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Table 3 New pCRMs from genome-wide eCIS-ANALYST (75 highest scoring predictions)

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 PCE8050 h stripes 3/4,6,7 [73] 3L 8,622,879 8,626,839 3,961 CG6486 +14646 h -7829 36 62 9 16 20.1   
2 PCE8051 kni upstream [74] 3L 20,614,714 20,617,020 2,307 kni -813 CG13253 +20716 25 31 11 13 13.2   
3 PCE8052 nub blastoderm 2L 12,604,311 12,606,913 2,603 CG15488 +1653 nub -304 20 33 8 13 11.6   
4 PCE8053 eve stripes 3/7 [75] 2R 5,035,493 5,037,290 1,798 CG12134 +3712 eve -2433 21 24 12 13 11.5 Adam +5901
5 PCE8054 hairy stripes 1,5 [73] 3L 8,628,846 8,631,011 2,166 CG6486 +20613 h -3657 17 29 8 13 10.5   
6 PCE8055 runt stripe 3 [76] X 20,356,848 20,360,054 3,207 CG1338 -9192 run -6801 17 34 5 11 10.3   
7 PCE8056   X 20,323,964 20,326,397 2,434 CG11692 -12536 Cyp6v1 -4186 16 28 7 12 9.6   
8 PCE8057 hb HZ1.4 [77] 3R 4,526,225 4,527,991 1,767 hb -2670 CG8112 +1273 17 21 10 12 9.5   
9 PCE8059 eve stripes 4/6 [78] 2R 5,044,597 5,046,030 1,434 eve +4874 TER94 -3763 15 18 10 13 9.0 Adam +15005
10 PCE8060 gt posterior [11] X 2,186,709 2,189,069 2,361 gt -974 tko +11679 18 21 8 9 8.9   
11 PCE8061   X 3,169,806 3,172,348 2,543 CG12535 -17954 CG14269 +21857 13 29 5 11 8.8   
12 PCE8063 CE8021 3L 18,339,914 18,341,941 2,028 grim -86621 rpr +5341 16 20 8 10 8.5   
13 PCE8064   3R 6,255,663 6,256,945 1,283 CG6345 -13879 Cyp12e1 -3594 13 17 10 13 8.4   
14 PCE8065   3R 4,026,032 4,027,816 1,785 grn -18853 CG7800 -15898 15 19 8 11 8.4   
15 PCE8066   X 20,348,460 20,352,624 4,165 CG1338 -804 run -14231 16 28 4 7 8.3   
16 PCE8067 ftz upstream [23] 3R 2,682,314 2,684,591 2,278 Scr -7972 ftz -5455 15 22 7 10 8.3   
17 PCE8068   X 18,701,007 18,702,700 1,694 CG32541 +39691 CG32541 +39691 12 22 7 13 8.2   
18 PCE8069   2R 17,274,311 17,276,017 1,707 CG3380 -2521 dve -11496 14 19 8 11 8.2   
19 PCE8070   2L 7,616,050 7,618,366 2,317 CG6739 +15430 CG13792 +19862 14 23 6 10 8.1   
20 PCE8071 sqz neurogenic 3R 14,999,463 15,001,552 2,090 sqz +9504 CG14282 -1186 12 24 6 11 8.0 nos +16485
21 PCE8072   X 5,674,422 5,676,386 1,965 CG3726 +16870 CG12728 -6597 11 24 6 12 7.8   
22 PCE8073   2R 14,903,099 14,903,925 827 Toll-7 +12482 Obp56i -27903 11 11 13 13 7.8   
23 PCE8074   3R 23,192,304 23,192,750 447 CG13980 +8073 side +40862 7 8 16 18 7.7   
24 PCE8075   3R 10,762,920 10,764,750 1,831 CG3837 +18501 CG14861 -75759 13 19 7 10 7.6   
25 PCE8076 eve stripe 2 [75] 2R 5,038,454 5,039,041 588 CG12134 +6673 eve -682 8 10 14 17 7.6 Adam +8862
26 PCE8077   2L 13,541,662 13,542,651 990 kuz +9371 kuz +9371 11 13 11 13 7.6   
27 PCE8078   2L 14,424,056 14,425,158 1,103 BG:DS06238.4 -16773 BG:DS08340.1 +7810 12 13 11 12 7.6   
28 PCE8080 odd stripes 3/6 2L 3,601,045 3,602,748 1,704 odd -1728 Dot -9112 12 19 7 11 7.5   
29 PCE8081   3L 17,412,324 17,413,414 1,091 CG18265 +24035 CG7603 -1413 11 14 10 13 7.5   
30 PCE8083   3L 14,121,556 14,123,127 1,572 Sox21b -41352 D +4373 12 17 8 11 7.3   
31 PCE8084   2L 4,098,489 4,099,006 518 ed +74542 ed +74542 7 9 14 17 7.3   
32 PCE8085   2R 12,253,766 12,255,302 1,537 CG10953 -23540 CG10950 -3625 13 15 8 10 7.2   
33 PCE8086   3L 20,612,647 20,614,073 1,427 kni +1254 CG13253 +23663 11 17 8 12 7.2   
34 PCE8087   2R 3,391,037 3,391,561 525 CG30358 +10444 CG14755 -16724 7 9 13 17 7.2   
35 PCE8088   3L 16,418,107 16,418,469 363 CG33158 +49435 argos +14111 6 6 17 17 7.2   
36 PCE8089   3R 12,368,159 12,368,687 529 CG11769 +28970 CG31448 -670 7 9 13 17 7.2 CG14889 -13735
37 PCE8091   3L 11,213,064 11,213,664 601 scylla +3224 CG32083 +24695 8 9 13 15 7.1   
38 PCE8092   2L 1,233,357 1,235,228 1,872 CG5156 +3715 CG5397 -6475 9 23 5 12 7.1   
39 PCE8093   3L 15,688,222 15,691,204 2,983 comm -10920 CG13445 -67172 13 22 4 7 7.0   
40 PCE8094   2R 10,492,861 10,493,546 686 CG30472 -5321 CG12959 -26488 9 9 13 13 7.0   
41 PCE8095   3R 23,894,562 23,895,459 898 CG12870 +31901 CG12870 +31901 10 11 11 12 7.0   
42 PCE8096   3L 6,762,543 6,765,157 2,615 vvl +12855 Prat2 +108336 13 20 5 8 6.9   
43 PCE8097   3R 10,238,130 10,238,652 523 CG14846 -1983 CG14847 +4557 7 8 13 15 6.8   
44 PCE8099   2L 18,305,051 18,306,251 1,201 Fas3 +6868 Fas3 +6868 10 14 8 12 6.7   
45 PCE8100 eve early APR [79] 2R 5,042,174 5,042,884 711 eve +2451 TER94 -6909 8 10 11 14 6.7 Adam +12582
46 PCE8102 tll posterior [80] 3R 26,663,942 26,665,204 1,263 CG15544 +21005 tll -2251 11 13 9 10 6.6   
47 PCE8104 ems neurogenic [81] 3R 9,723,602 9,724,936 1,335 E5 -23682 ems -2663 12 12 9 9 6.6   
48 PCE8105   3R 17,817,909 17,818,791 883 Eip93F +25598 Eip93F +25598 9 11 10 12 6.6   
49 PCE8106   3L 10,499,018 10,501,551 2,534 CG32062 +25485 CG32062 +25485 11 21 4 8 6.6   
50 PCE8107   3L 4,612,891 4,614,005 1,115 CG13716 -161 CG13715 +1681 11 11 10 10 6.6   
51 PCE8108   2L 14,403,771 14,404,937 1,167 CG15284 -4301 BG:DS06238.4 +2346 10 13 9 11 6.5   
52 PCE8109   3R 7,941,601 7,942,426 826 CG31361 +17775 CG4702 +11512 9 10 11 12 6.5   
53 PCE8110   2L 8,804,166 8,805,336 1,171 CG9468 -30684 SoxN -12519 10 13 9 11 6.5   
54 PCE8111   3L 8,612,337 8,613,016 680 CG6486 +4104 h -21652 8 9 12 13 6.5   
55 PCE8112   3L 4,377,989 4,379,208 1,220 CG7447 +13842 Syx17 -3984 11 12 9 10 6.5   
56 PCE8113   2L 14,113,291 14,113,893 603 CG15292 -3974 CG31768 -6693 7 9 12 15 6.5   
57 PCE8114   3L 3,997,600 3,998,923 1,324 CG14985 +13500 fd64A -799 11 13 8 10 6.5   
58 PCE8115 eve stripe 1 [79] 2R 5,046,559 5,047,297 739 eve +6836 TER94 -2496 8 10 11 14 6.5 Adam +16967
59 PCE8116   2R 16,921,501 16,922,240 740 CG13493 -11091 PpN58A +4194 8 10 11 14 6.5   
60 PCE8118   3R 14,822,848 14,823,484 637 gukh +13085 gukh +13085 8 8 13 13 6.4   
61 PCE8119   3R 12,671,525 12,672,987 1,463 abd-A -15737 CG10349 -32477 11 14 8 10 6.4   
62 PCE8120   3L 10,492,688 10,495,539 2,852 CG32062 +19155 CG32062 +19155 10 23 4 8 6.4   
63 PCE8121   2L 16,841,696 16,842,392 697 CG6012 -2193 CG31781 -5178 8 9 11 13 6.4   
64 PCE8122   3L 6,885,832 6,887,436 1,605 Prat2 -11445 CG14820 -5022 11 15 7 9 6.4   
65 PCE8123   2L 15,162,778 15,164,524 1,747 BG:DS03192.2 -6373 BG:DS07295.1 +59479 11 16 6 9 6.4   
66 PCE8124   2R 6,888,483 6,889,700 1,218 CG12443 +13963 CG13192 -428 10 13 8 11 6.4   
67 PCE8125   2L 20,466,022 20,467,708 1,687 CG2493 -32831 CG15476 +4184 10 17 6 10 6.4   
68 PCE8126   3L 2,779,198 2,779,658 461 CG2083 +1101 CG2083 +1101 6 7 13 15 6.3   
69 PCE8127   X 4,630,473 4,632,106 1,634 CG12681 +14179 CG15470 -3196 9 18 6 11 6.3   
70 PCE8128   3R 27,713,381 27,715,087 1,707 heph +35171 heph +35171 10 17 6 10 6.3   
71 PCE8130   3R 12,383,752 12,385,269 1,518 CG14889 +1858 CG14889 +1858 11 14 7 9 6.3   
72 PCE8131   3R 21,329,716 21,331,058 1,343 CG5111 +8355 msi -2351 8 17 6 13 6.3   
73 PCE8132   3R 16,242,660 16,243,128 469 CG10881 +8657 CG17208 +20535 6 7 13 15 6.3   
74 PCE8133   3R 24,120,296 24,122,240 1,945 CG12516 -668 larp +19112 12 15 6 8 6.2   
75 PCE8134   3L 8,733,754 8,734,394 641 CG32030 +8601 CG32030 +8601 7 9 11 14 6.2   
  1. Seventy-five top pCRMs, 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.
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