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Table 4 Additional new pCRMs within 20 kb of genes with anterior-posterior patterns

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

  CRM Known element overlap Arm pCRM start pCRM end pCRM length 5' gene pCRM relative position 3' gene pCRM relative position Conserved sites Conserved site density z score Additional Gap/pair-rule gene within 20 kb pCRM relative position
            A A+P A A+P    
1 PCE8137   3R 12,053,627 12,055,472 1,846 tara +2239 tara +2239 10 17 5 9 6.1   
2 PCE8139   2R 6,573,169 6,574,383 1,215 inv +32752 CG30034 +12378 10 12 8 10 6.1 en +19407
3 PCE8140   2R 15,167,055 15,168,270 1,216 CG16898 -98356 18w -6952 10 12 8 10 6.1   
4 PCE8144   3L 3,503,831 3,504,156 326 Eip63E +7518 Eip63E +7518 4 6 12 18 6.1 ImpE2 -10525
5 PCE8145   3R 4,536,237 4,536,936 700 CG8112 +1795 CG8112 +1795 8 8 11 11 6.0 hb -12682
6 PCE8150   3R 6,379,567 6,380,474 908 hth +50936 hth +50936 8 11 9 12 6.0   
7 PCE8165   X 8,390,109 8,392,075 1,967 oc -513 CG12772 -23984 10 16 5 8 5.8   
8 PCE8166   3R 12,570,467 12,571,123 657 Ubx -10101 CG31275 +5951 7 8 11 12 5.7   
9 PCE8167 Ubx S1 [82] 3R 12,589,099 12,589,755 657 CG31275 (Ubx adjacent) -11970 Glut3 -24295 7 8 11 12 5.7   
10 PCE8169 ftz stripes 1/5 [51] 3R 2,693,336 2,694,915 1,580 ftz +3290 Antp +63624 11 12 7 8 5.7   
11 PCE8170   3R 2,670,658 2,672,242 1,585 Scr +2100 Scr +2100 9 15 6 9 5.7 ftz -19388
12 PCE8177   2R 5,634,520 5,635,604 1,085 psq +4661 psq +4661 8 12 7 11 5.7   
13 PCE8183   2L 7,305,525 7,305,940 416 wg +4205 wg +4205 5 6 12 14 5.6   
14 PCE8187   2L 8,286,022 8,287,399 1,378 Btk29A +5904 Btk29A +5904 9 13 7 9 5.6   
15 PCE8190   3L 6,589,453 6,590,721 1,269 Glu-RI +5891 Glu-RI +5891 9 12 7 9 5.6   
16 PCE8193 Kr CD2 [83] 2R 20,268,656 20,269,940 1,285 CG9380 -36249 Kr -244 7 15 5 12 5.5   
17 PCE8195   3L 5,126,445 5,126,805 361 CG32423 +17297 CG32423 +17297 4 6 11 17 5.5   
18 PCE8198   2L 3,767,311 3,769,396 2,086 bowl +2110 bowl +2110 9 17 4 8 5.5   
19 PCE8210   3L 7,925,371 7,926,049 679 exex +17651 RNaseX25 -4074 6 9 9 13 5.4   
20 PCE8214   2L 12,601,146 12,602,225 1,080 ref2 -895 CG15488 -433 8 11 7 10 5.4 nub -6071
21 PCE8218   2L 10,545,226 10,547,197 1,972 CG31721 +7937 CG31721 +7937 10 14 5 7 5.3   
22 PCE8226   2L 12,541,433 12,542,145 713 bun -11992 CG15489 -40512 6 9 8 13 5.2   
23 PCE8235   X 2,190,216 2,191,697 1,482 gt -4481 tko +9051 9 12 6 8 5.2   
24 PCE8237   2L 12,670,755 12,671,417 663 pdm2 +3280 pdm2 +3280 6 8 9 12 5.2   
25 PCE8258   3L 15,491,385 15,492,925 1,541 CrebA +7093 CrebA +7093 7 15 5 10 5.1   
26 PCE8270   3L 16,421,730 16,422,846 1,117 argos +9734 argos +9734 8 10 7 9 5.0   
27 PCE8275   3L 18,329,419 18,330,261 843 grim -76126 rpr +17021 6 10 7 12 5.0   
28 PCE8277   3R 6,448,750 6,449,993 1,244 hth +8759 hth +8759 6 14 5 11 5.0   
29 PCE8297   2R 20,280,374 20,281,018 645 Kr +10190 CG30429 -9080 6 7 9 11 4.9   
30 PCE8306   3L 12,278,550 12,279,346 797 CG4328 -28041 CG32105 -7436 6 9 8 11 4.9   
31 PCE8307   3L 5,580,997 5,581,649 653 CG12756 -13449 CG5249 -8641 6 7 9 11 4.9   
32 PCE8309   2L 3,825,809 3,827,419 1,611 slp1 +7561 slp2 -1991 8 13 5 8 4.9   
33 PCE8314   2L 3,842,537 3,843,621 1,085 slp2 +13127 CG3964 -11628 6 12 6 11 4.8   
34 PCE8328   2L 16,418,533 16,419,580 1,048 BG:DS02780.1 +8016 Idgf1 -3783 7 10 7 10 4.8   
35 PCE8331   3L 5,582,709 5,583,340 632 CG12756 -15161 CG5249 -6950 5 8 8 13 4.8   
36 PCE8332   3R 2,725,376 2,726,195 820 Antp +32344 Antp +32344 6 9 7 11 4.8   
37 PCE8338   3R 3,987,824 3,989,532 1,709 grn +17647 grn +17647 8 13 5 8 4.7   
38 PCE8348   3L 18,966,181 18,967,380 1,200 nkd +26830 nkd +26830 7 11 6 9 4.7   
39 PCE8355   3R 6,421,647 6,422,583 937 hth +8827 hth +8827 6 10 6 11 4.7   
40 PCE8356   3L 22,244,275 22,244,894 620 Ten-m +80890 CG32450 -2161 6 6 10 10 4.7   
41 PCE8358   3R 26,740,914 26,742,495 1,582 Ptx1 +2496 Ptx1 +2496 8 12 5 8 4.7   
42 PCE8361 Ubx BRE [84] 3R 12,526,665 12,527,949 1,285 Ubx +32417 Ubx +32417 6 13 5 10 4.6   
43 PCE8367   2R 4,771,288 4,771,881 594 CG10459 +3018 dap -1074 5 7 8 12 4.6   
44 PCE8369   3L 14,540,753 14,541,382 630 HGTX +7066 HGTX +7066 6 6 10 10 4.6   
45 PCE8370   3L 2,395,158 2,396,393 1,236 CG13800 +12412 CG32306 -13538 5 14 4 11 4.6   
46 PCE8391   3L 5,254,002 5,254,895 894 CG32423 -16750 lama +55892 6 9 7 10 4.5   
47 PCE8394 Kr 730 [83] 2R 20,266,323 20,267,047 725 CG9380 -33916 Kr -3137 6 7 8 10 4.5   
48 PCE8398   3R 2,770,846 2,771,901 1,056 Antp +12307 Antp +12307 7 9 7 9 4.5   
49 PCE8401   2L 12,660,502 12,661,614 1,113 CG15485 -2463 pdm2 +5861 6 11 5 10 4.5   
50 PCE8408   X 8,379,690 8,381,014 1,325 oc +8582 oc +8582 5 14 4 11 4.4   
51 PCE8415   3R 13,867,601 13,868,164 564 CG7794 +18158 htl +6934 5 6 9 11 4.4   
52 PCE8417   2L 587,804 588,638 835 Gsc +7714 Gsc +7714 6 8 7 10 4.4   
53 PCE8418   3R 18,950,000 18,950,634 635 CG31457 -5638 hh +7739 5 7 8 11 4.4 cenB1A 12397
54 PCE8425   2R 18,693,096 18,694,318 1,223 retn +16917 CG5411 -6825 7 10 6 8 4.4   
55 PCE8439   X 4,770,587 4,771,859 1,273 CG12680 +32240 ovo -17051 7 10 5 8 4.3   
56 PCE8444   3L 18,330,763 18,332,045 1,283 grim -77470 rpr +15237 7 10 5 8 4.3   
57 PCE8450   3L 5,141,131 5,141,793 663 CG32423 +2971 CG10677 -438 5 7 8 11 4.3   
58 PCE8458   3L 19,101,833 19,102,666 834 fz2 +6194 fz2 +6194 5 9 6 11 4.2   
59 PCE8464   3L 17,314,105 17,314,815 711 tap +5577 Cad74A +13577 6 6 8 8 4.2   
60 PCE8483   2L 8,265,854 8,267,283 1,430 Btk29A +2646 Btk29A +2646 4 15 3 10 4.1   
61 PCE8493   3R 6,403,852 6,405,604 1,753 hth +25806 hth +25806 7 12 4 7 4.1   
62 PCE8494   3R 7,931,641 7,932,680 1,040 CG31361 +7815 CG31361 +7815 6 9 6 9 4.1   
63 PCE8495   2L 5,214,677 5,215,845 1,169 CG6514 +3847 tkv +14084 6 10 5 9 4.1   
64 PCE8501   2L 5,247,719 5,248,767 1,049 tkv +10898 Cyp4ac1 -7804 6 9 6 9 4.1   
65 PCE8511   3R 6,469,170 6,470,599 1,430 hth -4766 CG6465 +32311 7 10 5 7 4.0   
66 PCE8512 pdm2 neurogenic 2L 12,663,453 12,664,721 1,269 pdm2 +2754 pdm2 +2754 5 12 4 9 4.0   
67 PCE8513   3L 14,550,945 14,551,746 802 HGTX -2497 Cyp314a1 -16963 5 8 6 10 4.0   
68 PCE8515   2L 16,390,610 16,392,235 1,626 BG:DS02780.1 +34314 BG:DS02780.1 +34314 7 11 4 7 4.0   
69 PCE8519   3L 8,975,309 8,975,873 565 Doc2 +2077 Doc2 +2077 5 5 9 9 4.0 Doc3 11402
70 PCE8520   2L 12,080,772 12,081,448 677 prd -5445 CG5325 -1193 4 8 6 12 4.0   
71 PCE8521   2L 7,252,370 7,253,008 639 CG31909 +2569 Wnt4 +16391 5 6 8 9 4.0 Ndae1 -19639
72 PCE8528   X 14,366,706 14,367,311 606 NetA +17535 NetA +17535 4 7 7 12 4.0   
73 PCE8531   3R 6,363,866 6,364,968 1,103 CG31394 -8970 hth +66442 6 9 5 8 4.0   
74 PCE8533   3R 24,402,963 24,403,946 984 fkh -2792 Noa36 +10421 6 8 6 8 3.9   
75 PCE8536   3R 12,764,472 12,765,970 1,499 Abd-B +4036 Abd-B +4036 7 10 5 7 3.9   
  1. Seventy-five top pCRMs within 20 kb of a gene with early anterior-posterior expression, excluding those already listed in Table 3, are ranked by a z-score based on the number and density of conserved binding sites (see text for details). Site density columns list the number of conserved sites per kilobase (relative to the D. melanogaster sequence). The number and density of conserved sites are shown under two conditions - aligned sites only (A), or aligned + preserved sites (A+P) (see Materials and methods). 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 italicized. The names of genes with early anterior-posterior patterns are in bold. Early anterior-posterior genes that start within 20 kb of the pCRM (but are not the immediate annotation in the 5' or 3' direction) are also listed. Named enhancers without a reference are from this study.