- Region 'REG00000730'
Cis-regulatory Region
Name
Ci-Hox1 -2488/502 Intron 2 added
Short name
n/a
Region ID
REG00000730
Status
Curated
Origin
engineered region from C. robusta formely Ciona int. type A
Type of Activity
regulatory_region
(complex_region)
Author
Miyuki Kanda (2010-06-16)
Annotator
Clara Degos (2010-06-16)
Curator
Delphine Dauga (2011-08-16)
Region upstream of Ci-Hox1 from -2488 to +502bp leading expression in epidermis, posterior trunk, and anterior tail. Be careful, in the paper the coordinates are different : -2505/485.
This region was named Ci-Hox(intron 2) in the paper. In this construct, a part (1.9kb) of the second intron of Ci-Hox gene was added between the nucleotide position -972 and -878 (the region between was deleted) in the regulatory region.
There is two conserved elements between Ciona species in the sequence : one from 1317 to 1336 and an other from 1387 to 1466.
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 -2488/502 by insertion
187,934192,735
| Motif Name | Binding Factor(s) | Sequence | Position in Region | Comment | |
|---|---|---|---|---|---|
| 1 | ZnF_(nuclear receptor) | n/a | tgaacttttcaccc | [1,409 / 1,422] |
Aniseed Coordinates: [187,934 / 192,735] on scaffold KhL171
The sequence was found thanks to the primers used in the paper. <br />The coordinates were based on the first exon on the KH transcript. <br />
Show sequence
Length: 4,802
TAGATTGATGATTCAATATGAGGAACGTAATTTCGGTTATAATAGGACTCAGCGAGCATT
CAAAATTACAATCTTGTTTAAGGATCTCCTACTTAGGTTTTATGGGCATACTCAAGAGGC
ATACCAACAAAAGTTCAAAATTTATTAGGCGGAGTTGCTAAATATTCTTTAAAAGTACCA
CTAAAGTTTCAAAATACCAAAAAGCTTTTAAAAAAATGGCGTGAAATTAAAAAGTTGTAT
GGCGAACTCACACTCAACTTAGATTGGTAGCTTCTACTGCAAAAATGTTACATCTCGTGT
CGTATTTTTTTCAGCTCTCAATAACACCGCAATAACATGTTAAAAACTGTTATTGCGGTG
TTTCGATAAAAGGAACACTTTCGATAAAAGGAACATGGTGATATTTATTTAAAAAGAGGG
AAAAAATGGCTTAACTGCGATTTTAGGATATTTTGGCGAACCTAACCTGTTATATAGGCT
ATTATGTTACTCATGTGCGAGTTTACTTAATATACATTATTGAGTAGGCCATGACGCGCT
TAAACTTGTAGAAGAAATAAATTAAACTCTACAAATATATTAGATAGTACTTTAAGCTAA
ATCCACCGTTACATTTATTGCTGTTTAAAACGGTACCGATTTCGAGTTACTGTCACTTAC
ATATTTTAGCGGTAACGTAACTGGTGCATCTTGATTGTGCACAGCCAATCTCTTACAATG
GAAAATGCCGTGCTGCATATTTTCTTTTGGCGATGTCTTGGAAGCGGCTAAAGATTTTTA
TTTCACAGACGCATAAATACTTTTAGCCTAATATTTGTCAAATATTTATTATCTACAAAC
GTTGCTTTAACGCAAATAATTTTCAAAGTAAAAGTCCGCTATATCGGTCTGTGTTAACTT
TGGTGTATTTTATTTTCTCGATTTTAAATGACGCCCGTATACTTAATAGCCACCTGCTGG
TAAAGCTGCAGTGCATAAAAATCGTTTCTAAAAATCAATAAAATCCTATCAAATACAGTT
AACCAATATGCATCCAAATTTTATGATTGATTTATGATACATACCAAATACTAAAGTATT
AACCGCAATCACGCTTTTAACCTGTTACGATAGTATTTATGAGTTAATAGAGTATTTATA
TAGCTCGAGCCATGGCCTACTCGAACATATGTTTCAGTAGGCCATGCTCGAACATAAGAA
ATTCAGATATAGGAACCTGTTTGTTCTTCATCGCACAGCATTTTCTTTTTGTCATCACAT
AAACGAGGAAAAGTGTAGAAATGTGTATTTTCAACGGCTTTATGCCTAAACTTCCCACTC
ACGAATCAACTTTCAAATATATATTCACTCGGTAATATTGCATATAGTTTTTAATATTAT
GTAATTGATAAAAGAAATATGCACAGACTATACGTACTAGAATATTATTCAAAGCAGAAA
AGTCTAATTTTATTAAAACTTCGCCCCAAATCCTTGTTGCATTAGTTTAGCCGGTCTTAA
ATATCCTTATTGTCGACCTCGAGCGTTTCTCTCTATCAGATCCCGCGTGACATCATAATA
GAGAAAGTAGTGAAATAAAAGACAGATTGAGTAGTTACTTGCTTTATTTATTGGCGCATC
GTAGGTTCGCCTCATTGCGCGTATTTTACGAGGCGGGTAGTGACTATTATCATATTTTAT
CTAAGGTATTTATACGCGTCATTATAGAAAATATTTTGAATTTATAAATTTAGGCCGTGA
CATGCTTTAACAACTTTTTGTACGGTTAAAACTAATCGCAATATATAAAGTCCTAATAGT
AGGGTTGTGACACCTTTTCATTCGATTTTATCGTCACATTTAAACAAAAAATATTCAAAA
AATATATAAAACCGTATCCTCATGAGACTACTATAGACCGGTGTTAATTGTTTTAAACAC
GATCCGAAAATGTGGACATTATGTACCAAAGGTGTTCCGTCTTCTCCCATAGTACTTGAT
ATCAATGCCTAATAAGGCTATGTGTCCACTATTTGTTTTTGAATTTTGTGCCCAACGTTT
TGCTAATGCAGCAGTCATTGTGCTTATCTTGGTTTAAAAGGTAATCGTTCCGCATAATTA
GCATGTTGCTTTAGTAAAGGAGATATGGTCACGTGGTGTGTCGATCACCGTTTTTCGACT
TTCTGTTTATAAAATACATTACAACATCACCAATACTATACCACCAAAAGGAACACGCTA
TTACGCTTAAAAATACAAGTTTCGTATAGAGTAGGTTACGATGAGATGGTCTATGTTTTC
ATTCTCTATTATAATCCCATTTAGTATTAAACAACGAATATTTGTGGGTTTATATAATCG
TATCTTCGCGACCTTGAAAGCGCGTGATTATTTGTTTAAAACACGGTTAGAAAAAAATAT
GGAATTTTATGTGCAAATGGTACCCTACTATATTTATTGGCATTAAAATTGCGTGGTCAA
AGGGAACGTTGTCGTTTCAATGGTCCCTTTATCCGTCATGTGAATGATATCGAAACGCCG
CGGGGTAGATGCTGGGTTCATGAACTCTCTGTCCTTTCGCTCACACTATATCTTTGCGGC
GTTGGGCGTATCGATACCACGGTAAATATGTACACATCGTCGTGTCCTTGTCTACCAGTC
ATCCGTAAAATCGACCCAAAACCACAAAAAATTCTACGGGTTTTCCGCTGCCCGACGCGA
ACGGCTATGCGTTACTTTCAGCTAAAGTACTCTTTTAACATGTATTGCTCTTTATTGCTG
TTATTAGATTTATAAAACTTGTTTCCAAATAAGAATTATAGTGTGGTTATCTGTGCAGCA
CAATGTGCTTATATACGACGCCAGGTTAGAACACCTTGAACTGGAGTATAGATGCTAAAT
TTCTCGAATAAAAGCAATGCACATTGAAAACAGATTTTACCTAAAATATATAAAATTAAG
CCGAGTATATTTGTACTAACGTTGCTATGTTGCGTCTTGTTCAAGCAACAAGATATTGCC
GCTTAATGCACTGGGAAACCGTGGAACATCAAGTACGGTAACCATTAAGACGAATAGCGC
ACAGCACGCGTATTTCTATTTATCATTAGCGTGTAATATTGGAGTTATAATTACGGAATG
CAGATTACAATATCTGTTTTGCTCCCATGGCCTCGATCAATTGCATTGTGTCCTCATTTG
TCAACTGAAGCATTGCAATTGGCATTATTATTCCATTATCGAAACAAAAGCTGGCGTTAC
GCGTGGTTGGTCCACGGAGACCAATCTCAGTCACGCGTTTGGGTGTCGCTTTTCGTCACT
TCGATTTTTAAACAAAATGTGAGATATCGTTCACCATCTGACAATTTTTATATTGTAAAC
CAACATTGATCATTCGAAAAAATCTTTTATCGTTTTTTAACTTTTTCAAAAAGAAGCGTT
TCTCGCGACCTGTTTCGGTTTATTCCATTACAATAGACCGACATGTCGACGAACGATCAT
CATGCCAACATTTAAAATACAACTTTAGGTATTTTCCATTGGATTTAGAGCTTACAAAGA
CCAGATTGTGTTACCTAGTGTTCAACCATATTCAAATGCAATTAAATGCACTGCCAACAG
CGTGTTTATAAACACTATTCGGTGCTTCTATGGGATGCGTGAGCAATCTATATGTGAAGT
ATAATAAATCTTCGTGTAGTAAAATTGTTGTCAATATAAATTTGTAAACATTTTTTTTTT
GGTTACGAATTTACCAAAACGTAATGTGGTTAAAGCGACTAAAATTTGCAGGAGATTTGC
TATGTTTCTTATATTAAAATTGGAGATAATGGGCATTGTTTCTGTGACCGGACACTGGAA
ACAACAACAAAATGAGAAACGCGCCGAAAGCTCGAAGATAATAAGCAAACAAACGATGAA
CTTTTCACCCTAGAGTGAAGACCGGACAAGTGCTCTTGTCCGAGCGCGGACATTGCTGTT
TTTACAAGATGAATAAAAGAAACAAAAAACTCTCGTGTGCGTGGAGAAACAAGGAGAGAA
TAGAAACGAAAAAGTGTGAAAGAAATAGGGGAGCTTGCGTTTGTATAAAACGAGGTGCTG
GACGGGTTAGAAACTTCTCTGCCACAGATTGTAAAAGGCAACAAACCATATTTAGTATGT
TTCGCTTTGAAAGAAATAGTGTTTGCATTTTGGACCAGTGTTATATTGTATTGCTTTATA
CTAGTAGGTAAAGAAAAAACTAAAAAATTACTATTACATCGATGCAAACATTGGCTAAAT
ATGAAGTTGGGGTGTTGCGTTTAATCTTTGCTAGTACAGTATTGTGGTTTACTAGGTTGT
TTAGACTTTAGGTAAAATTAAAGTTAAAACAAAAATTGTAGCAGCAACACACGAAGGATC
TGCACAGCTCGTTAATAGGTATGTGTAATTATTTTTACTGATAAAATTAGCATTTAAGAG
TAGCCGCTGCGGCATTGGTATTCTGTTTCTATTTTTATATTTAGTCATTTTGATAGTAAT
TCAACATCAATTAAATTAACGTACCATTATTATTATTCCTACCAATGTTTACCTAAAATT
CAAGCAGATACATTTGTAATTAACCATATAACGTTTATTATTCGATTTACACGCGTATTT
GAAGGACTGAAAATGAAGTTTGCTTCAATTTAGGAATCTCATTGTACGTCGATATAGCTT
TGCGAATTTGGGTAAAAAGCGTTACACAACAACGGCTTATTAGAACCTTATTTACTGCCA
AGACTATTAAATACTCTTTTGTTAGAAAGGTGTAAGATGAATTCGTACATGAAATACCCG
GT
