Aniseed - Cis-regulation

Cis-regulatory Region

Name

Ci-fibrn -3016/38 delta -2781/-875

Short name

n/a

Region ID

REG00000828

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Hiroki Takahashi (2010-07-06)

Annotator

Clara Degos (2010-07-07)

Curator

Delphine Dauga (2010-07-15)

View position in WashU

Description

Region upstream of Ci-fibrn from -3016bp to +38bp. In this region a deletion from -875bp to -2781bp was performed. This deletion results in a loss of notochord expression, but an ectopic staining is observed in mesenchymal cells.

The corresponding construct is named p(-3.0 k (delta 2.7-0.8))fibrn/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-fibrn -3016/38 by deletion

Ci-fibrn -3016/38 REG00000825 [ regulatory_region (extended_promoter) ]

Regulated gene(s)

KH2012:KH.C1.832 (FGL1; FGL2; FIBCD1)

Construct(s) made to test this region

CONS00000791: pCi-fibrn -3016/38 delta -2781/-875::LacZ

Show in situ data

Overview of functional TF binding sites in this region

1,753,0561,756,109

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

Sequence

Aniseed Coordinates: [1,753,056 / 1,756,109] on scaffold KhC1

The deleted sequence was replaced by "-".

Show sequence

Length: 3,054

TGGACAGCATTATAACCTGCCTTATAGTGTATTGACCCCTGCATGGAAAAAGATGTATAT
GAAAATAGACAAACTGGTACATTTAACGGTAAGTCAACGAAGTGTTAAACTGGTACATTT
AACGGTAAGTCAACGAAGCCGTATAAATAGTCAAACTATAACTAAAAGTGCTCATTCGCA
TACTGCAATAGTTTCAGCAATACGACTGTGGGCATAGCAACTACTGATGTTATAATCTGT
ACTAACCGCTATACCTGCGTTTGCTTTATTAACTACGTAATATACATACTACCTTGTAAG
TTGGTACGAGGTGTATAAACACCCGCGTTATACCGACTGTCATGTTCCGGCCACGCGAGG
ATAAAAAAGTAAGTTACAAGTTATAAGTTATTCCACATTGTACAGTACATGAAGCGTTTA
TATAGAGCGGACTTTACCATCCGTTCAATCCACATTACTGGCTATAAGTTGAGCTTAGCA
TCTTAATACTGATGGCCGCAGGATGTATTGCTGTCTGTACATACAAACCTAATCTTCACC
CGATCTCTGCACATTGTTTACATTAAGTTAAGCCATCTATACAGTTTAAGTTAAAAACTC
AATGTGTTTTTGAAATATTTTAGAATAGCTGACTAGAAATAAATCTGCAATAAAACATAT
CGTTCAAAATATATACCTTGTTTAAAAGCAGCATTTATAAAGGTTTACACTGGTGCTTTT
TTTGCAACACGCCAATTTTTTAAATATATAGGTATAAATTACTTTTTTTTATTCCAAACA
GGCCAGTTCCTAACATTTATAACTACCCAGGCCCTCAATAGTCCAAGCATTCATATGCTC
TACTAACGGGTTGTCGCCAGCTTATATATAGGCCATTTAAAATGTGTCTGTTCAGATCAA
AGTTAGGGCCC-------------------------------------------------
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ATTGACTAAAAATGTATGTACTGTATACGCTTTACACGTATATAGCGTATATGTACCCCT
TCGCTTAAAAGTATATACAATTAGCGTAAGCAAATGTTATAACCAAAGAAAACAGTACAT
ATATATGCTGTAAGTATAGTTACTAATGGTATAACGCGTTTGCATGCGTTCTTTAGATGA
GTTTTCGACACGGTTTATCGTCAGCGTCGATGGTGTAACGGTTAGCATTGGTGC

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