Aniseed - Article

Pub 'PMID:10385620' >
Pub 'PMID:20434338'

Title

A cis-regulatory signature in ascidians and flies, independent of transcription factor binding sites.

Authors

Khoueiry P, Rothbächer U, Ohtsuka Y, Daian F, Frangulian E, Roure A, Dubchak I, Lemaire P

Journal

Curr. Biol. 2010; 20(9):792-802

PubMed ID

PMID:20434338

Abstract

Transcription initiation is controlled by cis-regulatory modules. Although these modules are usually made of clusters of short transcription factor binding sites, a small minority of such clusters in the genome have cis-regulatory activity. This paradox is currently unsolved.

Data related to this article

Fates affected

No result

Gene involved	Fates

Genes functionally analyzed

No result

Gene Name	Experimental evidence

Genes whose regulation was studied

48 results

Gene Name	Experimental evidence
KH.S544.3 (DMRT1; DMRTA1; DMRTA2)	Show experimental evidence
KH.L142.14 (EMX1; EMX2; VAX1)	Show experimental evidence
KH.C3.52 (EFNA1; EFNB1; EFNB3)	Show experimental evidence
KH.C10.113 (ETS1; ETS2; ETV1)	Show experimental evidence
KH.C4.341 (FOXA2; FOXB1; FOXB2)	Show experimental evidence
KH.L13.24 (FOXN1; FOXN2; FOXN3)	Show experimental evidence
KH.S696.1 (GATA2; GATA3; GATA4)	Show experimental evidence
KH.C9.616 (LHX1; LMX1A; LMX1B)	Show experimental evidence
KH.C6.129 (NEUROG1; NEUROG2; NEUROG3)	Show experimental evidence
KH.L116.39 (KH.L116.39)	Show experimental evidence
KH.C1.99 (SOX14; SOX2; SOX21)	Show experimental evidence
KH.C7.523 (SOX11; SOX12; SOX4)	Show experimental evidence
KH.C5.154 (KLF1; KLF2; KLF4)	Show experimental evidence
KH.C4.182 (ZFP36; ZFP36L1; ZFP36L2)	Show experimental evidence
KH.C3.348 (TCF12; TCF3; TCF4)	Show experimental evidence
KH.C3.17 (RORA; RORB; RORC)	Show experimental evidence
KH.L152.45 (WNT4; WNT5A; WNT5B)	Show experimental evidence
KH.C8.863 (TRIM2; TRIM3; TRIM71)	Show experimental evidence
KH.S2739.1 (TEAD1; TEAD3; TEAD4)	Show experimental evidence
KH.C3.257 (SPTB; SPTBN1; SPTBN2)	Show experimental evidence
KH.C7.576 (SERPINB11; SERPINB6; SERPINE1)	Show experimental evidence
KH.C2.380 (LARP4; LARP6; LARP7)	Show experimental evidence
KH.L96.100 (NWD1; NWD2; TEP1)	Show experimental evidence
KH.C10.571 (KH.C10.571)	Show experimental evidence
KH.C4.140 (ARF1; ARF3; ARF6)	Show experimental evidence
KH.S522.3 (KH.S522.3)	Show experimental evidence
KH.C4.366 (ERF; ETV3; ETV3L)	Show experimental evidence
KH.C9.608 (PDE2A; PDE8A; PDE9A)	Show experimental evidence
KH.C8.280 (KH.C8.280)	Show experimental evidence
KH.C3.716 (EFNA1; EFNA4; EFNA5)	Show experimental evidence
KH.L57.25 (FOXC1; FOXC2; FOXL1)	Show experimental evidence
KH.C2.489 (TAF11)	Show experimental evidence
KH.S215.4 (LHX3; LHX4; LHX5)	Show experimental evidence
KH.C14.520 (FOXE3; FOXI2; FOXI3)	Show experimental evidence
KH.C5.34 (ALX3; ALX4; UNCX)	Show experimental evidence
KH.C11.485 (IRX3; IRX4; IRX6)	Show experimental evidence
KH.L106.16 (BMP10; GDF2; NODAL)	Show experimental evidence
KH.C14.514 (KIF27; KIF4A; KIF4B)	Show experimental evidence
KH.C8.352 (KH.C8.352)	Show experimental evidence
KH.C1.26 (ATF1; CREB1; CREM)	Show experimental evidence
KH.C14.88 (FAT1; FAT3)	Show experimental evidence
KH.C12.670 (CSMD1; CSMD2; MASP1)	Show experimental evidence
KH.C8.227 (PDZRN3; PDZRN4; RNF151)	Show experimental evidence
KH.C3.923 (MKL1; MKL2; MYOCD)	Show experimental evidence
KH.C9.176 (NOTCH1; NOTCH2; NOTCH3)	Show experimental evidence
KH.C8.316 (PRICKLE1; PRICKLE2; PRICKLE3)	Show experimental evidence
KH.C4.707 (C16orf96; MYH7; QRICH2)	Show experimental evidence
KH.S816.1 (ZIC2; ZIC3; ZIC4)	Show experimental evidence

Genes with description of Wild Type Expression

No result

Gene Name	Experimental evidence

Molecular Tools

No result

Molecular Tool Name

Cis-regulatory regions

80 results

Cis-reg Name
Prickle Like 10773/10946
Ci-ELK 7029/7163
Ci-Nodal -1918/-1771
Nodal -1918/-1772bp Fox2 mutated
ZicL -200/-81
SPCB 5453/5600
Rorb -616/-456
ci0100138569/TBCE -236/-40
TEAD-3/4 3287/3493
CREB/ATF-c 3238/3404
KH2012:KH.C8.227.v1.C.SL1-1 -129/34
Ci-ELK -829/18
Ci-ELK 3450/3786
Ci-ELK 5385/6163
Ci-ELK 7073/7392
Ci-GABPa -2409/-1891
Ci-Unc4A -4987/-4857
Ci-FoxN2/3 -2270/-98
Ci-FoxN2/3 -2270/-1899
Ci-FoxN2/3 -1205/-98
Ci-Lhx3 -4480/-4185
IrxB-LacZ -2402/-1581
Ci-ELK -981/7393
Ci-FoxC -1023/-71
Ci-FoxC -493/-71
Ci-Nodal -2260/-2078
Ci-TGFbeta -252/-75
Ci-Znf(C3H) -212/24
Ci-COE -1043/-480
E12/E47 4415/5422
Rorc -716/-582
Ci-neurogenin -444/-61
Ci-GATA -1010/-76
Ci-GATA -278/-76
Ci-GATA -1010/-804
Ci-orphanFox1 -3554/-3273
Ci-Emc Scaffold_107: 31400-44900
Ci-ets/pointed2 -960/-206
Ci-Znf(C2H2)-24 -951/-301
Ci-Hes-a -1624/-1410
Ci-ZicL -162/78
Ci-PTFb -1665/-1407
Ci-FoxB -4260/-759
Ci-FoxB -3952/-3521
Ci-FoxB -1129/-867
Ci-RAR -4608/-4372
Ci-RAR -697/-394
Ci-SoxB1 -2021/80
Ci-SoxB1 -505/-215
Ci-SoxB1 -1911/-1541
Ci-Lmx -1270/106
Ci-DMRT1-1242/51
Ci-DMRT1 -335/51
Ci-Emx -525/-111
Ci-EphrinA-c -763/-23
Ci-EphrinA-d -742/-75
Ci-SoxC -881/-234
Trim 2/3 127/250
Wnt5 -784/-664
Notch 5332/5452
ci0100145875 2469/2603
ci0100137874 4403/4524
Ci-Erfa 11091/11293
Serpin2 3107/3243
ci0100147026 509/639
ci0100150529 -1956/-1822
Titin 7335/7458
ci0100149039 3158/3290
Ci-Ends2 -7852/-7993
myocardin 6166/6294
KH2012:KH.C12.670.v1.A.ND1-1 5736/5845
ci0100139092 897/1026
FATH2 18783/18923
QRICH2 6830/6960
Ci-Chromosome-associated kinesin KIF4A like 655/778
KH2012:KH.C8.244.v1.A.ND1-1 699/819
CREB/ATF-c 3238/5659
CREB/ATF-c 5494/5659
Ci-PDE9 -4412/6333
Ci-PDE9 6166/6329

Constructs

No result

Construct Name	Experimental evidence

RNA-Seq data

No result

Studied Transcriptome	Experiment ID

Show in situ data