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 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

*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.

Back to article page

ISSN: 1474-760X

Contact us

Submission enquiries: editorial@genomebiology.com
General enquiries: info@biomedcentral.com

Genome Biology

Contact us