# Pair analysis: ctdspl2a / ctdspl2b  (run 2026-09-28)

## 0. Ensembl Compara homologies

ctdspl2a: danio_rerio ENSDARG00000060586 within_species_paralog (node Osteoglossocephalai)
ctdspl2a: danio_rerio ENSDARG00000089646 within_species_paralog (node Bilateria)
ctdspl2a: danio_rerio ENSDARG00000035781 within_species_paralog (node Opisthokonta)
ctdspl2a: danio_rerio ENSDARG00000031098 within_species_paralog (node Opisthokonta)
ctdspl2a: danio_rerio ENSDARG00000016519 within_species_paralog (node Opisthokonta)
ctdspl2a: danio_rerio ENSDARG00000071673 other_paralog (node Opisthokonta)
ctdspl2a: danio_rerio ENSDARG00000036102 other_paralog (node Opisthokonta)
ctdspl2a: danio_rerio ENSDARG00000040674 other_paralog (node Opisthokonta)
ctdspl2a: danio_rerio ENSDARG00000062116 other_paralog (node Opisthokonta)
ctdspl2a: lepisosteus_oculatus ENSLOCG00000013760 ortholog_one2many (node Neopterygii)
ctdspl2a: homo_sapiens ENSG00000137770 ortholog_one2many (node Chordata)
ctdspl2a: oryzias_latipes ENSORLG00000005035 ortholog_one2one (node Clupeocephala)
ctdspl2b: danio_rerio ENSDARG00000061587 within_species_paralog (node Osteoglossocephalai)
ctdspl2b: danio_rerio ENSDARG00000089646 within_species_paralog (node Bilateria)
ctdspl2b: danio_rerio ENSDARG00000035781 within_species_paralog (node Opisthokonta)
ctdspl2b: danio_rerio ENSDARG00000031098 within_species_paralog (node Opisthokonta)
ctdspl2b: danio_rerio ENSDARG00000016519 within_species_paralog (node Opisthokonta)
ctdspl2b: danio_rerio ENSDARG00000071673 other_paralog (node Opisthokonta)
ctdspl2b: danio_rerio ENSDARG00000036102 other_paralog (node Opisthokonta)
ctdspl2b: danio_rerio ENSDARG00000040674 other_paralog (node Opisthokonta)
ctdspl2b: danio_rerio ENSDARG00000062116 other_paralog (node Opisthokonta)
ctdspl2b: lepisosteus_oculatus ENSLOCG00000013760 ortholog_one2many (node Neopterygii)
ctdspl2b: homo_sapiens ENSG00000137770 ortholog_one2many (node Chordata)
ctdspl2b: oryzias_latipes ENSORLG00000006288 ortholog_one2one (node Clupeocephala)

Compara node of the ctdspl2a/ctdspl2b duplication: ['Osteoglossocephalai']

## 1. Sequence lengths and pairwise identities

human CTDSPL2: UniProt Q05D32
human CTDSP1: UniProt Q9GZU7
human CTDSP2: UniProt O14595
human CTDSPL: UniProt O15194
length ctdspl2a: 469 aa
length ctdspl2b: 460 aa
length CTDSPL2: 466 aa
length CTDSP1: 261 aa
length CTDSP2: 271 aa
length CTDSPL: 276 aa
length gar_ENSLOCG00000013760: 488 aa
length medaka_ENSORLG00000005035(orth of ctdspl2a): 473 aa
length medaka_ENSORLG00000006288(orth of ctdspl2b): 474 aa
identity ctdspl2a vs ctdspl2b: 70.9% over 477 columns
identity ctdspl2a vs CTDSPL2: 73.2% over 477 columns
identity ctdspl2a vs CTDSP1: 23.5% over 469 columns
identity ctdspl2a vs CTDSP2: 24.1% over 469 columns
identity ctdspl2a vs CTDSPL: 25.4% over 472 columns
identity ctdspl2a vs gar_ENSLOCG00000013760: 74.4% over 496 columns
identity ctdspl2a vs medaka_ENSORLG00000005035(orth of ctdspl2a): 75.7% over 474 columns
identity ctdspl2a vs medaka_ENSORLG00000006288(orth of ctdspl2b): 72.2% over 482 columns
identity ctdspl2b vs CTDSPL2: 69.7% over 479 columns
identity ctdspl2b vs CTDSP1: 22.4% over 460 columns
identity ctdspl2b vs CTDSP2: 23.7% over 473 columns
identity ctdspl2b vs CTDSPL: 25.9% over 460 columns
identity ctdspl2b vs gar_ENSLOCG00000013760: 71.0% over 504 columns
identity ctdspl2b vs medaka_ENSORLG00000005035(orth of ctdspl2a): 69.0% over 477 columns
identity ctdspl2b vs medaka_ENSORLG00000006288(orth of ctdspl2b): 71.4% over 482 columns
identity CTDSPL2 vs CTDSP1: 23.3% over 468 columns
identity CTDSPL2 vs CTDSP2: 24.9% over 469 columns
identity CTDSPL2 vs CTDSPL: 26.0% over 469 columns
identity CTDSPL2 vs gar_ENSLOCG00000013760: 77.4% over 495 columns
identity CTDSPL2 vs medaka_ENSORLG00000005035(orth of ctdspl2a): 69.9% over 478 columns
identity CTDSPL2 vs medaka_ENSORLG00000006288(orth of ctdspl2b): 69.1% over 486 columns
identity CTDSP1 vs CTDSP2: 59.5% over 279 columns
identity CTDSP1 vs CTDSPL: 65.7% over 277 columns
identity CTDSP1 vs gar_ENSLOCG00000013760: 21.5% over 493 columns
identity CTDSP1 vs medaka_ENSORLG00000005035(orth of ctdspl2a): 21.8% over 478 columns
identity CTDSP1 vs medaka_ENSORLG00000006288(orth of ctdspl2b): 22.5% over 475 columns
identity CTDSP2 vs CTDSPL: 63.6% over 283 columns
identity CTDSP2 vs gar_ENSLOCG00000013760: 23.7% over 493 columns
identity CTDSP2 vs medaka_ENSORLG00000005035(orth of ctdspl2a): 24.1% over 474 columns
identity CTDSP2 vs medaka_ENSORLG00000006288(orth of ctdspl2b): 22.9% over 477 columns
identity CTDSPL vs gar_ENSLOCG00000013760: 23.8% over 488 columns
identity CTDSPL vs medaka_ENSORLG00000005035(orth of ctdspl2a): 25.2% over 473 columns
identity CTDSPL vs medaka_ENSORLG00000006288(orth of ctdspl2b): 25.5% over 474 columns
identity gar_ENSLOCG00000013760 vs medaka_ENSORLG00000005035(orth of ctdspl2a): 72.1% over 499 columns
identity gar_ENSLOCG00000013760 vs medaka_ENSORLG00000006288(orth of ctdspl2b): 69.7% over 511 columns
identity medaka_ENSORLG00000005035(orth of ctdspl2a) vs medaka_ENSORLG00000006288(orth of ctdspl2b): 69.7% over 485 columns

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

Domain: FCP1 homology [283-442] ctdspl2a: aligned 160/160, identical 156/160 (97.5%)
Domain: FCP1 homology [283-442] ctdspl2b: aligned 160/160, identical 154/160 (96.2%)
Domain: FCP1 homology [283-442] gar_ENSLOCG00000013760: aligned 160/160, identical 158/160 (98.8%)
Region: Disordered [1-140] ctdspl2a: aligned 134/140, identical 73/140 (52.1%)
Region: Disordered [1-140] ctdspl2b: aligned 124/140, identical 66/140 (47.1%)
Region: Disordered [1-140] gar_ENSLOCG00000013760: aligned 139/140, identical 92/140 (65.7%)
Region: Disordered [220-240] ctdspl2a: aligned 20/21, identical 9/21 (42.9%)
Region: Disordered [220-240] ctdspl2b: aligned 21/21, identical 11/21 (52.4%)
Region: Disordered [220-240] gar_ENSLOCG00000013760: aligned 21/21, identical 14/21 (66.7%)
motif DxDx(T/V) /D.D.[TV]/ in ctdspl2a: [(296, 'DLDET')]
motif DxDx(T/V) /D.D.[TV]/ in ctdspl2b: [(287, 'DLDET')]
motif DxDx(T/V) /D.D.[TV]/ in gar_ENSLOCG00000013760: [(315, 'DLDET')]
motif DxDx(T/V) /D.D.[TV]/ in CTDSPL2: [(293, 'DLDET')]
human CTDSPL2 residue D293 aligned to -> ctdspl2a: D; ctdspl2b: D; gar_ENSLOCG00000013760: D
human CTDSPL2 residue L294 aligned to -> ctdspl2a: L; ctdspl2b: L; gar_ENSLOCG00000013760: L
human CTDSPL2 residue D295 aligned to -> ctdspl2a: D; ctdspl2b: D; gar_ENSLOCG00000013760: D
human CTDSPL2 residue E296 aligned to -> ctdspl2a: E; ctdspl2b: E; gar_ENSLOCG00000013760: E
human CTDSPL2 residue T297 aligned to -> ctdspl2a: T; ctdspl2b: T; gar_ENSLOCG00000013760: T

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

gar positions aligned in both copies: 441
changes unique to ctdspl2a (m1): 38; unique to ctdspl2b (m2): 38; chi2 (1 df) = 0.00 (not significant at 0.05)

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

| stage | ctdspl2a | ctdspl2b |
|---|---|---|
| zygote | 59 | 26 |
| cleavage 2-cell | 111 | 48 |
| blastula 128-cell | 246 | 73 |
| blastula 1k-cell | 224 | 96 |
| blastula dome | 203 | 67 |
| gastrula 50%-epiboly | 77 | 34 |
| gastrula shield | 54 | 18 |
| gastrula 75%-epiboly | 53 | 14 |
| segmentation 1-4 somites | 54 | 23 |
| segmentation 14-19 somites | 57 | 23 |
| segmentation 20-25 somites | 60 | 23 |
| pharyngula prim-5 | 55 | 20 |
| pharyngula prim-15 | 48 | 18 |
| pharyngula prim-25 | 53 | 22 |
| hatching long-pec | 38 | 17 |
| larval protruding mouth | 36 | 18 |
| larval day 4 | 34 | 18 |
| larval day 5 | 34 | 17 |

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

### ctdspl2a: 27 calls
- early embryo: 95.5 (gold; RNA-Seq)
- blastula: 93.7 (gold; Affymetrix,RNA-Seq)
- camera-type eye: 89.2 (gold; Affymetrix,RNA-Seq)
- retina: 89.0 (gold; Affymetrix,RNA-Seq)
- gastrula: 88.7 (gold; Affymetrix,RNA-Seq)
- mature ovarian follicle: 88.1 (gold; RNA-Seq)
- cleaving embryo: 88.0 (gold; Affymetrix)
- spleen: 85.2 (gold; RNA-Seq)
- granulocyte: 85.2 (gold; RNA-Seq)
- pharyngeal gill: 83.1 (gold; RNA-Seq)
- brain: 83.0 (gold; Affymetrix,RNA-Seq)
- swim bladder: 82.9 (gold; RNA-Seq)
- integument: 82.8 (gold; Affymetrix,RNA-Seq)
- zone of skin: 82.7 (gold; RNA-Seq)
- larva: 82.2 (gold; Affymetrix,RNA-Seq)
- caudal fin: 82.2 (gold; Affymetrix)
- presomitic mesoderm: 81.9 (gold; Affymetrix)
- testis: 81.8 (gold; RNA-Seq)
- heart: 81.2 (gold; Affymetrix,RNA-Seq)
- muscle tissue: 80.6 (gold; RNA-Seq)
- cardiac ventricle: 79.7 (gold; Affymetrix)
- somite: 79.3 (gold; Affymetrix)
- bone element: 77.3 (gold; RNA-Seq)
- head kidney: 77.3 (gold; RNA-Seq)
- tail bud paraxial mesoderm: 75.1 (gold; Affymetrix)
- intestine: 74.6 (gold; RNA-Seq)
- liver: 74.0 (gold; Affymetrix,RNA-Seq)
### ctdspl2b: 27 calls
- early embryo: 90.5 (gold; RNA-Seq)
- mature ovarian follicle: 89.0 (gold; RNA-Seq)
- cleaving embryo: 87.2 (gold; Affymetrix)
- testis: 86.0 (gold; RNA-Seq)
- blastula: 85.8 (gold; Affymetrix,RNA-Seq)
- gastrula: 83.6 (gold; Affymetrix,RNA-Seq)
- somite: 83.2 (gold; Affymetrix)
- swim bladder: 83.1 (gold; RNA-Seq)
- brain: 83.0 (gold; Affymetrix,RNA-Seq)
- presomitic mesoderm: 82.1 (gold; Affymetrix)
- larva: 80.7 (gold; Affymetrix,RNA-Seq)
- head: 80.1 (gold; Affymetrix,RNA-Seq)
- muscle tissue: 79.4 (gold; RNA-Seq)
- camera-type eye: 79.0 (gold; Affymetrix,RNA-Seq)
- granulocyte: 79.0 (gold; RNA-Seq)
- cardiac ventricle: 78.7 (gold; Affymetrix)
- tail bud paraxial mesoderm: 78.5 (gold; Affymetrix)
- caudal fin: 77.3 (gold; Affymetrix)
- integument: 75.8 (gold; Affymetrix,RNA-Seq)
- zone of skin: 75.5 (gold; RNA-Seq)
- retina: 75.1 (gold; Affymetrix,RNA-Seq)
- head kidney: 72.3 (gold; RNA-Seq)
- bone element: 69.8 (gold; RNA-Seq)
- pharyngeal gill: 69.4 (gold; RNA-Seq)
- intestine: 68.4 (gold; RNA-Seq)
- spleen: 67.6 (gold; RNA-Seq)
- liver: 63.5 (gold; Affymetrix,RNA-Seq)
### gar ENSLOCG00000013760: 14 calls
- brain: 83.8 (gold; RNA-Seq)
- testis: 80.9 (gold; RNA-Seq)
- bone element: 80.6 (gold; RNA-Seq)
- intestine: 80.5 (gold; RNA-Seq)
- camera-type eye: 79.9 (gold; RNA-Seq)
- heart: 78.2 (gold; RNA-Seq)
- zone of skin: 77.8 (gold; RNA-Seq)
- ovary: 77.1 (gold; RNA-Seq)
- embryo: 76.5 (gold; RNA-Seq)
- mesonephros: 76.4 (gold; RNA-Seq)
- larva: 75.4 (gold; RNA-Seq)
- muscle tissue: 75.0 (gold; RNA-Seq)
- liver: 72.5 (gold; RNA-Seq)
- pharyngeal gill: 71.3 (gold; RNA-Seq)

RNA-Seq-supported entities: ctdspl2a only: ['heart']
RNA-Seq-supported entities: ctdspl2b only: ['head']
RNA-Seq-supported entities: both: ['blastula', 'bone element', 'brain', 'camera-type eye', 'early embryo', 'gastrula', 'granulocyte', 'head kidney', 'integument', 'intestine', 'larva', 'liver', 'mature ovarian follicle', 'muscle tissue', 'pharyngeal gill', 'retina', 'spleen', 'swim bladder', 'testis', 'zone of skin']

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

### ctdspl2a: 0 records
### ctdspl2b: 0 records

anatomy terms ctdspl2a only: []
anatomy terms ctdspl2b only: []
anatomy terms both: []

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

ctdspl2a: chr25:32496723-32519415
ctdspl2b: chr7:31374383-31395511

ctdspl2a +/- 1.5 Mb: 44 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 ctdspl2b:
- eif3ja -> eif3jb (chr7:31425976)
- apba2a -> apba2b (chr7:30787903)
- tjp1b -> tjp1a (chr7:30930653)
- tln2b -> tln2a (chr7:29863548)
- ENSDARG00000112342 -> tln2a (chr7:29863548)
- isl2a -> isl2b (chr7:29992889)
16 have their partner anywhere on chr7 (1356 protein-coding genes):
- lsp1a -> lsp1b (chr7:39410180)
- eif3ja -> eif3jb (chr7:31425976)
- apba2a -> apba2b (chr7:30787903)
- tjp1b -> tjp1a (chr7:30930653)
- tln2b -> tln2a (chr7:29863548)
- anxa2a -> anxa2b (chr7:29518396)
- tnni2a.1 -> tnni2b.2 (chr7:39385540)
- tnni2a.1 -> tnni2b.1 (chr7:39399747)
- tnni2a.2 -> tnni2b.2 (chr7:39385540)
- tnni2a.2 -> tnni2b.1 (chr7:39399747)
- tnni2a.3 -> tnni2b.1 (chr7:39399747)
- tnni2a.3 -> tnni2b.2 (chr7:39385540)
- tnni2a.4 -> tnni2b.1 (chr7:39399747)
- tnni2a.4 -> tnni2b.2 (chr7:39385540)
- ENSDARG00000112342 -> tln2a (chr7:29863548)
- isl2a -> isl2b (chr7:29992889)

ctdspl2b +/- 1.5 Mb: 60 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 ctdspl2a:
- tln2a -> tln2b (chr25:33033633)
- tln2a -> ENSDARG00000112342 (chr25:33002963)
- apba2b -> apba2a (chr25:31912153)
- tjp1a -> tjp1b (chr25:32031536)
- isl2b -> isl2a (chr25:32746014)
- eif3jb -> eif3ja (chr25:31900825)
12 have their partner anywhere on chr25 (806 protein-coding genes):
- adam10a -> adam10b (chr25:150570)
- lipca -> lipcb (chr25:135932)
- gas2b -> gas2a (chr25:35304903)
- tmem276b -> tmem276a (chr25:35533790)
- slc17a6b -> slc17a6a (chr25:35250976)
- tln2a -> tln2b (chr25:33033633)
- tln2a -> ENSDARG00000112342 (chr25:33002963)
- ano5b -> ano5a (chr25:35189555)
- apba2b -> apba2a (chr25:31912153)
- tjp1a -> tjp1b (chr25:32031536)
- isl2b -> isl2a (chr25:32746014)
- eif3jb -> eif3ja (chr25:31900825)