Aniseed - Cis-regulation

Cis-regulatory Region

Name

Ci-Noto8 -1737/-218

Short name

n/a

Region ID

REG00000817

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Hiroki Takahashi (2010-07-02)

Annotator

Clara Degos (2010-07-02)

Curator

Delphine Dauga (2010-07-15)

View position in WashU

Description

Region upstream of Ci-Noto8 from -1737bp to -218bp, driving notochord expression.

The corresponding construct is named p(-1.5 k)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

CONS00000780: pCi-Noto8 -1737/-218::LacZ

Show in situ data

Overview of functional TF binding sites in this region

1,072,4751,073,993

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

Sequence

Aniseed Coordinates: [1,072,475 / 1,073,993] on scaffold KhC11

Sequence found thanks to the primers used in the paper. Coordinates were based on the first exon of the KH transcript.

Show sequence

Length: 1,519

CTTGAGACATATTTCCTTTGCAGCGTCCTTCTTATAATATATGCTACGGTGTATTTGATG
AATAACTGCAAAAACACTAGAGCGACCAATGACGCTACCATTTTATATGACAACAACGAG
AGGAAGTAACGTCATAGCGCTGAAACATCCGCAACATTCCACTGTGGTGTTAAAACCAGA
GTGTGATTTTTAAACATTAGATTTAGTGAACCAAGTTATAAAAGCTTTTCGCGTAAATTG
TCTTGCAACAACTGTCATTTAGGTTGGTTTACGATAGGAAGTTCTTATAATTCATATGCT
TATTTGGCATTTGCACAATTATAGAGCTTACAAATTATAATAATAAGGACGACTTTGGTG
GTAGCAGTTGTAGTCTCCACTAAGTATAGCTTTGCAATTGTTCGAGAAATAATAGTGTCG
TCGTTGCGGTGTGTTATACGTTCAAATTAATCCAGTGCGTACTTTTGATTTGTATTGTTT
GTTAGTATCGTAAAACTAAAATACAAGAATTACAATACAAAAAAAATGCAAATATGCCAT
GTAACAAGAGCAACAGAAAGTAAAATATATGTAGAATTGTGAAGCATTACAGCAGGTATA
TCAAACAAATTTAGTAGGGTGAATATGGGACACCTTTGTGTTTCATTTTATCGTCCCATT
TGGTAGTAAACAAAGAACATTCAAAGAATTATAAAACCGTATCCTTTGGGCTCCCATAGA
CCGTGTTGTAATATGTTTAAAACTCGATCAGGATATTTGGATATTACGTGTTAAAGGTGT
CCCATCTTCCCCCACCCTACTATATATAGGTTATGCATTCACATTTATTTGACAGACAGT
AATTCGTGCTAACTAGGTTACATTAGGTTAGCTGAACACAATTGTGTAACTGGAAGATCA
AATGCCGGGGTAAGATTGACCAATCCATGGTCGGAGGTGGTTGAACTTGGTGGTCTAATG
CTAAGCCTCAAACCGGTGTCGGTCGGATCTCCCCTATACGGAGTACCAGGGTGCCAATCT
CCATTATACCCAGGATTTCCATTGCTTTGTGTTACTGTATCAGCCTGTGGATAAATATAT
ATAACAAGTTCTTAACTCGGGAAATTAACTTTTCGTGTCTCCATTAATTGTCGACTATTG
TGCAGTGTCTTAAACTATTAAAAAATTTGGTGGCTTGTGGGCGTGTAAGTTAGGCTATTT
AGAAGGAGAAAGACATGTCTCCGCTTGTTATTCCCTATGAGTTTTGCAAACTCACTCTCG
AAAATGTACAAATTCACTTACAGAATGGAATGTAGCAGGTTAAGTCTAGTATTTCAAACT
TACCACTGTGTTGTAACTTGAACCGAGCCAAATATCAGCATGGGTAGCTGGTCTGATGGG
GAATACGATGGTTTGTCGACAGTAGTTATAAACTATGTCGTACATCGCTTTATCCACAAT
ATCCACCAATCGACCGCCGCTTTCGGCGCAAAATTTTATTGCTTGAGTGAGGTTTAATTC
TTTTACAACTGAAGCACCA

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