samsn1a notes

Provenance and setup

• Record: B3DH22 (TrEMBL, 621 aa), ZFIN ZDB-GENE-030131-8639, Ensembl ENSDARG00000054543 (chr15).
• Paralog: samsn1b (A0A8M2BH30). Pair drawn at random for DANRE_DUPLICATION batch 4
  (PANTHER TGD_tree, Ensembl Compara duplication node Osteoglossocephalai).
• Deep research was not available for this gene (Edison returned 402 Payment Required; the OpenAI
  key is invalid). Literature was searched by hand through Europe PMC (queries: samsn1a OR samsn1b;
  (samsn1 OR HACS1 OR SASH2 OR NASH1) AND zebrafish; title search for HACS1/SAMSN1/NASH1).
• No functional study of zebrafish samsn1a or samsn1b exists. Zebrafish mentions are marker-gene
  statements in single-cell RNA-seq papers.

Mammalian SAMSN1 (HACS1, SLy2, NASH1)

• SH3-SAM adaptor, hematopoietic, human chr21q11.2
  PMID:11536050
  PMID:11536050
• NASH1 identified in mast cells, nuclear
  PMID:11594764
• Up-regulated in B-cell activation; binds tyrosine-phosphorylated proteins and PIR-B
  PMID:15381729
  PMID:15381729
• Mouse knockout: enhanced B-cell responses (source of the IBA for negative regulation of B cell
  activation, MGI:1914992)
  PMID:19923443
  PMID:19923443
• SH3 domain binds a motif near ITIM3 of PIRB (NMR structure)
  PMID:33188360
• Family: SLy1/SASH3, SLy2/HACS1 (SAMSN1), SASH1/SLy3
  PMID:33710696

Zebrafish / teleost expression

• Retinal bipolar-cell marker in two independent zebrafish scRNA-seq studies:
  PMID:37988404
  PMID:36047082
• Channel catfish spleen single-nucleus data place samsn1a in a myeloid cluster (catfish, an
  otophysan like zebrafish; not zebrafish data):
  PMID:39325796
• My analysis (file:DANRE/samsn1a/samsn1a-bioinformatics/RESULTS.md):
• ZFIN curated in situ (Covassin et al. 2006, ZDB-PUB-060927-11): samsn1a in blood, macrophage and
  solid lens vesicle at prim-5. samsn1b: epiphysis (pineal) and retinal photoreceptor layer
  (Thisse et al. 2004 direct submission).
• E-ERAD-475: samsn1a zygotic, rising from hatching to 28 TPM at day 5; samsn1b has a small
  gastrula peak (5 TPM) then silent until larval stages (10-17 TPM).
• Bgee: both copies have RNA-seq calls in granulocyte, spleen, head kidney, retina, gill, intestine,
  liver; samsn1a has top scores in granulocyte/spleen/head kidney, samsn1b in retina.

Protein

• samsn1a and samsn1b are only 37.8% identical over the full length, but SH3 domains are 82.3% and
  77.4% identical to human SAMSN1 SH3; both keep the 14-3-3 motif region. Both zebrafish proteins
  (621/676 aa) and the gar protein (690 aa) are much longer than human SAMSN1 (373 aa).
  No relative-rate asymmetry (gar outgroup).

Annotation decisions

• Only two IBA process rows on each copy. Both accepted; the B-cell row is a phylogenetic inference
  from the mouse knockout, consistent with the hematopoietic expression of both copies. No NEW rows.