# Pair analysis: prom1a / prom1b  (run 2026-09-28)

## 1. Sequence lengths and pairwise identities

length prom1a: 826 aa
length prom1b: 867 aa
length PROM1: 865 aa
length PROM2: 834 aa
length gar_PROM1: 895 aa
length medaka_ortholog_of_prom1a: 857 aa
length medaka_ortholog_of_prom1b: 837 aa
length zebrafish_prom1a_ensembl_canonical: 849 aa
length zebrafish_prom1b_ensembl_canonical: 853 aa
identity prom1a vs prom1b: 54.4% over 867 columns
identity prom1a vs PROM1: 41.2% over 880 columns
identity prom1a vs PROM2: 27.6% over 870 columns
identity prom1a vs gar_PROM1: 60.3% over 899 columns
identity prom1a vs medaka_ortholog_of_prom1a: 62.5% over 858 columns
identity prom1a vs medaka_ortholog_of_prom1b: 56.9% over 842 columns
identity prom1a vs zebrafish_prom1a_ensembl_canonical: 97.1% over 849 columns
identity prom1a vs zebrafish_prom1b_ensembl_canonical: 55.3% over 853 columns
identity prom1b vs PROM1: 39.1% over 898 columns
identity prom1b vs PROM2: 27.1% over 885 columns
identity prom1b vs gar_PROM1: 60.8% over 911 columns
identity prom1b vs medaka_ortholog_of_prom1a: 53.7% over 881 columns
identity prom1b vs medaka_ortholog_of_prom1b: 67.4% over 869 columns
identity prom1b vs zebrafish_prom1a_ensembl_canonical: 56.3% over 867 columns
identity prom1b vs zebrafish_prom1b_ensembl_canonical: 98.4% over 867 columns
identity PROM1 vs PROM2: 25.4% over 891 columns
identity PROM1 vs gar_PROM1: 46.3% over 905 columns
identity PROM1 vs medaka_ortholog_of_prom1a: 41.9% over 887 columns
identity PROM1 vs medaka_ortholog_of_prom1b: 39.8% over 883 columns
identity PROM1 vs zebrafish_prom1a_ensembl_canonical: 41.6% over 882 columns
identity PROM1 vs zebrafish_prom1b_ensembl_canonical: 39.7% over 885 columns
identity PROM2 vs gar_PROM1: 27.8% over 915 columns
identity PROM2 vs medaka_ortholog_of_prom1a: 26.8% over 874 columns
identity PROM2 vs medaka_ortholog_of_prom1b: 26.7% over 875 columns
identity PROM2 vs zebrafish_prom1a_ensembl_canonical: 27.2% over 887 columns
identity PROM2 vs zebrafish_prom1b_ensembl_canonical: 27.3% over 871 columns
identity gar_PROM1 vs medaka_ortholog_of_prom1a: 58.1% over 907 columns
identity gar_PROM1 vs medaka_ortholog_of_prom1b: 59.4% over 896 columns
identity gar_PROM1 vs zebrafish_prom1a_ensembl_canonical: 62.3% over 900 columns
identity gar_PROM1 vs zebrafish_prom1b_ensembl_canonical: 59.6% over 911 columns
identity medaka_ortholog_of_prom1a vs medaka_ortholog_of_prom1b: 52.8% over 865 columns
identity medaka_ortholog_of_prom1a vs zebrafish_prom1a_ensembl_canonical: 63.4% over 866 columns
identity medaka_ortholog_of_prom1a vs zebrafish_prom1b_ensembl_canonical: 53.8% over 873 columns
identity medaka_ortholog_of_prom1b vs zebrafish_prom1a_ensembl_canonical: 57.3% over 850 columns
identity medaka_ortholog_of_prom1b vs zebrafish_prom1b_ensembl_canonical: 67.3% over 863 columns
identity zebrafish_prom1a_ensembl_canonical vs zebrafish_prom1b_ensembl_canonical: 56.0% over 861 columns

## 1b. Zebrafish copies vs each isoform of the human reference

identity prom1a vs O43490 (865 aa): 41.2% over 880 columns; N-terminal 60 aa: 26.9%
identity prom1b vs O43490 (865 aa): 39.0% over 899 columns; N-terminal 60 aa: 12.0%
identity prom1a vs O43490-2 (856 aa): 41.6% over 865 columns; N-terminal 60 aa: 26.9%
identity prom1b vs O43490-2 (856 aa): 38.4% over 899 columns; N-terminal 60 aa: 12.0%
identity prom1a vs O43490-3 (830 aa): 42.9% over 839 columns; N-terminal 60 aa: 26.9%
identity prom1b vs O43490-3 (830 aa): 39.4% over 875 columns; N-terminal 60 aa: 12.0%
identity prom1a vs O43490-4 (833 aa): 42.8% over 842 columns; N-terminal 60 aa: 26.9%
identity prom1b vs O43490-4 (833 aa): 39.2% over 876 columns; N-terminal 60 aa: 12.0%
identity prom1a vs O43490-5 (825 aa): 43.2% over 834 columns; N-terminal 60 aa: 26.9%
identity prom1b vs O43490-5 (825 aa): 39.5% over 870 columns; N-terminal 60 aa: 12.0%
identity prom1a vs O43490-6 (834 aa): 42.8% over 849 columns; N-terminal 60 aa: 26.9%
identity prom1b vs O43490-6 (834 aa): 40.2% over 870 columns; N-terminal 60 aa: 12.0%
identity prom1a vs O43490-7 (842 aa): 42.4% over 857 columns; N-terminal 60 aa: 26.9%
identity prom1b vs O43490-7 (842 aa): 39.8% over 876 columns; N-terminal 60 aa: 12.0%

## 2. Regions of human PROM1 (UniProt features), N-glycosylation sites, cysteines, R373

Topological domain: Extracellular [20-108] prom1a: aligned 74/89, identical 32/89 (36.0%)
Topological domain: Extracellular [20-108] prom1b: aligned 88/89, identical 37/89 (41.6%)
Topological domain: Extracellular [20-108] gar_PROM1: aligned 89/89, identical 37/89 (41.6%)
Transmembrane: Helical [109-129] prom1a: aligned 21/21, identical 11/21 (52.4%)
Transmembrane: Helical [109-129] prom1b: aligned 21/21, identical 10/21 (47.6%)
Transmembrane: Helical [109-129] gar_PROM1: aligned 21/21, identical 12/21 (57.1%)
Topological domain: Cytoplasmic [130-157] prom1a: aligned 28/28, identical 18/28 (64.3%)
Topological domain: Cytoplasmic [130-157] prom1b: aligned 28/28, identical 20/28 (71.4%)
Topological domain: Cytoplasmic [130-157] gar_PROM1: aligned 28/28, identical 19/28 (67.9%)
Transmembrane: Helical [158-178] prom1a: aligned 21/21, identical 5/21 (23.8%)
Transmembrane: Helical [158-178] prom1b: aligned 21/21, identical 3/21 (14.3%)
Transmembrane: Helical [158-178] gar_PROM1: aligned 21/21, identical 8/21 (38.1%)
Topological domain: Extracellular [179-433] prom1a: aligned 255/255, identical 96/255 (37.6%)
Topological domain: Extracellular [179-433] prom1b: aligned 255/255, identical 97/255 (38.0%)
Topological domain: Extracellular [179-433] gar_PROM1: aligned 255/255, identical 111/255 (43.5%)
Transmembrane: Helical [434-454] prom1a: aligned 21/21, identical 7/21 (33.3%)
Transmembrane: Helical [434-454] prom1b: aligned 21/21, identical 8/21 (38.1%)
Transmembrane: Helical [434-454] gar_PROM1: aligned 21/21, identical 8/21 (38.1%)
Topological domain: Cytoplasmic [455-486] prom1a: aligned 32/32, identical 26/32 (81.2%)
Topological domain: Cytoplasmic [455-486] prom1b: aligned 32/32, identical 23/32 (71.9%)
Topological domain: Cytoplasmic [455-486] gar_PROM1: aligned 32/32, identical 24/32 (75.0%)
Transmembrane: Helical [487-507] prom1a: aligned 21/21, identical 10/21 (47.6%)
Transmembrane: Helical [487-507] prom1b: aligned 21/21, identical 12/21 (57.1%)
Transmembrane: Helical [487-507] gar_PROM1: aligned 21/21, identical 14/21 (66.7%)
Topological domain: Extracellular [508-792] prom1a: aligned 284/285, identical 126/285 (44.2%)
Topological domain: Extracellular [508-792] prom1b: aligned 284/285, identical 109/285 (38.2%)
Topological domain: Extracellular [508-792] gar_PROM1: aligned 284/285, identical 132/285 (46.3%)
Transmembrane: Helical [793-813] prom1a: aligned 21/21, identical 12/21 (57.1%)
Transmembrane: Helical [793-813] prom1b: aligned 21/21, identical 10/21 (47.6%)
Transmembrane: Helical [793-813] gar_PROM1: aligned 21/21, identical 12/21 (57.1%)
Topological domain: Cytoplasmic [814-865] prom1a: aligned 17/52, identical 14/52 (26.9%)
Topological domain: Cytoplasmic [814-865] prom1b: aligned 23/52, identical 16/52 (30.8%)
Topological domain: Cytoplasmic [814-865] gar_PROM1: aligned 44/52, identical 34/52 (65.4%)
human PROM1 annotated N-glycosylation sites [220, 274, 395, 414, 548, 580, 729, 730]: Asn kept in prom1a: [548, 580, 730]
human PROM1 annotated N-glycosylation sites [220, 274, 395, 414, 548, 580, 729, 730]: Asn kept in prom1b: [580, 729, 730]
human PROM1 annotated N-glycosylation sites [220, 274, 395, 414, 548, 580, 729, 730]: Asn kept in gar_PROM1: [220, 580, 730]
human PROM1 cysteines (22): prom1a keeps 15; changed: ['C14->T', 'C113->A', 'C157->L', 'C166->T', 'C461->L', 'C494->S', 'C624->T']; total Cys in prom1a: 22
human PROM1 cysteines (22): prom1b keeps 15; changed: ['C14->W', 'C112->L', 'C113->S', 'C157->F', 'C166->S', 'C494->S', 'C624->T']; total Cys in prom1b: 21
human PROM1 cysteines (22): gar_PROM1 keeps 17; changed: ['C14->W', 'C113->A', 'C166->S', 'C494->S', 'C624->T']; total Cys in gar_PROM1: 24
N-glycosylation sequons (N-X-S/T, X!=P) in prom1a: 13
N-glycosylation sequons (N-X-S/T, X!=P) in prom1b: 9
N-glycosylation sequons (N-X-S/T, X!=P) in gar_PROM1: 14
N-glycosylation sequons (N-X-S/T, X!=P) in PROM1: 9
human PROM1 disease variant position 373 (R): prom1a: A, prom1b: E, gar_PROM1: N

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

gar positions aligned in both copies: 821
changes unique to prom1a (m1): 107; unique to prom1b (m2): 118; chi2 (1 df) = 0.54 (not significant at 0.05)

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

| stage | prom1a | prom1b |
|---|---|---|
| zygote | 3 | 0 |
| cleavage 2-cell | 11 | 0 |
| blastula 128-cell | 11 | 0 |
| blastula 1k-cell | 12 | 0 |
| blastula dome | 12 | 0 |
| gastrula 50%-epiboly | 9 | 0 |
| gastrula shield | 5 | 0 |
| gastrula 75%-epiboly | 2 | 0 |
| segmentation 1-4 somites | 1 | 2 |
| segmentation 14-19 somites | 4 | 2 |
| segmentation 20-25 somites | 4 | 0.8 |
| pharyngula prim-5 | 3 | 0.3 |
| pharyngula prim-15 | 4 | 0.7 |
| pharyngula prim-25 | 5 | 2 |
| hatching long-pec | 5 | 6 |
| larval protruding mouth | 14 | 49 |
| larval day 4 | 15 | 29 |
| larval day 5 | 14 | 26 |

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

### prom1a: 46 calls
- eyeball of camera-type eye: 96.8 (gold; in situ hybridization,RNA-Seq)
- retina: 96.8 (gold; in situ hybridization,RNA-Seq)
- brain: 92.6 (gold; in situ hybridization,RNA-Seq)
- diffuse nuclei: 87.5 (gold; in situ hybridization)
- early embryo: 81.2 (gold; RNA-Seq)
- blastula: 76.0 (gold; RNA-Seq)
- mature ovarian follicle: 75.3 (gold; RNA-Seq)
- facial lobe: 75.0 (gold; in situ hybridization)
- periventricular grey zone: 75.0 (gold; in situ hybridization)
- muscle tissue: 73.9 (gold; RNA-Seq)
- bone element: 73.7 (gold; RNA-Seq)
- pallium: 73.1 (gold; in situ hybridization)
- larva: 71.3 (gold; RNA-Seq)
- torus longitudinalis: 66.7 (gold; in situ hybridization)
- outer nuclear layer of retina: 66.7 (gold; in situ hybridization)
- dorsal thalamus: 65.0 (gold; in situ hybridization)
- ventral part of telencephalon: 64.3 (gold; in situ hybridization)
- swim bladder: 63.7 (silver; RNA-Seq)
- tail: 63.7 (gold; RNA-Seq)
- olfactory epithelium: 63.6 (gold; in situ hybridization)
- torus semicircularis: 62.5 (gold; in situ hybridization)
- testis: 62.1 (gold; RNA-Seq)
- gastrula: 61.4 (gold; RNA-Seq)
- preoptic area: 61.1 (gold; in situ hybridization)
- inner nuclear layer of retina: 59.6 (gold; in situ hybridization)
- head kidney: 58.0 (gold; RNA-Seq)
- granulocyte: 57.6 (gold; RNA-Seq)
- lens of camera-type eye: 57.5 (gold; in situ hybridization)
- zone of skin: 57.3 (gold; RNA-Seq)
- eye epithelium: 57.1 (gold; in situ hybridization)
- ventricular system of central nervous system: 55.4 (gold; in situ hybridization)
- epithalamus: 54.8 (gold; in situ hybridization)
- cerebellum: 54.6 (gold; in situ hybridization)
- gland of diencephalon: 54.5 (gold; in situ hybridization)
- ventricular zone: 54.5 (gold; in situ hybridization)
- midbrain-hindbrain boundary: 54.0 (gold; in situ hybridization)
- ectoderm: 53.2 (gold; in situ hybridization)
- pineal body: 53.0 (gold; in situ hybridization)
- ear vesicle: 52.8 (gold; in situ hybridization)
- midbrain tegmentum: 51.5 (gold; in situ hybridization)
- central nucleus of ventral telencephalon (Danio): 50.0 (gold; in situ hybridization)
- epithelium of lens: 50.0 (gold; in situ hybridization)
- spleen: 48.1 (gold; RNA-Seq)
- heart: 46.9 (silver; RNA-Seq)
- intestine: 42.8 (silver; RNA-Seq)
- pharyngeal gill: 41.4 (gold; RNA-Seq)
### prom1b: 5 calls
- retina: 86.3 (gold; Affymetrix,RNA-Seq)
- larva: 76.0 (gold; Affymetrix,RNA-Seq)
- brain: 67.0 (gold; Affymetrix,RNA-Seq)
- embryo: 38.0 (gold; Affymetrix,RNA-Seq)
- bone element: 36.2 (gold; RNA-Seq)
### gar_PROM1 (spotted gar): 13 calls
- camera-type eye: 96.8 (gold; RNA-Seq)
- ovary: 79.1 (gold; RNA-Seq)
- larva: 77.1 (gold; RNA-Seq)
- brain: 74.7 (gold; RNA-Seq)
- embryo: 64.4 (gold; RNA-Seq)
- bone element: 57.4 (gold; RNA-Seq)
- testis: 52.5 (gold; RNA-Seq)
- mesonephros: 50.2 (gold; RNA-Seq)
- zone of skin: 39.2 (gold; RNA-Seq)
- muscle tissue: 36.2 (silver; RNA-Seq)
- liver: 35.9 (silver; RNA-Seq)
- intestine: 30.8 (silver; RNA-Seq)
- heart: 29.6 (silver; RNA-Seq)

RNA-Seq-supported entities: prom1a only: ['blastula', 'early embryo', 'eyeball of camera-type eye', 'gastrula', 'granulocyte', 'head kidney', 'heart', 'intestine', 'mature ovarian follicle', 'muscle tissue', 'pharyngeal gill', 'spleen', 'swim bladder', 'tail', 'testis', 'zone of skin']
RNA-Seq-supported entities: prom1b only: ['embryo']
RNA-Seq-supported entities: both: ['bone element', 'brain', 'larva', 'retina']

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

prom1a: chr14:46456091-46617228
prom1b: chr1:22712931-22757145

prom1a +/- 1.5 Mb: 61 other protein-coding genes (0 homology queries failed); 18 have a teleost-level (Osteoglossocephalai/Clupeocephala) zebrafish paralogue; 6 such paralogue pairs have their partner within 1.5 Mb of prom1b:
- anxa5a -> anxa5b (chr1:22654875)
- fgfbp1a -> fgfbp1b (chr1:22677429)
- fgfbp2a -> fgfbp2b (chr1:22685961)
- tapt1a -> tapt1b (chr1:22770255)
- ldb2a -> ldb2b (chr1:22805398)
- qdpra -> qdprb.1 (chr1:22845225)
Of the teleost-level paralogue pairs, 13 have their partner anywhere on chr1 (the chromosome of prom1b, 1179 protein-coding genes):
- cabp2b -> cabp2a (chr1:44127292)
- anxa5a -> anxa5b (chr1:22654875)
- fgfbp1a -> fgfbp1b (chr1:22677429)
- fgfbp2a -> fgfbp2b (chr1:22685961)
- tapt1a -> tapt1b (chr1:22770255)
- ldb2a -> ldb2b (chr1:22805398)
- qdpra -> qdprb.3 (chr1:24387659)
- qdpra -> qdprb.1 (chr1:22845225)
- qdpra -> qdprb.2 (chr1:24382651)
- qdpra -> qdprb.4 (chr1:24376394)
- nocta -> noctb (chr1:13930625)
- elf2a -> elf2b (chr1:13957235)
- naa15a -> naa15b (chr1:40613292)

prom1b +/- 1.5 Mb: 53 other protein-coding genes (0 homology queries failed); 12 have a teleost-level (Osteoglossocephalai/Clupeocephala) zebrafish paralogue; 6 such paralogue pairs have their partner within 1.5 Mb of prom1a:
- anxa5b -> anxa5a (chr14:46410766)
- fgfbp2b -> fgfbp2a (chr14:46449070)
- tapt1b -> tapt1a (chr14:46629941)
- ldb2b -> ldb2a (chr14:46678711)
- qdprb.1 -> qdpra (chr14:46873229)
- fgfbp1b -> fgfbp1a (chr14:46441617)
Of the teleost-level paralogue pairs, 12 have their partner anywhere on chr14 (the chromosome of prom1a, 823 protein-coding genes):
- anxa5b -> anxa5a (chr14:46410766)
- fgfbp2b -> fgfbp2a (chr14:46449070)
- tapt1b -> tapt1a (chr14:46629941)
- ldb2b -> ldb2a (chr14:46678711)
- qdprb.1 -> qdpra (chr14:46873229)
- tmem144a -> tmem144b (chr14:35884853)
- glrba -> glrbb (chr14:35691889)
- ube2kb -> ube2ka (chr14:683947)
- frmpd1a -> frmpd1b (chr14:4191136)
- chrna9a -> chrna9b (chr14:669982)
- chrnb3a -> chrnb3b (chr14:41518257)
- fgfbp1b -> fgfbp1a (chr14:46441617)