 84 TPM in 5-day whole larvae (gad1a 4 TPM); 88 Bgee calls, mostly in situ
  in brain nuclei, retina, spinal interneurons, Kolmer-Agduhr neurons and Purkinje cells; 247 ZFIN
  records from 69 publications.

Function

• Morphants (translation-blocking MO): craniofacial defects not seen in the mutant:
  PMID:30200754
  PMID:30200754
• CRISPR null allele gav2303 (10-bp deletion, exon 4), abnormal brain activity like PTZ:
  PMID:30200754
  PMID:30200754
  Full characterization "submitted" (VanLeuven et al.); a 2024 preprint on reduced GABA and tectal
  connectivity exists but has no PMID and was not used. PMID:42610151 cites earlier 2D seizure
  imaging of gad1b null mutants.
• Splice MO (intron 8 retention) raises locomotor activity:
  PMID:34650032
• No enzyme assay of zebrafish Gad1b; activity inferred (catalytic residues kept, 82.7% identical to
  human GAD1). Mammalian: PMID:17384644
• Transcriptional adaptation (gad1a upregulation in gad1b mutants) has not been measured.

Annotation decisions

• IEP GABA biosynthetic process (PMID:9634146): ACCEPT. The GAD67 cDNA of that paper is gad1b by
  sequence, and GABA co-localizes with GAD expression. The process term is right; the evidence is
  expression-based.
• IBA/IEA MF rows: ACCEPT. Cytoplasm: ACCEPT. Presynaptic active zone (IBA): KEEP_AS_NON_CORE (ZFIN
  curates Gad1b-antibody staining at presynaptic active zones in adult cerebellum from Bae et al. 2009,
  PMID:19371731, abstract only in cache, so not quoted).
• No NEW rows: the mutant/morphant phenotypes (seizure-like activity, locomotion) are downstream
  consequences of GABA deficiency, not processes Gad1b performs.