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CIS-REGULATION

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  1. Clone 'ma339m24' > 
  2. Region 'REG00000555' > 
  3. Region 'REG00000855'

Cis-regulatory Region

Name

Ci-Tbx6b -827/-13

Short name

n/a

Region ID

REG00000855

Status

Not Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Jamie E. Kugler (2010-07-08)

Annotator

Clara Degos (2010-07-23)

Curator

Clara Degos (2010-07-08)

View position in WashU

Description

Region upstream of Ci-Tbx6b from -827bp to -13bp. This region can drive muscle expression from neurula stage.
Region named 862bp fragment in the paper.
Binding sites are present in this region : one E-box site, one CREB binding site and one T-box site. All the macho1 sites are absent of this region.


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 -2339/-13 by deletion

Regulated gene(s)

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

Construct(s) made to test this region

CONS00000818: pCi-Tbx6b -827/-13::LacZ

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

26,96027,773

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 bHLH n/a CAACTG [-778 / -773]
2 T-Box n/a TCAGTGTGAC [-707 / -698]
3 bZIP n/a TGACG [-701 / -697]

Sequence

Aniseed Coordinates: [26,960 / 27,773] on scaffold KhS654

Show sequence

Length: 814


GAGACTCGTTTTCGATGCCACTTTGATCTTAACGAGTCATTAACAAGGACAACTGCTTCC
TGATAAGCCTCCGAACTCTCCTGCTGATTCAAGTCTAGCGCATGCAGAACACTCCAAAAC
TCAGTGTGACGCATACCGTCTTGCATGTGGCGCGTTGGTTTGATGAAATCGCTTTAAAAA
TGTGTTTGATAATTTCATTATTATGGTTTGATGTAGAATAGCCTTGTTAGTTTTTTTTAT
TAAACAGCTTCGTTTATAGAGATTTAAAGGTAATTTTGACAACTAAGTTGACAGTCCGCC
ATATGAAGCCATTTCCTAAATATGTTATGTGTTAAGTCTATTGTTATTAGTAGACAATAG
TTATCGTACGTTGTTACCAATGTCACCTTCGCTTTTGCAAGCTTGTTACGTTGTTAACCA
GTTGGGGATCATCCGTTTAAGAATGCGACATAAGTCTGTCACAAAAACTAAAATTTTATT
ATATAGTGCTGTGGGGTAAGATGGGACACATTCAGAACATAATATCCTTATCGTGTTTTT
AAACAATTAACAACGGTATATAGGATTCGTAAGAAAACGGTTTTCCATTTCTTTGAATGT
TCTTCTTAAAAATAGAACGAAAAGGTCTTCAAAAAAGTAACGATAATTGTAAAACGTTTC
CATCGATGGCTAAAACCACATACGTTTAGGTTAAACCCTTATTCTACTCAAAGTTGCCTA
ATAGTTTTAAAAATATTTTAAATCAATTTGATTAAAACTAATATATGGGTATGTCTTGCA
TAGTTTTATATACCGCCGTATTTAGTGTAGGCCT

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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