Login
Help

CIS-REGULATION

Submit your Data

  1. Region 'REG00000665'

Cis-regulatory Region

Name

Ci-RhoD 448/835

Short name

n/a

Region ID

REG00000665

Status

Curated

Origin

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

Type of Activity

regulatory_region
(enhancer)

Author

Lionel Christiaen (2010-04-25)

Annotator

Clara Degos (2010-04-25)

Curator

Delphine Dauga (2010-05-05)

View position in WashU

Description

Region from +448bp to +835 of the RhoD/F gene, containing the second exon, and the two last FoxF sites were absent.



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

Coordinates in the paper : +380/+768

Hierarchy of Regulatory Regions

Modification of Ci-RhoD 448/990 by deletion

Regulated gene(s)

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

Construct(s) made to test this region

CONS00000647: pCi-RhoD 448/835 bpFOG::LacZ

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

7,847,9687,848,355

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]

Sequence

Aniseed Coordinates: [7,847,968 / 7,848,355] on scaffold KhC1

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

Show sequence

Length: 388


CCACCATACTATATATGACAGTCCGTATATATACTAGGGCGAGCAGGATAATTGGATAAT
ATGTGCTAAAGGAATCCCATATCTTCCTTAACAGTACTATTTGGTATAGTTTGCTTATAC
TAAATTTAATTAGCAACCCGCTGTTGTTCAAAGGTGTACACGCCCACGGTGTTTGAGAAT
TACAGCAGAGAGGTGGAATTAAATCGAAAGAAGGCGGTGCTAACATTGTGGGATACGGCG
GGTATATATTAGTACATACGTGTTTATGCAAGACATCGTAGGCTTGTTGACTTAGTTTCG
GTTAGCATGGAAGTGTAGTCTATGTTCTACGTGGGTTATGTTCTTGTCGAGGATCTGGGA
TTAGGGCTAAATTCAGCCTATTATTACC

Reference(s)

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

Back to Top