Aniseed - Cis-regulation

CIS-REGULATION

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Region 'REG00000305'

Cis-regulatory Region

Name

Ci-msxb 130/238

Short name

n/a

Region ID

REG00000305

Status

Curated

Origin

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

Type of Activity

inactive_region

Author

Monia Teresa Russo (2007-12-04)

Annotator

Delphine Dauga (2007-12-04)

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 : 119bp/227bp

Hierarchy of Regulatory Regions

Modification of Ci-msxb -117/238 by deletion

Ci-msxb -3792/238 REG00000076 [ regulatory_region (extended_promoter) ]
- Ci-msxb -2545/238 REG00000300 [ regulatory_region (extended_promoter) ]
  - Ci-msxb -818/238 REG00000301 [ regulatory_region (extended_promoter) ]
    - Ci-msxb -457/238 REG00000302 [ regulatory_region (extended_promoter) ]
      - Ci-msxb -457/238 delta -205/130 REG00000077 [ regulatory_region (extended_promoter) ]
      - Ci-msxb -227/238 REG00000303 [ regulatory_region (extended_promoter) ]
        
        Ci-msxb -227/238 delta -84/130 REG00000079 [ regulatory_region (extended_promoter) ]
        
        Ci-msxb -117/238 REG00000080 [ inactive_region ]
        
        Ci-msxb -117/238 N3 motif added REG00000081 [ regulatory_region (enhancer) ]
        
        Ci-msxb -117/238 N3 motif added/mutated REG00000082 [ regulatory_region (enhancer) ]
        
        Ci-msxb 130/238 REG00000305 [ inactive_region ]
        
        Ci-msxb 130/238 N3 motif added REG00000083 [ regulatory_region (enhancer) ]
        
        Ci-msxb 130/238 N3 motif added/mutated REG00000084 [ regulatory_region (enhancer) ]
    - Cirobu.REG.KH2012:KH.C2.5770855-5775557 REG00000992 [ regulatory_region (enhancer) ]

Regulated gene(s)

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

Construct(s) made to test this region

CONS00000288: pMsxb 130/238::LacZ

Show in situ data

Overview of functional TF binding sites in this region

5,773,6435,773,750

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

Sequence

Aniseed Coordinates: [5,773,643 / 5,773,750] on scaffold KhC2

This sequence was found using blast on JGI version 1 with the sequence in the paper.

Show sequence

Length: 108

GGTAAGAAAATATTTGTATAAATTTTTTTCAGACACTTATGGTAAATAATATTACTCAGA
TAATGTAACCTGTGGTTTAAGATTAGTTTTTTAACATCTTTGCGTTGC

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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