Aniseed - Cis-regulation

Region 'REG00001546'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.C12:1333885-1333914|Rx

Short name

J-C_Rx-547/-518

Region ID

REG00001546

Status

Curated

Origin

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

Type of Activity

inactive_region

Author

D Aniello Enrico (2022-10-11)

Annotator

Marion Gueroult-Bellone (2022-10-11)

Curator

Marion Gueroult-Bellone (2022-10-11)

View position in WashU

Description

This 30bp element is located upstream (-547/-518bp) of Rx TSS. Associated with the basal promoter of the human β-globin, it is not able to drive reporter gene activity.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.C12:1333829-1334025|Rx by deletion

Ci-Rx -3kb/1 REG00000281 [ regulatory_region (extended_promoter) ]
- Cirobu.REG.KH2012.C12:1331487-1333133|Rx REG00001531 [ inactive_region ]
  - Cirobu.REG.KH2012.C12:1331896-1331990|Rx REG00001532 [ inactive_region ]
- Cirobu.REG.KH2012.C12:1333114-1334401|Rx REG00001533 [ regulatory_region (complex_region) ]

Regulated gene(s)

KH2012:KH.C12.152 (PAX6; RAX; RAX2)

Construct(s) made to test this region

CONS00001620: p.Cirobu.REG.KH2012.C12:1333885-1333914>LacZ

Show in situ data

Overview of functional TF binding sites in this region

1,333,8851,333,914

	Motif Name	Binding Factor(s)	Sequence	Position in Region	Comment

Sequence

Aniseed Coordinates: [1,333,885 / 1,333,914] on scaffold KhC12

This 30bp DNA fragment was amplified using the following annealing oligonucleotides : J-C up: TTAGTGCAAATTGCCCTAATCCTTATTAAA and J-C down: TTTAATAAGGATTAGGGCAATTTGCACTAA

Show sequence

Length: 30

TTAGTGCAAATTGCCCTAATCCTTATTAAA

Reference(s)

D'Aniello et al. (2011). Onecut is a direct neural-specific transcriptional activator of Rx in Ciona intestinalis. Dev. Biol. 355(2):358-71