# Pair analysis: samsn1a / samsn1b  (run 2026-09-28)

## 0. Ensembl Compara homologies

samsn1a: danio_rerio ENSDARG00000078647 within_species_paralog (node Osteoglossocephalai)
samsn1a: danio_rerio ENSDARG00000007179 other_paralog (node Vertebrata)
samsn1a: danio_rerio ENSDARG00000058853 other_paralog (node Vertebrata)
samsn1a: danio_rerio ENSDARG00000016541 other_paralog (node Vertebrata)
samsn1a: lepisosteus_oculatus ENSLOCG00000000927 ortholog_one2many (node Neopterygii)
samsn1a: homo_sapiens ENSG00000155307 ortholog_one2many (node Euteleostomi)
samsn1a: oryzias_latipes ENSORLG00000014201 ortholog_one2one (node Clupeocephala)
samsn1b: danio_rerio ENSDARG00000054543 within_species_paralog (node Osteoglossocephalai)
samsn1b: danio_rerio ENSDARG00000007179 other_paralog (node Vertebrata)
samsn1b: danio_rerio ENSDARG00000058853 other_paralog (node Vertebrata)
samsn1b: danio_rerio ENSDARG00000016541 other_paralog (node Vertebrata)
samsn1b: lepisosteus_oculatus ENSLOCG00000000927 ortholog_one2many (node Neopterygii)
samsn1b: homo_sapiens ENSG00000155307 ortholog_one2many (node Euteleostomi)

Compara node of the samsn1a/samsn1b duplication: ['Osteoglossocephalai']

## 1. Sequence lengths and pairwise identities

human SAMSN1: UniProt Q9NSI8
human SASH1: UniProt O94885
human SASH3: UniProt O75995
length samsn1a: 621 aa
length samsn1b: 676 aa
length SAMSN1: 373 aa
length SASH1: 1247 aa
length SASH3: 380 aa
length gar_ENSLOCG00000000927: 690 aa
length medaka_ENSORLG00000014201(orth of samsn1a): 523 aa
identity samsn1a vs samsn1b: 37.8% over 727 columns
identity samsn1a vs SAMSN1: 27.1% over 671 columns
identity samsn1a vs SASH1: 17.4% over 1313 columns
identity samsn1a vs SASH3: 24.3% over 671 columns
identity samsn1a vs gar_ENSLOCG00000000927: 43.3% over 714 columns
identity samsn1a vs medaka_ENSORLG00000014201(orth of samsn1a): 40.0% over 658 columns
identity samsn1b vs SAMSN1: 28.0% over 700 columns
identity samsn1b vs SASH1: 18.7% over 1328 columns
identity samsn1b vs SASH3: 26.1% over 693 columns
identity samsn1b vs gar_ENSLOCG00000000927: 46.4% over 714 columns
identity samsn1b vs medaka_ENSORLG00000014201(orth of samsn1a): 33.8% over 734 columns
identity SAMSN1 vs SASH1: 14.3% over 1256 columns
identity SAMSN1 vs SASH3: 44.0% over 402 columns
identity SAMSN1 vs gar_ENSLOCG00000000927: 30.3% over 707 columns
identity SAMSN1 vs medaka_ENSORLG00000014201(orth of samsn1a): 33.3% over 553 columns
identity SASH1 vs SASH3: 14.8% over 1264 columns
identity SASH1 vs gar_ENSLOCG00000000927: 19.3% over 1329 columns
identity SASH1 vs medaka_ENSORLG00000014201(orth of samsn1a): 16.6% over 1285 columns
identity SASH3 vs gar_ENSLOCG00000000927: 26.4% over 712 columns
identity SASH3 vs medaka_ENSORLG00000014201(orth of samsn1a): 30.3% over 554 columns
identity gar_ENSLOCG00000000927 vs medaka_ENSORLG00000014201(orth of samsn1a): 37.6% over 716 columns

## 2. Regions of the human reference (UniProt features), motifs and key residues

Domain: SH3 [163-224] samsn1a: aligned 62/62, identical 51/62 (82.3%)
Domain: SH3 [163-224] samsn1b: aligned 62/62, identical 48/62 (77.4%)
Domain: SH3 [163-224] gar_ENSLOCG00000000927: aligned 62/62, identical 52/62 (83.9%)
Domain: SAM [241-305] samsn1a: aligned 62/65, identical 34/65 (52.3%)
Domain: SAM [241-305] samsn1b: aligned 65/65, identical 39/65 (60.0%)
Domain: SAM [241-305] gar_ENSLOCG00000000927: aligned 64/65, identical 40/65 (61.5%)
Region: Disordered [1-72] samsn1a: aligned 66/72, identical 37/72 (51.4%)
Region: Disordered [1-72] samsn1b: aligned 61/72, identical 30/72 (41.7%)
Region: Disordered [1-72] gar_ENSLOCG00000000927: aligned 70/72, identical 40/72 (55.6%)
Region: Disordered [91-153] samsn1a: aligned 54/63, identical 29/63 (46.0%)
Region: Disordered [91-153] samsn1b: aligned 60/63, identical 29/63 (46.0%)
Region: Disordered [91-153] gar_ENSLOCG00000000927: aligned 55/63, identical 31/63 (49.2%)
Region: Disordered [337-359] samsn1a: aligned 8/23, identical 5/23 (21.7%)
Region: Disordered [337-359] samsn1b: aligned 23/23, identical 15/23 (65.2%)
Region: Disordered [337-359] gar_ENSLOCG00000000927: aligned 23/23, identical 14/23 (60.9%)
Motif: Important for interaction with 14-3-3 proteins [20-25] samsn1a: aligned 6/6, identical 5/6 (83.3%)
Motif: Important for interaction with 14-3-3 proteins [20-25] samsn1b: aligned 6/6, identical 5/6 (83.3%)
Motif: Important for interaction with 14-3-3 proteins [20-25] gar_ENSLOCG00000000927: aligned 6/6, identical 6/6 (100.0%)

## 3. Tajima-style relative-rate test (outgroup = gar)

gar positions aligned in both copies: 573
changes unique to samsn1a (m1): 96; unique to samsn1b (m2): 93; chi2 (1 df) = 0.05 (not significant at 0.05)

## 4. Whole-embryo time course, E-ERAD-475 (TPM, median of replicates)

| stage | samsn1a | samsn1b |
|---|---|---|
| zygote | 0 | 0 |
| cleavage 2-cell | 0 | 0 |
| blastula 128-cell | 0 | 0 |
| blastula 1k-cell | 0 | 0 |
| blastula dome | 0 | 0 |
| gastrula 50%-epiboly | 0 | 5 |
| gastrula shield | 0 | 5 |
| gastrula 75%-epiboly | 0 | 1 |
| segmentation 1-4 somites | 0 | 0 |
| segmentation 14-19 somites | 0 | 0 |
| segmentation 20-25 somites | 1 | 0.6 |
| pharyngula prim-5 | 1 | 0 |
| pharyngula prim-15 | 0.9 | 0 |
| pharyngula prim-25 | 0.9 | 0 |
| hatching long-pec | 4 | 0 |
| larval protruding mouth | 17 | 17 |
| larval day 4 | 21 | 10 |
| larval day 5 | 28 | 10 |

## 5. Bgee expressed calls per anatomical entity (score 0-100; only 'expressed' calls are returned)

### samsn1a: 18 calls
- granulocyte: 94.6 (gold; RNA-Seq)
- spleen: 94.5 (gold; RNA-Seq)
- head kidney: 90.1 (gold; RNA-Seq)
- swim bladder: 81.9 (gold; RNA-Seq)
- retina: 80.9 (gold; Affymetrix,RNA-Seq)
- larva: 69.1 (gold; Affymetrix,RNA-Seq)
- zone of skin: 65.9 (gold; RNA-Seq)
- liver: 63.6 (gold; Affymetrix,RNA-Seq)
- bone element: 62.0 (gold; RNA-Seq)
- heart: 61.5 (gold; Affymetrix,RNA-Seq)
- intestine: 61.3 (gold; RNA-Seq)
- caudal fin: 59.9 (gold; Affymetrix)
- pharyngeal gill: 58.8 (gold; RNA-Seq)
- brain: 56.1 (gold; Affymetrix,RNA-Seq)
- lens vesicle: 53.0 (gold; in situ hybridization)
- macrophage: 52.0 (gold; in situ hybridization)
- muscle tissue: 48.5 (gold; RNA-Seq)
- embryo: 37.5 (gold; Affymetrix,RNA-Seq)
### samsn1b: 19 calls
- retina: 89.3 (gold; in situ hybridization,RNA-Seq)
- granulocyte: 88.4 (gold; RNA-Seq)
- pharyngeal gill: 69.2 (gold; RNA-Seq)
- spleen: 63.7 (gold; RNA-Seq)
- photoreceptor layer of retina: 61.9 (gold; in situ hybridization)
- dorsal plus ventral thalamus: 61.3 (gold; in situ hybridization)
- epithalamus: 61.2 (gold; in situ hybridization)
- head kidney: 61.1 (gold; RNA-Seq)
- gland of diencephalon: 60.6 (gold; in situ hybridization)
- pineal body: 60.1 (gold; in situ hybridization)
- intestine: 52.4 (gold; RNA-Seq)
- gastrula: 51.8 (gold; RNA-Seq)
- zone of skin: 50.5 (gold; RNA-Seq)
- liver: 50.0 (silver; RNA-Seq)
- larva: 48.3 (gold; RNA-Seq)
- bone element: 47.9 (gold; RNA-Seq)
- testis: 41.8 (gold; RNA-Seq)
- muscle tissue: 39.6 (silver; RNA-Seq)
- tail: 26.7 (silver; RNA-Seq)
### gar ENSLOCG00000000927: 12 calls
- bone element: 92.3 (gold; RNA-Seq)
- camera-type eye: 91.6 (gold; RNA-Seq)
- pharyngeal gill: 83.9 (gold; RNA-Seq)
- intestine: 80.5 (gold; RNA-Seq)
- mesonephros: 77.2 (gold; RNA-Seq)
- heart: 66.7 (gold; RNA-Seq)
- liver: 65.8 (gold; RNA-Seq)
- larva: 55.6 (gold; RNA-Seq)
- zone of skin: 52.0 (gold; RNA-Seq)
- muscle tissue: 50.0 (gold; RNA-Seq)
- brain: 43.3 (gold; RNA-Seq)
- embryo: 36.7 (gold; RNA-Seq)

RNA-Seq-supported entities: samsn1a only: ['brain', 'embryo', 'heart', 'swim bladder']
RNA-Seq-supported entities: samsn1b only: ['gastrula', 'tail', 'testis']
RNA-Seq-supported entities: both: ['bone element', 'granulocyte', 'head kidney', 'intestine', 'larva', 'liver', 'muscle tissue', 'pharyngeal gill', 'retina', 'spleen', 'zone of skin']

## 6. ZFIN curated wild-type expression (wildtype-expression_fish.txt)

### samsn1a: 3 records
- blood | Pharyngula:Prim-5 | mRNA in situ hybridization | ZDB-PUB-060927-11
- macrophage | Pharyngula:Prim-5 | mRNA in situ hybridization | ZDB-PUB-060927-11
- solid lens vesicle | Pharyngula:Prim-5 | mRNA in situ hybridization | ZDB-PUB-060927-11
### samsn1b: 5 records
- epiphysis | Pharyngula:High-pec | mRNA in situ hybridization | ZDB-PUB-040907-1
- epiphysis | Pharyngula:Prim-15 | mRNA in situ hybridization | ZDB-PUB-040907-1
- epiphysis | Segmentation:14-19 somites | mRNA in situ hybridization | ZDB-PUB-040907-1
- epiphysis | Segmentation:20-25 somites | mRNA in situ hybridization | ZDB-PUB-040907-1
- retinal photoreceptor layer | Larval:Day 5 | mRNA in situ hybridization | ZDB-PUB-040907-1

anatomy terms samsn1a only: ['blood', 'macrophage', 'solid lens vesicle']
anatomy terms samsn1b only: ['epiphysis', 'retinal photoreceptor layer']
anatomy terms both: []

## 7. Local synteny between the copies (neighbour paralogues with a teleost-level node)

samsn1a: chr15:29564364-29586747
samsn1b: chr10:38417512-38428094

samsn1a +/- 1.5 Mb: 63 other protein-coding genes (0 homology queries failed); 15 have a teleost-level (Teleostei/Osteoglossocephalai/Clupeocephala) zebrafish paralogue; 6 such pairs have their partner within 1.5 Mb of samsn1b:
- gdpd5b -> gdpd5a (chr10:38430359)
- serpinh1b -> serpinh1a (chr10:38512270)
- nrip1a -> nrip1b (chr10:38256556)
- msi2b -> msi2a (chr10:37500234)
- omgb -> omga (chr10:37334270)
- ksr1b -> ksr1a (chr10:37173029)
8 have their partner anywhere on chr10 (943 protein-coding genes):
- gdpd5b -> gdpd5a (chr10:38430359)
- serpinh1b -> serpinh1a (chr10:38512270)
- nrip1a -> nrip1b (chr10:38256556)
- msi2b -> msi2a (chr10:37500234)
- slc43a2a -> slc43a2b (chr10:24371921)
- pitpnaa -> pitpnab (chr10:24323751)
- omgb -> omga (chr10:37334270)
- ksr1b -> ksr1a (chr10:37173029)

samsn1b +/- 1.5 Mb: 41 other protein-coding genes (0 homology queries failed); 18 have a teleost-level (Teleostei/Osteoglossocephalai/Clupeocephala) zebrafish paralogue; 6 such pairs have their partner within 1.5 Mb of samsn1a:
- ksr1a -> ksr1b (chr15:31070603)
- omga -> omgb (chr15:30917282)
- msi2a -> msi2b (chr15:30424645)
- nrip1b -> nrip1a (chr15:29662401)
- gdpd5a -> gdpd5b (chr15:29387910)
- serpinh1a -> serpinh1b (chr15:29382454)
12 have their partner anywhere on chr15 (953 protein-coding genes):
- cuedc1a -> cuedc1b (chr15:31188016)
- ksr1a -> ksr1b (chr15:31070603)
- omga -> omgb (chr15:30917282)
- msi2a -> msi2b (chr15:30424645)
- nrip1b -> nrip1a (chr15:29662401)
- gdpd5a -> gdpd5b (chr15:29387910)
- serpinh1a -> serpinh1b (chr15:29382454)
- igsf5a -> igsf5b (chr15:5973909)
- mipepb -> mipepa (chr15:8192715)
- hmgn1b -> hmgn1a (chr15:5898410)
- sez6a -> sez6b (chr15:24212847)
- vezf1a -> vezf1b (chr15:31244025)