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CIS-REGULATION

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  1. Clone 'cicl089f03' > 
  2. Region 'REG00000780'

Cis-regulatory Region

Name

Ci-Nut1 -733/94

Short name

n/a

Region ID

REG00000780

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Kotaro Shimai (2010-06-29)

Annotator

Clara Degos (2011-08-10)

Curator

Delphine Dauga (2011-08-10)

View position in WashU

Description

Region upstream of Ci-Nut1 from -733bp to +94bp, named -729bp in the paper. This region can drive expression in neural tube.

Three putative regulatory motifs were present in this region : 2 ZicL binding sites and one Fox binding site.


Transcription start site is based on the start of the first exon of the KH transcript model.

Be carefull the coordinates in the paper may be different from ANISEED coordinates.

Hierarchy of Regulatory Regions

Modification of Ci-Nut1 -824/94 by deletion

Regulated gene(s)

KH2012:KH.C14.4 (ADRB2; P2RY12; RGR)

Construct(s) made to test this region

CONS00000743: pCi-Nut1 -733/94 pVenus::EGFP

Show in situ data
Overview of functional TF binding sites in this region

1,413,7951,414,621

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 ZnF_(C2H2) n/a CATGCTGTG [-74 / -66]
2 Fox n/a TGTATTGTTT [-63 / -54]
3 ZnF_(C2H2) n/a GTCGCTTTG [-41 / -33]

Sequence

Aniseed Coordinates: [1,413,795 / 1,414,621] on scaffold KhC14

Transcription start site is based on the start of the first exon of the KH transcript model.

Show sequence

Length: 827


ATATGCTTTGTTTACTACAAAATGGGACGGGAAAATAAAATAAAAAGGTGTCCTATCTTC
CCCCATCCTACTATATATATCATATTTTCTAATCCTGTTTTAGCAATTAACAACGCTCGT
TTAAAGTCGTGGGTATATGCGGTTACATAAATTTAAAAATATTATTTGTTTACTTCAAAA
TAGAACGATAAAAGCGTGTATAAACATGTTGTATCATCTTACCCCATCCTGCTACAAATA
TAAACAATTTCATGATAAGAAAATGCACATGTTTGTTATGCCGCGTGTTGTGTACAGTTC
TGGTTAGGATTTCAGAACACACACACAGAAAATCGGTCGTGCCTGCTGCTGCAACTAGTG
CGACACCTCAATAATTATGAGACTGCCTCAGTGCATTCCTATCAACGTGTTTTGCGCTCG
TATCACCCAAAAAGCGTGCCTCGTGCTGCCTACACGGTGTGGCTACATAAAAACGTCGCG
TGTTTTACTGTTCCAGTTCGTTTTTGTATTCGTGGAAATAGGTTCGCATTTTTTATTAAG
AAAGAGTTTGGTTTTCGAGGTCACTGAATTGCAATTAGAAGGCATTTAATAGTAGCACTA
GGACACTCTATTCACTGCGTTGTCTAAATCCATGCGAAACAACAAAATAAGTCGCAAGAC
ATGCTGTGCGTGTATTGTTTTTTTGAAACCCCGTCGCTTTGTGAAAATCTGGTTGATTAT
TTTTTCGTACCAGTTTTACAGTTTAAATACGACTGTGCTTCAGTTTTTGTTAGTATTGAG
TTGTACACTATATCAACAACATGGAAATTGATTTTGGATTTGCAAGA

Reference(s)

Shimai et al. (2010). Upstream regulatory sequences required for specific gene expression in the ascidian neural tube. Zool. Sci. 27(2):76-83

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