# Pair analysis: mapre3a / mapre3b  (run 2026-09-28)

## 0. Ensembl Compara homologies of the two zebrafish genes

mapre3a: within-species paralogue ENSDARG00000102878 (within_species_paralog), duplication node Clupeocephala
mapre3a: ortholog_one2many lepisosteus_oculatus ENSLOCG00000016310 (node Gnathostomata)
mapre3a: ortholog_one2many homo_sapiens ENSG00000084764 (node Gnathostomata)
mapre3a: ortholog_one2one oryzias_latipes ENSORLG00000028482 (node Clupeocephala)
mapre3b: within-species paralogue ENSDARG00000020231 (within_species_paralog), duplication node Clupeocephala
mapre3b: ortholog_one2many lepisosteus_oculatus ENSLOCG00000016310 (node Gnathostomata)
mapre3b: ortholog_one2many homo_sapiens ENSG00000084764 (node Gnathostomata)
mapre3b: ortholog_one2one oryzias_latipes ENSORLG00000017672 (node Clupeocephala)
gar orthologue gene(s): ['ENSLOCG00000016310']

## 1. Sequence lengths and pairwise identities (global, BLOSUM62, -10/-0.5)

length mapre3a: 273 aa
length mapre3b: 278 aa
length mapre3a_NP_Q4V903: 259 aa
length mapre3b_NP_Q6GMJ3: 262 aa
length MAPRE3: 281 aa
length MAPRE1: 268 aa
length MAPRE2: 327 aa
length gar_ENSLOCG00000016310: 323 aa
length medaka_ENSORLG00000028482_orth_of_mapre3a: 262 aa
length medaka_ENSORLG00000017672_orth_of_mapre3b: 273 aa
identity mapre3a vs mapre3b: 83.0% over 282 columns
identity mapre3a vs mapre3a_NP_Q4V903: 94.9% over 273 columns
identity mapre3a vs mapre3b_NP_Q6GMJ3: 81.3% over 278 columns
identity mapre3a vs MAPRE3: 77.9% over 281 columns
identity mapre3a vs MAPRE1: 64.1% over 276 columns
identity mapre3a vs MAPRE2: 50.8% over 333 columns
identity mapre3a vs gar_ENSLOCG00000016310: 72.1% over 323 columns
identity mapre3a vs medaka_ENSORLG00000028482_orth_of_mapre3a: 79.7% over 276 columns
identity mapre3a vs medaka_ENSORLG00000017672_orth_of_mapre3b: 74.6% over 276 columns
identity mapre3b vs mapre3a_NP_Q4V903: 80.7% over 280 columns
identity mapre3b vs mapre3b_NP_Q6GMJ3: 94.2% over 278 columns
identity mapre3b vs MAPRE3: 76.6% over 282 columns
identity mapre3b vs MAPRE1: 63.9% over 288 columns
identity mapre3b vs MAPRE2: 51.9% over 335 columns
identity mapre3b vs gar_ENSLOCG00000016310: 71.3% over 324 columns
identity mapre3b vs medaka_ENSORLG00000028482_orth_of_mapre3a: 76.1% over 280 columns
identity mapre3b vs medaka_ENSORLG00000017672_orth_of_mapre3b: 79.6% over 279 columns
identity mapre3a_NP_Q4V903 vs mapre3b_NP_Q6GMJ3: 85.6% over 264 columns
identity mapre3a_NP_Q4V903 vs MAPRE3: 76.9% over 281 columns
identity mapre3a_NP_Q4V903 vs MAPRE1: 64.0% over 275 columns
identity mapre3a_NP_Q4V903 vs MAPRE2: 50.3% over 332 columns
identity mapre3a_NP_Q4V903 vs gar_ENSLOCG00000016310: 70.6% over 323 columns
identity mapre3a_NP_Q4V903 vs medaka_ENSORLG00000028482_orth_of_mapre3a: 84.0% over 262 columns
identity mapre3a_NP_Q4V903 vs medaka_ENSORLG00000017672_orth_of_mapre3b: 73.6% over 276 columns
identity mapre3b_NP_Q6GMJ3 vs MAPRE3: 75.8% over 281 columns
identity mapre3b_NP_Q6GMJ3 vs MAPRE1: 65.6% over 273 columns
identity mapre3b_NP_Q6GMJ3 vs MAPRE2: 51.7% over 327 columns
identity mapre3b_NP_Q6GMJ3 vs gar_ENSLOCG00000016310: 70.0% over 323 columns
identity mapre3b_NP_Q6GMJ3 vs medaka_ENSORLG00000028482_orth_of_mapre3a: 80.7% over 264 columns
identity mapre3b_NP_Q6GMJ3 vs medaka_ENSORLG00000017672_orth_of_mapre3b: 78.9% over 279 columns
identity MAPRE3 vs MAPRE1: 64.6% over 288 columns
identity MAPRE3 vs MAPRE2: 49.9% over 345 columns
identity MAPRE3 vs gar_ENSLOCG00000016310: 73.7% over 323 columns
identity MAPRE3 vs medaka_ENSORLG00000028482_orth_of_mapre3a: 74.4% over 281 columns
identity MAPRE3 vs medaka_ENSORLG00000017672_orth_of_mapre3b: 70.0% over 283 columns
identity MAPRE1 vs MAPRE2: 46.9% over 339 columns
identity MAPRE1 vs gar_ENSLOCG00000016310: 57.1% over 331 columns
identity MAPRE1 vs medaka_ENSORLG00000028482_orth_of_mapre3a: 65.1% over 275 columns
identity MAPRE1 vs medaka_ENSORLG00000017672_orth_of_mapre3b: 64.2% over 285 columns
identity MAPRE2 vs gar_ENSLOCG00000016310: 58.5% over 340 columns
identity MAPRE2 vs medaka_ENSORLG00000028482_orth_of_mapre3a: 50.5% over 327 columns
identity MAPRE2 vs medaka_ENSORLG00000017672_orth_of_mapre3b: 50.5% over 329 columns
identity gar_ENSLOCG00000016310 vs medaka_ENSORLG00000028482_orth_of_mapre3a: 68.1% over 323 columns
identity gar_ENSLOCG00000016310 vs medaka_ENSORLG00000017672_orth_of_mapre3b: 63.7% over 325 columns
identity medaka_ENSORLG00000028482_orth_of_mapre3a vs medaka_ENSORLG00000017672_orth_of_mapre3b: 73.7% over 278 columns

## 2. Regions of the human reference (UniProt features) and C-terminal tails

Domain: Calponin-homology (CH) [14-116] mapre3a: aligned 103/103, identical 92/103 (89.3%)
Domain: Calponin-homology (CH) [14-116] mapre3b: aligned 103/103, identical 94/103 (91.3%)
Domain: Calponin-homology (CH) [14-116] mapre3a_NP_Q4V903: aligned 103/103, identical 92/103 (89.3%)
Domain: Calponin-homology (CH) [14-116] mapre3b_NP_Q6GMJ3: aligned 103/103, identical 94/103 (91.3%)
Domain: Calponin-homology (CH) [14-116] gar_ENSLOCG00000016310: aligned 103/103, identical 97/103 (94.2%)
Domain: EB1 C-terminal [194-264] mapre3a: aligned 69/71, identical 58/71 (81.7%)
Domain: EB1 C-terminal [194-264] mapre3b: aligned 68/71, identical 57/71 (80.3%)
Domain: EB1 C-terminal [194-264] mapre3a_NP_Q4V903: aligned 69/71, identical 58/71 (81.7%)
Domain: EB1 C-terminal [194-264] mapre3b_NP_Q6GMJ3: aligned 68/71, identical 57/71 (80.3%)
Domain: EB1 C-terminal [194-264] gar_ENSLOCG00000016310: aligned 71/71, identical 62/71 (87.3%)
Region: Disordered [157-181] mapre3a: aligned 22/25, identical 13/25 (52.0%)
Region: Disordered [157-181] mapre3b: aligned 25/25, identical 13/25 (52.0%)
Region: Disordered [157-181] mapre3a_NP_Q4V903: aligned 21/25, identical 13/25 (52.0%)
Region: Disordered [157-181] mapre3b_NP_Q6GMJ3: aligned 24/25, identical 13/25 (52.0%)
Region: Disordered [157-181] gar_ENSLOCG00000016310: aligned 25/25, identical 15/25 (60.0%)
Region: DCTN1-binding [217-281] mapre3a: aligned 65/65, identical 54/65 (83.1%)
Region: DCTN1-binding [217-281] mapre3b: aligned 64/65, identical 51/65 (78.5%)
Region: DCTN1-binding [217-281] mapre3a_NP_Q4V903: aligned 65/65, identical 54/65 (83.1%)
Region: DCTN1-binding [217-281] mapre3b_NP_Q6GMJ3: aligned 64/65, identical 51/65 (78.5%)
Region: DCTN1-binding [217-281] gar_ENSLOCG00000016310: aligned 65/65, identical 55/65 (84.6%)
Region: APC-binding [217-260] mapre3a: aligned 44/44, identical 38/44 (86.4%)
Region: APC-binding [217-260] mapre3b: aligned 44/44, identical 36/44 (81.8%)
Region: APC-binding [217-260] mapre3a_NP_Q4V903: aligned 44/44, identical 38/44 (86.4%)
Region: APC-binding [217-260] mapre3b_NP_Q6GMJ3: aligned 44/44, identical 36/44 (81.8%)
Region: APC-binding [217-260] gar_ENSLOCG00000016310: aligned 44/44, identical 41/44 (93.2%)
Region: Disordered [261-281] mapre3a: aligned 21/21, identical 16/21 (76.2%)
Region: Disordered [261-281] mapre3b: aligned 20/21, identical 15/21 (71.4%)
Region: Disordered [261-281] mapre3a_NP_Q4V903: aligned 21/21, identical 16/21 (76.2%)
Region: Disordered [261-281] mapre3b_NP_Q6GMJ3: aligned 20/21, identical 15/21 (71.4%)
Region: Disordered [261-281] gar_ENSLOCG00000016310: aligned 21/21, identical 14/21 (66.7%)
C-terminal 12 aa of MAPRE3: IEEHQQEDQDEY
C-terminal 12 aa of MAPRE1: DEGGPQEEQEEY
C-terminal 12 aa of MAPRE2: AHEQQPPQQEEY
C-terminal 12 aa of mapre3a: IDEQSHLDQDEY
C-terminal 12 aa of mapre3b: EIDEQPQDQEEY
C-terminal 12 aa of mapre3a_NP_Q4V903: IDEQSHLDQDEY
C-terminal 12 aa of mapre3b_NP_Q6GMJ3: EIDEQPQDQEEY
C-terminal 12 aa of gar_ENSLOCG00000016310: IDEQPHDDQDEY
C-terminal 12 aa of medaka_ENSORLG00000028482_orth_of_mapre3a: LDEQAHLDQDEY
C-terminal 12 aa of medaka_ENSORLG00000017672_orth_of_mapre3b: LDEGPRGDQEEF

Alignment mapre3a (top) vs mapre3b (bottom):
MAVNVYSTSVTIENLSRHDMLAWVNDSLQLTYTKIEQLCSGAAYCQFMEMLFPGCILLKKVKFQAKLEHE
|||||||||.|||||||||||||||||||||||||||||||.||||||.|||||||||||||||||||||
MAVNVYSTSMTIENLSRHDMLAWVNDSLQLTYTKIEQLCSGVAYCQFMDMLFPGCILLKKVKFQAKLEHE

FIHNFKVLQAAFKRMNVDKIIPVERLVKGKFQDNFEFVQWFKKFFDANYDGKEYDPIQARQGQDVAPPPN
.|||||||||||||||||||||||.|||||||||||||||||||||||||||||||..|||||||.||||
YIHNFKVLQAAFKRMNVDKIIPVEKLVKGKFQDNFEFVQWFKKFFDANYDGKEYDPQLARQGQDVTPPPN

PGEHF-SHK---PKRTGPSGPQRTSPTVPKNMPTPQRV-----TTTIRKNPTHARNGGSDAEITELNQQL
|||.| .||   |.|.  |||||||||.||.||||||.     .|.||.|....|||| ||||.||||||
PGEVFLFHKLKSPSRS--SGPQRTSPTAPKTMPTPQRAISSTPSTGIRRNTPISRNGG-DAEIMELNQQL

MELKLTVDGLEKERDFYFSKLRDIELICQDHEAESSPVISRIIDILYATEDGFAPPEDDEIDEQSHLDQD
|.|||||||||||||||||||||||||||.||..|.||...|||||||||||||||||.|||||.. ||.
MDLKLTVDGLEKERDFYFSKLRDIELICQEHESDSNPVLGKIIDILYATEDGFAPPEDEEIDEQPQ-DQE

EY
||
EY


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

gar_ENSLOCG00000016310: positions aligned in both copies: 271
changes unique to mapre3a (m1): 14; unique to mapre3b (m2): 17; chi2 (1 df) = 0.29 (not significant at 0.05)

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

| stage | mapre3a | mapre3b |
|---|---|---|
| zygote | 0 | 4 |
| cleavage 2-cell | 0 | 5 |
| blastula 128-cell | 0 | 20 |
| blastula 1k-cell | 0 | 34 |
| blastula dome | 0 | 17 |
| gastrula 50%-epiboly | 0 | 7 |
| gastrula shield | 0 | 6 |
| gastrula 75%-epiboly | 0 | 8 |
| segmentation 1-4 somites | 0 | 8 |
| segmentation 14-19 somites | 0 | 7 |
| segmentation 20-25 somites | 0.6 | 8 |
| pharyngula prim-5 | 2 | 9 |
| pharyngula prim-15 | 2 | 10 |
| pharyngula prim-25 | 4 | 12 |
| hatching long-pec | 7 | 14 |
| larval protruding mouth | 12 | 29 |
| larval day 4 | 14 | 35 |
| larval day 5 | 16 | 41 |

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

### mapre3a: 13 calls
- retina: 88.8 (gold; RNA-Seq)
- brain: 87.0 (gold; RNA-Seq)
- testis: 79.2 (gold; RNA-Seq)
- larva: 62.4 (gold; RNA-Seq)
- swim bladder: 55.0 (gold; RNA-Seq)
- heart: 52.6 (gold; RNA-Seq)
- bone element: 50.1 (gold; RNA-Seq)
- tail: 40.8 (gold; RNA-Seq)
- embryo: 40.7 (gold; RNA-Seq)
- muscle tissue: 40.2 (silver; RNA-Seq)
- mesonephros: 39.0 (gold; RNA-Seq)
- head kidney: 37.0 (silver; RNA-Seq)
- zone of skin: 34.5 (silver; RNA-Seq)
### mapre3b: 20 calls
- brain: 95.8 (gold; RNA-Seq)
- muscle tissue: 94.2 (gold; RNA-Seq)
- retina: 92.8 (gold; RNA-Seq)
- heart: 91.5 (gold; RNA-Seq)
- swim bladder: 88.9 (gold; RNA-Seq)
- bone element: 88.0 (gold; RNA-Seq)
- pharyngeal gill: 86.6 (gold; RNA-Seq)
- intestine: 83.8 (gold; RNA-Seq)
- head kidney: 80.6 (gold; RNA-Seq)
- spleen: 80.0 (gold; RNA-Seq)
- testis: 79.2 (gold; RNA-Seq)
- larva: 78.8 (gold; RNA-Seq)
- liver: 75.9 (gold; RNA-Seq)
- mature ovarian follicle: 75.6 (gold; RNA-Seq)
- zone of skin: 73.3 (gold; RNA-Seq)
- tail: 68.5 (gold; RNA-Seq)
- early embryo: 66.9 (gold; RNA-Seq)
- blastula: 63.3 (gold; RNA-Seq)
- gastrula: 62.8 (gold; RNA-Seq)
- granulocyte: 51.2 (gold; RNA-Seq)
### gar ENSLOCG00000016310: 14 calls
- brain: 94.6 (gold; RNA-Seq)
- camera-type eye: 92.6 (gold; RNA-Seq)
- muscle tissue: 85.8 (gold; RNA-Seq)
- zone of skin: 82.1 (gold; RNA-Seq)
- larva: 81.9 (gold; RNA-Seq)
- mesonephros: 79.3 (gold; RNA-Seq)
- bone element: 78.7 (gold; RNA-Seq)
- heart: 77.1 (gold; RNA-Seq)
- liver: 73.8 (gold; RNA-Seq)
- testis: 73.1 (gold; RNA-Seq)
- embryo: 72.4 (gold; RNA-Seq)
- pharyngeal gill: 68.2 (gold; RNA-Seq)
- intestine: 64.6 (gold; RNA-Seq)
- ovary: 45.3 (gold; RNA-Seq)

entities called for mapre3a only: ['embryo', 'mesonephros']
entities called for mapre3b only: ['blastula', 'early embryo', 'gastrula', 'granulocyte', 'intestine', 'liver', 'mature ovarian follicle', 'pharyngeal gill', 'spleen']
entities called for both: ['bone element', 'brain', 'head kidney', 'heart', 'larva', 'muscle tissue', 'retina', 'swim bladder', 'tail', 'testis', 'zone of skin']

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

### mapre3a: 0 records
### mapre3b: 1 records
- unspecified | Zygote:1-cell - Hatching:Pec-fin | mRNA in situ hybridization | ZDB-PUB-040907-1

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

mapre3a: chr17:36867281-36896560
mapre3b: chr4:783644-797858

mapre3a +/- 1.5 Mb: 34 other protein-coding genes (0 homology queries failed); 8 have a teleost-level (Clupeocephala/Osteoglossocephalai/Teleostei) zebrafish paralogue; 1 such pairs have their partner within 1.5 Mb of mapre3b:
- dpysl5a -> dpysl5b (chr4:798696)
Of the teleost-level paralogue pairs, 1 have their partner anywhere on chr4 (the chromosome of mapre3b, 1475 protein-coding genes):
- dpysl5a -> dpysl5b (chr4:798696)

mapre3b +/- 1.5 Mb: 78 other protein-coding genes (0 homology queries failed); 15 have a teleost-level (Clupeocephala/Osteoglossocephalai/Teleostei) zebrafish paralogue; 1 such pairs have their partner within 1.5 Mb of mapre3a:
- dpysl5b -> dpysl5a (chr17:36898874)
Of the teleost-level paralogue pairs, 3 have their partner anywhere on chr17 (the chromosome of mapre3a, 898 protein-coding genes):
- tulp4a -> tulp4b (chr17:8183393)
- dpysl5b -> dpysl5a (chr17:36898874)
- crybg1b -> crybg1a (chr17:25481466)