Aniseed - Cis-regulation

Region 'REG00000157'

Cis-regulatory Region

Name

Ci-IkB -885/115

Short name

n/a

Region ID

REG00000157

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Narudo Kawai (2007-01-24)

Annotator

Jonathan Luchino (2007-08-05)

Curator

Delphine Dauga (2010-04-08)

View position in WashU

Description

Data of promoter from Kawai, N., Takahashi, H., Nishida, H., Yokosawa, H. 2005. Regulation of NF-kB/rel by IkB is essential for ascidian notochord formation. Dev Biol (277): 80-91.

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

Coordinates in the paper : -1,0kb/-1bp

Hierarchy of Regulatory Regions

Ci-IkB -885/115 REG00000157 [ regulatory_region (extended_promoter) ]
- Ci-IkB -885/115 NF-kB mutated REG00000190 [ regulatory_region (extended_promoter) ]
- Ci-IkB -885/115 delta NF-kB REG00000191 [ regulatory_region (extended_promoter) ]

Regulated gene(s)

KH2012:KH.C4.206 (BCL3; NFKBIA; NFKBIE)

Construct(s) made to test this region

CONS00000187: pIkB -885/115::LacZ

Show in situ data

Overview of functional TF binding sites in this region

2,383,6272,384,626

	Motif Name	Binding Factor(s)	Sequence	Position in Region	Comment
1	NF-kb/Rel/Dorsal	n/a	GGGAATCCCC	[2,383,734 / 2,383,743]

Sequence

Aniseed Coordinates: [2,383,627 / 2,384,626] on scaffold KhC4

This sequence was found using JGI V1.0.

Show sequence

Length: 1,000

AACAAACTATATATGGAAAATTACTACCAAAATGTGATTATTATTACTGTATTACTCCCG
TTCATACTACTGTGTTCTTGCTCTGGATAAAACCTTATTGTAAAATGGGGAATCCCCAAT
ATCAAGAATTGAGTGTTGTGTACAGAAAGATTGCAAGTCTCCTCATAGTATTTTTAGGAA
TCGCACAGAATAATTCTGTTTAACTTAAGGGGTTTTCTAATCTCGTTTACATGAAACTTT
GTTTGTGACGCCGCATAGCATTATTGTTGGTGTATTTGCCAAGCAATAAAAACGCATTCC
AACCGGCCAATATAATATTAAAACCCTATTACTTTTTGTTTGAACAAGAAAGAATGACCT
TTTGCAGTGTTGCAAATATGTGGAAGTGAATGCATTCACTTGTTTCGATTGCGTTGTGCC
AGTGTAATGAGTATGTACGAAACCTAGTAGGCGAAAAGATATTTGTAGCGCTATTCACGC
TTTGTTTGGATGGTGTGACTAAGAGAATCGTGATTCAAGTCAAATTATCGGAGCTGACCT
CGGCACGGAACAAATATAAACCACCACAGACTACGTTTCAATTGGTTTGTATGTACTGGT
GGTGAAACGACGTAAAGTCCCGGATGTCTAGCTGACAGTGTTACACGATAACATATTTCA
CAAACCATTGCGATTTTGAATATTTAGCCAATAGCGTATAAAGATAAACGCTGTAGAGTA
ATTAATACCAAACTACCAAGCTGTGTTTTACTTATAAAGGTTTTTGTGTGAATATTAGTA
AAAGATATATCTTTACGTTTGTATGAAAAATTAGTCTCGGCAACACTGCAAATTTCGGTA
CTTTCCAAAACTCCGCCGTAAGAAAAAAAGCTTATTCAGCTCTTGCCTTTGTCTGTTGGT
TTGGGTAATTTCGTTGTTCGAAGCGTTGAGTTAAGAGTTGTAGATTACCATTTTAGTTGA
TTTGTTATGCTTTTAACCAGTTATAGTTCATTTCGTCAAA

Reference(s)

Kawai et al. (2005). Regulation of NF-kappaB/Rel by IkappaB is essential for ascidian notochord formation. Dev. Biol. 277(1):80-91