- Region 'REG00000080'
Cis-regulatory Region
Name
Ci-msxb -117/238
Short name
n/a
Region ID
REG00000080
Status
Curated
Origin
natural region from C. robusta formely Ciona int. type A
Type of Activity
inactive_region
Author
Monia Teresa Russo (2007-03-03)
Annotator
Clara Degos (2010-07-22)
Curator
Delphine Dauga (2010-04-07)
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 : -129bp/227bp
Modification of Ci-msxb -227/238 delta -84/130 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) ]
- Cirobu.REG.KH2012:KH.C2.5770855-5775557 REG00000992 [ regulatory_region (enhancer) ]
- Ci-msxb -457/238 REG00000302 [ regulatory_region (extended_promoter) ]
- Ci-msxb -818/238 REG00000301 [ regulatory_region (extended_promoter) ]
- Ci-msxb -2545/238 REG00000300 [ regulatory_region (extended_promoter) ]
5,773,3965,773,750
| Motif Name | Binding Factor(s) | Sequence | Position in Region | Comment |
|---|
Aniseed Coordinates: [5,773,396 / 5,773,750] on scaffold KhC2
This sequence was found using blast on the JGI site with the sequence in the publication listed bellow.
Show sequence
Length: 355
GAACGCGCGCTGGCGACTGAAGGATGCTGTATAATTGGGGGTAATGGGGAAATATCGGGA
GAAAAAATATGGCGATCTGCGGGAGAGGATAGTCGCTTACATAATCTCTGGAGTTTAGTT
GAAGCAGTTCATATTGAGAGAAGCATCCCTCAGACGAGTAGTTCGTAAATTTTAGAATAT
TGAAGAATAAATAAAATATTCAAGAAATTTTTAAGAAAATTGAAAAGAGTTTAAATTAAA
AATGACAGGTAAGAAAATATTTGTATAAATTTTTTTCAGACACTTATGGTAAATAATATT
ACTCAGATAATGTAACCTGTGGTTTAAGATTAGTTTTTTAACATCTTTGCGTTGC
