Login
Help

CIS-REGULATION

Submit your Data

  1. Transcript 'KH2012:KH.C2.1094.v1...' > 
  2. Transcript 'KH2012:KH.C11.388.v1...' > 
  3. Region 'REG00001240'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.L5:133066-133414_Bra3mut|Pavarotti-like

Short name

Pavarotti_CRM96-251pb_Bra3mut

Region ID

REG00001240

Status

Curated

Origin

engineered 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 251pb sequence, located in an intronic region of Pavarotti-like (KH.L5.8), drives reporter gene expression in notochord, even when its third Brachyury putative binding site is mutated. Additional activity is observed in mesenchyme and central nervous system.

Hierarchy of Regulatory Regions

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

Regulated gene(s)

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

Construct(s) made to test this region

CONS00001243: p.Cirobu.REG.KH2012.L5:133066-133414_Bra3mut>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 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 third Brachyury putative binding site is mutated : TAACAC is replaced by TCAAGA.

Show sequence

Length: 349


cagtggacaagtttgtgaaggaatcaattctatttctttcgtctggaaaataaaatataa
taaatgaatgtaacttatttatcctcgcgtggtgaggcaacgacagtcgttataacactg
gtgttctgtttcatacacctcgtgcccgcttacaagttaccacgtatgtaacttatttat
cctcgcatggggaagcaacgatagtcgctataacactggtgttctgtttcatacaccttg
tgctcgcttacaagttaccacgcatgtaacttgtttattcaaccatggcggggcaacgat
agtcgttatcaagacggtgctctgtttcacacacctcgtgctcgcttac

Reference(s)

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

Back to Top