| arxb / aristaless related homeobox b / ARX* / Q96QS3* / aristaless related homeobox* | ENSDARG00000101523 | 49 |
| alx4b / ALX homeobox 4b / ALX4* / O35137* / Q9H161* / ALX homeobox 4* / Homeobox protein aristaless-like 4 * | ENSDARG00000074442 | 22 |
| alx4a / ALX homeobox 4a / ALX4* / O35137* / Q9H161* / ALX homeobox 4* / Homeobox protein aristaless-like 4 * | ENSDARG00000088332 | 22 |
| vsx2 / visual system homeobox 2 | ENSDARG00000005574 | 20 |
| rx1 / retinal homeobox gene 1 / RAX2* / Q96IS3* / retina and anterior neural fold homeobox 2* | ENSDARG00000071684 | 20 |
| alx1 / Q1LVQ7 / ALX homeobox 1 / Q15699* / Q8C8B0* / ALX homeobox protein 1 * | ENSDARG00000062824 | 20 |
| rx2 / retinal homeobox gene 2 / RAX2* / Q96IS3* / retina and anterior neural fold homeobox 2* | ENSDARG00000040321 | 19 |
| rx3 / retinal homeobox gene 3 / RAX* / Q9Y2V3* / O35602* / Retinal homeobox protein Rx * / retina and anterior neural fold homeobox* | ENSDARG00000052893 | 19 |
| drgx / dorsal root ganglia homeobox / A6NNA5* / Prrxl1* / Q8BYH0* / paired related homeobox protein-like 1* | ENSDARG00000069329 | 18 |
| phox2bb / paired-like homeobox 2bb / Q99453* / O35690* / PHOX2B* / paired like homeobox 2b* / Paired mesoderm homeobox protein 2B * | ENSDARG00000091029 | 17 |
| phox2a / paired-like homeobox 2a / O14813* / Q62066* / Paired mesoderm homeobox protein 2A * | ENSDARG00000007406 | 17 |
| uncx4.1 / Unc4.1 homeobox (C. elegans) / UNCX* / A6NJT0* / O08934* / UNC homeobox* | ENSDARG00000037760 | 16 |
| uncx / UNC homeobox / A6NJT0* / O08934* | ENSDARG00000102976 | 15 |
| vsx1 / visual system homeobox 1 homolog, chx10-like / Q91V10* / Q9NZR4* / visual system homeobox 1* | ENSDARG00000056292 | 15 |
| si:dkey-43p13.5 | ENSDARG00000104199 | 13 |
| phox2ba / paired-like homeobox 2ba | ENSDARG00000075330 | 13 |
