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  1. Region 'REG00000141'

Cis-regulatory Region

Name

Ci-RAR -4038/312

Short name

n/a

Region ID

REG00000141

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Fujiwara team (2006-12-15)

Annotator

Daniel Sobral (2007-01-31)

Curator

Delphine Dauga (2010-06-23)

View position in WashU

Description

4350-bp-genomic DNA fragment containing the Ci-RAR promoter region, including putative transcription and translation initiation sites (Fujiwara, 2005).

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.


Hierarchy of Regulatory Regions

Modification of Ci-RAR -4739/312 by deletion

Regulated gene(s)

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

Construct(s) made to test this region
n/a
Overview of functional TF binding sites in this region

3,688,4783,692,827

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: [3,688,478 / 3,692,827] on scaffold KhC9

Sequence obtained using the primers as in Fujiwara (2005). ANISEED coordinates may differ from the coordinates defined in the publication because of polymorphisms.

Show sequence

Length: 4,350


CTGTCAACCAAGCCATCGTATAATTACATCCGCCCAGCAATAAGTGACGTTCGTATTAAT
GCTGGCAAGGATAGGGATAGCAAGTTCACTGTTTGTTGTTGCTTTCTTTGCTCGCTGGTG
TGCCACTCGTGAGCAAAATGCCAAGTCCGTGCTGGGCATTAAGCGGATTAGGATAAACAA
TTGTCTGCGATAAGGCGTATTTACCGCACGCTATGTACACCCAGCATGCCGATCGTTGCT
GATGCAAGCTGAGCATGCGGTATCACCATGTAAGCGCTGTAAAGCAAGGGTTCACCGAAG
GGTCACACCTGGTTCATCGAAAGGTCACGCACATGTGCAAACATTGGCGCCAGCATGCGG
CTATACGTCACAGTACACATTCACTAGTATCTTTCACCAGTACACTTTACTTTTAGCAGT
TTTTCGGTTAGAAAATAACTGTAAATTAAATTTAAGTTATTTTTCCATGATCCGCTGTAT
CTATTTCATCAGTTTATTTCAGCCTATTATTCCCTGTATACAGTTTCAATGTTATCTCCA
ATTTGCGGTCCAGTCTCTGCTGGTGTAGTATTTTCTCCGAGGCCCTGTGGTCTCATAAAT
TAGCCATGCTATTTATATGTGCGATCGTGTTCGTATATCCCATCTCAATCATTCGTTCTT
GTCGCCCCATCCGGTATTTCAGTTCGCTTGTCCTACCCTTCATGTAATTCCTATACGAAA
CACCACAAATCCCCAACATACTAAATCTGCATGGCACAAACAATCCACGTAAAACATCAA
CAAAAGAACGGTGAGAAACGTTCTGTCTTTATTTATCTTGCCCGAGCGGTTAGCTTATCT
TGTTTCACCAGTGCGTTGGGACGATTAAACGTGGGAATATTCAAGTTATCACGACTGCTG
ATACACTCCTTTTGTACCAAGGCCTATATTGCACAGACAAAGATTCATAATTTCATATCG
ATGCCGCCTATAGTAGTTAACGTAGGTTTTAACCAGTTCTTACTTCAAAGTTCAAAATAA
GCCTTGTTCATTCCTTTTCTTTATCTATACCACTAAACTGAGATTGTGGTCACAAAATTG
CAAGATATATCTGATAGATTGATACACTGGGAAAGGATTAAATCACCCGCTAATAACGCG
TCGTTCTTTGCTCTTTTACCAACAACGTAAAGGTTATTACATTCCACGCGTTTTATCTAT
ACACAAGCAATGCCATGTCGGTCAGGTTCAACTTTTCGGTTCACGCAGAGGTTACAACGA
ACGTTGAATGTTTCTACGAAACAACGAATGTTATTTTTCCTAATTGTGGAAAACTTGTTC
TTCTCTGCACGAGATATCTCGGATTCTTAGAACAAAAACAACTTTATTATTTTGACTGTT
CTGTGATTTTAATCAATTAATATTGCTTGAAAGTTGTCAAAAAATCCGCTTGTTTATTTC
CAAAGCATTGGCCATTACGTTGTAAAACAAGAATCGACCATTTGTGTGTGTGTGATAACT
TAACACGTCGTACACTGAACATGAAAGCAAATTAAATCTGATATAGCGGAAAGCCCACGA
GACCAGTATGTATGATATAATTATATCGCTGAAAATCCCATCCTATAATTTCAACTTAAC
ATACCATTGCGATACACGGGAATCGAGTAATTATCTGACCTAACTTATGTAGGTTGTGGT
ATTGAGTAATGTTATTTAGTTCATGTTATCTTGTTTTTCACCAAGAACAGACACCTAAGG
TGGGAGTTAGCGATTGTTTGTGTGCGGTGGTATTAGCGTTTCGTAAGATGCCCTGGAGAC
AAAAATCTTTTGTTTGTTTTTGTTGACGTGGATCGTAAGTTGTGGGCCAAGCGTCTTGAC
CTTCTTCATAAGTATTATGTGTTGTTACCACCATAATACACTTCTTATCAGTTGTTTTTA
AATCAAGAGATAAACTCCCAACGAAGTTCTAACCACAGTGTATCTCAATGCACTTGATTG
ACTCGTCGCGGTAGATTGACACGTTTCTCTTATAATAAGCATTATAATAGGATGGGGAAG
ACGGGACACCTTTAGCACAAAAAAAACAGCGGTCTATGGATGTCGTAAGGATACTGTTTT
ACAACACTTTGAATGTTCTTTGTTTACTACTAAGTGGGGCGAGAAAATAAAATGCGAAGG
TGTCCCATCTTTCCCCATCCTACTGTATGTTGTAATTATCCGAAGCTCGAATGTAACCCA
ATATTAATAAATATCCATTTTTTATGACGTCATTTTTAGCTATGAAAAACATTATGTACA
ACGTTTTTCAAATATTTCTGTATGTTGTGCGAATTTTTTTTTTTTAAAGAGTACACGGTT
AGCTAAAGCTGTAATGTATTATGATGTCAGCAAGGGGGTATCTCGCGAAGTTTGTAATAT
TTGTTCAGCTGGACGGAGTGCTCATCATTCAGCACTGTTTGTTATGTAATGCTAATGTAC
GGTTCCCCATAAACAGTCGCACATATTCAGTTGACGTTACTACCGATTACTACGTAAAGC
GACAAGATAATTATTTCTTTTTTGTGGAATGTGTTTGTTATTCTTGAAACGTGGAGTTCC
TGGTATGCGATCTTGCGTGACTAAATGTTGTAGGGCGTGACGGAGCAAAACGCTCAACAA
ACTTGTAATGGGTTTTTACACTCCGTACTTTCAACCGTAAAGGCCATAATTTTTAATTAA
TTTTTGTGTGTTGACTTACATATGAGTAATTATTTTGTGTATTGGTGTACATGTGATGTC
ATAGTTCTGTTATTTTAATGGCACATCATTGTTTTAGCACGTCTTAGTATGTAGCTGGAG
GAAATTTGCGTTTTTGTTGCCTTTTTCGGTTGGGACATTAGTGGTAGATTATTTATTGTT
TAAAACCCTCATTAATTTCTGCTCGATAAATCGCCGCAAGCGTCAAGCTTTGCGATCTGG
TAAACGTCCTTTTGTTTTGTAACAATTAAATTTTACCAGACAATGGTTTAGTTTTCAGAC
GAAGTAATTATCGAAAGAAGTACAGTTCGCAATGGTTTTGTTGCATCGTTAAGAGTTAAT
TATATCAGTTGTTGAACATGGATGGTTAGACACGAGCTGTTTTGCAAACTCTCGCATACT
GTTTGTGTTGCTGACATAGAAAGGCGACGTTATTATAGCTGCTATGACCGACATTTTTAC
AGCGTTGTATCTTTTCTGTGTATTAATTGGACGTGTTATTTAAGCATAATACCCCGTTAG
GTCGCTTAAGTTTAAATATGAATTAGCGCAAGCATATATTAGTGATTAGTAAGGGCAGTG
CATATTTATATCAAACAGTAGCTGCGTGATAGGCAGTTAAGTACGTGAAGCAGGCATGAC
AGTGCAAACAAGTCATATTGTGAGAGCTCTCCTGCTCCTCATTAGAGAAAAAGGCAATTA
GTTGGTGAGAGAAGTGAGAGAAAAGCAACGTCACTTGTATTGGAGAAGTGCTGATGCTTG
TTGGTCCGCGGTCACTGGTGAGGGAAGGCAGAAGCTGCTATGTATTGTTTGGAAATTCGC
TGCGCAGGAAATCGCTAATAAAAGCTTGATATTTTCCACGATAGGACTTGCGATAAGGTT
AAGCCATGGTAAACTGCAACGTGCGTTCTTCCCACGTTACTACACTTATAGAGCGTTATG
CGAGACGCCGAATTCGGTTGCTGCAATATAGTAATGTTGCCACGTAGAAAGATTTTGTAG
ATACAAAAAGAGCTTTTAAATTTTGAGAGTCTAGACAGTAAAGTGTCAAGCTATTGCATT
TAGTGCCACGTGTTATTACTGTCAGGAATGTAACAACTGCTTGCTAACAGGGGTCAACTG
CGTGATAATCTTCTGTTGAGCTTGAAGAGAGTATTCGTCACCTAATCACGTTTAAACTGT
CGTCACTATAGCTGGTAGTTTATCACTGTAGTTGCTTTTTTCCTGGTAAGCACTTCAGCT
TAAAGAACAACATTGGCAGCCGCCCAAAATGTAACGTAACATCCGAAATGTCGTTTTAAC
GTTTTCATATCGTTGCAGTTTGTTCTAGTTAATTAGTACAAAGCATTGAGCTTCCAGCAA
GCAACTTGTTTTATTGTGGTGTCAGTATCAGCGTGATAGCGTTGTTGAACTCTGCGTGAA
TACTATAGCATGATGAACGTTATGGAGTTTCAAGAACAATGGAGAAACCGAATGAATGGA
ATCTTGAGCGACATGTTTCATCCTACATCTACAATATGCGATGCTATGACTGGCATGCCA
CGTTCGCATAATACAATGGCATCTATGATAGATTCCCCGCCACCGTTACAGAATCTGACC
ATTCATTCGAATAACTATCCTCGGCAATAT

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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