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CIS-REGULATION

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  1. Transcript 'KH2012:KH.C2.821.v1....' > 
  2. Region 'REG00001236'

Cis-regulatory Region

Name

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

Short name

Pavarotti_CRM96-251pb

Region ID

REG00001236

Status

Curated

Origin

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

Type of Activity

regulatory_region
(enhancer)

Author

Diana S. José-Edwards (2017-09-08)

Annotator

Marion Gueroult-Bellone (2017-09-08)

Curator

Marion Gueroult-Bellone (2018-05-09)

View position in WashU

Description

This 251pb sequence, located in an intronic region of Pavarotti-like (KH.L5.8), drives reporter gene expression in notochord. It contains 4 Brachyury and 2 Fox putative binding sites.

Hierarchy of Regulatory Regions

Regulated gene(s)

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

Construct(s) made to test this region

CONS00001239: p.Cirobu.REG.KH2012.L5:133066-133414>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 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.
5 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.
6 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

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

Show sequence

Length: 349


cagtggacaagtttgtgaaggaatcaattctatttctttcgtctggaaaataaaatataa
taaatgaatgtaacttatttatcctcgcgtggtgaggcaacgacagtcgttataacactg
gtgttctgtttcatacacctcgtgcccgcttacaagttaccacgtatgtaacttatttat
cctcgcatggggaagcaacgatagtcgctataacactggtgttctgtttcatacaccttg
tgctcgcttacaagttaccacgcatgtaacttgtttattcaaccatggcggggcaacgat
agtcgttataacaccggtgctctgtttcacacacctcgtgctcgcttac

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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