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CIS-REGULATION

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  1. Transcript 'KH2012:KH.C1.1001.v1...' > 
  2. Transcript 'Boleac.CG.SB_v3.S171...' > 
  3. Region 'REG00000860'

Cis-regulatory Region

Name

Ci-Tbx6b -145/-13 T-box mutated

Short name

n/a

Region ID

REG00000860

Status

Not Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Jamie E. Kugler (2010-07-09)

Annotator

Clara Degos (2010-07-09)

Curator

Clara Degos (2010-07-09)

View position in WashU

Description

Region upstream of Ci-Tbx6b from -145bp to -13bp.
Region named 112bp Ci-Tbx6b CRM fragment in the paper.
Binding sites are present in this region : one E-box site, one CREB binding site and one T-box site.
The T-box site was mutated (TCAGTGTGAC=>TCAGTTGTAC), this mutation results in a loss of the muscle expression.

ANISEED coordinates are different from the coordinates in the paper. Coordinates are based on KH transcript model.

Hierarchy of Regulatory Regions

Modification of Ci-Tbx6b -145/-13 by substitution

Regulated gene(s)

KH2012:KH.S654.3 (TBX2; TBX4; TBX6)

Construct(s) made to test this region

CONS00000821: pCi-Tbx6b -145/-13 T-box mutated pFoxAa::LacZ

Show in situ data
Overview of functional TF binding sites in this region

26,96027,091

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 bHLH n/a CAACTG [-96 / -91]
2 bZIP n/a TGACG [-19 / -15]

Sequence

Aniseed Coordinates: [26,960 / 27,091] on scaffold KhS654

The T-box site was replaced by the mutated sequence.

Show sequence

Length: 132


GAGACTCGTTTTCGATGCCACTTTGATCTTAACGAGTCATTAACAAGGACAACTGCTTCC
TGATAAGCCTCCGAACTCTCCTGCTGATTCAAGTCTAGCGCATGCAGAACACTCCAAAAC
TCAGTTGTACGC

Reference(s)

Erives et al. (2009). Non-homologous structured CRMs from the Ciona genome. J. Comput. Biol. 16(2):369-77

Kugler et al. (2010). Temporal regulation of the muscle gene cascade by Macho1 and Tbx6 transcription factors in Ciona intestinalis. J. Cell. Sci. 123(Pt 14):2453-63

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