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  1. Region 'REG00000301'

Cis-regulatory Region

Name

Ci-msxb -818/238

Short name

n/a

Region ID

REG00000301

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Monia Teresa Russo (2007-12-04)

Annotator

Clara Degos (2010-07-22)

Curator

Delphine Dauga (2010-04-07)

View position in WashU

Description

A 3.8 kb region located upstream of the gene contains all the regulatory elements able to reproduce its spatial expression pattern. Analyzing progressively truncated fragments of this region; three discrete and separate regions driving LacZ reporter gene expression in the ventral epidermis, primordial pharynx and neural territories have been identified :


- Region - 2546 bp/- 818 bp : Drives the expression in the ventral epidermis


- Region -457 bp/ - 227 bp : Drives the expression in the pharynx


- Region - 227 bp/- 84 bp : Drives the expression in the visceral ganglion, the sensory vesicle, the otolith-ocellus precursor and in the neural tube.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.

Coordinates in the paper : -830bp/227bp

Hierarchy of Regulatory Regions

Modification of Ci-msxb -2545/238 by deletion

Regulated gene(s)

KH2012:KH.C2.957 (DLX1; MSX1; MSX2)

Construct(s) made to test this region

CONS00000285: pMsxb -818/238::LacZ

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

5,772,6955,773,750

Motif Name Binding Factor(s) Sequence Position in Region Comment

Sequence

Aniseed Coordinates: [5,772,695 / 5,773,750] on scaffold KhC2

This sequence was found using blast on JGI Version 1.0 with the sequence in the paper.

Show sequence

Length: 1,056

AAGCTTAATTAAAATAATAAGCGTTGTTAATAAATATTAGCATATAGACCAAACACCAAA
TTGTGTGCAATCAGTTTTTGCATCTTTAAAACTATTAATTTTTTATGTTCGCCGTGCGAA
TTTTTATTTGAATGATTCTATTAATAAAGCCTGAAATCCTAGCAATCATTTTGAGCTTCC
ACATTTGATATTAAAATTCTCGTATTTGTTGTTATTTATTAATGATTTTGAGTGACTTTT
TTAGACTCAGTTTTTGTTTTGTTTTTCAATTATTCAAGTTCGGATGTGTGGAGATACGGG
ATTAATACAATGAATGTTCAATTAAAAACACAAAAGTTTTAATTTGAATTAATGTCGGCG
CTGCAGACGAGCCGAGAGCTTGTCGGATTTAAAATGTAATCCTCCAATTTTGTCTGGCAC
TGACGGTGTAGATGCAATCTGAAAATGGCGACTGAGCAGGATCGGGTCGCGGCTGGAGCT
CCGGCGGGCTCGGGACGCTCATAATTCCGCCGGTAATCCCCGTAACGTCGATGAAAGCGA
ACGCGCCGACAAAAGTGACGAAGATTAAGTGTAACAACATGGTTTAAACAAACAGACTGG
AGCAGCGGAGACGAGAGAGAGAGGGAACGTAATCGCCGCGGCCGAAGCGTGACCAAGTCG
TTGTATTGTTATAATAGAAAATCGTTTTATTATGATTTAATGAACGCGCGCTGGCGACTG
AAGGATGCTGTATAATTGGGGGTAATGGGGAAATATCGGGAGAAAAAATATGGCGATCTG
CGGGAGAGGATAGTCGCTTACATAATCTCTGGAGTTTAGTTGAAGCAGTTCATATTGAGA
GAAGCATCCCTCAGACGAGTAGTTCGTAAATTTTAGAATATTGAAGAATAAATAAAATAT
TCAAGAAATTTTTAAGAAAATTGAAAAGAGTTTAAATTAAAAATGACAGGTAAGAAAATA
TTTGTATAAATTTTTTTCAGACACTTATGGTAAATAATATTACTCAGATAATGTAACCTG
TGGTTTAAGATTAGTTTTTTAACATCTTTGCGTTGC

Reference(s)

Russo et al. (2004). Regulatory elements controlling Ci-msxb tissue-specific expression during Ciona intestinalis embryonic development. Dev. Biol. 267(2):517-28

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