Aniseed - Cis-regulation

Cis-regulatory Region

Name

Cirobu.REG.KH2012.L5:133335-133414|Pavarotti-like

Short name

Pavarotti_CRM96-80pb

Region ID

REG00001237

Status

Curated

Origin

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

Type of Activity

regulatory_region
(enhancer)

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 80pb sequence, located in an intronic region of Pavarotti-like (KH.L5.8), drives reporter gene expression in notochord and mesenchyme. It contains 2 Brachyury and 1 Fox putative binding sites.

Hierarchy of Regulatory Regions

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

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

CONS00001240: p.Cirobu.REG.KH2012.L5:133335-133414>LacZ

Show in situ data

Overview of functional TF binding sites in this region

133,335133,414

	Motif Name	Binding Factor(s)	Sequence	Position in Region	Comment
1	Fox	n/a	tgtttat	[133,337 / 133,344]	Pavarotti-like (KH.L5.8) enhancer is a cluster of Brachyury and Fox binding sites. Mutation of this second Fox site abolishes enhancer activity.
2	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.
3	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: [133,335 / 133,414] on scaffold KhL5

Sequence of the primers used : Forward : ActcgagCTTGTTTATTCAACCATGGCGG Reverse : TTCGtctagaGTAAGCGAGCACGAGGTGTGTG Lowercase letters correspond to XhoI/XbaIb and XhoI/XbaI restriction sites respectively

Show sequence

Length: 80

cttgtttattcaaccatggcggggcaacgatagtcgttataacaccggtgctctgtttca
cacacctcgtgctcgcttac

Reference(s)

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