# Pair analysis: abi1a / abi1b  (run 2026-09-28)

## 1. Sequence lengths and pairwise identities

length abi1a: 522 aa
length abi1b: 507 aa
length ABI1: 508 aa
length ABI2: 513 aa
length ABI3: 366 aa
length gar_ABI1: 625 aa
length medaka_ortholog_of_abi1a: 641 aa
length medaka_ortholog_of_abi1b: 496 aa
identity abi1a vs abi1b: 79.2% over 543 columns
identity abi1a vs ABI1: 81.6% over 526 columns
identity abi1a vs ABI2: 62.5% over 549 columns
identity abi1a vs ABI3: 36.1% over 526 columns
identity abi1a vs gar_ABI1: 72.5% over 633 columns
identity abi1a vs medaka_ortholog_of_abi1a: 64.9% over 646 columns
identity abi1a vs medaka_ortholog_of_abi1b: 80.7% over 529 columns
identity abi1b vs ABI1: 77.5% over 530 columns
identity abi1b vs ABI2: 57.6% over 569 columns
identity abi1b vs ABI3: 36.5% over 507 columns
identity abi1b vs gar_ABI1: 68.8% over 634 columns
identity abi1b vs medaka_ortholog_of_abi1a: 57.1% over 662 columns
identity abi1b vs medaka_ortholog_of_abi1b: 86.8% over 516 columns
identity ABI1 vs ABI2: 63.6% over 555 columns
identity ABI1 vs ABI3: 36.8% over 517 columns
identity ABI1 vs gar_ABI1: 74.3% over 626 columns
identity ABI1 vs medaka_ortholog_of_abi1a: 61.4% over 650 columns
identity ABI1 vs medaka_ortholog_of_abi1b: 79.0% over 515 columns
identity ABI2 vs ABI3: 35.7% over 513 columns
identity ABI2 vs gar_ABI1: 54.6% over 657 columns
identity ABI2 vs medaka_ortholog_of_abi1a: 48.3% over 662 columns
identity ABI2 vs medaka_ortholog_of_abi1b: 60.5% over 554 columns
identity ABI3 vs gar_ABI1: 29.9% over 625 columns
identity ABI3 vs medaka_ortholog_of_abi1a: 25.5% over 647 columns
identity ABI3 vs medaka_ortholog_of_abi1b: 36.4% over 506 columns
identity gar_ABI1 vs medaka_ortholog_of_abi1a: 54.9% over 748 columns
identity gar_ABI1 vs medaka_ortholog_of_abi1b: 67.2% over 632 columns
identity medaka_ortholog_of_abi1a vs medaka_ortholog_of_abi1b: 58.8% over 646 columns

## 2. Identity per region of the human reference, and key residues

N-terminal WAVE-binding region (UniProt 'Required for binding to WASF1') [18-79] abi1a: aligned 62/62, identical 59/62 (95.2%)
N-terminal WAVE-binding region (UniProt 'Required for binding to WASF1') [18-79] abi1b: aligned 62/62, identical 57/62 (91.9%)
N-terminal WAVE-binding region (UniProt 'Required for binding to WASF1') [18-79] gar_ABI1: aligned 62/62, identical 59/62 (95.2%)
t-SNARE coiled-coil homology domain [45-107] abi1a: aligned 63/63, identical 63/63 (100.0%)
t-SNARE coiled-coil homology domain [45-107] abi1b: aligned 63/63, identical 63/63 (100.0%)
t-SNARE coiled-coil homology domain [45-107] gar_ABI1: aligned 63/63, identical 63/63 (100.0%)
central disordered / proline-rich region [159-421] abi1a: aligned 259/263, identical 202/263 (76.8%)
central disordered / proline-rich region [159-421] abi1b: aligned 240/263, identical 186/263 (70.7%)
central disordered / proline-rich region [159-421] gar_ABI1: aligned 262/263, identical 232/263 (88.2%)
SH3 domain [446-505] abi1a: aligned 60/60, identical 54/60 (90.0%)
SH3 domain [446-505] abi1b: aligned 60/60, identical 55/60 (91.7%)
SH3 domain [446-505] gar_ABI1: aligned 60/60, identical 55/60 (91.7%)
human ABI1 Y53: abi1a=Y, abi1b=Y, gar_ABI1=Y
human ABI1 Y213: abi1a=Y, abi1b=Y, gar_ABI1=Y
human ABI1 Y455: abi1a=Y, abi1b=Y, gar_ABI1=Y
abi1a: 0 residues precede the alignment to human ABI1 residue 1 (N-terminal extension)
abi1b: 13 residues precede the alignment to human ABI1 residue 1 (N-terminal extension)

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

gar positions aligned in both copies: 480
changes unique to abi1a (m1): 17; unique to abi1b (m2): 28; chi2 (1 df) = 2.69 (not significant at 0.05)

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

| stage | abi1a | abi1b |
|---|---|---|
| zygote | 7 | 8 |
| cleavage 2-cell | 4 | 15 |
| blastula 128-cell | 5 | 28 |
| blastula 1k-cell | 4 | 26 |
| blastula dome | 2 | 16 |
| gastrula 50%-epiboly | 6 | 11 |
| gastrula shield | 13 | 9 |
| gastrula 75%-epiboly | 26 | 6 |
| segmentation 1-4 somites | 35 | 4 |
| segmentation 14-19 somites | 29 | 3 |
| segmentation 20-25 somites | 36 | 4 |
| pharyngula prim-5 | 33 | 3 |
| pharyngula prim-15 | 28 | 3 |
| pharyngula prim-25 | 22 | 6 |
| hatching long-pec | 26 | 6 |
| larval protruding mouth | 29 | 4 |
| larval day 4 | 29 | 7 |
| larval day 5 | 25 | 7 |

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

### abi1a: 25 calls
- caudal fin: 94.8 (gold; Affymetrix)
- presomitic mesoderm: 93.1 (gold; Affymetrix)
- pharyngeal gill: 92.1 (gold; RNA-Seq)
- cardiac ventricle: 88.3 (gold; Affymetrix)
- somite: 88.3 (gold; Affymetrix)
- intestine: 88.1 (gold; RNA-Seq)
- granulocyte: 87.8 (gold; RNA-Seq)
- tail bud paraxial mesoderm: 87.2 (gold; Affymetrix)
- zone of skin: 86.2 (gold; RNA-Seq)
- spleen: 85.0 (gold; RNA-Seq)
- swim bladder: 84.0 (gold; RNA-Seq)
- liver: 83.5 (gold; Affymetrix,RNA-Seq)
- camera-type eye: 83.4 (gold; Affymetrix,RNA-Seq)
- retina: 83.2 (gold; Affymetrix,RNA-Seq)
- brain: 81.5 (gold; Affymetrix,RNA-Seq)
- larva: 80.1 (gold; Affymetrix,RNA-Seq)
- head kidney: 80.1 (gold; RNA-Seq)
- mature ovarian follicle: 75.0 (gold; RNA-Seq)
- muscle tissue: 70.6 (gold; RNA-Seq)
- gastrula: 70.2 (gold; Affymetrix,RNA-Seq)
- bone element: 66.3 (gold; RNA-Seq)
- early embryo: 64.0 (gold; RNA-Seq)
- testis: 63.8 (gold; RNA-Seq)
- cleaving embryo: 59.6 (gold; Affymetrix)
- blastula: 56.2 (gold; Affymetrix,RNA-Seq)
### abi1b: 8 calls
- early embryo: 78.6 (gold; RNA-Seq)
- blastula: 74.8 (gold; RNA-Seq)
- retina: 70.1 (gold; RNA-Seq)
- gastrula: 67.9 (gold; RNA-Seq)
- mature ovarian follicle: 62.2 (silver; RNA-Seq)
- brain: 60.4 (gold; RNA-Seq)
- larva: 43.8 (gold; RNA-Seq)
- bone element: 26.0 (silver; RNA-Seq)
### gar_ABI1 (spotted gar): 14 calls
- zone of skin: 88.3 (gold; RNA-Seq)
- camera-type eye: 87.7 (gold; RNA-Seq)
- liver: 84.3 (gold; RNA-Seq)
- larva: 83.8 (gold; RNA-Seq)
- mesonephros: 83.1 (gold; RNA-Seq)
- testis: 82.4 (gold; RNA-Seq)
- intestine: 82.1 (gold; RNA-Seq)
- brain: 81.6 (gold; RNA-Seq)
- bone element: 81.2 (gold; RNA-Seq)
- heart: 80.8 (gold; RNA-Seq)
- embryo: 80.5 (gold; RNA-Seq)
- ovary: 78.7 (gold; RNA-Seq)
- pharyngeal gill: 78.4 (gold; RNA-Seq)
- muscle tissue: 62.7 (gold; RNA-Seq)

RNA-Seq-supported entities: abi1a only: ['camera-type eye', 'granulocyte', 'head kidney', 'intestine', 'liver', 'muscle tissue', 'pharyngeal gill', 'spleen', 'swim bladder', 'testis', 'zone of skin']
RNA-Seq-supported entities: abi1b only: []
RNA-Seq-supported entities: both: ['blastula', 'bone element', 'brain', 'early embryo', 'gastrula', 'larva', 'mature ovarian follicle', 'retina']

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

abi1a: chr24:5935377-6012786
abi1b: chr2:9868601-9915870

abi1a +/- 1.5 Mb: 40 other protein-coding genes (0 homology queries failed); 3 have a Clupeocephala-level zebrafish paralogue; 0 such paralogue pairs have their partner within 1.5 Mb of abi1b:
Of the Clupeocephala-level paralogue pairs, 3 have their partner anywhere on chr2 (the chromosome of abi1b, 1188 protein-coding genes):
- si:dkeyp-101e12.1 -> si:ch211-182e10.4 (chr2:53114476)
- kmt2ca -> kmt2cb (chr2:12847602)
- agtr1b -> agtr1a (chr2:24931677)

abi1b +/- 1.5 Mb: 66 other protein-coding genes (0 homology queries failed); 17 have a Clupeocephala-level zebrafish paralogue; 0 such paralogue pairs have their partner within 1.5 Mb of abi1a:
Of the Clupeocephala-level paralogue pairs, 1 have their partner anywhere on chr24 (the chromosome of abi1a, 687 protein-coding genes):
- ENSDARG00000098557 -> si:dkeyp-88h4.2 (chr24:29860769)