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CIS-REGULATION

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Cis-regulatory Region

Name

Cirobu.REG.KH2012.C9:5648367-5650489|DDR1; DDR2; MUSK

Short name

DDR1/2_CRM24_2123pb

Region ID

REG00001242

Status

Curated

Origin

natural region from C. robusta formely Ciona int. type A

Type of Activity

regulatory_region
(extended_promoter)

Author

Diana S. José-Edwards (2017-09-09)

Annotator

Marion Gueroult-Bellone (2017-09-09)

Curator

Marion Gueroult-Bellone (2018-05-09)

View position in WashU

Description

This 2.1kb region, located upstream of DDR1/DDR2/MUSK (KH.C9.371), drives reporter gene expression in notochord. It contains a cluster of Fox and Brachyury putative binding sites.

Hierarchy of Regulatory Regions

Regulated gene(s)

KH2012:KH.C9.371 (DDR1; DDR2)

Construct(s) made to test this region

CONS00001245: p.Cirobu.REG.KH2012.C9:5648367-5650489>LacZ

Show in situ data
Overview of functional TF binding sites in this region

5,648,3675,650,489

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 T-Box n/a tctcac [5,648,369 / 5,648,375] First Brachyury binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer.
2 T-Box n/a gtgaca [5,648,387 / 5,648,393] Second Brachyury binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of all four Brachyury sites strongly reduces enhancer activity in the notochord.
3 T-Box n/a gtgtga [5,648,400 / 5,648,406] Third Brachyury binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of all four Brachyury sites strongly reduces enhancer activity in the notochord.
4 Fox n/a tatttac [5,648,424 / 5,648,431] First Fox binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of this site alone does not affect enhancer activity in the notochord, but creates new activity in central nervous system and tail muscle. Mutation of this site and of the fourth Brachyury site strongly reduces enhancer activity in the notochord. Mutation of three Fox sites and of the fourth Brachyury site abolishes enhancer activity in the notochord.
5 T-Box n/a gtgtaa [5,648,439 / 5,648,445] Fourth Brachyury binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of this site alone does not affect enhancer activity in the notochord, but creates new mesenchyme activity. Mutation of this site and of the first Fox site strongly reduces enhancer activity in the notochord. Mutation of all four Brachyury sites strongly reduces enhancer activity in the notochord.
6 Fox n/a gtaaata [5,648,441 / 5,648,448] Second Fox binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of three Fox sites and of the fourth Brachyury site abolishes enhancer activity in the notochord.
7 Fox n/a ataaaca [5,648,445 / 5,648,452] Third Fox binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of three Fox sites and of the fourth Brachyury site abolishes enhancer activity in the notochord.
8 Fox n/a acaaata [5,648,449 / 5,648,456] Fourth Fox binding site of the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer. Mutation of the three other three Fox sites and of the fourth Brachyury site abolishes enhancer activity in the notochord.
9 Helix Turn Helix / Tryptophane clusters n/a attgaa [5,648,477 / 5,648,483] This Myb#2 binding site is located in the notochord-active enhancer of KH.C9.371.
10 ZnF_(C2H2) n/a ccacc [5,648,492 / 5,648,497] Sp1/Klf binding site located next to the Brachyury/Fox sites cluster contained in DDR1/2 139pb enhancer.

Sequence

Aniseed Coordinates: [5,648,367 / 5,650,489] on scaffold KhC9

This sequence was retrieved using ANISEED Blast tool, thanks to the information provided in FigS2.a of Jose-Edwards et al. 2015.

Show sequence

Length: 2,123


aatctcacttacttgcgaaggtgacatcacccggtgtgacggatctcaaaccaggtttat
ttacttcctcgtgtgtaaataaacaaatacagatcgcaaggctttgtcatattgaactct
gaaagccaccgctgttgcgccaataacagggaccataaccggcacaactaccagtacaaa
gttgcatgaaacaatatcgacagtttcaatacaaacaaattatcatagttttatgcaaac
atttgttcaagcgacgtattatccaaacatagaaaaaatacatttcttttcaaagaagtc
attgtgaaaaaatcctatgaaatggttgtatacccacttttaaattcgtcataccaagtt
caaacaaaagaacaaaaatagcgattacgtaatttgagttgtaagaaggtgaccgattct
tgacacgttccggggccgggtcgtctttttgccggggagcgtgctcaaattttacgatca
ttctcggagtagctgaacgacgtccgtgaggtaattataaggcggggtcaattccacgaa
aacgcactgctggagatacggtgttcagagacgcattgttcaacgagggtttacgacagg
cagttacagtaaattgctgctaataattcgttaaatagtgccaagtaattttagaagatc
ttcggaattaaaatgaaaattattttcaaatgattcgattgatttgatagtttgataacg
ctagaagttcgtcccaatatgacctttccacattacgatgtcggtccttcaaaagtatgt
tgtgttaacggcgagtgtactactttcaatcgagcaaatattagatacaaaaatgggtca
gtacttcaaacttaaggtttcgcgattgctggcgctctctgtttgtgtagtagggaataa
attataaccattggtgtttgtaaaccggtcaaatgttgtcttggttcaacaaaacctgga
cagtttgattggtgttaatttatgagcaacaaaatgcgctcccatgtttaaacaggcctt
gacatgaagttggttatgtttatatgtggctattttgtcatgggcttaggataaattcga
ttttccggagatacatatttttgtctcaaaatatccaacgcgttttcggctacaaagatc
aaaccccgctgagctattgtgcctcacgtcatacgcagacgcggtaatctggtgttgcct
ttttctcgacgtggtttcgtctaattttgaagagaaggcaatatcggcgctcctttagtt
ctgatagcattgcggtgttgaacgctctgtcaataccaggagagagcgggcttgagtatg
ttagcggaatagatgctgacttagtcatatagtgctaacaaggctgaaacggcgctcaag
ttattttgttttctcgtcgaagtatcaggtgttagtgtgcttacgtagaagcggtatctt
gtaaaatatcacgtgtcagattacagtcggatcgaatgttaaacagtgatgtaatttcta
ttttgtatctttgtagtttaggtctctcaaagttgtttactgtcaggtcattttcgaatc
cacgcagcggaaccttgacaacaggttacagtttacgcgtgctcgtaaagaactcgcaat
ttgcgcaagcgtaactgatcattacgtttgtttctccagtgcggcttgatttagttgggg
ccgcggcgagacaacgcttataatctgaacgtctgactgtcaattattaaaccgtagacg
agttaggctgtgcctgggctttggattagaattggagttaaagaaactgttccctttggg
aaaacgtcaacgctgaaaagcttgtgcaaggttcaccatgaagtcgaagtcattaccacc
gagtgatcgatcgagtattataattacgttgctgttctgtcttctgctgtcagaggtaca
accgactacagcacaaatagatacaggtaagatggaaatacttttgttgattttattaaa
gttttggttgattttatttaaagttataatatgttatgttcataaaaacacgggttttct
tggcggcttcaatacaaacatgaatatacatatatgcatgatgcaattttcatctcgaac
gttacggtttaaataccaaaacc

Reference(s)

José-Edwards et al. (2015). Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord. PLoS Genet. 11(12):e1005730

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