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CIS-REGULATION

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  1. Region 'REG00000009'

Cis-regulatory Region

Name

Otx -1541/161

Short name

n/a

Region ID

REG00000009

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

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 -1723/161 by deletion

Regulated gene(s)

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

Construct(s) made to test this region

CONS00000003: pOtx -1541/161::NLSLacZ

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

4,313,9964,315,697

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 ZnF_(GATA) n/a TTATCT [4,314,067 / 4,314,072]
2 Ets n/a CGGAAG [4,314,077 / 4,314,082]
3 Ets n/a AGGAAA [4,314,092 / 4,314,097]
4 ZnF_(GATA) n/a ATATCT [4,314,105 / 4,314,110]
5 ZnF_(GATA) n/a AGATAG [4,314,112 / 4,314,117]

Sequence

Aniseed Coordinates: [4,313,996 / 4,315,697] on scaffold KhC4

JGI v1.0 version

Show sequence

Length: 1,702


CGTGTGATAGTGCGTGATAACTCGTATCCTTTCGCACTGCGTTCCTATCCGTACTTTGGA
TCTGAAGCTCGTTATCTCTAACGGAAGTTTTCGAAAAGGAAATTGTTCAATATCTAAGAT
AGGAGACAATAACGAAGCTCCGCAATGTTTTGGTAAGATAATAACTTGGAAAAACACAGA
ACGTACAAGCGAAAATGCGTGTCGTACATGAGTTACGACAGCTGTGGTTGTTTATCGTTA
ATATCTATTTTAAAGTAAGCACCTTAAAATTTAGCAAACGAAATCGTGTTCGTTGTGCAT
AACAGTCTATTTCCTTCGTCTTCTGTGTTTGTTCCGTCCATTCTAATTGTGTGTAACTAT
GTCTGTGCTTGCTGGTCTGTGTTTGAGTGGCCACAGTCGAATTAATGGCCATCGCCGCTG
CCACAGTGCAAATACAGAAGGTAGGGGAACATACGGGCACTTTGTACGCAGTCTGGATAC
AACATAAGCCGTAACTGAGACCTCAGATCTGCTATCACTACAATTTGCCCCGTTTTACTT
TAAAATTTACCCAACTCAGCAATTGTACATGACTATATTATACCACAGGGGTTTCGTTAC
AACTTAAAAATATGAAAACCTTATTTTCAAATGCCCTCGGTTTGGGATAAGTTTGGGCTT
CGGCGTACCGCACGTAACTTGATACGCTTTGGTCAGTTAAAATCGAGCGGACCGGTTGCG
CTAAGATGGACTGACGAGTGGTTGGTAGAATTTCCGGGGTACGGAAGGCGCGCAATTTAT
ACCAGGCGAGAAATCTTGCACCGGCAGATGACGTCGCTCTGACGTCATTCCGCCCTTAAG
AATCTTCCTAATTAAATTCTAATTGCAGATTGAAAGACGGTCGTATTTTTAGCATGACAA
CAACTCTTAGCGGGTGGTAGCACCTGCCGGGTCAGGCCAGTCCTTGTCTCATGCTCCAGA
TTCAAGCTCGGCAGACCATTTGCCGCACTTCATTTCGGCTTCTCGCTCCGACCCCCCAAC
GTCCGCTATTCACACTTGGAGCGCAGCTTTGTTTCTTTCTTTATCTTATCGGAGGCGCCA
AGCGATTGCTTCCGAATTTCCAGGCCTTCCCCGCTTGCAAGGGCGGCCTCTCACTCCTTC
CCTCGCTCCCGCCTTTCTCTTTTTTCCTCGCTCGATTTTAATTAATCGGGTATTTAAATT
CGTCACCACTTCCATTTGAATCATTAAGTAGCTTGTGGTCCTCTTAGTCACAAGGCGGGA
TCTCCCCAATCTAGATACTTGGTCCAAGCATAGCAAAAAAGCCTAACTCATATAATAATA
CATTAGCAGAATAGCCATCCTTGAAAGTTATCCCAGTTCGAAAAGTCAGTTTAAATAGTA
AATCAAATCAGTCTTTGTAATCACGAATAATCTTAGTCGTATTCGAGCATACATGTATGG
AACATTGAAATGAAATCAAAGAAAATCAGGCATTCACATTACATTACATGCTATTTTCAG
TTCGTATTTTAACTTTTATAATTCTTTCTACAGATATTAGGCTTCAACCTGATAATTTTG
AAAAATAGAGGTTTATTAAATTTGTAAAATAAGTTGATTGATTACAATCTACAAGCAAGA
AGTTTGAAAAGTAAAAAATCAAGTTGAAAAACGAAGACATTTTGAACGAAAAAACAAATT
CATTTCAAGTACCACGGGTGAG

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

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