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CIS-REGULATION

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  1. Clone 'cien52383' > 
  2. Transcript 'KH2012:KH.C14.52.v2....' > 
  3. Region 'REG00000214'

Cis-regulatory Region

Name

Ci-Sna -3200/codon 15 delta 1.5kb

Short name

n/a

Region ID

REG00000214

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Albert Erives (2007-11-06)

Annotator

Clara Degos (2010-07-23)

Curator

Delphine Dauga (2010-02-26)

View position in WashU

Description

This region goes from 3,2Kb upstream the start of cDNA AF002987 to 1,3 kb downstream (corresponding to the midle of exon 2). A 1.5kb EcoR1 internal deletion (from -1.7kb to -0.2kb) only leaves the anterior sensory vesicle and secondary tail muscle activity.

This region is named delta EcoRI in the paper (Erives et al 1998).

Hierarchy of Regulatory Regions

Modification of Ci-Sna -3200/codon 15 by deletion

Regulated gene(s)

KH2012:KH.C3.751 (SNAI1; SNAI2; SNAI3)

Construct(s) made to test this region

CONS00000034: pCi-Sna -3200/codon 15 delta 1,5kb:: NLS LacZ

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

5,676,0835,680,582

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

Sequence

Aniseed Coordinates: [5,676,083 / 5,680,582] on scaffold KhC3

JGI v1.0 sequence for this region, as the sequence reported in the article is not available in Genbank. E-box site E5 is not found in the JGI assembly sequence. The "-" in the middle of the Ecor1 site used to create an internal deletion, mark the position of the missing sequence.

Show sequence

Length: 4,500

ATAATAAAATACGTAAAGGATTTTTTGATACGGACCAATTTGCGAATCCGCAAGGACTGT
AAAGTATAGGATAGAGGTTGATATATGAATAATAAGTGCTATTTTGTACACCTCATCAGA
GAAATGGCTAACTGTAACTTGCGATAAATTCTTTCGCAGTTTACGGTGTATCGTGGGCTT
TAATAAACAATGCACCTGTTTAAAACCGGCGTTCTGTATAGCGCCTATCACATTACCACG
CCTCGTGTGTCTTTACCCAAGAGACGTATATTTCAATCACTTAACGGCTTAATTCGAAAC
CGAGCAAGTGTTATGGTTAGATACGTCATGTTTCTAATGCAAGGGTATTTTAATCTATAT
CTCTATATACTATTAATAGACAATCATTATTCCTATGTAGTTAGAATTTCATCACATTCA
GTATTTTATTTGTATATAAGCCATCTTTGATTTTAAAATAATTTTATTGCCGCCTTAGCC
GAGAGCAAACTAATAACTGGACTTTAAACGATACGTCACTCGTTACGGATTTTTTCCAGA
CTATATTAAAGTGACGTCAGTGAAATGAATGCATGCGCGTGTCGCACTTTGTTATTTAAT
GACGTAATCTTGATGCGGCCACATAGATTAATGGGTGCACCGAGTACTTTCATCATACCA
GGCGTCCGGTGCCGAAGCAACAGGCGGCTAACCGAAATAGAACAACGACCAGCAGGAGCG
AGCCAACAACTGTTACCGAAGCGGTCCACTTAATCCCGGGACACGCGCGAACTGTACGCG
ACAAATATCAAAATATAAACAACGGCATTCAACTATTAATATTGCGCCTTTGGTTACGTT
CAACCGAGTTTTAAAAACCTGTCACATTTTTAAACTGAAGGCTGTCTGTATAGTCATCGA
AAGAATATCCCACGACCCAGCGTGCACACTTGGCCCGTATAACCTTCCGTTTGTGTTGGT
TTTTATTCCGAATACTCCAAATGATTGTAGCGCCGGGATACCTTAGTTGGCTTAGTACAC
CGATAGCAGACCGCCCCTCCACGAAATACAGACACTCTGTTTGTCACCAGTGTTCTATCA
ACTGTCTCGTTTAGCTACGGTGTACACATGCTTCTACATACGTTCCGCGGGTGTCTATTG
TTGCCCTTGTCCTTACAGTGCGTCTAGAGTAAACTAACCAAGATACGATTGCGTATACCG
GGACAATAGGATAACATTTGCACGGAGACACGTGGTCAACTATACGAGGCACGTAACCGC
AGGGCACTACCAAAGTCCGGTTATTTAAGTTTATATTTTTGCCTAGCCGTCGAAAAAACA
TGCATATATTAAAATTAATAAAACCGTTTATTCTCTATATCGTACATTGGTTATGAGCGC
TTTAGCACCAAAATATAACGAGTTCTATAAACGCAGTTAAATTCAATTGATTTTACCTTA
CCAGCAGGCAGTTTCTCTCCACAAACATTTAAGCCTCATTCCTAACGTGCGGGGAATT--
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-----------------------------------------------CTAAAGTGATTAT
ATTTAGAAATGGGCTATCAGTGCTTGATTACTGTTGCAGGGTTATTTAAAAATGCAGTCG
AACAGTCTAAGAAAGCTTAGCTATATTTGAAGGATTATGTATACTTATTTCATTAGAGCA
ATATTTTTTTTTTTATTTTAGACTTTTGGTACATATTCAAAATATCAAAATTCTCACTGT
GAAATATATTACTGTGATTACATCATGACCTCCGTCGAGCCCATGCTTTATCAAGGCAAG
CACGCCGTTCAGAAAAATGAAGGTATATATGCAGTCCTATTTATATTATAATTCATCGCG
GCAATTGTTTCTCTTATAAAAATCAAACGCGATCATTTTAAATGTTGTAAACAGAGCAGA
TGCCTTTGTAAATATGCATCATCTTGTACCGAGAATCCAGCAGAATTTTCCATGAGACTT
TCGTTCACGTAAAAGTTAAATTATTTTCGGAGGTTATTTGCGCACGGCGCGGTGTTGGAA
CTTTTCGCTAATCCGACTGTTTGTTTCCGCCTAAATTAATCACAAGTAACAGTTGCGATA
AAACAAGGAAACGACTGGATCTCCCGCTGTTATAGGATGCCACCTCGCACGTCAAACCCC
ACACATACCGTAACTTTTACCTAAATAATGGAAATGCAATTATTTAATTACCTGTGGAAG
AATCCGGACTAAGCCGAGATTGCCTAATATAGTTAGACAAGGTCCGGTCACTCGGGCTAA
ACATTCAAACAGGTGGTGCCTAAAATAGATGCGAGCTGGTACCAAGTGTTTTGCTCGCAC
CGTTCCTCCCATGGGTGACTGGCTGGCTTTAAGGATGGAACGCTACCGATATAAGTTTGA
CGTAATCTCGGTCTGGATGAAAGCGTTGACAGCACTACCTGTTTGCACACTCGGCACAAC
TGCTGCTTATGGAAGTGAACTGCGGTTTCCCGATATGGAAACCGTATGGCTCAATAACAA
ATTATTTACGGCCCTCAGGACAGCCCGCCATGCAGTCTGCACCATATTTTTAATCCTGGC
TTTTGCCAAGACCAAATATTACAAAGTTAAATCTTCTTTAGGCGAATCTACCCGTCCTTG
CACTTTGAGTGGAGATGACAGTTTTTACTGCAGCGGCGAATCAACAAATTCGACGTCATC
TCCCACGTCATCCATTACGTCATCGCGTTCATGTGGACCTGACAGCGACGAAGGTTTTCC
GAGACAGGATGACCTGGATTTGCGTGACAAAGCCAGCAAAAACTTGCAACATAGCGTTGA
GCTTTTTTGCCCTATTAAGAGCAAGTCAGTTGATCATGATAACGATTTAATGCCTATGGA
TCTCTCGTGCAAAAAGAGAACTTTCCCAAAACAAAATTGCAAAACTGCTAGCATGCCTAA
AACGAGCCCAACCATAAAATCAGAACCGATTGATGACTATCCAGCTTCACTTACACGCAA

Reference(s)

Erives et al. (1998). Lineage-specific regulation of the Ciona snail gene in the embryonic mesoderm and neuroectoderm. Dev. Biol. 194(2):213-25

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