Aniseed - Cis-regulation

Cis-regulatory Region

Name

Cirobu.REG.KH2012.L5:133344-133414|Pavarotti-like

Short name

Pavarotti_CRM96-71pb

Region ID

REG00001238

Status

Curated

Origin

natural 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

This 71pb sequence, located in an intronic region of Pavarotti-like (KH.L5.8), is not able to drive reporter gene expression in the notochord. It contains 2 Brachyury putative binding sites and lacks one Fox binding site compared to Pavarotti 80pb minimal enhancer.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.L5:133335-133414|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

CONS00001241: p.Cirobu.REG.KH2012.L5:133344-133414>LacZ

Show in situ data

Overview of functional TF binding sites in this region

133,344133,414

	Motif Name	Binding Factor(s)	Sequence	Position in Region	Comment
1	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.
2	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: [133,344 / 133,414] on scaffold KhL5

Sequence of the primers used : Forward : TctcgagTCAACCATGGCGGGGCAAC Reverse : TTCGtctagaGTAAGCGAGCACGAGGTGTGTG Lowercase letters correspond to XhoI/XbaI restriction site.

Show sequence

Length: 71

tcaaccatggcggggcaacgatagtcgttataacaccggtgctctgtttcacacacctcg
tgctcgcttac

Reference(s)

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