Aniseed - Cis-regulation

Region 'REG00000010'

Cis-regulatory Region

Name

Otx -1541/-1417

Short name

n/a

Region ID

REG00000010

Status

Curated

Origin

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

Type of Activity

regulatory_region
(enhancer)

Author

Vincent Bertrand (2007-01-19)

Annotator

Guillaume Luxardi (2007-01-19)

Curator

Delphine Dauga (2010-03-01)

View position in WashU

Description

This region, also called otx a-element, drives expression in the induced animal territories a6.5 and b6.5 at the late 32-cell stage.

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

Hierarchy of Regulatory Regions

Modification of Otx -1541/161 by deletion

Otx -3541/1333 REG00000007 [ regulatory_region (extended_promoter) ]
- Otx -3541/161 REG00000008 [ regulatory_region (extended_promoter) ]
  - Otx -2165/161 REG00000242 [ regulatory_region (extended_promoter) ]
    - Otx -1723/161 REG00000243 [ regulatory_region (extended_promoter) ]
      - Otx -1541/161 REG00000009 [ regulatory_region (extended_promoter) ]
        
        Otx -1541/-1417 REG00000010 [ regulatory_region (enhancer) ]
        
        Otx -1541/-1417 Ets2 mutated REG00000011 [ regulatory_region (enhancer) ]
        
        Otx -1541/-1417 Ets1 mutated REG00000012 [ regulatory_region (enhancer) ]
        
        Otx -1541/-1417 Ets1-2 mutated REG00000013 [ regulatory_region (enhancer) ]
        
        Otx -1541/-1417 GATA2-3 mutated REG00000014 [ no_output ]
        
        Otx -1541/-1417 GATA1 mutated REG00000015 [ inactive_region ]
        
        Otx -1472/-1417 REG00000016 [ regulatory_region (enhancer) ]
        
        Otx -1464/-1436 REG00000246 [ regulatory_region (enhancer) ]
        
        Otx -1472/-1417 delta -1464/-1436 REG00000248 [ regulatory_region (enhancer) ]
        
        Otx -1472/-1417 delta -1464/-1436 dimer REG00000439 [ regulatory_region (enhancer) ]
        
        Otx -1417/161 REG00000017 [ regulatory_region (extended_promoter) ]
        
        Otx -1133/161 REG00000244 [ regulatory_region (extended_promoter) ]
        
        Otx -706/161 REG00000018 [ regulatory_region (extended_promoter) ]
        
        Otx -271/161 REG00000019 [ inactive_region ]
      - Cirobu.REG.KH2012.C4.4315574-4315776 REG00001207 [ regulatory_region (extended_promoter) ]
- Otx -271/1333 REG00000245 [ regulatory_region (extended_promoter) ]

Regulated gene(s)

KH2012:KH.C4.84 (CRX; OTX1; OTX2)

Construct(s) made to test this region

CONS00000004: pOtx -1541/-1417 pBra::NLSLacZ

CONS00001199: p.Cirobu.REG.KH2012.C4:4315574-4315697>LacZ

Show in situ data

Overview of functional TF binding sites in this region

4,315,5744,315,697

	Motif Name	Binding Factor(s)	Sequence	Position in Region
1	ZnF_(GATA)	n/a	TTATCT	[4,315,645 / 4,315,650]
2	Ets	n/a	CGGAAG	[4,315,655 / 4,315,660]
3	Ets	n/a	AGGAAA	[4,315,670 / 4,315,675]
4	ZnF_(GATA)	n/a	ATATCT	[4,315,683 / 4,315,688]
5	ZnF_(GATA)	n/a	AGATAG	[4,315,690 / 4,315,695]

Sequence

Aniseed Coordinates: [4,315,574 / 4,315,697] on scaffold KhC4

BASE COUNT 32A 24C 27G 41T

Show sequence

Length: 124

CGTGTGATAGTGCGTGATAACTCGTATCCTTTCGCACTGCGTTCCTATCCGTACTTTGGA
TCTGAAGCTCGTTATCTCTAACGGAAGTTTTCGAAAAGGAAATTGTTCAATATCTAAGAT
AGGA

Reference(s)

Bertrand et al. (2003). Neural tissue in ascidian embryos is induced by FGF9/16/20, acting via a combination of maternal GATA and Ets transcription factors. Cell 115(5):615-27