Aniseed - Cis-regulation

Region 'REG00000735'

Cis-regulatory Region

Name

Ci-Hox1 -2488/502 Intron 2 added DR-2 type RARE mutated

Short name

n/a

Region ID

REG00000735

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Miyuki Kanda (2010-06-17)

Annotator

Clara Degos (2010-07-22)

Curator

Delphine Dauga (2011-08-16)

View position in WashU

Description

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. In this construction this motif was mutated (ATGAACTTTTCACCC=>TCTAGCTTTTCACCC). The mutation results in a complete loss of epidermal expression.

Hierarchy of Regulatory Regions

Modification of Ci-Hox1 -2488/502 Intron 2 added by substitution

Ci-Hox1 -2488/553 REG00000727 [ regulatory_region (extended_promoter) ]
- Ci-Hox1 -2488/502 REG00000728 [ regulatory_region (extended_promoter) ]
  - Ci-Hox1 -2488/502 Intron 2 added REG00000730 [ regulatory_region (complex_region) ]
    - Ci-Hox1 -2488/502 Intron 2 added delta 821bp REG00000731 [ regulatory_region (complex_region) ]
    - Ci-Hox1 -2488/502 Intron 2 added DR-2 type RARE mutated REG00000735 [ regulatory_region (extended_promoter) ]
- Ci-Hox1 -836/553 REG00000729 [ regulatory_region (extended_promoter) ]

Regulated gene(s)

KH2012:KH.L171.16 (HOXA1; HOXB1; HOXD1)

Construct(s) made to test this region

CONS00000702: pCi-Hox1 -2488/502 Intron 2 added DR-2 type RARE mutated::LacZ

Show in situ data

Overview of functional TF binding sites in this region

187,934190,923

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

Sequence

Aniseed Coordinates: [187,934 / 190,923] 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.

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
ACAACAACAAAATGAGAAACGCGCCGAAAGCTCGAAGATAATAAGCAAACAAACGTCTAG
CTTTTCACCCTAGAGTGAAGACCGGACAAGTGCTCTTGTCCGAGCGCGGACATTGCTGTT
TTTACAAGATGAATAAAAGAAACAAAAAACTCTCGTGTGCGTGGAGAAACAAGGAGAGAA
TAGAAACGAAAAAGTGTGAAAGAAATAGGGGAGCTTGCGTTTGTATAAAACGAGGTGCTG
GACGGGTTAGAAACTTCTCTGCCACAGATTGTAAAAGGCAACAAACCATATTTAGTATGT
TTCGCTTTGAAAGAAATAGTGTTTGCATTTTGGACCAGTGTTATATTGTATTGCTTTATA
CTAGTAGGTAAAGAAAAAACTAAAAAATTACTATTACATCGATGCAAACATTGGCTAAAT
ATGAAGTTGGGGTGTTGCGTTTAATCTTTGCTAGTACAGTATTGTGGTTTACTAGGTTGT
TTAGACTTTAGGTAAAATTAAAGTTAAAACAAAAATTGTAGCAGCAACACACGAAGGATC
TGCACAGCTCGTTAATAGGTATGTGTAATTATTTTTACTGATAAAATTAGCATTTAAGAG
TAGCCGCTGCGGCATTGGTATTCTGTTTCTATTTTTATATTTAGTCATTTTGATAGTAAT
TCAACATCAATTAAATTAACGTACCATTATTATTATTCCTACCAATGTTTACCTAAAATT
CAAGCAGATACATTTGTAATTAACCATATAACGTTTATTATTCGATTTACACGCGTATTT
GAAGGACTGAAAATGAAGTTTGCTTCAATTTAGGAATCTCATTGTACGTCGATATAGCTT
TGCGAATTTGGGTAAAAAGCGTTACACAACAACGGCTTATTAGAACCTTATTTACTGCCA
AGACTATTAAATACTCTTTTGTTAGAAAGGTGTAAGATGAATTCGTACATGAAATACCCG
GT

Reference(s)

Kanda et al. (2009). Epidermal expression of Hox1 is directly activated by retinoic acid in the Ciona intestinalis embryo. Dev. Biol. 335(2):454-63