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Table 1 Genomic location of pCRMs and neighboring genes

From: Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura

  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
  1. *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.
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Genome Biology

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