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CIS-REGULATION

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  1. Region 'REG00000778'

Cis-regulatory Region

Name

Ci-Nut1 -927/94

Short name

n/a

Region ID

REG00000778

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 -927bp to +94bp, named -923 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 -1030/94 by deletion

Regulated gene(s)

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

Construct(s) made to test this region

CONS00000741: pCi-Nut1 -927/94 pVenus::EGFP

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

1,413,7951,414,815

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 / 1,414,815] on scaffold KhC14

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

Show sequence

Length: 1,021


TATCTAACTGCAGCCGGAAATACGTGCTCTTTGCAGAAAGGAAAATCCATTTCTCGTGTA
TTGCAACATACGGTATAGTAGGTTTAGATGGGTCACCTTTACCACAAATAACATCCAAAT
ATCCTGAGCATGTTTTAAACATTTAACAACGGTATATGTGGAAGTTGCGAGAATACGGTT
TGATAATTCATTAAATATGCTTTGTTTACTACAAAATGGGACGGGAAAATAAAATAAAAA
GGTGTCCTATCTTCCCCCATCCTACTATATATATCATATTTTCTAATCCTGTTTTAGCAA
TTAACAACGCTCGTTTAAAGTCGTGGGTATATGCGGTTACATAAATTTAAAAATATTATT
TGTTTACTTCAAAATAGAACGATAAAAGCGTGTATAAACATGTTGTATCATCTTACCCCA
TCCTGCTACAAATATAAACAATTTCATGATAAGAAAATGCACATGTTTGTTATGCCGCGT
GTTGTGTACAGTTCTGGTTAGGATTTCAGAACACACACACAGAAAATCGGTCGTGCCTGC
TGCTGCAACTAGTGCGACACCTCAATAATTATGAGACTGCCTCAGTGCATTCCTATCAAC
GTGTTTTGCGCTCGTATCACCCAAAAAGCGTGCCTCGTGCTGCCTACACGGTGTGGCTAC
ATAAAAACGTCGCGTGTTTTACTGTTCCAGTTCGTTTTTGTATTCGTGGAAATAGGTTCG
CATTTTTTATTAAGAAAGAGTTTGGTTTTCGAGGTCACTGAATTGCAATTAGAAGGCATT
TAATAGTAGCACTAGGACACTCTATTCACTGCGTTGTCTAAATCCATGCGAAACAACAAA
ATAAGTCGCAAGACATGCTGTGCGTGTATTGTTTTTTTGAAACCCCGTCGCTTTGTGAAA
ATCTGGTTGATTATTTTTTCGTACCAGTTTTACAGTTTAAATACGACTGTGCTTCAGTTT
TTGTTAGTATTGAGTTGTACACTATATCAACAACATGGAAATTGATTTTGGATTTGCAAG
A

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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