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  1. Region 'REG00000658'

Cis-regulatory Region

Name

Ci-RhoD -645/1049

Short name

n/a

Region ID

REG00000658

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Lionel Christiaen (2010-04-25)

Annotator

Clara Degos (2010-04-25)

Curator

Delphine Dauga (2010-05-04)

View position in WashU

Description

This cis regulatory region drives RhoD expression in TVCS, muscles and mesenchyme.



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

Coordinates in the paper : -711/+982

Hierarchy of Regulatory Regions

Modification of Ci-RhoD -1005/1048 by deletion

Regulated gene(s)

KH2012:KH.C1.129 (RHOA; RHOB; RHOF)

Construct(s) made to test this region

CONS00000628: pCi-RhoD -645/1049::LacZ

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

7,847,7547,849,446

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 Fox n/a TGTTTGA [616 / 622]
2 Fox n/a TGTTTAT [707 / 713]
3 Ets n/a TGGAAG [754 / 759]
4 Ets n/a AGGATC [796 / 801]
5 Fox n/a TGTTTAT [896 / 902]
6 Fox n/a TGTTTGT [925 / 931]

Sequence

Aniseed Coordinates: [7,847,754 / 7,849,446] on scaffold KhC1

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

Show sequence

Length: 1,693


CTGGCCTACTATATCACCGAAGACGTAATAGACTATATATGCATAACACGCACATGCTTT
GCGCCATGTATATATATGATATTTGAATATAGATTTGATCACGCCGAAAGCTGTCCAGAC
TAAGAATGCTTACAAAGGTAAGTTTCAGACAGTTCTATAAAGTTACACCAGCGTTATACA
AAGGATCTGTATGGCAACGTCAGACAATTTGCGTAACAGGAAGCAGAACTACTTGTTTCT
AACGTCACAGTCCCCTAGCGGCCTAGTGAATAACGGTGGCGAAAGATAGATAGTAAGTTT
TTTTTATTGTTTTATGTCCTTGGAGAGGTAAATAAATTAACTAGGAGATGATTGAAAAAA
CATTATTACGTCCACAATATGAGTATAGTATAGCATTGTAAGGTTGTATGTTTGAGTAAG
ACTATCTAAAAAAGATAAAAAAGAGATGAAGTCTAGGATTTGTTTTTCTTTTTACAGCAT
TGTCGTTCAATTACCGCGTATATATGTATTTGTATTTTTAAAATTTAGCGTATATTTAGC
TGCATTTAAAGATAAAATGGGCTACTAAAGAATCCTCCCCAACTAACTGCTAGTCTAAAT
AGTATTCTTCACTACTGTAACAAAGTTGCATTTCTTCTTTTAGTGACTGGCATCACTTCT
TAGAATGTAGTTGCTAATTTTAACTTGTAAAGCCAAAACTATACACAAACAATGGAAAGG
ATACCCAATGACGTCAAAGGTGCTTTCCCCGAGCAGCAACCCAAAATTAAATGTGTTATA
GTTGGGGATGGTGGATGCGGTAAAACTTCAATGCTGGTTGTATATACGGAAGGCGAATTC
CCTGAAGTAAGTTTACGTTTAATTATAAACTTTTTTGTATAGTTGTCAGTTTCAATACAA
ATATAGTGGGATGGGGAAAGATGGGACAACTTTAACACCTAATATCCAAATATTCTGGTG
GTGTTTTAAAGAATAAACAATGGTCTACGCCCTACGGGGTCGTAAGGATACGGTTTTATG
ATTCTTTGTATGTTCTTTGTTTACTACCAAATGGGACGAGAAAATCGAATGAAAAGGTGT
CCCATCTCCCCCCACCATACTATATATGACAGTCCGTATATATACTAGGGCGAGCAGGAT
AATTGGATAATATGTGCTAAAGGAATCCCATATCTTCCTTAACAGTACTATTTGGTATAG
TTTGCTTATACTAAATTTAATTAGCAACCCGCTGTTGTTCAAAGGTGTACACGCCCACGG
TGTTTGAGAATTACAGCAGAGAGGTGGAATTAAATCGAAAGAAGGCGGTGCTAACATTGT
GGGATACGGCGGGTATATATTAGTACATACGTGTTTATGCAAGACATCGTAGGCTTGTTG
ACTTAGTTTCGGTTAGCATGGAAGTGTAGTCTATGTTCTACGTGGGTTATGTTCTTGTCG
AGGATCTGGGATTAGGGCTAAATTCAGCCTATTATTACCACAACATTCAGACTGCTTTTG
TAGGTCCAAATGTAACATATGACTAGTGTGTTCTGATGTGTGTTTATAATACAATAAACT
AGCGCAAACTGTTTGTCCCATTATGTTTAGTCATATAGGTCATATGAGAGTAAATGAAGT
GTAAACCAAATGTTTACTTGTACCAGGTCAGGAAGATTATGACCGGCTTCGACCTCTCTC
TTACAACAACGCA

Reference(s)

Christiaen et al. (2008). The transcription/migration interface in heart precursors of Ciona intestinalis. Science 320(5881):1349-52

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