# Pair analysis: olfm3a / olfm3b  (run 2026-09-28)

## 1. Sequence lengths and pairwise identities

length olfm3a: 457 aa
length olfm3b: 457 aa
length OLFM3: 478 aa
length OLFM1: 485 aa
length OLFM2: 454 aa
length gar_OLFM3: 375 aa
length medaka_ortholog_of_olfm3a: 457 aa
length medaka_ortholog_of_olfm3b: 485 aa
identity olfm3a vs olfm3b: 83.2% over 457 columns
identity olfm3a vs OLFM3: 79.7% over 478 columns
identity olfm3a vs OLFM1: 58.7% over 489 columns
identity olfm3a vs OLFM2: 59.0% over 459 columns
identity olfm3a vs gar_OLFM3: 71.6% over 457 columns
identity olfm3a vs medaka_ortholog_of_olfm3a: 84.9% over 457 columns
identity olfm3a vs medaka_ortholog_of_olfm3b: 69.5% over 492 columns
identity olfm3b vs OLFM3: 77.6% over 478 columns
identity olfm3b vs OLFM1: 58.4% over 486 columns
identity olfm3b vs OLFM2: 58.5% over 458 columns
identity olfm3b vs gar_OLFM3: 69.1% over 457 columns
identity olfm3b vs medaka_ortholog_of_olfm3a: 80.1% over 457 columns
identity olfm3b vs medaka_ortholog_of_olfm3b: 71.7% over 492 columns
identity OLFM3 vs OLFM1: 66.3% over 486 columns
identity OLFM3 vs OLFM2: 58.4% over 483 columns
identity OLFM3 vs gar_OLFM3: 68.2% over 478 columns
identity OLFM3 vs medaka_ortholog_of_olfm3a: 76.8% over 478 columns
identity OLFM3 vs medaka_ortholog_of_olfm3b: 69.5% over 485 columns
identity OLFM1 vs OLFM2: 54.9% over 486 columns
identity OLFM1 vs gar_OLFM3: 48.5% over 491 columns
identity OLFM1 vs medaka_ortholog_of_olfm3a: 59.7% over 486 columns
identity OLFM1 vs medaka_ortholog_of_olfm3b: 55.2% over 491 columns
identity OLFM2 vs gar_OLFM3: 46.5% over 458 columns
identity OLFM2 vs medaka_ortholog_of_olfm3a: 56.8% over 458 columns
identity OLFM2 vs medaka_ortholog_of_olfm3b: 51.9% over 486 columns
identity gar_OLFM3 vs medaka_ortholog_of_olfm3a: 67.2% over 457 columns
identity gar_OLFM3 vs medaka_ortholog_of_olfm3b: 56.3% over 492 columns
identity medaka_ortholog_of_olfm3a vs medaka_ortholog_of_olfm3b: 67.5% over 492 columns

## 1b. Zebrafish copies vs each human OLFM3 isoform

identity olfm3a vs Q96PB7 (478 aa): 79.7% over 478 columns; N-terminal 60 aa: 25.9%
identity olfm3b vs Q96PB7 (478 aa): 77.6% over 478 columns; N-terminal 60 aa: 25.9%
identity olfm3a vs Q96PB7-3 (458 aa): 83.8% over 458 columns; N-terminal 60 aa: 70.5%
identity olfm3b vs Q96PB7-3 (458 aa): 81.0% over 458 columns; N-terminal 60 aa: 63.9%
identity olfm3a vs Q96PB7-2 (235 aa): 34.1% over 478 columns; N-terminal 60 aa: 25.9%
identity olfm3b vs Q96PB7-2 (235 aa): 33.3% over 478 columns; N-terminal 60 aa: 25.9%
identity olfm3a vs Q96PB7-4 (215 aa): 36.2% over 458 columns; N-terminal 60 aa: 70.5%
identity olfm3b vs Q96PB7-4 (215 aa): 34.7% over 458 columns; N-terminal 60 aa: 63.9%
identity olfm3a vs Q96PB7-5 (383 aa): 71.3% over 457 columns; N-terminal 60 aa: 15.4%
identity olfm3b vs Q96PB7-5 (383 aa): 69.8% over 457 columns; N-terminal 60 aa: 11.8%
identity olfm3a vs Q96PB7-6 (140 aa): 23.6% over 457 columns; N-terminal 60 aa: 15.4%
identity olfm3b vs Q96PB7-6 (140 aa): 23.4% over 457 columns; N-terminal 60 aa: 11.8%

## 2. Regions of human OLFM3 (UniProt features), cysteines, sequons, Ca-site residues

Signal [1-23] olfm3a: aligned 17/23, identical 5/23 (21.7%)
Signal [1-23] olfm3b: aligned 22/23, identical 6/23 (26.1%)
Signal [1-23] gar_OLFM3: aligned 15/23, identical 4/23 (17.4%)
Domain: Olfactomedin-like [218-470] olfm3a: aligned 253/253, identical 219/253 (86.6%)
Domain: Olfactomedin-like [218-470] olfm3b: aligned 253/253, identical 215/253 (85.0%)
Domain: Olfactomedin-like [218-470] gar_OLFM3: aligned 179/253, identical 156/253 (61.7%)
Coiled coil [77-217] olfm3a: aligned 141/141, identical 120/141 (85.1%)
Coiled coil [77-217] olfm3b: aligned 141/141, identical 116/141 (82.3%)
Coiled coil [77-217] gar_OLFM3: aligned 141/141, identical 133/141 (94.3%)
human OLFM3 cysteines (6): olfm3a keeps 6; changed: none; total Cys in olfm3a: 6
human OLFM3 cysteines (6): olfm3b keeps 6; changed: none; total Cys in olfm3b: 8
human OLFM3 cysteines (6): gar_OLFM3 keeps 5; changed: ['C401->None']; total Cys in gar_OLFM3: 5
N-glycosylation sequons (N-X-S/T, X!=P) in olfm3a: 4 at [74, 158, 278, 444]
N-glycosylation sequons (N-X-S/T, X!=P) in olfm3b: 4 at [74, 158, 278, 444]
N-glycosylation sequons (N-X-S/T, X!=P) in gar_OLFM3: 3 at [74, 158, 278]
N-glycosylation sequons (N-X-S/T, X!=P) in OLFM3: 5 at [33, 95, 179, 299, 465]
mouse Olfm1 (O88998) Ca-site residues aligned in olfm3a: E404->E, D453->D
mouse Olfm1 (O88998) Ca-site residues aligned in olfm3b: E404->E, D453->D
mouse Olfm1 (O88998) Ca-site residues aligned in gar_OLFM3: E404->E, D453->None
mouse Olfm1 (O88998) Ca-site residues aligned in OLFM3: E404->E, D453->D

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

gar positions aligned in both copies: 375
changes unique to olfm3a (m1): 21; unique to olfm3b (m2): 32; chi2 (1 df) = 2.28 (not significant at 0.05)

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

| stage | olfm3a | olfm3b |
|---|---|---|
| zygote | 0 | 0 |
| cleavage 2-cell | 0 | 0.6 |
| blastula 128-cell | 0 | 1 |
| blastula 1k-cell | 0 | 0.3 |
| blastula dome | 0 | 0.3 |
| gastrula 50%-epiboly | 0 | 0 |
| gastrula shield | 0 | 0 |
| gastrula 75%-epiboly | 0 | 0 |
| segmentation 1-4 somites | 0 | 0 |
| segmentation 14-19 somites | 0 | 0 |
| segmentation 20-25 somites | 0 | 0 |
| pharyngula prim-5 | 0 | 0 |
| pharyngula prim-15 | 0.6 | 0 |
| pharyngula prim-25 | 2 | 0 |
| hatching long-pec | 3 | 0 |
| larval protruding mouth | 9 | 0.4 |
| larval day 4 | 9 | 0.6 |
| larval day 5 | 11 | 1 |

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

### olfm3a: 4 calls
- brain: 70.4 (gold; Affymetrix,RNA-Seq)
- retina: 53.3 (gold; Affymetrix,RNA-Seq)
- larva: 52.3 (gold; Affymetrix,RNA-Seq)
- bone element: 45.1 (gold; RNA-Seq)
### olfm3b: 7 calls
- brain: 55.0 (gold; RNA-Seq)
- intestine: 50.2 (gold; RNA-Seq)
- early embryo: 45.4 (silver; RNA-Seq)
- blastula: 42.1 (gold; RNA-Seq)
- ovary: 35.7 (silver; RNA-Seq)
- tail: 28.7 (silver; RNA-Seq)
- bone element: 24.4 (silver; RNA-Seq)
### gar_OLFM3 (spotted gar): 10 calls
- brain: 75.2 (gold; RNA-Seq)
- ovary: 71.7 (gold; RNA-Seq)
- camera-type eye: 65.0 (gold; RNA-Seq)
- heart: 62.1 (gold; RNA-Seq)
- mesonephros: 57.2 (gold; RNA-Seq)
- larva: 45.2 (gold; RNA-Seq)
- embryo: 44.9 (gold; RNA-Seq)
- bone element: 40.7 (gold; RNA-Seq)
- testis: 39.6 (gold; RNA-Seq)
- muscle tissue: 36.7 (silver; RNA-Seq)

RNA-Seq-supported entities: olfm3a only: ['larva', 'retina']
RNA-Seq-supported entities: olfm3b only: ['blastula', 'early embryo', 'intestine', 'ovary', 'tail']
RNA-Seq-supported entities: both: ['bone element', 'brain']

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

olfm3a: chr24:28686287-28711176
olfm3b: chr2:15341689-15362923

olfm3a +/- 1.5 Mb: 41 other protein-coding genes (0 homology queries failed); 6 have a Clupeocephala-level zebrafish paralogue; 1 such paralogue pairs have their partner within 1.5 Mb of olfm3b:
- abca4a -> abca4b (chr2:15203322)
Of the Clupeocephala-level paralogue pairs, 6 have their partner anywhere on chr2 (the chromosome of olfm3b, 1188 protein-coding genes):
- aglb -> agla (chr2:20472150)
- si:dkeyp-88h4.2 -> ENSDARG00000098557 (chr2:10597810)
- plppr4b -> plppr4a (chr2:20331445)
- hs6st1b -> hs6st1a (chr2:40901997)
- abca4a -> abca4b (chr2:15203322)
- ENSDARG00000106630 -> agla (chr2:20472150)

olfm3b +/- 1.5 Mb: 41 other protein-coding genes (0 homology queries failed); 7 have a Clupeocephala-level zebrafish paralogue; 1 such paralogue pairs have their partner within 1.5 Mb of olfm3a:
- abca4b -> abca4a (chr24:28561038)
Of the Clupeocephala-level paralogue pairs, 4 have their partner anywhere on chr24 (the chromosome of olfm3a, 687 protein-coding genes):
- hccsa.2 -> hccsb (chr24:31081504)
- hccsa.1 -> hccsb (chr24:31081504)
- si:dkey-10f21.4 -> tlcd4a (chr24:31098534)
- abca4b -> abca4a (chr24:28561038)