- Region 'REG00000732'
Cis-regulatory Region
Name
Ci-Hox1 -836/553 delta -496/-477
Short name
n/a
Region ID
REG00000732
Status
Curated
Origin
engineered region from C. robusta formely Ciona int. type A
Type of Activity
regulatory_region
(extended_promoter)
Author
Miyuki Kanda (2010-06-16)
Annotator
Clara Degos (2010-07-22)
Curator
Delphine Dauga (2011-08-16)
Region upstream of Ci-Hox1 from -836 to +553bp leading expression in epidermis, posterior trunk, and anterior tail. Be careful, in the paper the coordinates are different : -853/536.
This region was named Ci-Hox(del1) in the paper.
There is two conserved elements between Ciona species in the sequence : one from -496 to -477 and an other from -426 to -347. The first element was deleted. This deletion seems have no effect on epidermal expression.
The second conserved element contains a RARE regulatory motif, Ci-RAR and Ci-RXR can bind this motif. Moreover the deletion or mutation of this motif results in a loss of epidermal expression.
Modification of Ci-Hox1 -836/553 by deletion
187,883189,271
| Motif Name | Binding Factor(s) | Sequence | Position in Region | Comment | |
|---|---|---|---|---|---|
| 1 | ZnF_(nuclear receptor) | n/a | tgaacttttcaccc | [-404 / -391] |
Aniseed Coordinates: [187,883 / 189,271] on scaffold KhL171
The sequence was found thanks to the primers used in the paper.
The coordinates were based on the first exon on the KH transcript.
The deleted sequence was replaced by "-".
Show sequence
Length: 1,389
GTCGACGAACGATCATCATGCCAACATTTAAAATACAACTTTAGGTATTTTCCATTGGAT
TTAGAGCTTACAAAGACCAGATTGTGTTACCTAGTGTTCAACCATATTCAAATGCAATTA
AATGCACTGCCAACAGCGTGTTTATAAACACTATTCGGTGCTTCTATGGGATGCGTGAGC
AATCTATATGTGAAGTATAATAAATCTTCGTGTAGTAAAATTGTTGTCAATATAAATTTG
TAAACATTTTTTTTTTGGTTACGAATTTACCAAAACGTAATGTGGTTAAAGCGACTAAAA
TTTGCAGGAGATTTGCTATGTTTCTTATATTAAAATTGGA--------------------
TGACCGGACACTGGAAACAACAACAAAATGAGAAACGCGCCGAAAGCTCGAAGATAATAA
GCAAACAAACGATGAACTTTTCACCCTAGAGTGAAGACCGGACAAGTGCTCTTGTCCGAG
CGCGGACATTGCTGTTTTTACAAGATGAATAAAAGAAACAAAAAACTCTCGTGTGCGTGG
AGAAACAAGGAGAGAATAGAAACGAAAAAGTGTGAAAGAAATAGGGGAGCTTGCGTTTGT
ATAAAACGAGGTGCTGGACGGGTTAGAAACTTCTCTGCCACAGATTGTAAAAGGCAACAA
ACCATATTTAGTATGTTTCGCTTTGAAAGAAATAGTGTTTGCATTTTGGACCAGTGTTAT
ATTGTATTGCTTTATACTAGTAGGTAAAGAAAAAACTAAAAAATTACTATTACATCGATG
CAAACATTGGCTAAATATGAAGTTGGGGTGTTGCGTTTAATCTTTGCTAGTACAGTATTG
TGGTTTACTAGGTTGTTTAGACTTTAGGTAAAATTAAAGTTAAAACAAAAATTGTAGCAG
CAACACACGAAGGATCTGCACAGCTCGTTAATAGGTATGTGTAATTATTTTTACTGATAA
AATTAGCATTTAAGAGTAGCCGCTGCGGCATTGGTATTCTGTTTCTATTTTTATATTTAG
TCATTTTGATAGTAATTCAACATCAATTAAATTAACGTACCATTATTATTATTCCTACCA
ATGTTTACCTAAAATTCAAGCAGATACATTTGTAATTAACCATATAACGTTTATTATTCG
ATTTACACGCGTATTTGAAGGACTGAAAATGAAGTTTGCTTCAATTTAGGAATCTCATTG
TACGTCGATATAGCTTTGCGAATTTGGGTAAAAAGCGTTACACAACAACGGCTTATTAGA
ACCTTATTTACTGCCAAGACTATTAAATACTCTTTTGTTAGAAAGGTGTAAGATGAATTC
GTACATGAAATACCCGGTTCATGCTTCAAACTCAAATTCCTATACCAACCACATCACCCC
GCAAGGCCC
