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CIS-REGULATION

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  1. Transcript 'Moocci.CG.ELv1_2.S61...' > 
  2. Clone 'cijm006c18' > 
  3. Region 'REG00000684' > 
  4. Region 'REG00001383' > 
  5. Region 'REG00000861'

Cis-regulatory Region

Name

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

Short name

n/a

Region ID

REG00000861

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. This region can drive muscle expression from neurula stage.
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. Here the E-box site was mutated (CAACTG=>ACCAGT). This mutation has no effect on 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)
n/a
Construct(s) made to test this region

CONS00000822: pCi-Tbx6b -145/-13 E-box mutated

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 T-Box n/a TCAGTGTGAC [-25 / -16]
2 bZIP n/a TGACG [-19 / -15]

Sequence

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

The E-box site was replaced by the mutated sequence (CAACTG=>ACCAGT).

Show sequence

Length: 132


GAGACTCGTTTTCGATGCCACTTTGATCTTAACGAGTCATTAACAAGGAACCAGTCTTCC
TGATAAGCCTCCGAACTCTCCTGCTGATTCAAGTCTAGCGCATGCAGAACACTCCAAAAC
TCAGTGTGACGC

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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