Table 1.
Genomic location of pCRMs and neighboring genes
| pCRM | ID* | Name | CRM activity | Arm | pCRM start | pCRM end | pCRM length | 5' gene | pCRM relative position | 3' gene | pCRM relative position | |
| 1 | PCE7001 | runt stripe 3 | + | X | 20,357,206 | 20,358,294 | 1,089 | CG1338 | -9,550 | run | -8,561 | |
| 2 | PCE7002 | eve stripes 3/7 | + | 2R | 5,035,494 | 5,036,771 | 1,278 | CG12134 | 3,713 | eve | -2,952 | |
| 3 | PCE7003 | eve stripe 2 | + | 2R | 5,038,454 | 5,039,040 | 587 | CG12134 | 6,673 | eve | -683 | |
| 4 | PCE7004 | eve stripes 4/6 | + | 2R | 5,044,597 | 5,045,395 | 799 | eve | 4,874 | TER94 | -4,398 | |
| 5 | PCE7005 | hairy stripe 7 | + | 3L | 8,624,351 | 8,625,245 | 895 | CG6486 | 16,118 | h | -9,423 | |
| 6 | PCE7006 | hairy stripe 6 | + | 3L | 8,625,452 | 8,626,319 | 868 | CG6486 | 17,219 | h | -8,349 | |
| 7 | PCE7007 | hairy stripes 1,5 | + | 3L | 8,629,180 | 8,629,966 | 787 | CG6486 | 20,947 | h | -4,702 | |
| 8 | PCE7008 | kni upstream | + | 3L | 20,615,070 | 20,616,425 | 1,356 | kni | -1,169 | CG13253 | 21,311 | |
| 9 | PCE7009 | hb HZ1.4 | + | 3R | 4,526,315 | 4,527,521 | 1,207 | hb | -2,760 | CG8112 | 403 | |
| 10 | PCE8001 | 1 | gt posterior domain | + | X | 2,187,439 | 2,188,382 | 944 | gt | -1,704 | tko | 12,366 |
| 11 | PCE8010 | 2 | odd stripes 3/6 | + | 2L | 3,601,750 | 3,602,509 | 760 | odd | -2,433 | Dot | -9,351 |
| 12 | PCE8011 | 3 | nub blastoderm | + | 2L | 12,605,345 | 12,606,039 | 695 | CG15488 | 2,687 | nub | -1,178 |
| 13 | PCE8024 | 4 | ftz stripes 1/5 | + | 3R | 2,693,713 | 2,694,405 | 693 | ftz | 3,667 | Antp | 131,873 |
| 14 | PCE8012 | 5 | pdm2 neurogenic | + | 2L | 12,663,878 | 12,664,600 | 723 | pdm2 | 2,875 | pdm2 | 2,875 |
| 15 | PCE8027 | 6 | sqz neurogenic | + | 3R | 15,000,096 | 15,000,905 | 810 | sqz | 10,137 | CG14282 | -1,833 |
| 16 | PCE8005 | 7 | cluster_at_7A | amb. | X | 6,996,209 | 6,996,756 | 548 | CG32725 | -17,671 | CG1958 | -10,524 |
| 17 | PCE8016 | 8 | cluster_at_55C | amb. | 2R | 13,354,407 | 13,355,109 | 703 | CG14502 | 957 | CG14502 | 957 |
| 18 | PCE8020 | 9 | cluster_at_70F | amb. | 3L | 14,665,967 | 14,666,676 | 710 | ome | 10,334 | ome | 10,334 |
| 19 | PCE8006 | 13 | cluster_at_7B | - | X | 7,239,486 | 7,240,124 | 639 | CG11368 | 46,902 | CG32719 | 13,096 |
| 20 | PCE8008 | 15 | cluster_at_8F | - | X | 9,457,631 | 9,458,375 | 745 | btd | 24,460 | Sp1 | -33,567 |
| 21 | PCE8013 | 17 | cluster_at_34E | - | 2L | 13,989,283 | 13,990,132 | 850 | rk | -5,879 | bgm | -5,767 |
| 22 | PCE8014 | 18 | cluster_at_36F | - | 2L | 18,400,758 | 18,401,458 | 701 | CG31749 | 36,362 | RpS26 | 19,862 |
| 23 | PCE8015 | 19 | cluster_at_47A | - | 2R | 5,664,440 | 5,665,094 | 655 | psq | 45,904 | psq | 45,904 |
| 24 | PCE8017 | 20 | cluster_at_56B | - | 2R | 14,266,629 | 14,267,261 | 633 | CG7097 | 24,156 | CG7097 | 24,156 |
| 25 | PCE8018 | 21 | cluster_at_59B | - | 2R | 17,995,894 | 17,996,609 | 716 | CG32835 | 759 | CG32835 | 759 |
| 26 | PCE8019 | 22 | cluster_at_67B | - | 3L | 9,529,913 | 9,530,579 | 667 | CG32048 | 10,499 | CG32048 | 10,499 |
| 27 | PCE8021 | 23 | cluster_at_75C | - | 3L | 18,339,914 | 18,340,665 | 752 | grim | -86,621 | rpr | 6,617 |
| 28 | PCE8022 | 24 | cluster_at_76C | - | 3L | 19,594,180 | 19,594,883 | 704 | CG8786 | -1,409 | CG8782 | 4,923 |
| 29 | PCE8023 | 25 | cluster_at_84A | - | 3R | 2,595,162 | 2,595,926 | 765 | Ama | 6,847 | Dfd | -21,632 |
| 30 | PCE8025 | 26 | cluster_at_85C | - | 3R | 4,944,607 | 4,945,444 | 838 | pum | 117,315 | pum | 117,315 |
| 31 | PCE8026 | 27 | cluster_at_88F | - | 3R | 11,424,315 | 11,424,996 | 682 | CG18516 | -45,803 | CG5302 | -33,626 |
| 32 | PCE8028 | 28 | cluster_at_95C | - | 3R | 19,757,908 | 19,758,531 | 624 | Gdh | 950 | Gdh | 950 |
| 33 | PCE8003 | 11 | cluster_at_5C.1 | - | X | 5,658,504 | 5,659,131 | 628 | CG3726 | 952 | CG3726 | 952 |
| 34 | PCE8004 | 12 | cluster_at_5C.2 | - | X | 5,674,913 | 5,675,606 | 694 | CG3726 | 17,361 | CG3726 | 17,361 |
| 35 | PCE8009 | 16 | cluster_at_12E | - | X | 14,146,556 | 14,147,218 | 663 | CG32600 | 93,317 | CG32600 | 93,317 |
| 36 | PCE8002 | 10 | cluster_at_4B | - | X | 4,124,119 | 4,125,459 | 1,341 | CG12688 | 2,032 | CG32773 | 3,408 |
| 37 | PCE8007 | 14 | cluster_at_7F | Unknown | X | 8,350,658 | 8,351,315 | 658 | Caf1-180 | -5,486 | oc | 38,281 |
*IDs in this column are taken from [11]. Genomic locations of the 37 pCRMs identified in our previous genome search. All coordinates are from D. melanogaster Release 3 [68]. pCRMs 1-9 were reported prior to our original search, and we attempted to characterize 10-37 in the current study (we reported PCE8001 in our previous publication). pCRMs10-15 recapitulate endogenous expression patterns of embryonic genes, and 16-18 drive ambiguous (amb.) expression patterns, as described in the text. pCRMs 19-36 drove no detectable expression in the embryo, and pCRM 37 was not tested. Orthologous regions were identified in D. pseudoobscura for all but pCRMs 33-37. The 5' and 3' gene columns correspond to the closest transcription (or annotation) start 5' and 3' of the pCRM. If a pCRM is within an intron, only the intron-containing gene is reported and its name is given in italics. The names of genes with early anterior-posterior patterns are in bold.