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CIS-REGULATION

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  1. Region 'REG00000885' > 
  2. Molecular Tool 'Hr-beta-catenin mRNA (Kumano 2006)' > 
  3. Transcript 'KH2012:KH.C1.373.v1....' > 
  4. Region 'REG00000879' > 
  5. Region 'REG00000682'

Cis-regulatory Region

Name

Ci-Pitx -2735/-2540

Short name

n/a

Region ID

REG00000682

Status

Curated

Origin

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

Type of Activity

regulatory_region
(enhancer)

Author

Maximilian Haeussler (2010-06-01)

Annotator

Clara Degos (2010-06-02)

Curator

Delphine Dauga (2011-08-08)

View position in WashU

Description

Minimal enhancer upstream of Pitx gene from -2735 to -2540, called D1bcde in the paper. The Pax binding site is absent. This region can drive expression in the neurohypophysis primordium.

KH transcript model was taken as reference for the region s coordinates.

Hierarchy of Regulatory Regions

Modification of Ci-Pitx -7865/140 by deletion

Regulated gene(s)

KH2012:KH.L153.79 (PITX1; PITX2; PITX3)

Construct(s) made to test this region

CONS00000652: pCi-Pitx -2735/-2540::LacZ

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

197,517197,711

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 Homeobox n/a GATTA [-2,732 / -2,728]
2 Fox n/a TAATATTTCTTT [-2,724 / -2,713]
3 MAD n/a GCCG [-2,705 / -2,702]
4 Homeobox n/a TGACAA [-2,688 / -2,683]
5 Homeobox n/a TGACAG [-2,677 / -2,672]
6 Fox n/a AAAAAACACTA [-2,640 / -2,630]
7 Homeobox n/a TAATC [-2,628 / -2,624]
8 MAD n/a GCCG [-2,583 / -2,580]
9 MAD n/a CGAC [-2,572 / -2,569]
10 MAD n/a GCCG [-2,550 / -2,547]

Sequence

Aniseed Coordinates: [197,517 / 197,711] on scaffold KhL153

The sequence is based on the first codon on the KH transcript.

Show sequence

Length: 195


ACGGATTAAGGTAATATTTCTTTTTATGTTGCCGCCCAGTCGGTTCCTGACAATACACTG
ACAGGTAGTGCGAATAAAAGGCGCTCGTGGATGTAAAAAAACACTAATAATCTTCAGTAA
TTTCCGTGCCTTTCCTATGGGCGAAAACTCCCGCCGTGTGAAACGACTTCAAAAGGCGGA
CAGTCGCCGCCAAGG

Reference(s)

Haeussler et al. (2010). A cis-regulatory signature for chordate anterior neuroectodermal genes. PLoS Genet. 6(4):e1000912

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