Aniseed - Cis-regulation

Region 'REG00000015'

Cis-regulatory Region

Name

Otx -1541/-1417 GATA1 mutated

Short name

n/a

Region ID

REG00000015

Status

Curated

Origin

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

Type of Activity

inactive_region

Author

Vincent Bertrand (2007-01-19)

Annotator

Guillaume Luxardi (2007-01-19)

Curator

Delphine Dauga (2010-03-01)

View position in WashU

Description

This regulatory region is segmented in Four parts:
Region -1541/-1417 mainly drives expression during cleavage stages in a- and b-line neural precursors as a result of induction by FGF9/16/20
Region -1417/-1133 drives expression in A-line cells from the 64-cell stage onwards
Region -706/-271 drives cleavage stage expression in b- and B-line cells
the first intron drives later expression in the palps and anterior ventral epidermis.

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/-1417 by substitution

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

CONS00001568: test2 chris

CONS00000009: pOtx -1541/-1417 GATA1 mutated pBra::NLSLacZ

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	Ets	n/a	CGGAAG	[4,315,655 / 4,315,660]
2	Ets	n/a	AGGAAA	[4,315,670 / 4,315,675]
3	ZnF_(GATA)	n/a	ATATCT	[4,315,683 / 4,315,688]
4	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 34A 21C 25G 44T

Show sequence

Length: 124

CGTGTAATAGTGCGTAATAACTCGTATTCTTTCGCACTGCGTTCCTATTCGTACTTTGGA
TCTGAAGCTCGTTATTTCTAACGGAAGTTTTCGAAAAGGAAATTGTTCAATATCTAAGAT
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