cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers

Brody, Thomas; Rasband, Wayne; Baler, Kevin; Kuzin, Alexander; Kundu, Mukta; Odenwald, Ward F

doi:10.1186/gb-2007-8-5-r75

Table 1 Enhancers analyzed

From: cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers

Enhancer	Class	Reference
*Drosophila*
anterior open/yan	neur	[61]
atonal F:2.6 PNS	neur	[62]
bagpipe DS3.5	meso	[63]
bearded PNS	neur	[57]
biparous/tap CNS	neur	[64]
charlatan PNS	neur	[65]
deadpan CNS	neur	[5]
deadpan PNS	neur	[5]
dpp 813	meso	[28]
eve neuronal CNS	neur	[66]
eve EL CNS	neur	[18]
eve MES	meso	[67]
eve stripe 1	seg	[18]
eve stripe 2	seg	[68]
eve stripe 4+6	seg	[18]
eve stripe 5	seg	[18]
eve stripe 3+7	seg	[69]
eve ftz-like	seg	[18]
eyeless 12 PNS	neur	[16]
ftz distal	meso	[70]
ftz proxA	meso	[70]
ftz CE8024	seg	[71]
ftz neuro CNS	neur	[72]
ftz PS4*	seg	[70]
giant 1	seg	[24]
giant 3	seg	[24]
giant 6	seg	[24]
giant 10	seg	[24]
gooseberry-n CNS	neur	[73]
gooseberry GLE	neur	[74]
gooseberry fragIV	seg	[74]
hairy h7	seg	[75]
hairy stripe 0	seg	[44]
hairy stripe 1	seg	[17]
hairy stripe 5	seg	[76]
hairy stripe 3+4	seg	[77]
hairy stripe 6+2	seg	[77]
heartless early	meso	[78]
huckebein ventral	seg	[79]
hunchback CNS	neur	[19]
hunchback ant	seg	[80]
hunchback upstr	seg	[20]
knirps 5	seg	[24]
Krüppel CD1	seg	[10]
mir-1	meso	[81]
Mef2 I-D	meso	[82]
Mef2 II-E	meso	[79]
nerfin-1 CNS	neur	AK (pers. com.)
odd skipped-3	seg	[24]
odd skipped-5	seg	[24]
paired cc	seg	[80]
paired O-E	seg	[44]
paired stripe P	seg	[83]
paired stripe 1	seg	[84]
paired stripe 2P	seg	[83]
paired zebra	seg	[79]
pdm-1 Gap+CNS	seg/n	[84]
pdm-2 CE8012	neur	[71]
pdp1 intron 1	meso	[85]
pdp1 intron 2	meso	[85]
runt stripe 1E+6	seg	[86]
runt stripe 1+7	seg	[86]
runt stripe 3+7	seg	[86]
runt stripe 5	seg	[86]
runt 15G CNS	neur	[86]
Schizo/loner PNS	neur	[65]
scratch sA	neur	[5]
scratch PNS	neur	[5]
Scr 3.0RR	meso	[23]
Scr 7.0RR	meso	[23]
Scr 8.2XX	meso	[23]
scute SCM	neur	[87]
serpent-A7.1EB	meso	[22]
snail CNS	neur	[4]
snail PNS	neur	[4]
snail MES	meso	[4]
string b-5.8 CNS	neur	[88]
teashirt del-1-5	meso	[89]
tinman B	meso	[21]
tinman C	meso	[21]
tinman D	meso	[21]
toll-6.5RL	meso	[90]
β-tub 56DAS1	meso	[91]
Tropomyosin1-M	meso	[92]
Tropomyosin1-P	meso	[92]
twist-del	meso	[48]
vnd CNS	neur	[93]
vnd A CNS	neur	[93]
wor CNS	neur	[94]
Mammalian
bagpipe Hox 1	meso	[95]
Cbfa1 non-coding	meso	[96]
Dll1 HI CNS	neur	[35]
Dll1 HII CNS	neur	[35]
Dll1 msd	meso	[35]
Dll1 msd II	meso	[35]
forkhead box f1	meso	[97]
Gata6	meso	[38]
dHAND	meso	[98]
Hes 7	meso	[99]
HoxA-5	meso	[100]
H. domain only	neur	[101]
IA-1 CNS	neur	[102]
α7 integrin	meso	[103]
Mef2c	meso	[104]
Mash1 CNS	neur	[105]
Math1 CNS	neur	[27]
Myogenic factor-5	meso	[106]
Nestin CNS	neur	[107]
Nfatc1	meso	[108]
Neurogenin 2:5'	neur	[109]
Neurogenin 2:3'	neur	[109]
Nkx-2.5	meso	[110]
Otx 2 CNS	neur	[111]
Pax 3	meso	[112]
Phox2b CNS	neur	[25]
Serum response f	meso	[113]
Six2	meso	[114]
Sox-2 CNS	neur	[115]
Sox-2 #2 CNS	neur	[116]
Sox 9^p CNS	neur	[37]
Stem cell leukemia	meso	[117]
Tbx1	meso	[118]
Wnt-1	neur	[36]

Meso, mesodermal; neur, neural; seg, segmental.

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