Aniseed - Cis-regulation

Cis-regulatory Region

Name

Ci-Rora -4493/-421

Short name

n/a

Region ID

REG00000441

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Hélène Auger (2009-04-07)

Annotator

Clara Degos (2009-04-07)

Curator

Delphine Dauga (2010-02-26)

View position in WashU

Description

Transcription start site is based on the start of the first exon of the KH transcript model. Construct used to test this sequence is named AL in the paper. This construct recapitulates the endogenous expression of Ci-Rora.

Hierarchy of Regulatory Regions

Ci-Rora -4493/-421 REG00000441 [ regulatory_region (extended_promoter) ]
- Ci-Rora -678/-421 REG00000442 [ regulatory_region (extended_promoter) ]
  - Ci-Rora -658/-539 REG00000443 [ regulatory_region (extended_promoter) ]
    - Ci-Rora -658/-539 Fox mutated REG00000638 [ regulatory_region (extended_promoter) ]
  - Ci-Rora -545/-423 REG00000444 [ regulatory_region (RNApol_II_core_promoter) ]

Regulated gene(s)

KH2012:KH.C8.101 (MUSK; ROR1; ROR2)

Construct(s) made to test this region

CONS00000421: pCi-Rora -4493/-421::EGFP

Show in situ data

Overview of functional TF binding sites in this region

2,731,7632,735,834

	Motif Name	Binding Factor(s)	Sequence	Position in Region
1	Fox	n/a	tgttt	[2,731,887 / 2,731,891]
2	Fox	n/a	tgttt	[2,731,934 / 2,731,938]
3	Fox	n/a	tgttt	[2,731,949 / 2,731,953]
4	Fox	n/a	aaaca	[2,731,972 / 2,731,976]
5	Fox	n/a	tgttt	[2,731,991 / 2,731,995]

Sequence

Aniseed Coordinates: [2,731,763 / 2,735,834] on scaffold KhC8

Sequence from JGI Version 1 thanks to coordinates and primers found in the paper.

Show sequence

Length: 4,072

CAATAATTCGAATATACACACCCGCTAGGTGGCAGTCAGTAGCAAAACGGCACATCACAC
TGTTCGGTGCTTCAAATAGTCTAACATCCCCCGTTGAGCTTTTGATTGAGCTGTTTCGTA
CACAATCGGGACTTTAAGGGGGTTGGGCTTAATACTTACCCAGACAAGTTAAAATTGTTA
AAAAATCTGCTTAGATCCTTATACAAGTCTGTAATAACACCGGTTATCCTGCTGTTCCAT
ATGGCTGAGGCAGGCAAGTGGGCTTGGAATTTGAATGTGACTCTGCCCATTGCCTAACTC
GTTATTTTATCGTTACATCACGTTGCAAAATTCTGCTGATCCACCAATTTAACTTGGTAC
ATTCCGAAAAACAAATAAGGCTTAAAACTTTGCTATGTTTCTACTTATCCTCATATTCAT
CTCTAGATGAGGCATCTATAGGTATAAGTGCGTTTCAACACTTAAAATATTTCGACAGAT
ACTCCGACCTGCTGTTGTTTTTTCGTAGACCTGTTGAGAAAATTGTTATTTCAGTACCGC
CTGTTGTTTTTGTTCTGTTTGTACAAGACACAAAATTTATCACTTCTACCCGTGCCAAGG
TTTAATTAGTGTACACTGAAGTAGGATTCTGAGTAATTTGCGTTGTAAGTCAAAAACAGA
GCATTTAGCAAAGCAGCTGCTTCCACTTTCGTCGGTGCTTTACTTTCAAAAACCGTGACC
ATGTACCAGAGGGGACACGCCCGTTAGTCAACCTTGATTCGACACTTAGTCGGCCAGGTT
TAGCTTCTGCTACAACGGATAACAAAGAACATTTTACTGGCACTAAATGTGAGGCCCACT
TACAATCTTCTGAAGCAGTTTACACCTGTTGTACTTGTATGCTTTTAGATTTATTTGGTG
GCAAAGGCCATATCTTGCAATATCGTGCATTATGAATAAACATATACAGTAAGGTGGGAT
AAGTGGGACATCTTATCATTATATTTTCCCGTTCCATTTGGTAGTAACCAAAGAACATTC
AAAGAATTATAAAACCGTATCCCCACGACTTCTATAGACCGTCGTTAATTAAAACCAATA
AAGATATTTGAATATTATGTGCTAAAGTTGTCCCGCCTTTCCCCACTTTACCATATATAA
GCAAATGGTTTACAAAAAATCGTGCAACAAATATAAATTGGTTTACAAAAATATGTTCTT
GCTCTCATTACGCTGTATAGTGTATAGGGTCTGTAGTGTAGAAGCAGCATCAAACAGATT
GGTTTAACCTCTTTGGGCAGCAAGACGGAAAAGAGCATGCTTGTGTATACACGAGATAGC
TGAGTATATATTGCATACTCTGCATATTTCCCAGGACTTTGTGACAAATACAGCACTTTT
AAAGCAACCACAATATTGGATTGAGGTGTGAACGTCACTAATGGTTTGTTACGTCACGGA
TCTGAGTTTAAAAATCAACAACATTTCATTTACAACGTCGTAGTATGTTTGGTAATGGGA
AAATACAATTTCACACGCTCGCATACCATAACTTTTAAAGGTTTGTAAAAGTTCTAACCG
CTAGCCACCATTTTTGCTTGCATTTAAAACAAACTGTACTGTTAAATGCAACATATATAC
TAATGAAAATAATCTGACACATTTGCCCTGGATTCGAACCCAATACCTCTAGGACTACCT
CCCTCTATATTTTTTTTAATTAATAACATAAATTACTTCGTAACGAATCGCATTCGAGTG
ATTTCCGTTTTTTTTTATTAAAAATCGTTTGCATTTTTGGTCTCTTGTACAAAAACATTC
CTTGTTGCCATGATTACAAATGTTCCCGGTTGTGCACTCCTAACAATAAATGCTTTTATA
AGATTGTTATGTCTCATTTTAGCGGTCTGTACTTTCGAGGTAACTCCCACTTTAATTTGC
GATCTAAAGAGATTAAATTAACCCTGTAACGAAGTTACTGTAATTTATCTTTATTGGGTA
ACTTAAAATGATAAATGTTTTGTTGTTTTAAGGTTAATTGTGCATTTCCCCAGCTGTGGT
GTTCGAGAATTTATAGTTTCAGCTTTGATCCTGTAGAAAATCAGCAAAACATCTAGTTTT
AGCTCCACCGTTCACTTTGTCAGCTTGATTTTGGTCTGCAGCAAATCAAACAAATTCTCT
CCTTGCCTCATTGGCAGAATTTAAAGACTCGACTGTTAAGCCTAACAAAGGGTCTCACGA
AAACAAGGGGTCCCATGTTAACAAAACTTTCATGTTTAGTCTTGAGTGAAAATCAAGTAT
TTTTGTTATGCAGAAACTAAAGCTGGTTTTAAAACTCTGCTTAATAAATTTACTTTTTAA
TGATTTTGTTTATAAGCTATCCTTGTCCACAGTTGAATAAACTAGTTTAAATTTAAATTA
CTAAAAAACATTCAAAAGATAAAGTTGTAAACGGACTCGGACTCGAACCGATATACTTCC
CGAACCACACACATTCAAAAGATAAAGTTGTAAACGGACTCGGACTGGACTCGAACCGAT
ATACCTCCCGAACCACACGTTTCGCCAGCATGGTTATAACACGAGCTGTATATATCACTC
TCATTATCTGAGAGATTTATATGACTGTTGTGGGCCATAAGTCTGCTTTTAATGGCCGGT
TGACTTATGATGGCATAAATGTTGTAAAGCCTCTGTGGTATAAACTTAACGATGTAATTT
GTTTCGCATCTTACACGTCGTTATTAATAATCGTGCGGTTACACTTCATAGGAGGCAGTT
TCGAAGTGAAACGCGAGGGTGCGAAAACTGTTTTCATTATATTTTTGTTTGTGTACAAAG
CATATGGAAAATGTCTTTAATAAAATAACTTGTAACTTTCTATAGGTGCGTATGGTACAA
CAAAAGTCGTAAAATATGCTGTAGGTATATATTAAAAAATATGCAATTAATTTATCGTTT
TCGTGCTAACTTCAACAAAATATTTGCTTAAAAATTGCATTATTCGCTCATATAACAGTT
GTTCGTCACAATCTACATGTTAAGTTCCGGAAGTTCTAATGTCACTGAATAAACATCATT
ATGACGTCACAATCGCTAAAAATGATCGATTCTCACTATCGCGTGTCTATCTTGGGTGTA
TTTGGTCATTGCATGTCTAATAATCTGTTTTATCACGTCACTGACGTATTCTAATGACAT
AATCTGTGTTTAGCGAACGCTATGCTTGCAATCCAGAACCATGTGAAACGCAAACAGTGT
CTTGGTTTAAAGTATTTGTTGCATAACAATTGCTATTGTTTCATTGGACACGGATCAGTG
GTTTTGGCGGGTGTCAGTTTTTAAGACTTGGGTCTTAATTCGCCAGTGACTTTGGTGGTC
GAATCAAATATTTCCGAAGGAAAAAACGTTGAGATGCCTGCATGGCTGGGATATGCTCTC
TTTCCTCGTTCGAAAACGAAAAAATAGTAAAAATAGAAAAATGCGTTTTTTCGGCAGTTT
CAGCTTTAAAATTTTTATAATGCGTCTCAATTAAAAATAATTTCGCGTATATTTATTCAG
CAATAGCATTTTTTACCTAAATTGTTCATTTGTGATGCGATGGAGCCATTGCACCTGGGA
AAATGCGCCTTCTAAAATAGACTAAAGAGCGTGTCATAGGATTAGCATAGCACAAATATG
AACGTATACGCAACGTGTCCTAAGTACCAGGTATGCACTAATCTTCTGGAAATTTGTCTG
TCGTTGTCGAGCTATTAATTTGCTGGTAGAAGACAAAACAATGCAGCCAACAAGGAACGA
CAATCGTAATCGATGCATTTAACGGTAGCTTGTACAACGAACGACGTAACAATGCACGTT
GTTTGCTCAGAAGAGCCGAAACAAGCATTACGGTGTCGTCGTGTTTGCATTTGGCGTGTT
TAATTGATAGCGCCATTCGCGAGTCTAAAGACGCGAAAGATAATGTTTTGCTTGCTGATG
AGAGCGCCGCGATACCCGCCCGCCCTTTATTGACGTTCTGGAACGCGGTCGCTTCGGGTA
GAAGATTGTGACGTAATAAAGCGCAGCGTGCTATCGCTCGACCATCACTCGT

Reference(s)

Auger et al. (2009). Similar regulatory logic in Ciona intestinalis for two Wnt pathway modulators, ROR and SFRP-1/5. Dev. Biol. 329(2):364-73