samsn1b notes

Provenance and setup

• Record: A0A8M2BH30 (TrEMBL, 676 aa, RefSeq XP_005169221.2 isoform X1), ZFIN ZDB-GENE-041010-135
  (synonym zgc:103427), Ensembl ENSDARG00000078647 (chr10).
• Paralog: samsn1a (B3DH22). DANRE_DUPLICATION batch 4 random pair (PANTHER TGD_tree; Ensembl
  Compara duplication node Osteoglossocephalai).
• Deep research was not available (Edison 402 Payment Required; OpenAI key invalid). Literature
  searched by hand in Europe PMC; see samsn1a-notes.md for queries. No paper mentions samsn1b in
  its text beyond gene lists; no functional study exists.

Mammalian SAMSN1

See genes/DANRE/samsn1a/samsn1a-notes.md. Key points with provenance:
- PMID:15381729
- PMID:19923443
- PMID:11536050

Expression and protein (file:DANRE/samsn1a/samsn1a-bioinformatics/RESULTS.md)

• ZFIN curated in situ (Thisse et al. 2004 direct submission, ZDB-PUB-040907-1): epiphysis (pineal)
  from 14-19 somites to high-pec; retinal photoreceptor layer at day 5. No curated blood or
  macrophage expression (those are samsn1a records).
• E-ERAD-475: small gastrula peak (5 TPM), silent through pharyngula, 10-17 TPM in larvae.
• Bgee RNA-seq: highest in retina (89.3) and granulocyte (88.4); also spleen, head kidney, gill,
  intestine, testis.
• Protein 37.8% identical to samsn1a; SH3 77.4% identical to human SAMSN1; SAM 60%.
• Compara gives samsn1b no medaka orthologue (medaka's single copy is assigned to samsn1a).

Annotation decisions

• Three root ND rows accepted as accurate placeholders.
• Two IBA process rows accepted, as for samsn1a; bulk RNA-seq keeps samsn1b in hematopoietic
  tissues, so there is no expression argument for loss of the immune role.