Table 1. Tetrapod-Teleost Conserved Non-Coding elements (CNEs) from Introns of Human GLI3 Selected for Functional Analysis.
| Region | Element | Amplicon Coordinates Chr7 | Amplicon Size | Conservation Human-Fugu 50%; >60 bp | In Vitro Activity | In Vivo Activity | Conserved Putative TFBSs |
| Intron 1 | CNE12 | 42239221-42239879 | 659 bp | 190 bp | A/R | n.a. | TBX5, PITX2, PAX6, GATA1, POU6F1 |
| Intron 2 | CNE1 | 42219598-42220542 | 945 bp | 935 bp | A/R | (+) | ATF1, CDPCR1, CDXA, EBOX, FOXM1, FOXP3, GABP, GATA1, PBX1, HOXA3, LMO2COM, MSX1, MYOGENIN, NFY, NMYC, POU3F2, USF, YY1, IRF1, AFP1, VJUN, dHAND |
| Intron 2 | CNE2 | 42159050-42159483 | 434 bp | 401 bp | n.a. | n.a. | CEBPDELTA, CHCH, HOX13, IRF2, LEF1B, MSX1, SP3, TCF4, EN1 |
| Intron 3 | CNE3 | 42131347-42131748 | 400 bp | 378 bp | R | (−) | AREB6, ATF, EBOX, GATA1, GATA2, GATA3, LEF1B, LMO2COM, MYOD, NMYC, TCF4, USF |
| Intron 3 | CNE10 | 42125837-42126969 | 1133 bp | 105 bp | A/R | (+) | CART1, CDP, CLOX, P53, E2F1, SOX5, EN1, PBX1 |
| Intron 4 | CNE4 | 42079507-42079678 | 172 bp | 160 bp | R | (−) | CREL, LEF1B, NKX25, PTF1BETA, STAT1, STAT4, STAT6 |
| Intron 4 | CNE5 | 42068665-42069242 | 578 bp | 255 bp | A/R | (−) | AREB6, E2F, FREAC2, GATA1, GATA6, HNF1, HNF3 ALPHA, MEIS1, OCT1, PAX2, PBX1, PBX, TBP, XFD1 |
| Intron 6 | CNE7 | 42049418-42050221 | 804 bp | 337 bp | A/R | (+) | NKX61, OCT1, POU3F2, SRY, MEF2, STAF |
| Intron 10 | CNE8 | n.a. | n.a. | 123 bp | n.a. | n.a. | n.a |
| Intron 10 | CNE6 | 42018164-42019025 | 862 bp | 179 bp | A/R | (+) | OCT1, PPARA, TBX5, PBX1, PAX4 |
| Intron 10 | CNE11 | 42002211-42003395 | 1185 bp | 129 bp | A/R | (+) | SMAD3, LEF1B |
| Intron 13 | CNE9 | 41975857-41976525 | 669 bp | 108 bp | A/R | (+) | OCT1, PPARA, TBX5, PAX3, STAT5A |
Location, size, coordinates (NCBI 36, Oct 2005), and human-Fugu conserved transcriptional factor binding sites (union of results from rVISTA and ConSite) are indicated. Dual nature and repressor elements are represented by “A/R” (activator/repressor) and “R” symbols, respectively. The (+) sign indicates the elements which induced GFP expression in zebrafish embryos, while (−) sign indicates those which could not drive GFP expression significantly. n.a.: not analyzed. The analysis of CNE2 is reported elsewhere.