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CIS-REGULATION

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  1. Region 'REG00000690'

Cis-regulatory Region

Name

Ci-Pitx -2735/-2540 Second, Third, Fourth Smad site mutated

Short name

n/a

Region ID

REG00000690

Status

Curated

Origin

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

Type of Activity

regulatory_region
(enhancer)

Author

Maximilian Haeussler (2010-06-02)

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. The three last Smad regulatory motifs were mutated (GCCG=>ACCG, CGAC=>CGAA, GCCG => ACCG). The mutations (m7/8/9 in the paper) affect the expression in the neurohypophysis primordium, anterior epidermis, ventral anterior sensory vesicle, but in the mesenchyme it seems that expression is higher.

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

Hierarchy of Regulatory Regions

Modification of Ci-Pitx -2735/-2540 by substitution

Regulated gene(s)

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

Construct(s) made to test this region

CONS00000658: pCi-Pitx -2735/-2540 Second, Third, Fourth Smad site mutated:CES2: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]

Sequence

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

The three last Smad sites were mutated (GCCG=>ACCG, CGAC=>CGAA, GCCG => ACCG).

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

Show sequence

Length: 195


ACGGATTAAGGTAATATTTCTTTTTATGTTGCCGCCCAGTCGGTTCCTGACAATACACTG
ACAGGTAGTGCGAATAAAAGGCGCTCGTGGATGTAAAAAAACACTAATAATCTTCAGTAA
TTTCCGTGCCTTTCCTATGGGCGAAAACTCCCACCGTGTGAAACGAATTCAAAAGGCGGA
CAGTCACCGCCAAGG

Reference(s)

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

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