Aniseed - Cis-regulation

Cis-regulatory Region

Name

Cirobu.REG.KH2012.L5:133066-133414_Fox2mut|Pavarotti-like

Short name

Pavarotti_CRM96-251pb_Fox2mut

Region ID

REG00001239

Status

Curated

Origin

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

Type of Activity

no_output

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

Mutation of the second Fox binding site of Pavarotti-like (KH.L5.8) abolishes the enhancer activity of this fragment in the notochord, but new activity is observed in the mesenchyme.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.L5:133066-133414|Pavarotti-like by substitution

Cirobu.REG.KH2012.L5:133066-133414|Pavarotti-like REG00001236 [ regulatory_region (enhancer) ]

Regulated gene(s)

KH2012:KH.L5.8 (KIF20A; KIF20B; KIF23)

Construct(s) made to test this region

CONS00001242: p.Cirobu.REG.KH2012.L5:133066-133414_Fox2mut>LacZ

Show in situ data

Overview of functional TF binding sites in this region

133,066133,414

	Motif Name	Binding Factor(s)	Sequence	Position in Region	Comment
1	Fox	n/a	tatttat	[133,239 / 133,246]	Pavarotti-like (KH.L5.8) enhancer is a cluster of Brachyury and Fox binding sites.
2	T-Box	n/a	taacac	[133,276 / 133,282]	Pavarotti-like (KH.L5.8) enhancer is a cluster of Brachyury and Fox binding sites.
3	T-Box	n/a	taccac	[133,321 / 133,327]	Pavarotti-like (KH.L5.8) enhancer is a cluster of Brachyury and Fox binding sites.
4	T-Box	n/a	taacac	[133,374 / 133,380]	Pavarotti-like (KH.L5.8) enhancer is a cluster of Brachyury and Fox binding sites. Mutation of this third Brachyury site does not impact enhancer activity.
5	T-Box	n/a	tcacac	[133,392 / 133,398]	Pavarotti-like (KH.L5.8), enhancer is a cluster of Brachyury and Fox binding sites. Mutation of this (4th) Brachyury site abolishes enhancer activity.

Sequence

Aniseed Coordinates: [133,066 / 133,414] on scaffold KhL5

The second Fox binding site was mutated : TGTTTAT replaced by TGGGGCG.

Show sequence

Length: 349

cagtggacaagtttgtgaaggaatcaattctatttctttcgtctggaaaataaaatataa
taaatgaatgtaacttatttatcctcgcgtggtgaggcaacgacagtcgttataacactg
gtgttctgtttcatacacctcgtgcccgcttacaagttaccacgtatgtaacttatttat
cctcgcatggggaagcaacgatagtcgctataacactggtgttctgtttcatacaccttg
tgctcgcttacaagttaccacgcatgtaacttggggcgtcaaccatggcggggcaacgat
agtcgttataacaccggtgctctgtttcacacacctcgtgctcgcttac

Reference(s)

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