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- Region 'REG00000081'
Cis-regulatory Region
Name
Ci-msxb -117/238 N3 motif added
Short name
n/a
Region ID
REG00000081
Status
Curated
Origin
engineered region from C. robusta formely Ciona int. type A
Type of Activity
regulatory_region
(enhancer)
Author
Monia Teresa Russo (2007-03-03)
Annotator
Clara Degos (2010-07-22)
Curator
Delphine Dauga (2010-04-08)
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 -117/238 by insertion
- 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) ]
5,773,3955,773,750
| Motif Name | Binding Factor(s) | Sequence | Position in Region | Comment |
|---|
Aniseed Coordinates: [5,773,395 / 5,773,750] on scaffold KhC2
This sequence was found using blast on the JGI version 1.0 with the sequence found in the paper. Two motifs N3 (atcgtcgcggccgaagcgtgaccaagtcgt) was fused to the -129bp/+227bp Ci-msxb enhancer sequence.
Show sequence
Length: 390
ATCGTCGCGGCCGAAGCGTGACCAAGTCGT-----GAACGCGCGCTGGCGACTGAAGGAT
GCTGTATAATTGGGGGTAATGGGGAAATATCGGGAGAAAAAATATGGCGATCTGCGGGAG
AGGATAGTCGCTTACATAATCTCTGGAGTTTAGTTGAAGCAGTTCATATTGAGAGAAGCA
TCCCTCAGACGAGTAGTTCGTAAATTTTAGAATATTGAAGAATAAATAAAATATTCAAGA
AATTTTTAAGAAAATTGAAAAGAGTTTAAATTAAAAATGACAGGTAAGAAAATATTTGTA
TAAATTTTTTTCAGACACTTATGGTAAATAATATTACTCAGATAATGTAACCTGTGGTTT
AAGATTAGTTTTTTAACATCTTTGCGTTGC
