Aniseed - Cis-regulation

Cis-regulatory Region

Name

Short name

n/a

Region ID

REG00000803

Status

Curated

Origin

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

Type of Activity

regulatory_region
(complex_region)

Author

Kotaro Shimai (2010-06-30)

Annotator

Clara Degos (2010-07-22)

Curator

Delphine Dauga (2011-08-11)

View position in WashU

Description

Region upstream of Ci-Nut2 from -1068bp to +146bp (named CiNut2-1196 in the paper). Upstream of this region, a part of the Ci-Nut1 region (from -123bp to -10bp, and named -119/-27 in the paper) was added to the sequence. This part of Ci-Nut1 regulatory region contains two ZicL binding sites and one Fox binding site, required for the neural tube expression.

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

Hierarchy of Regulatory Regions

Modification of Ci-Nut2 -1068/+146 by insertion

Ci-Nut2 -1068/+146 REG00000801 [ regulatory_region (extended_promoter) ]
- REG00000802 [ regulatory_region (extended_promoter) ]
- REG00000803 [ regulatory_region (complex_region) ]

Regulated gene(s)

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

Construct(s) made to test this region

CONS00000766: pCi-Nut2 -1068/+146 & Ci-Nut1 -123/-10 added:Venus:EGFP

Show in situ data

Overview of functional TF binding sites in this region

1,405,7851,406,998

	Motif Name	Binding Factor(s)	Sequence	Position in Region
1	ZnF_(C2H2)	n/a	CATGCTGTG	[-1,019 / -1,011]
2	Fox	n/a	TGTATTGTTT	[-1,008 / -999]
3	ZnF_(C2H2)	n/a	GTCGCTTTG	[-986 / -978]

Sequence

Aniseed Coordinates: [1,405,785 / 1,406,998] on scaffold KhC14

Transcription start site is based on the start of the first exon of the KH transcript model. Sequence found thanks to the primers used in the paper.

Show sequence

Length: 1,327

TTCACTGCGTTGTCTAAATCCATGCGAAACAACAAAATAAGTCGCAAGACATGCTGTGCG
TGTATTGTTTTTTTGAAACCCCGTCGCTTTGTGAAAATCTGGTTGATTATTTTAATGAAA
AATATGTCTCATATTGCCCCACCCTACTAGTTACAAATTTTTCGTTGGTATATGCGCTTT
AGCACACAGTATAGCAGCGAAAAACTTGTTCGATTACGAAAGAGGTCATCATAAGGTGAA
TCCTGATTACAGTTTTCCGAGTAAACATAGTTTTAATACTTCAATCTGCAGCGTTAAATA
GAATGTTAAAAGTGAACTTTGCACGACTCTAGCCTTTATCAATATTTAAACGAGACGGTT
AAACTAAGCGTAAAAGTTTGACCCACGTTTGACCGGCACCACATAAAACGTATACAGACA
TGATGTCAAATTTATGACGAAATCGCGATATATAAAAACGTACGCAGCTCTGAGTCACAC
ATAGTGATGGTATACGGTGATAAACGCGTGTTAAAGAGTGAAGTTTTACTTATGTATGGT
AGGGTGGGGAAAGATAGGACACGTGTTTATTTTCTTTTCTCGTCCCGTTTGGGAGTAATT
AAAAATGTTTAACGTAATATATAACTGTAGATCAGCGATTTTAAAACGGCGTTGTTAATT
GTTAAAAACACGACCAGGAAATATGGGTTTTAGGTGGAGAGGTATATCCTATTTCAACCC
ACACCACTATTTTAAAAATACAGGATTATAGTAGAGTGGGGGAAGTTGGGACACCTTTAG
CACAGAATATCCAAATATCTTGATCGTGTTTTAAACAATTAACAACGTTCTATGGGAGTC
GTGAGGATACGGTTTTACAATTCTTTGAATGTTCTTTGTTTACTAGCAAATGAGGCGAGG
AAATAGAATGAAAAGGTGTCCCATTTTCCCCCATCCTACTATATATTAAAAATACGTTCA
ATTTAAGACCCTTTTAAAAAACATTTATGGTCATAGTATATGTTATAATTTTAGACTGCT
TTTAGTTGACGCCCTCGGTCTCATACCTATATACGTACTTACACGTCTATATTAATCTGT
GTACGGTACATTAAAAGCGCTTAAGGCAGCGCGAAATTGACAACCTATAAATGATGAAAC
CATTTGATAATTTATATAATTATTCCTAAATTAATCTGAAGTTTTAAGAAGTGGCCATTA
CAGCAACCAATTACTCCGCGTAAAGTATCGCATTTGTTTTACACTTAGAAGACGTACGGG
ATTTTAAAATGGAGCTGGAATTCGGTATAACACGAACTGCTTATGGAATCGCAATGCTTA
TGATGGG

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