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CIS-REGULATION

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  1. Region 'REG00000146' > 
  2. Clone 'citb4g19' > 
  3. Region 'REG00000143' > 
  4. Region 'REG00000154' > 
  5. Region 'REG00000142'

Cis-regulatory Region

Name

Ci-RAR -4008/281

Short name

n/a

Region ID

REG00000142

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Fujiwara team (2007-01-19)

Annotator

Daniel Sobral (2007-05-21)

Curator

Delphine Dauga (2010-06-23)

View position in WashU

Description

Be careful, coordinates in the paper may differ from ANISEED coordinates (coordinates in the paper: -4037). We took the KH transcript model as reference.


Hierarchy of Regulatory Regions

Modification of Ci-RAR -4038/312 by deletion

Regulated gene(s)

KH2012:KH.C9.580 (RARA; RARB; RARG)

Construct(s) made to test this region

CONS00000134: pRAR -4008/281::LacZ

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

3,688,5093,692,797

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 bHLH n/a CACGTG [-252 / -247]
2 bHLH n/a CAACTG [-225 / -220]

Sequence

Aniseed Coordinates: [3,688,509 / 3,692,797] on scaffold KhC9

Sequence obtained using the primers described in Fujiwara (2005) with Ciona JGI V1.0. ANISEED coordinates may differ from the coordinates defined in the publication because of polymorphisms.

Show sequence

Length: 4,289


CGCCCAGCAATAAGTGACGTTCGTATTAATGCTGGCAAGGATAGGGATAGCAAGTTCACT
GTTTGTTGTTGCTTTCTTTGCTCGCTGGTGTGCCACTCGTGAGCAAAATGCCAAGTCCGT
GCTGGGCATTAAGCGGATTAGGATAAACAATTGTCTGCGATAAGGCGTATTTACCGCACG
CTATGTACACCCAGCATGCCGATCGTTGCTGATGCAAGCTGAGCATGCGGTATCACCATG
TAAGCGCTGTAAAGCAAGGGTTCACCGAAGGGTCACACCTGGTTCATCGAAAGGTCACGC
ACATGTGCAAACATTGGCGCCAGCATGCGGCTATACGTCACAGTACACATTCACTAGTAT
CTTTCACCAGTACACTTTACTTTTAGCAGTTTTTCGGTTAGAAAATAACTGTAAATTAAA
TTTAAGTTATTTTTCCATGATCCGCTGTATCTATTTCATCAGTTTATTTCAGCCTATTAT
TCCCTGTATACAGTTTCAATGTTATCTCCAATTTGCGGTCCAGTCTCTGCTGGTGTAGTA
TTTTCTCCGAGGCCCTGTGGTCTCATAAATTAGCCATGCTATTTATATGTGCGATCGTGT
TCGTATATCCCATCTCAATCATTCGTTCTTGTCGCCCCATCCGGTATTTCAGTTCGCTTG
TCCTACCCTTCATGTAATTCCTATACGAAACACCACAAATCCCCAACATACTAAATCTGC
ATGGCACAAACAATCCACGTAAAACATCAACAAAAGAACGGTGAGAAACGTTCTGTCTTT
ATTTATCTTGCCCGAGCGGTTAGCTTATCTTGTTTCACCAGTGCGTTGGGACGATTAAAC
GTGGGAATATTCAAGTTATCACGACTGCTGATACACTCCTTTTGTACCAAGGCCTATATT
GCACAGACAAAGATTCATAATTTCATATCGATGCCGCCTATAGTAGTTAACGTAGGTTTT
AACCAGTTCTTACTTCAAAGTTCAAAATAAGCCTTGTTCATTCCTTTTCTTTATCTATAC
CACTAAACTGAGATTGTGGTCACAAAATTGCAAGATATATCTGATAGATTGATACACTGG
GAAAGGATTAAATCACCCGCTAATAACGCGTCGTTCTTTGCTCTTTTACCAACAACGTAA
AGGTTATTACATTCCACGCGTTTTATCTATACACAAGCAATGCCATGTCGGTCAGGTTCA
ACTTTTCGGTTCACGCAGAGGTTACAACGAACGTTGAATGTTTCTACGAAACAACGAATG
TTATTTTTCCTAATTGTGGAAAACTTGTTCTTCTCTGCACGAGATATCTCGGATTCTTAG
AACAAAAACAACTTTATTATTTTGACTGTTCTGTGATTTTAATCAATTAATATTGCTTGA
AAGTTGTCAAAAAATCCGCTTGTTTATTTCCAAAGCATTGGCCATTACGTTGTAAAACAA
GAATCGACCATTTGTGTGTGTGTGATAACTTAACACGTCGTACACTGAACATGAAAGCAA
ATTAAATCTGATATAGCGGAAAGCCCACGAGACCAGTATGTATGATATAATTATATCGCT
GAAAATCCCATCCTATAATTTCAACTTAACATACCATTGCGATACACGGGAATCGAGTAA
TTATCTGACCTAACTTATGTAGGTTGTGGTATTGAGTAATGTTATTTAGTTCATGTTATC
TTGTTTTTCACCAAGAACAGACACCTAAGGTGGGAGTTAGCGATTGTTTGTGTGCGGTGG
TATTAGCGTTTCGTAAGATGCCCTGGAGACAAAAATCTTTTGTTTGTTTTTGTTGACGTG
GATCGTAAGTTGTGGGCCAAGCGTCTTGACCTTCTTCATAAGTATTATGTGTTGTTACCA
CCATAATACACTTCTTATCAGTTGTTTTTAAATCAAGAGATAAACTCCCAACGAAGTTCT
AACCACAGTGTATCTCAATGCACTTGATTGACTCGTCGCGGTAGATTGACACGTTTCTCT
TATAATAAGCATTATAATAGGATGGGGAAGACGGGACACCTTTAGCACAAAAAAAACAGC
GGTCTATGGATGTCGTAAGGATACTGTTTTACAACACTTTGAATGTTCTTTGTTTACTAC
TAAGTGGGGCGAGAAAATAAAATGCGAAGGTGTCCCATCTTTCCCCATCCTACTGTATGT
TGTAATTATCCGAAGCTCGAATGTAACCCAATATTAATAAATATCCATTTTTTATGACGT
CATTTTTAGCTATGAAAAACATTATGTACAACGTTTTTCAAATATTTCTGTATGTTGTGC
GAATTTTTTTTTTTTAAAGAGTACACGGTTAGCTAAAGCTGTAATGTATTATGATGTCAG
CAAGGGGGTATCTCGCGAAGTTTGTAATATTTGTTCAGCTGGACGGAGTGCTCATCATTC
AGCACTGTTTGTTATGTAATGCTAATGTACGGTTCCCCATAAACAGTCGCACATATTCAG
TTGACGTTACTACCGATTACTACGTAAAGCGACAAGATAATTATTTCTTTTTTGTGGAAT
GTGTTTGTTATTCTTGAAACGTGGAGTTCCTGGTATGCGATCTTGCGTGACTAAATGTTG
TAGGGCGTGACGGAGCAAAACGCTCAACAAACTTGTAATGGGTTTTTACACTCCGTACTT
TCAACCGTAAAGGCCATAATTTTTAATTAATTTTTGTGTGTTGACTTACATATGAGTAAT
TATTTTGTGTATTGGTGTACATGTGATGTCATAGTTCTGTTATTTTAATGGCACATCATT
GTTTTAGCACGTCTTAGTATGTAGCTGGAGGAAATTTGCGTTTTTGTTGCCTTTTTCGGT
TGGGACATTAGTGGTAGATTATTTATTGTTTAAAACCCTCATTAATTTCTGCTCGATAAA
TCGCCGCAAGCGTCAAGCTTTGCGATCTGGTAAACGTCCTTTTGTTTTGTAACAATTAAA
TTTTACCAGACAATGGTTTAGTTTTCAGACGAAGTAATTATCGAAAGAAGTACAGTTCGC
AATGGTTTTGTTGCATCGTTAAGAGTTAATTATATCAGTTGTTGAACATGGATGGTTAGA
CACGAGCTGTTTTGCAAACTCTCGCATACTGTTTGTGTTGCTGACATAGAAAGGCGACGT
TATTATAGCTGCTATGACCGACATTTTTACAGCGTTGTATCTTTTCTGTGTATTAATTGG
ACGTGTTATTTAAGCATAATACCCCGTTAGGTCGCTTAAGTTTAAATATGAATTAGCGCA
AGCATATATTAGTGATTAGTAAGGGCAGTGCATATTTATATCAAACAGTAGCTGCGTGAT
AGGCAGTTAAGTACGTGAAGCAGGCATGACAGTGCAAACAAGTCATATTGTGAGAGCTCT
CCTGCTCCTCATTAGAGAAAAAGGCAATTAGTTGGTGAGAGAAGTGAGAGAAAAGCAACG
TCACTTGTATTGGAGAAGTGCTGATGCTTGTTGGTCCGCGGTCACTGGTGAGGGAAGGCA
GAAGCTGCTATGTATTGTTTGGAAATTCGCTGCGCAGGAAATCGCTAATAAAAGCTTGAT
ATTTTCCACGATAGGACTTGCGATAAGGTTAAGCCATGGTAAACTGCAACGTGCGTTCTT
CCCACGTTACTACACTTATAGAGCGTTATGCGAGACGCCGAATTCGGTTGCTGCAATATA
GTAATGTTGCCACGTAGAAAGATTTTGTAGATACAAAAAGAGCTTTTAAATTTTGAGAGT
CTAGACAGTAAAGTGTCAAGCTATTGCATTTAGTGCCACGTGTTATTACTGTCAGGAATG
TAACAACTGCTTGCTAACAGGGGTCAACTGCGTGATAATCTTCTGTTGAGCTTGAAGAGA
GTATTCGTCACCTAATCACGTTTAAACTGTCGTCACTATAGCTGGTAGTTTATCACTGTA
GTTGCTTTTTTCCTGGTAAGCACTTCAGCTTAAAGAACAACATTGGCAGCCGCCCAAAAT
GTAACGTAACATCCGAAATGTCGTTTTAACGTTTTCATATCGTTGCAGTTTGTTCTAGTT
AATTAGTACAAAGCATTGAGCTTCCAGCAAGCAACTTGTTTTATTGTGGTGTCAGTATCA
GCGTGATAGCGTTGTTGAACTCTGCGTGAATACTATAGCATGATGAACGTTATGGAGTTT
CAAGAACAATGGAGAAACCGAATGAATGGAATCTTGAGCGACATGTTTCATCCTACATCT
ACAATATGCGATGCTATGACTGGCATGCCACGTTCGCATAATACAATGGCATCTATGATA
GATTCCCCGCCACCGTTACAGAATCTGAC

Reference(s)

Fujiwara et al. (2005). Promoter activity of the retinoic acid receptor gene in the Ciona intestinalis embryo. Dev. Dyn. 232(4):1124-30

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