Aniseed - Cis-regulation

Region 'REG00000819'

Cis-regulatory Region

Name

Ci-Noto8 -3248/-218 delta -1143/-2147

Short name

n/a

Region ID

REG00000819

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Hiroki Takahashi (2010-07-05)

Annotator

Clara Degos (2010-07-19)

Curator

Delphine Dauga (2010-07-26)

View position in WashU

Description

Region of Ci-Noto8 from -3248bp to -218bp, driving notochord expression. In this region, a deletion from -1143bp to -2147bp was performed, and had no effect on notochord expression.

The correponding construct was named p(-3.0 k)(delta 2.0k-0.8k)Noto8/lacZ in the paper.

Be careful, coordinates in the paper may be different from ANISEED coordinates. We took the KH transcript model as reference.

Hierarchy of Regulatory Regions

Modification of Ci-Noto8 -3248/-218 by deletion

Ci-Noto8 -3248/-218 REG00000816 [ regulatory_region (extended_promoter) ]
- Ci-Noto8 -1737/-218 REG00000817 [ regulatory_region (extended_promoter) ]
  - Ci-Noto8 -1353/-218 REG00000818 [ regulatory_region (extended_promoter) ]
    - Ci-Noto8 -1148/-218 REG00000820 [ regulatory_region (extended_promoter) ]
      - Ci-Noto8 -446/-218 REG00000821 [ regulatory_region (extended_promoter) ]
- Ci-Noto8 -3248/-218 delta -1143/-2147 REG00000819 [ regulatory_region (extended_promoter) ]

Regulated gene(s)

KH2012:KH.C11.665 (CALML3; CETN2; CETN3)

Construct(s) made to test this region

CONS00000782: pCi-Noto8 -3248/-218 delta -1143/-2147::LacZ

Show in situ data

Overview of functional TF binding sites in this region

1,070,9651,073,994

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

Sequence

Aniseed Coordinates: [1,070,965 / 1,073,994] on scaffold KhC11

Coordinates were based on the first exon of the KH transcript.
The deleted sequence was replaced by "-".

Show sequence

Length: 3,030

CCTTGAGACATATTTCCTTTGCAGCGTCCTTCTTATAATATATGCTACGGTGTATTTGAT
GAATAACTGCAAAAACACTAGAGCGACCAATGACGCTACCATTTTATATGACAACAACGA
GAGGAAGTAACGTCATAGCGCTGAAACATCCGCAACATTCCACTGTGGTGTTAAAACCAG
AGTGTGATTTTTAAACATTAGATTTAGTGAACCAAGTTATAAAAGCTTTTCGCGTAAATT
GTCTTGCAACAACTGTCATTTAGGTTGGTTTACGATAGGAAGTTCTTATAATTCATATGC
TTATTTGGCATTTGCACAATTATAGAGCTTACAAATTATAATAATAAGGACGACTTTGGT
GGTAGCAGTTGTAGTCTCCACTAAGTATAGCTTTGCAATTGTTCGAGAAATAATAGTGTC
GTCGTTGCGGTGTGTTATACGTTCAAATTAATCCAGTGCGTACTTTTGATTTGTATTGTT
TGTTAGTATCGTAAAACTAAAATACAAGAATTACAATACAAAAAAAATGCAAATATGCCA
TGTAACAAGAGCAACAGAAAGTAAAATATATGTAGAATTGTGAAGCATTACAGCAGGTAT
ATCAAACAAATTTAGTAGGGTGAATATGGGACACCTTTGTGTTTCATTTTATCGTCCCAT
TTGGTAGTAAACAAAGAACATTCAAAGAATTATAAAACCGTATCCTTTGGGCTCCCATAG
ACCGTGTTGTAATATGTTTAAAACTCGATCAGGATATTTGGATATTACGTGTTAAAGGTG
TCCCATCTTCCCCCACCCTACTATATATAGGTTATGCATTCACATTTATTTGACAGACAG
TAATTCGTGCTAACTAGGTTACATTAGGTTAGCTGAACACAATTGTGTAACTGGAAGATC
AAATGCCGGGGTAAGATTGACCAAT-----------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
---------CGTTGAACTTGTGGGGTAAAGATGGGTCGCTCGGTCTTGCTGTTGCGTGAA
CGTAATCTGGAGCTTTAGGCAAGCACATCATGTAGCCGATCTTTGCTTTTGTTTTAGCAT
TTGCCGAAAACGAAGATAATTCAAAACTCCCTCCGCTGGTCAGCGGTTTATCTGTTGATG
GATTTGTTTACTAGATATATATACTTACACTTTAATGATATATACTTATACTAACTTAAA
CGTAGACAACTTACTTGAATTGACCTCGCTTATAACTACAAGCAACATGAACCAAATGCA
CTTCATAATGACCAATGTTAATAAACCTAACCCCACAGAAATCTGTGTTGTGTTAAAGTG
GGTAGTTAATTAAAACAGCTTAGCGAACAATGCTGTCTGAACAATAAATAATGAATGCAT
ACCACAGGTATTGGATTGGTGTTTTGGCACGTTTTATGCAACACATCTTATAGTAGCAGT
ATATAGCAAACAGATTTACTTTATTTGGGGCCGTATTTTAAGATTAAAATACATCATGAT
TTACCCATGATATGTATAGTATTAACTAAACTTCTGCTCATTTAAATCAACCAAACTCTA
ACGAATACACAATCTAAACAACATGAGAGTCAAACTATATTGAACGGGCACGTATTATTA
CAAAAATAATTTATGTAGAAGATGCGGAAAAAACGGTACAACCTTCTGCCGAACTGTGAC
CTCAAAATATTAGCCTGGTCGTTCTGTATTTCAGTCAAAATATTGTTCTGCTGTTGTCCC
GAACATTCGTTTCCATGTTTTACAAAATGCGGGTCATGATTAAATAGAAAAAAATACACG
TGCATGTTGTCATCATACATTTACTTGGAACCGCAAAAACATATGTTTTGGTATTTAGGT
TAAAATCAACAGCTAATGCTATATATTGCTAAACAACGTAATTGCTGAAACCACAGATAC
ATAAACATATAGTGGGGTGGGGGAAGATGGGACACTTTTTAACTCTATTTACTCGTCCCA
GTTAGTAGTAAACAAAGAACATTCAAAGAATTATAATATATCCTTACGACTTCCATGAAC
CGTTGTTAATTGTTTAAAACACGATCAGTG

Reference(s)

Takahashi et al. (2010). Regulation of notochord-specific expression of Ci-Bra downstream genes in Ciona intestinalis embryos. Zool. Sci. 27(2):110-8