# Pair analysis: tusc2a / tusc2b  (run 2026-09-28)

## 1. Sequence lengths and pairwise identities

length tusc2a: 111 aa
length tusc2b: 111 aa
length TUSC2: 110 aa
length gar_TUSC2: 112 aa
length medaka_ortholog_of_tusc2a: 109 aa
length medaka_ortholog_of_tusc2b: 111 aa
identity tusc2a vs tusc2b: 80.2% over 111 columns
identity tusc2a vs TUSC2: 70.3% over 111 columns
identity tusc2a vs gar_TUSC2: 81.2% over 112 columns
identity tusc2a vs medaka_ortholog_of_tusc2a: 77.5% over 111 columns
identity tusc2a vs medaka_ortholog_of_tusc2b: 76.6% over 111 columns
identity tusc2b vs TUSC2: 65.8% over 111 columns
identity tusc2b vs gar_TUSC2: 77.7% over 112 columns
identity tusc2b vs medaka_ortholog_of_tusc2a: 75.7% over 111 columns
identity tusc2b vs medaka_ortholog_of_tusc2b: 79.3% over 111 columns
identity TUSC2 vs gar_TUSC2: 72.3% over 112 columns
identity TUSC2 vs medaka_ortholog_of_tusc2a: 66.7% over 111 columns
identity TUSC2 vs medaka_ortholog_of_tusc2b: 66.7% over 111 columns
identity gar_TUSC2 vs medaka_ortholog_of_tusc2a: 80.4% over 112 columns
identity gar_TUSC2 vs medaka_ortholog_of_tusc2b: 78.6% over 112 columns
identity medaka_ortholog_of_tusc2a vs medaka_ortholog_of_tusc2b: 72.1% over 111 columns

## 1b. Zebrafish copies vs each human isoform

identity tusc2a vs O75896 (110 aa): 70.3% over 111 columns
identity tusc2b vs O75896 (110 aa): 65.8% over 111 columns

## 2. Regions of the human protein (UniProt features) and of the zebrafish 'a' copy

### human TUSC2 (O75896) features
Chain: Tumor suppressor candidate 2 [2-110] tusc2a: aligned 109/109, identical 77/109 (70.6%)
Chain: Tumor suppressor candidate 2 [2-110] tusc2b: aligned 109/109, identical 72/109 (66.1%)
Chain: Tumor suppressor candidate 2 [2-110] gar_TUSC2: aligned 109/109, identical 80/109 (73.4%)
Modified residue: Phosphoserine [50-50] tusc2a: aligned 1/1, identical 1/1 (100.0%) residues: S50->S
Modified residue: Phosphoserine [50-50] tusc2b: aligned 1/1, identical 1/1 (100.0%) residues: S50->S
Modified residue: Phosphoserine [50-50] gar_TUSC2: aligned 1/1, identical 1/1 (100.0%) residues: S50->S
Lipidation: N-myristoyl glycine [2-2] tusc2a: aligned 1/1, identical 1/1 (100.0%) residues: G2->G
Lipidation: N-myristoyl glycine [2-2] tusc2b: aligned 1/1, identical 1/1 (100.0%) residues: G2->G
Lipidation: N-myristoyl glycine [2-2] gar_TUSC2: aligned 1/1, identical 1/1 (100.0%) residues: G2->G

### zebrafish tusc2a features (cached UniProt record) mapped to tusc2b

### literal motif search
motif CBM_exact (DEDGDLAHEFYEE) in tusc2a: [55]
motif CBM_exact (DEDGDLAHEFYEE) in tusc2b: [55]
motif CBM_exact (DEDGDLAHEFYEE) in TUSC2: [54]
motif CBM_exact (DEDGDLAHEFYEE) in gar_TUSC2: [56]
motif CBM_exact (DEDGDLAHEFYEE) in medaka_ortholog_of_tusc2a: [53]
motif CBM_exact (DEDGDLAHEFYEE) in medaka_ortholog_of_tusc2b: [55]
motif DxDxD (D.D.D) in tusc2a: [55]
motif DxDxD (D.D.D) in tusc2b: [55]
motif DxDxD (D.D.D) in TUSC2: [54]
motif DxDxD (D.D.D) in gar_TUSC2: [56]
motif DxDxD (D.D.D) in medaka_ortholog_of_tusc2a: [53]
motif DxDxD (D.D.D) in medaka_ortholog_of_tusc2b: [55]
N-terminus of tusc2a: MGGSGSKPKGVW (Gly at position 2: True)
N-terminus of tusc2b: MGGSGSKGKGYW (Gly at position 2: True)
N-terminus of TUSC2: MGASGSKARGLW (Gly at position 2: True)
N-terminus of gar_TUSC2: KMGGSGSKSRGF (Gly at position 2: False)

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

gar positions aligned in both copies: 111
changes unique to tusc2a (m1): 5; unique to tusc2b (m2): 9; chi2 (1 df) = 1.14 (not significant at 0.05)

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

| stage | tusc2a | tusc2b |
|---|---|---|
| zygote | 26 | 10 |
| cleavage 2-cell | 13 | 13 |
| blastula 128-cell | 5 | 31 |
| blastula 1k-cell | 6 | 38 |
| blastula dome | 5 | 31 |
| gastrula 50%-epiboly | 1 | 26 |
| gastrula shield | 2 | 30 |
| gastrula 75%-epiboly | 2 | 38 |
| segmentation 1-4 somites | 4 | 49 |
| segmentation 14-19 somites | 9 | 51 |
| segmentation 20-25 somites | 5 | 47 |
| pharyngula prim-5 | 7 | 44 |
| pharyngula prim-15 | 8 | 42 |
| pharyngula prim-25 | 11 | 45 |
| hatching long-pec | 16 | 43 |
| larval protruding mouth | 18 | 45 |
| larval day 4 | 18 | 42 |
| larval day 5 | 14 | 37 |

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

### tusc2a: 25 calls
- testis: 89.7 (gold; RNA-Seq)
- mature ovarian follicle: 87.3 (gold; RNA-Seq)
- muscle tissue: 84.2 (gold; RNA-Seq)
- cardiac ventricle: 83.4 (gold; Affymetrix)
- brain: 82.7 (gold; Affymetrix,RNA-Seq)
- head: 76.4 (gold; Affymetrix,RNA-Seq)
- early embryo: 75.2 (gold; RNA-Seq)
- camera-type eye: 73.9 (gold; Affymetrix,RNA-Seq)
- retina: 73.4 (gold; Affymetrix,RNA-Seq)
- larva: 73.1 (gold; Affymetrix,RNA-Seq)
- bone element: 67.8 (gold; RNA-Seq)
- liver: 66.0 (gold; Affymetrix,RNA-Seq)
- spleen: 65.1 (gold; RNA-Seq)
- pharyngeal gill: 62.3 (gold; RNA-Seq)
- caudal fin: 62.2 (gold; Affymetrix)
- cleaving embryo: 59.3 (gold; Affymetrix)
- integument: 57.6 (gold; Affymetrix,RNA-Seq)
- blastula: 57.6 (gold; Affymetrix,RNA-Seq)
- zone of skin: 57.4 (gold; RNA-Seq)
- gastrula: 55.5 (gold; Affymetrix,RNA-Seq)
- granulocyte: 53.0 (gold; RNA-Seq)
- intestine: 51.5 (gold; RNA-Seq)
- mesonephros: 49.0 (gold; RNA-Seq)
- head kidney: 46.5 (gold; RNA-Seq)
- swim bladder: 35.6 (gold; RNA-Seq)
### tusc2b: 31 calls
- muscle tissue: 91.8 (gold; RNA-Seq)
- somite: 88.8 (gold; Affymetrix)
- liver: 88.6 (gold; Affymetrix,RNA-Seq)
- bone element: 86.6 (gold; RNA-Seq)
- larva: 86.0 (gold; Affymetrix,RNA-Seq)
- brain: 84.3 (gold; Affymetrix,RNA-Seq)
- spleen: 84.0 (gold; RNA-Seq)
- head: 83.6 (gold; Affymetrix,RNA-Seq)
- camera-type eye: 83.4 (gold; Affymetrix,RNA-Seq)
- presomitic mesoderm: 82.8 (gold; Affymetrix)
- tail: 81.9 (gold; Affymetrix,RNA-Seq)
- granulocyte: 81.5 (gold; RNA-Seq)
- gastrula: 80.3 (gold; Affymetrix,RNA-Seq)
- tail bud paraxial mesoderm: 80.1 (gold; Affymetrix)
- retina: 79.8 (gold; Affymetrix,RNA-Seq)
- caudal fin: 79.6 (gold; Affymetrix)
- heart: 79.5 (gold; Affymetrix,RNA-Seq)
- testis: 78.6 (gold; RNA-Seq)
- ovary: 78.3 (gold; RNA-Seq)
- integument: 78.1 (gold; Affymetrix,RNA-Seq)
- zone of skin: 78.1 (gold; RNA-Seq)
- pharyngeal gill: 75.6 (gold; RNA-Seq)
- cardiac ventricle: 75.2 (gold; Affymetrix)
- blastula: 74.5 (gold; Affymetrix,RNA-Seq)
- intestine: 73.7 (gold; RNA-Seq)
- mesonephros: 73.1 (gold; RNA-Seq)
- cleaving embryo: 72.1 (gold; Affymetrix)
- head kidney: 70.5 (gold; RNA-Seq)
- swim bladder: 67.0 (gold; RNA-Seq)
- early embryo: 65.2 (gold; RNA-Seq)
- mature ovarian follicle: 64.3 (silver; RNA-Seq)
### gar_TUSC2 (spotted gar): 14 calls
- camera-type eye: 76.2 (gold; RNA-Seq)
- muscle tissue: 63.8 (gold; RNA-Seq)
- brain: 60.6 (gold; RNA-Seq)
- liver: 59.4 (gold; RNA-Seq)
- ovary: 58.6 (gold; RNA-Seq)
- testis: 56.9 (gold; RNA-Seq)
- zone of skin: 53.6 (gold; RNA-Seq)
- embryo: 52.4 (gold; RNA-Seq)
- larva: 50.9 (gold; RNA-Seq)
- heart: 49.8 (gold; RNA-Seq)
- mesonephros: 48.1 (gold; RNA-Seq)
- pharyngeal gill: 43.7 (gold; RNA-Seq)
- intestine: 33.6 (silver; RNA-Seq)
- bone element: 31.4 (silver; RNA-Seq)

RNA-Seq-supported entities: tusc2a only: []
RNA-Seq-supported entities: tusc2b only: ['heart', 'ovary', 'tail']
RNA-Seq-supported entities: both: ['blastula', 'bone element', 'brain', 'camera-type eye', 'early embryo', 'gastrula', 'granulocyte', 'head', 'head kidney', 'integument', 'intestine', 'larva', 'liver', 'mature ovarian follicle', 'mesonephros', 'muscle tissue', 'pharyngeal gill', 'retina', 'spleen', 'swim bladder', 'testis', 'zone of skin']
entities called for both: 25; tusc2a score higher in 4, median difference (tusc2a - tusc2b) = -16.9

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

### tusc2a (ZDB-GENE-061013-612): 0 rows
### tusc2b (ZDB-GENE-040718-99): 1 rows
- whole organism | Zygote:1-cell to Hatching:Pec-fin | assay mRNA in situ hybridization | ZDB-PUB-040907-1

## 7. Local synteny between the two copies (Ensembl REST)

tusc2a: chr6:54117004-54126463
tusc2b: chr22:10660140-10663935

tusc2a +/- 1.5 Mb: 72 other protein-coding genes (0 homology queries failed); 30 have a teleost-level (Clupeocephala, Osteoglossocephalai, Teleostei) zebrafish paralogue; 0 such paralogue pairs have their partner within 1.5 Mb of tusc2b:
Of the teleost-level paralogue pairs, 0 have their partner anywhere on chr22 (the chromosome of tusc2b, 1007 protein-coding genes):

tusc2b +/- 1.5 Mb: 102 other protein-coding genes (0 homology queries failed); 16 have a teleost-level (Clupeocephala, Osteoglossocephalai, Teleostei) zebrafish paralogue; 0 such paralogue pairs have their partner within 1.5 Mb of tusc2a:
Of the teleost-level paralogue pairs, 0 have their partner anywhere on chr6 (the chromosome of tusc2a, 1014 protein-coding genes):