Table 1. List of CNE and non-CNE fragments tested using in vivo enhancer assay.
| name | Location | Flanking genes (within 100 kb) | Enhancer activity | |||
| chr | start | end | 8 hpf (fold, qPCR) | 24 hpf (%) | ||
| CNEs | ||||||
| 13-29 | chr13 | 29550477 | 29550578 | zgc:153142, unc5b, chat | 1.88 | 29.69 |
| 17-24 | chr17 | 24095622 | 24095712 | otx1b | 1.42 | 34.48 |
| 15-26 | chr15 | 26812885 | 26812985 | brip, tbx4, tbx2b | 2.07 | 42.31 |
| 7-28 | chr7 | 28533221 | 28533276 | sox6 | 1.16 | 21.74 |
| 4-16 | chr4 | 16204706 | 16204764 | sox5, casc1, bcat1 | 0.91 | 0 |
| 13-16 | chr13 | 16987933 | 16987979 | c10orf11 | 1.66 | 45.16 |
| 20-4 | chr20 | 4566963 | 4567026 | - | 1.1 | 0 |
| 23-29 | chr23 | 29550522 | 29550546 | tardbp1, sst6, pgd, kif1b | 1.87 | 16.28 |
| 8-34 | chr8 | 34893735 | 34893847 | pbx3b | 2.62 | 53.42 |
| 21-14 | chr21 | 14240602 | 14240635 | zgc:101080, zgc:183801, lhx5 | 4.99 | 0 |
| 1-22 | chr1 | 22884044 | 22884087 | mab21l2 | 1.55 | 0 |
| 17-33 | chr17 | 33138334 | 33138419 | prox1, smyd2a | 1.41 | 68 |
| 9-32 | chr9 | 32394294 | 32394354 | zic5, zic2a | 2.04 | 7.69 |
| 25-15 | chr25 | 15101126 | 15101143 | dnajc24, mpped2 | 1.16 | 6.56 |
| 19-42 | chr19 | 42355789 | 42355849 | shfm1, dlx6a, dlx5a | 1.26 | 0 |
| Non-CNEs | ||||||
| 12-6 | chr12 | 6034509 | 6034630 | dlx4b, zgc:163073, ghrhr2, dlx3b | 1.89 | 0 |
| 16-296 | chr16 | 29652564 | 29652690 | invs, tex10, erp44 | 0.79 | 0 |
| 17-245 | chr17 | 24570163 | 24570239 | fam54b, sepn1, spdya | 0 | |
| 16-34 | chr16 | 34391029 | 34391168 | prpf31, leng1, cnot3a, mboat7, zgc:92763 | 3.01 | 0 |
| 20-33 | chr20 | 33776501 | 33776557 | hen1, fam102bb, zgc:110463, rock2b | 1.06 | |
| 17-25 | chr17 | 25263319 | 25263482 | zgc:165525, srrm1, clic4, zgc:154055, lck | 0.89 | 0 |
| 18-19 | chr18 | 19527760 | 19527861 | sma3b, aagab, iqch, LOC564395 | 0.71 | 0 |
| 6-28 | chr6 | 28633320 | 28633360 | tp63, tomm70a, tbc1d23, glmnb, gfi1.2 | 1.44 | 0 |
| 23-7 | chr23 | 7756857 | 7756924 | pofut1, kif3b, plag12 | 0 | |
| 14-09 | chr14 | 95269 | 95403 | zgc:158483, otop1, nkx3.2, zgc:110421, | 1.17 | 0 |
| 7-212 | chr7 | 21241201 | 21241282 | zgc:153917, zgc:114045, zgc:64136, prox1b | 0.8 | 0 |
| 3-42 | chr3 | 42787879 | 42787947 | litaf, snn, zc3h7a, zgc:92162 | 1.49 | 0 |
Enhancer activity at 8 hpf was assayed by qRT-PCR of gfp transcript. Enhancer activity at 24 hpf was determined through observation of GFP expression by immunohistochemistry staining. A positive enhancer activity is defined as either a positive enrichment (at least 1.5 fold by qRT-PCR) of gfp expression at 8 hpf or a consistent expression pattern other than the background cFos expression (in the muscle and blood cells) in at least 10% of injected embryos at 24 hpf. Typically, 50 to 100 injected embryos were assayed in each experimental time point.