Aniseed - Cis-regulation

Region 'REG00000727'

Cis-regulatory Region

Name

Ci-Hox1 -2488/553

Short name

n/a

Region ID

REG00000727

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Miyuki Kanda (2010-06-15)

Annotator

Clara Degos (2010-06-16)

Curator

Delphine Dauga (2011-08-16)

View position in WashU

Description

Region upstream of Ci-Hox1 from -2488 to 553bp leading to expression in epidermis, posterior trunk, and anterior tail. Be careful, in the paper the coordinates are different : -2505/536.

This region was deduced by assembling the two regions in the paper : Ci-Hox(1.0) and Ci-Hox(0.9).
There is two conserved elements between Ciona species in the sequence : one from -496 to -477 and an other from -426 to -347.

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.

Hierarchy of Regulatory Regions

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

n/a

Overview of functional TF binding sites in this region

187,883190,923

	Motif Name	Binding Factor(s)	Sequence	Position in Region	Comment
1	ZnF_(nuclear receptor)	n/a	tgaacttttcaccc	[-404 / -391]

Sequence

Aniseed Coordinates: [187,883 / 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: 3,041

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
ATATCCTTATTCTCGAGTAGGTGTGTAAAAGATGGCAAATTTTGAGGTAGAATGGCACTG
TGTTAGTGATCGGCAGAAGCAGTGAGATGTTCTCACTGGCGTTTTCGTTATCGCGACCTG
TTTCGGTTTATTCCATTACAATAGACCGACATGTCGACGAACGATCATCATGCCAACATT
TAAAATACAACTTTAGGTATTTTCCATTGGATTTAGAGCTTACAAAGACCAGATTGTGTT
ACCTAGTGTTCAACCATATTCAAATGCAATTAAATGCACTGCCAACAGCGTGTTTATAAA
CACTATTCGGTGCTTCTATGGGATGCGTGAGCAATCTATATGTGAAGTATAATAAATCTT
CGTGTAGTAAAATTGTTGTCAATATAAATTTGTAAACATTTTTTTTTTGGTTACGAATTT
ACCAAAACGTAATGTGGTTAAAGCGACTAAAATTTGCAGGAGATTTGCTATGTTTCTTAT
ATTAAAATTGGAGATAATGGGCATTGTTTCTGTGACCGGACACTGGAAACAACAACAAAA
TGAGAAACGCGCCGAAAGCTCGAAGATAATAAGCAAACAAACGATGAACTTTTCACCCTA
GAGTGAAGACCGGACAAGTGCTCTTGTCCGAGCGCGGACATTGCTGTTTTTACAAGATGA
ATAAAAGAAACAAAAAACTCTCGTGTGCGTGGAGAAACAAGGAGAGAATAGAAACGAAAA
AGTGTGAAAGAAATAGGGGAGCTTGCGTTTGTATAAAACGAGGTGCTGGACGGGTTAGAA
ACTTCTCTGCCACAGATTGTAAAAGGCAACAAACCATATTTAGTATGTTTCGCTTTGAAA
GAAATAGTGTTTGCATTTTGGACCAGTGTTATATTGTATTGCTTTATACTAGTAGGTAAA
GAAAAAACTAAAAAATTACTATTACATCGATGCAAACATTGGCTAAATATGAAGTTGGGG
TGTTGCGTTTAATCTTTGCTAGTACAGTATTGTGGTTTACTAGGTTGTTTAGACTTTAGG
TAAAATTAAAGTTAAAACAAAAATTGTAGCAGCAACACACGAAGGATCTGCACAGCTCGT
TAATAGGTATGTGTAATTATTTTTACTGATAAAATTAGCATTTAAGAGTAGCCGCTGCGG
CATTGGTATTCTGTTTCTATTTTTATATTTAGTCATTTTGATAGTAATTCAACATCAATT
AAATTAACGTACCATTATTATTATTCCTACCAATGTTTACCTAAAATTCAAGCAGATACA
TTTGTAATTAACCATATAACGTTTATTATTCGATTTACACGCGTATTTGAAGGACTGAAA
ATGAAGTTTGCTTCAATTTAGGAATCTCATTGTACGTCGATATAGCTTTGCGAATTTGGG
TAAAAAGCGTTACACAACAACGGCTTATTAGAACCTTATTTACTGCCAAGACTATTAAAT
ACTCTTTTGTTAGAAAGGTGTAAGATGAATTCGTACATGAAATACCCGGTTCATGCTTCA
AACTCAAATTCCTATACCAACCACATCACCCCGCAAGGCCC

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