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CIS-REGULATION

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  1. Transcript 'KH2012:KH.C1.920.v2....' > 
  2. Transcript 'Phfumi.CG.MTP2014.S1...' > 
  3. Clone 'cima821622' > 
  4. Region 'REG00000054'

Cis-regulatory Region

Name

Ci-Sna -2200/codon 15

Short name

n/a

Region ID

REG00000054

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Albert Erives (2006-10-01)

Annotator

Patrick Lemaire (2007-11-06)

Curator

Delphine Dauga (2011-11-14)

View position in WashU

Description

The sequence below extends from 2,2Kb upstream the start of cDNA AF002987 to 1,3 kb downstream (corresponding to the middle of exon 2). It has the same activity as the parental ci-Sna -3.2kb to Codon 15 region.

This region was named -2200bp 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

CONS00000039: pCi-Sna -2200/codon 15::NLS-LacZ

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

5,677,0835,680,582

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 bHLH n/a CAACTG [5,678,683 / 5,678,688]
2 T-Box n/a GATCCCACCT [5,678,737 / 5,678,746]
3 bHLH n/a CAACTG [5,678,786 / 5,678,791]
4 T-Box n/a TTTGGCACCT [5,678,873 / 5,678,882]
5 bHLH n/a CACCTG [5,678,929 / 5,678,934]
6 bHLH n/a CATATG [5,678,951 / 5,678,956]
7 bHLH n/a CATTTG [5,679,045 / 5,679,050]
8 bHLH n/a CAAATG [5,679,075 / 5,679,080]

Sequence

Aniseed Coordinates: [5,677,083 / 5,680,582] on scaffold KhC3

This sequence is the JGI v1.0 assembly version of this region. Note that the E5 sequence is absent from JGI assembly.

Show sequence

Length: 3,500


CCTTAGTTGGCTTAGTACACCGATAGCAGACCGCCCCTCCACGAAATACAGACACTCTGT
TTGTCACCAGTGTTCTATCAACTGTCTCGTTTAGCTACGGTGTACACATGCTTCTACATA
CGTTCCGCGGGTGTCTATTGTTGCCCTTGTCCTTACAGTGCGTCTAGAGTAAACTAACCA
AGATACGATTGCGTATACCGGGACAATAGGATAACATTTGCACGGAGACACGTGGTCAAC
TATACGAGGCACGTAACCGCAGGGCACTACCAAAGTCCGGTTATTTAAGTTTATATTTTT
GCCTAGCCGTCGAAAAAACATGCATATATTAAAATTAATAAAACCGTTTATTCTCTATAT
CGTACATTGGTTATGAGCGCTTTAGCACCAAAATATAACGAGTTCTATAAACGCAGTTAA
ATTCAATTGATTTTACCTTACCAGCAGGCAGTTTCTCTCCACAAACATTTAAGCCTCATT
CCTAACGTGCGGGAATTCTCCTCATCCGATAGAAACATATTAGTGTACGGACACTTCTCC
ATTCTTTGACAATGTGGTGACAGGGGAATATCATTTACGACAGTGCGAAGCGTCTCCTTT
ACCGAATAAACCTCATGATTCTAACATTAAAGTCGTTGCAATAGGTACGGATATTCTAAA
ATTGAAACTATGCACAATCACGGGTATACCATATATATATATAGTAGGGTGGGAAAAATA
GGACACCATTTTATTCTATTTTCTCGTCCCATTTTGTAGAAAACAAGGAACATTTAAAGA
ATTATAAAACCGTATCCGTACGACTACCATAGACCGTTGTAAATTGTTTAAACACGATCA
AGATATTTGGATATTATGTGCTAACGGTGTCTCATCTACCCCCACCCTATTATAACACCG
AACGTTAAAAATTCATTGCACCGAATGTTCCACCGTTTTAGTGTATTAGCGGATTCAGAA
TGTCGCACGCGTTCAAAGCGACCCAGTACCTATTGGTGTCAATTAACACCATTTTGGATC
GAATTTTCGGATGAGCCTTTGTGTGAAAATTAGCGGTTCACTCTGCCGGCCATCCTCAGG
TTGAGATAACGCATCTATCGCAAAGTAGCAGCTGAAGTGAAGACTTGCGATCGGAGAGAA
TTTAATTTCGATATTTTTATTTGCATTGATTTACAAAAATATTTATACAGTTTTTGATTT
TGAAAACAATAGAGTAGGGTGGGGGAAAATGGGATACCCTTTCATTCTATTTCCTTGTTC
CATTTAGTAGTAAACAAAGACCTTTTCAGAGAATTATAAAACCGTATTCTCACGACTCCC
ACAGCCCTTTGTTAATTATTTAAAACATGATTAGAATATTTAAATATAATGTCCCAAAGA
TGCCCCATCTTCCGCCACAGTACTATACTTGAAAAATATATTGTTCTGCCCCTGAAATAG
GAACTTTAGGGGGAGATTTTTCTTACGCACATGATAAATTAATATGTTGTTACCGATAAA
TTGTAGATACTTAAAATGAAAAGGTCGCAATTGTATTTACCATTATAAAACAGAAGATCG
GTGTGTTTTGCTGGACAAATATTGAGAAAATCTGTGGCGACAACTGTGGTCTGATTTACA
GGCGAGTTGGACGGAGTTGACAGGTCGCGAAAGCGATCCCACCTTCGTGTCTGGGTTTCG
AGGTGCCGCCCGTCGTGCAGTAGCAACTGTGCGGTCAAGTTGAGAGCAAGAAGACACTAC
AGCGCGCTTTGAAGCGTCCAAGCCGCCCGCTGAGCAGGGCGGATAGCTCGTTTGGCACCT
CGTCTGGCATCGTCCGCACTGTCAACCTTCTTCGTACAAACGTCCTCACCTGCCGCGCAG
GATTGCTTCATATGGCAGACCGAGTTGAGTGGGAAATCATATTCTGGTTGCTTCGCTTAT
AGAGCTAGCTCACTAGAGACTAGAGTGTTGTGAATGATGAATCATTTGAATTAAGCATTT
TGTTTAGTTGATCAAATGAGTTTCAGTTTGATGTTCAGGACTGCTAAGTAATGCAGTGAA
AGGAATTCTAAAGTGATTATATTTAGAAATGGGCTATCAGTGCTTGATTACTGTTGCAGG
GTTATTTAAAAATGCAGTCGAACAGTCTAAGAAAGCTTAGCTATATTTGAAGGATTATGT
ATACTTATTTCATTAGAGCAATATTTTTTTTTTTATTTTAGACTTTTGGTACATATTCAA
AATATCAAAATTCTCACTGTGAAATATATTACTGTGATTACATCATGACCTCCGTCGAGC
CCATGCTTTATCAAGGCAAGCACGCCGTTCAGAAAAATGAAGGTATATATGCAGTCCTAT
TTATATTATAATTCATCGCGGCAATTGTTTCTCTTATAAAAATCAAACGCGATCATTTTA
AATGTTGTAAACAGAGCAGATGCCTTTGTAAATATGCATCATCTTGTACCGAGAATCCAG
CAGAATTTTCCATGAGACTTTCGTTCACGTAAAAGTTAAATTATTTTCGGAGGTTATTTG
CGCACGGCGCGGTGTTGGAACTTTTCGCTAATCCGACTGTTTGTTTCCGCCTAAATTAAT
CACAAGTAACAGTTGCGATAAAACAAGGAAACGACTGGATCTCCCGCTGTTATAGGATGC
CACCTCGCACGTCAAACCCCACACATACCGTAACTTTTACCTAAATAATGGAAATGCAAT
TATTTAATTACCTGTGGAAGAATCCGGACTAAGCCGAGATTGCCTAATATAGTTAGACAA
GGTCCGGTCACTCGGGCTAAACATTCAAACAGGTGGTGCCTAAAATAGATGCGAGCTGGT
ACCAAGTGTTTTGCTCGCACCGTTCCTCCCATGGGTGACTGGCTGGCTTTAAGGATGGAA
CGCTACCGATATAAGTTTGACGTAATCTCGGTCTGGATGAAAGCGTTGACAGCACTACCT
GTTTGCACACTCGGCACAACTGCTGCTTATGGAAGTGAACTGCGGTTTCCCGATATGGAA
ACCGTATGGCTCAATAACAAATTATTTACGGCCCTCAGGACAGCCCGCCATGCAGTCTGC
ACCATATTTTTAATCCTGGCTTTTGCCAAGACCAAATATTACAAAGTTAAATCTTCTTTA
GGCGAATCTACCCGTCCTTGCACTTTGAGTGGAGATGACAGTTTTTACTGCAGCGGCGAA
TCAACAAATTCGACGTCATCTCCCACGTCATCCATTACGTCATCGCGTTCATGTGGACCT
GACAGCGACGAAGGTTTTCCGAGACAGGATGACCTGGATTTGCGTGACAAAGCCAGCAAA
AACTTGCAACATAGCGTTGAGCTTTTTTGCCCTATTAAGAGCAAGTCAGTTGATCATGAT
AACGATTTAATGCCTATGGATCTCTCGTGCAAAAAGAGAACTTTCCCAAAACAAAATTGC
AAAACTGCTAGCATGCCTAAAACGAGCCCAACCATAAAATCAGAACCGATTGATGACTAT
CCAGCTTCACTTACACGCAA

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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