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

Berman, Benjamin P; Pfeiffer, Barret D; Laverty, Todd R; Salzberg, Steven L; Rubin, Gerald M; Eisen, Michael B; Celniker, Susan E

doi:10.1186/gb-2004-5-9-r61

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

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.

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