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CIS-REGULATION

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  1. Transcript 'KH2012:KH.L153.32.v1...' > 
  2. Transcript 'KH2012:KH.L153.32.v2...' > 
  3. Transcript 'KH2012:KH.C5.12.v2.A...' > 
  4. Molecular Tool 'cieg43d06-MO (Hamada's MO)' > 
  5. Region 'REG00001100'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.C5:4201966-4206944

Short name

-4976/+3 (upstream region of KH.C5.12, cdc25)

Region ID

REG00001100

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Yosuke Ogura (2017-01-23)

Annotator

Marion Gueroult-Bellone (2017-01-23)

Curator

Delphine Dauga (2017-05-24)

View position in WashU

Description

This region is the largest one of the deletion analysis of the Ci-cdc25 upstream region. It contains the cis-regulatory modules CRM1 and CRM2 defined by Ogura&Sasakura, 2016.
Region called -4976 in the article.

Hierarchy of Regulatory Regions

Regulated gene(s)

KH2012:KH.C5.12 (CDC25A; CDC25B; CDC25C)

Construct(s) made to test this region

CONS00001068: pSP.Cirobu.REG.KH2012.C5:4201966-4206944:prCirobu.bpForkhead>Kaede

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

4,201,9664,206,944

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 ZnF_(GATA) n/a gata [4,203,954 / 4,203,958] This binding site is one of the two GATA binding sites of the CRM1 defined by Ogura et al., 2016. When both of them are mutated, this CRM is no longer able to drive expression in the epidermis.
2 ZnF_(GATA) n/a gata [4,203,975 / 4,203,979] This binding site is one of the two GATA binding sites of the CRM1 defined by Ogura et al., 2016. When both of them are mutated, this CRM is no longer able to drive expression in the epidermis.
3 SOX n/a ttcaacg [4,203,985 / 4,203,992] This binding site is one of the 3 Sox sites of the cis-regulatory module 2 of Cdc25 (KH.C5.12). When all of them are deleted, this CRM is no longer able to drive expression in the epidermis.
4 AP2/ERF n/a gtccacggc [4,204,012 / 4,204,021] This binding site is one of the two AP-2 sites of he cis-regulatory module 2 of Cdc25 (KH.C5.12). The mutation or deletion of one of them slighlty decrease the epidermal enhancer activity. When both of them are mutated or deleted, the epidermal activity of the enhancer is reduced by a half.
5 SOX n/a cattgtt [4,204,030 / 4,204,037] This binding site is one of the 3 Sox sites of the cis-regulatory module 2 of Cdc25 (KH.C5.12). When all of them are deleted, this CRM is no longer able to drive expression in the epidermis.
6 AP2/ERF n/a caggtgggc [4,204,053 / 4,204,062] This binding site is one of the two AP-2 sites of he cis-regulatory module 2 of Cdc25 (KH.C5.12). The mutation or deletion of one of them slighlty decrease the epidermal enhancer activity. When both of them are mutated or deleted, the epidermal activity of the enhancer is reduced by a half.
7 SOX n/a cattgtt [4,204,062 / 4,204,069] This binding site is one of the 3 Sox sites of the cis-regulatory module 2 of Cdc25 (KH.C5.12). When all of them are deleted, this CRM is no longer able to drive expression in the epidermis.

Sequence

Aniseed Coordinates: [4,201,966 / 4,206,944] on scaffold KhC5

5kpb region located upstream the start codon of cdc25 (KH5.12)

Show sequence

Length: 4,979


catattaaagacaggtgctgaagattgaccacaagtgtataacacccgctagcttacaac
agagtaagctctcaagataccgtatgtctaaaacgcaattagctacttcggatgtcaaat
aacctgaaattctgcaaaagaaaacagtttgcttactcgatcggcgaagatactctgcta
atccacgagatatcggcttatgacaaacgcccataagttacatcgccgatatgacccaat
tccatcggcaatacgaccactatgttattgcggtctttactaagtcataatccaacttta
taacgcttgcgtcgcagaacaactgttgcaataagctccaatggccacaccatatgttac
gctcgaggtataggaggccttttgagtatatacccgacattctaatactactcactcaat
ataatacacaatacaacgtatgtatgtatgctgcatggtactctcttaatcaacacaata
aaatgacatatccaaaaccccaataatactatagccagctaactagtatacgactcttag
attctagttattgtgcaatgaaccgtctagtatcgtcagttaaacaaccatgtaatagca
tagtctctttctctcagtgctcgaggagcattccactttagttttaacgcactacaaact
actatacatacgcaatttctttcagttaccaatacgctatagtcgctatataacgtggta
gcctcacgctacagttatgtgctttagatgtgaatacatccgcctgtcgatactggccac
ttgtcctatatacattggatacggcttatcggcacaaagtaaacaataacaatgcgtagt
atgtggtctgcaatgcgctgctctgggtatactggaacggtactacattgttgtacagta
atgataaagttttacgtagaccagtaactacctagaggtagctgaataggtgaatactgt
ttgactcttatgcttctgtctagtaatatataagagccgaagtctgtctcgctgcttaat
acgcgctcaaactgaaatcccaggcaagatgtctacgattaggaagttgagaaaaaaggc
ccaagagctatgagctaattcccttgcattgtccggtttggacgctaattgatattctga
aggcagctcatgtaaactggtttacgaagcatcttacaatccggccaagctgggacacag
cgtgcgagtgactacctttacctgtgacgcgattaccaagcgagagattaacctttttcc
tttggcggtgagtcgaaaaggaaacataccgctgggctctcgctcggtagcgagtttgct
gctggcaagtaaatcctacgaccaacaatactagcgcaccttggcccggctggatgcagt
caggatgtctcggttggctgtttgtacgctatgcgggcactatggatgcacgcaagtgga
ttaacgggtgggattcttgcttaatatatccgaagttgggaactagttacggattaggca
gcgagtcggttctaatttttatagaaaagtttgctccgcggagatatttacgagaagcac
cacatatatattgacgacgtatttttgcttactactactgtcctactaacgttgcacgaa
aaacacacaactagtcttcctttaactatgcaggcagaacatgagtgaatactagattag
ttttaattaacgaatcggtcactatcctgcactgttgcatattctccaattacatggaat
attgctaataatgcatgtataccgaatcgatctactaacaaattgaactcagctggttgt
gcgctgcatgtgcagttgaatgaatggtgccctgcatcgaaccgcagctgctattttaag
agtgctggtgcagtcgcctttttctcgctttactacaggttcagtgtgttttggtcgtcc
actgataagtagcgaaggccgaagcgtcgcggttcgggccccgaggcacgcactattcta
gcgtcatagataagagctggattcgttctgataggaccgttcaacgaattgcctctcctt
tcacctgtccacggctcaaaagtccattgttttcttctgtgacggcacaggtgggccatt
gttatacaggcattgtatatgctgaacagtaaaatacaagagcagaaccacggcgacaga
tttctgccacttaaagaaaacttgatatttttttaagactctcactgcagtaaaacatat
gtcgcccaactgccaacgccacctacttaacatcagcgctaaccaaagggcggtaagacc
gttacagcacgtcggaatctatacgcgtggctataagatatttcaaatatagccaactcg
cataaaaatatacttgcgtatatctcatggaaaatatttaaaccatgcgtttcaaataac
caaagaaacaaactcgacgtagctttacaaaatcgtagtaccgataaatcgtatataggc
ctataaaccaattatgatgtccaagcgggtcgttgttttccgctatatattatacacgac
tatataattatcaatataaaatattagcatgcttttaaaatcaaacaaaacttgacactt
tcaatttgtaagtgaaggtgttgctaaaagttggcacggatttagaatagcacactttgc
aactcggcaacgaaaagtacgagttttaacagctataggtaggaaactcgcaatgtttag
gtctctgtaaacatagaattgcaaacgtgacggaaagcgacgaaaaccgataactatttc
ctccgaatgtgcgacctgtttgcctcttgtgggccaacgtgttgtcggaatgcaaataca
caggtgtttattggtttactagcaaggttgcgcgatgtttgggcttggagtgtttatttg
aatgcgtatatcaggctaccggtcaagtgataaaatttgagcggtttttggaccgcggtt
gttggttgaattatagggaatgcattgaacggatagtgcggtaatcgattcgggtcatgg
taatttgtgttttgtgtgagaacctgccacgatttataggaccgacgcttttcgcaagtg
aacgacaacttaccggaaaattgaaaattgtttcgcttcgcggacgggttaaaataccat
gggagtatagattgctataattagtgtttctgggaattttaggaatcttatgggggcggg
cgtcgtgttcatggaacgccgacgatggtaatcctaaggtgtcgcgatgaggagccgcaa
aggagatcagaaagaacaaagccgcatctaagtgaatagctggcgctggacaatggacga
ctgggagtctagggcgacggataatcgcgaagatgagcggatagttcaaccaaagggttt
tggggaggcggtgtaatttgcgacggccacattgtctcctggatcgcactgcgtggctgt
aaaccagcgattaagtgaacgcgctcgggattacgaacccagctcgatgatcatgtatgt
gttttaacttcgcctgctgtcattgggatcgtgagtttttaacgttcggtgttgggatta
agttcgtggcctatttgacaataatacgcgattcccgtgccataatagtaaaagatcggg
ccaatctgttgaaaagaaattgaatctaaggcaaaaggattttgcttttttacgaacttt
gcgaaaaaaatcaaataacgcgagtgtcgaacccgagaaaagtcgttacgagaatttgag
cattttgaaacataatacaaaaataccaataacacattgctaactccaatatccgccaac
cggctggattatagtcattataccaacttttgtaaagccggtagtaccaattggtcatgc
tcacgagtggataatatcattaagaaggatgacgtggttttaaattatggcggacccaac
gtgctctatagcgacgacacgcggaaagacatttttacatagacgaggcatcaaaaatac
ctcaagttagtttttgagcgtttcttaaattcgtgattggtgaaatacatgcatatattc
tagtattatggaaatctaaaaaaaattcgaattgacaaaaaataacattctcattcatat
agaatagaatatatgtctaaaaatacaaacagcgtttcaaacatgtgcaacactgctgtt
cagttaccgtagttttagaaaagtattactatggataacgttctgcgaatgggcggtaga
atcttttctgattcttcgcaatatcttacgtaaacagggccgaactatacagataatctg
tgggtgtatgttcgttatctgggctgttgttccaacgaaactacggcgaacaatagacga
gcttcattaacgaaacaaaacagcgattacgacttattagcgttgtgcggccgataacga
caaaggcgatccgtggttgttcaatcaaatgttcataacatctgggtaaattagaagcgt
cccgacgaagtacaagtccgcctgcggtctgctaacttaattgacccggtgcaaggcgat
gattaaaagttggatggaactggttcgggtattgttaatttttttggaacgagatcggtt
ttaaggtgcgagacgttcgtggaatttagagttacaccagcactattgagaacgacagct
ggtcaaatgatctaaaagaacgacatctttaaaagtgattttcaaatacaaaagcagcca
actttttgggtctaactcacacatatacatattaacgttcgccaaaaaactcgccattta
cacgaaattttcccgtttttacgaacagcgattttgttacattaatcttaaataggactg
agacaacaacaaacacaaattagatcctaacagtttttgccacattagtgccgtctttca
acagtcttttaggcgcctatgttgttttttgggttcaaacaggtttgtgggaacagtgga
aatgggtcgtatatcagacccttcagaacacagtcttgtggagaattcgtgcacacttg

Reference(s)

Ogura et al. (2016). Developmental Control of Cell-Cycle Compensation Provides a Switch for Patterned Mitosis at the Onset of Chordate Neurulation. Dev. Cell 37(2):148-61

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