Aniseed - Cis-regulation

Region 'REG00000387'

Cis-regulatory Region

Name

Ci-Hox3 -1812/-1507

Short name

n/a

Region ID

REG00000387

Status

Curated

Origin

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

Type of Activity

regulatory_region
(enhancer)

Author

Annamaria Locascio (2008-03-21)

Annotator

Clara Degos (2010-07-22)

Curator

Delphine Dauga (2010-02-24)

View position in WashU

Description

JGI transcript model was taken as reference for the region's coordinates.

Hierarchy of Regulatory Regions

Modification of Ci-Hox3 -2022/-1507 by deletion

Ci-Hox3 -4200/174 REG00000047 [ regulatory_region (extended_promoter) ]
- Ci-Hox3 -3000/174 REG00000266 [ regulatory_region (extended_promoter) ]
- Ci-Hox3 -4200/-3000 REG00000267 [ regulatory_region (enhancer) ]

Regulated gene(s)

KH2012:KH.C1.38 (HOXA3; HOXB3; HOXD3)

Construct(s) made to test this region

CONS00000373: pHox3 -1812/-1507::LacZ

Show in situ data

Overview of functional TF binding sites in this region

9,906,7569,907,060

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

Sequence

Aniseed Coordinates: [9,906,756 / 9,907,060] on scaffold KhC1

This sequence was found with a blast on JGI version 1.0 with the sequence includes in the publication listed bellow. This sequence was not exactly the same in the publication, it seems that the publication lacks few nucleotides.

Show sequence

Length: 305

GCAGAAGTAGAAGCAGGTGTAGGGCAAATTTAAAATTCATATTCTTAATATATAATTTTA
AAATAATAAAAACTAAATCACTTGCGGTATAAACCTAATTTATTGACTTCTGGGTCGAAA
TGAAACTAAAATACGGAAATCTTTATATAGTTTATGTTTCCCTCGGTACTGGCGGGCCAT
GGGCTTTAATAATTTAGGACTAGGTTTTATTGAAATGCAGATATAAGTAAAAGGGGTTAT
ACTGAATGCTGAGGTTGTAAACTAAACAGAATTAAGCCCTGCTTTGATGGATGGAGCTGT
CAATA

Reference(s)

Locascio et al. (1999). Patterning the ascidian nervous system: structure, expression and transgenic analysis of the CiHox3 gene. Development 126(21):4737-48