Aniseed - Cis-regulation

Cis-regulatory Region

Name

Ci-Hox1 -836/553 DR-2 type RARE mutated

Short name

n/a

Region ID

REG00000734

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)

View position in WashU

Description

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(0.9)mut 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 second conserved element contains a RARE regulatory motif, Ci-RAR and Ci-RXR can bind this motif. In this construct, this site is mutated (tgaacttttcaccc => tctagcttttcaccc). The mutation of this motif results in a loss of epidermal expression.

Hierarchy of Regulatory Regions

Modification of Ci-Hox1 -836/553 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

CONS00000701: pCi-Hox1 -836/553 DR-2 type RARE mutated::LacZ

Show in situ data

Overview of functional TF binding sites in this region

187,883189,271

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

Sequence

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 sequence mutated was replaced by the new sequence.

Show sequence

Length: 1,389

GTCGACGAACGATCATCATGCCAACATTTAAAATACAACTTTAGGTATTTTCCATTGGAT
TTAGAGCTTACAAAGACCAGATTGTGTTACCTAGTGTTCAACCATATTCAAATGCAATTA
AATGCACTGCCAACAGCGTGTTTATAAACACTATTCGGTGCTTCTATGGGATGCGTGAGC
AATCTATATGTGAAGTATAATAAATCTTCGTGTAGTAAAATTGTTGTCAATATAAATTTG
TAAACATTTTTTTTTTGGTTACGAATTTACCAAAACGTAATGTGGTTAAAGCGACTAAAA
TTTGCAGGAGATTTGCTATGTTTCTTATATTAAAATTGGAGATAATGGGCATTGTTTCTG
TGACCGGACACTGGAAACAACAACAAAATGAGAAACGCGCCGAAAGCTCGAAGATAATAA
GCAAACAAACGTCTAGCTTTTCACCCTAGAGTGAAGACCGGACAAGTGCTCTTGTCCGAG
CGCGGACATTGCTGTTTTTACAAGATGAATAAAAGAAACAAAAAACTCTCGTGTGCGTGG
AGAAACAAGGAGAGAATAGAAACGAAAAAGTGTGAAAGAAATAGGGGAGCTTGCGTTTGT
ATAAAACGAGGTGCTGGACGGGTTAGAAACTTCTCTGCCACAGATTGTAAAAGGCAACAA
ACCATATTTAGTATGTTTCGCTTTGAAAGAAATAGTGTTTGCATTTTGGACCAGTGTTAT
ATTGTATTGCTTTATACTAGTAGGTAAAGAAAAAACTAAAAAATTACTATTACATCGATG
CAAACATTGGCTAAATATGAAGTTGGGGTGTTGCGTTTAATCTTTGCTAGTACAGTATTG
TGGTTTACTAGGTTGTTTAGACTTTAGGTAAAATTAAAGTTAAAACAAAAATTGTAGCAG
CAACACACGAAGGATCTGCACAGCTCGTTAATAGGTATGTGTAATTATTTTTACTGATAA
AATTAGCATTTAAGAGTAGCCGCTGCGGCATTGGTATTCTGTTTCTATTTTTATATTTAG
TCATTTTGATAGTAATTCAACATCAATTAAATTAACGTACCATTATTATTATTCCTACCA
ATGTTTACCTAAAATTCAAGCAGATACATTTGTAATTAACCATATAACGTTTATTATTCG
ATTTACACGCGTATTTGAAGGACTGAAAATGAAGTTTGCTTCAATTTAGGAATCTCATTG
TACGTCGATATAGCTTTGCGAATTTGGGTAAAAAGCGTTACACAACAACGGCTTATTAGA
ACCTTATTTACTGCCAAGACTATTAAATACTCTTTTGTTAGAAAGGTGTAAGATGAATTC
GTACATGAAATACCCGGTTCATGCTTCAAACTCAAATTCCTATACCAACCACATCACCCC
GCAAGGCCC

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