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CIS-REGULATION

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  1. Transcript 'KH2012:KH.C10.113.v5...' > 
  2. Clone 'cinc030a13' > 
  3. Region 'REG00000415' > 
  4. Region 'REG00000076'

Cis-regulatory Region

Name

Ci-msxb -3792/238

Short name

n/a

Region ID

REG00000076

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Monia Teresa Russo (2007-03-03)

Annotator

Jonathan Luchino (2007-07-17)

Curator

Delphine Dauga (2010-04-07)

View position in WashU

Description

A 3.8 kb region located upstream of the gene contains all the regulatory elements able to reproduce its spatial expression pattern. Analyzing progressively truncated fragments of this region; three discrete and separate regions driving LacZ reporter gene expression in the ventral epidermis, primordial pharynx and neural territories have been identified :


- Region - 2546 bp/- 818 bp : Drives the expression in the ventral epidermis


- Region -457 bp/ - 227 bp : Drives the expression in the pharynx


- Region - 227 bp/- 84 bp : Drives the expression in the visceral ganglion, the sensory vesicle, the otolith-ocellus precursor and in the neural tube.

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

Coordinates in the paper : -3804bp/227bp

Hierarchy of Regulatory Regions

Regulated gene(s)

KH2012:KH.C2.957 (DLX1; MSX1; MSX2)

Construct(s) made to test this region

CONS00000066: pMsxb -3792/238::LacZ

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

5,769,7215,773,750

Motif Name Binding Factor(s) Sequence Position in Region Comment

Sequence

Aniseed Coordinates: [5,769,721 / 5,773,750] on scaffold KhC2

This sequence was found using blast on JGI Version 1.0 with the sequence in the paper.

Show sequence

Length: 4,030

CCGAGCACACCCGCGACAGAAAGGCACTGGCATGCCTTAGCCACGTGACTTGTGCAATGT
GCCGTAGTCAGCGTGTTTCATTATTAGTTGTGTAGTTATGTAGTAATTAGTGTCGCTATG
TTGCAATTTAGTTCCCTTTATATACGTGTGTGCTCGCCTTAGTTTTCATTCTACAATTTG
GCGTCTCAATACAAACCCAAGAACACAACAGTAATGACAGACAAAACATTGGAAATAAAC
GCCTTTTCATACCAGAATAACCGTTGAAAGTTTATTCACATTATGCCTGGTAGCAGAAGT
AACAGAATCTTAATCTTTCTTCTACAACAGAGTGATGGCCGTGTTGGATCCTCTCAAGAT
CACCATCACCAACTTCCCAAGTGATGAGGGATCAATCGAGATCAAAGTTCCCAACTTCCC
TGCTGATGAATCGCGAGGACATCATTCATCCAACCTCACCAAGTCCTTATATATTGAAAG
AACAGATTTCATGGATGTAAGATTTTTATTTTCACAAGTGTTAAGATAAATTATATTTAT
TTCTTCATATATAATAGCAAAAATCAAATTAACCAAAACAAGAATAATTGAAAATAAACA
AATTATGACACACATTAAAATCTTTAAAAAAATATTTTCAACAGACATTTTTAATTTCAA
ATTTAATTTTCTGTACTTTTTCTTGCATTTTTCTTAGATTGCAGACAAAAACTACAAGAA
TTTTTTACTACAAGAAAAAATAAAAATTTTCTTGCATTTTTCTTAGATTGCAGACAAAAA
CTACAAGAGGTTCGCATCGAATCAGAGCGTCGGGTTACGTCATGCAGGTTTGGTTCTCAC
GCTTGACCGAGCAGTGAAAGGAGACAACGGTGACGTCACTGAGCTCATTGTGACGTGTAA
ATCGGTTGAAGAATCCCCGAAACCAAAAGCTTTTATCCACTGGGTGTCAGCAACGAGCAG
TCTGGCATGCGAGATTCGCGTGTACAGCAGATTGTAAGGAAAAATATATATTTTTTCATC
TGAATTTTAACACGTTTTTCATCACAGATTTAAGCACAAAAACCCGGAGGACCCAGCAGT
GGTTCCAGGCGGTTTTGTGACGGATTGCAACTCCAATACACTGACGGTTAACACTGCTGC
GAGGGTGGAAGCGTCGGTTAAAAATTCCAAAGTTTTCGACAAATTTCAGTTCGAGCGACT
TGGTTACTTCTGTGTGGATCCCGATACTAACGATAACAAGGTATATATATGTCACAACAC
TGTGCACTTATTCTTGGCGGCGATTGTGACGTAAGGGTACATCATTCTGACGTCACAATC
GCCGCTGTTCACGTGTTCACACAGCACAAACACTTTGTTTTTTTTACAGATTGTTTTTAA
CCGCACCATCCCACTGAAAGAGGACCCCGGTAAAAACTGAACTTCCGGTCGCGTATACGT
CATTTTGTGACGTAGTTATGACATCATCGTATGTAGCACAAACCAGAAGATATTTTTTGT
TTAGGGGAATTTTTGCGGTGACCTAATAAAATCTATGACATGTTATTTATTGTTTCTTTT
ATTATAACGTAACAAATTTCGTAATGACGTCACTTATCTAATGACGTCACACACTACGCA
TTGATGTCGCAATCTCCCCAAGTTTCCCACCACCTATATGAAAGCTACGAAGGCGGAAAG
ATTTCGGCATAATAACCTATTGTTGACGTCATAATCGACCGATAAATAAGCGGCGAAGAT
CGCGTCCTCTACAATAGGAGGTGGAACACTCATAAAAAATCACAGCGGTAAAGCCGCTAC
CACACGCTGCTAACATTTATTAAGGAGACATGCTACACTCGACGTCATAATGCGCGTGAC
GACTATATTGTGACGTCACAGAGAGATAAATAGGATATTTATTGCGCGGTAGAATAGAAC
GACGAGCAATAAAATGAAATGAATTTTGGAAATGGTAAATTAATTTATTTTATAAGTCGT
CTAAACTTTATCCATTTCCGTATAAAACACGACTTTTACCAACTGTTAATTTTTATTAAC
TTACCACATAAAGTAGTTTATTGGGCCGCTCTGAACGAATGGAAATCACCGTACTCTATT
AAGTTGATCGACCTTTTACATTTCAATATGTTAAAAATCGTACATTAAAAAAAGATATAG
TAGGATGGGGGGATGGGATACGTTTTCATTCTATTTTCTTGTCCAATTTGGTAGTAAAAA
AGGAACTTTCAAAGATTTATAAAACCGCATCCTTACGACTTTCATAGACGGATGGTAATT
GTTTAAAACACGAACAGTATATTAAGATAATATTTTCTAATGGCGTCCCGTCTTCCCCCG
CCCTACTATATTAAAAAGAGGCAATATGAACCAATACTTAAGATTTTAGTTGGTGCACAT
CAATTACTGTTTTTATAAGTCCATGCAGACCGATGTCCATTTACCAGTGATTAAACAGGG
CAATAAAATTACGAAGAATCGCCTTGCGTCGCTGCAAACATATTTATTAGGCATTAGCAA
GTGTGACGTAATAATGCCTCTTGTTCGACGTGACGGCGAGCGCTTGCTTTTGAAACACCG
CGACGTCGACGAAGACGGTGTCGTAACTTAACAATAGTCTGGGGCCTATGATGTCATAAT
GCCCATTTGGTGCACTCGCGTGCTGTCGCCCAAAATCGCAATTAACTCGATGACACTGGC
AGCATATGACGTCATAAAATGGTTGCCAGGGTCCCGGACCGAGACAGTAATTCACTTTTA
TGACCCGAATATCTAATGGGACCCATGATGTACACTTAGAAGCACGCAGCAACTGATTAT
TAATGTTGAGTGTGTTACGGATGACTGTTAATTTCACAAACAAACAAAAAAACAGAGTTC
GTTGGCCTTTAGATCACTATTAGAAACAACAGTAATTGGTGGGAACTTGTTTCGGAGCGA
GCCAAATAAAAAAGCTAAAACAAACATAACAGTAAAGCTTAATTAAAATAATAAGCGTTG
TTAATAAATATTAGCATATAGACCAAACACCAAATTGTGTGCAATCAGTTTTTGCATCTT
TAAAACTATTAATTTTTTATGTTCGCCGTGCGAATTTTTATTTGAATGATTCTATTAATA
AAGCCTGAAATCCTAGCAATCATTTTGAGCTTCCACATTTGATATTAAAATTCTCGTATT
TGTTGTTATTTATTAATGATTTTGAGTGACTTTTTTAGACTCAGTTTTTGTTTTGTTTTT
CAATTATTCAAGTTCGGATGTGTGGAGATACGGGATTAATACAATGAATGTTCAATTAAA
AACACAAAAGTTTTAATTTGAATTAATGTCGGCGCTGCAGACGAGCCGAGAGCTTGTCGG
ATTTAAAATGTAATCCTCCAATTTTGTCTGGCACTGACGGTGTAGATGCAATCTGAAAAT
GGCGACTGAGCAGGATCGGGTCGCGGCTGGAGCTCCGGCGGGCTCGGGACGCTCATAATT
CCGCCGGTAATCCCCGTAACGTCGATGAAAGCGAACGCGCCGACAAAAGTGACGAAGATT
AAGTGTAACAACATGGTTTAAACAAACAGACTGGAGCAGCGGAGACGAGAGAGAGAGGGA
ACGTAATCGCCGCGGCCGAAGCGTGACCAAGTCGTTGTATTGTTATAATAGAAAATCGTT
TTATTATGATTTAATGAACGCGCGCTGGCGACTGAAGGATGCTGTATAATTGGGGGTAAT
GGGGAAATATCGGGAGAAAAAATATGGCGATCTGCGGGAGAGGATAGTCGCTTACATAAT
CTCTGGAGTTTAGTTGAAGCAGTTCATATTGAGAGAAGCATCCCTCAGACGAGTAGTTCG
TAAATTTTAGAATATTGAAGAATAAATAAAATATTCAAGAAATTTTTAAGAAAATTGAAA
AGAGTTTAAATTAAAAATGACAGGTAAGAAAATATTTGTATAAATTTTTTTCAGACACTT
ATGGTAAATAATATTACTCAGATAATGTAACCTGTGGTTTAAGATTAGTTTTTTAACATC
TTTGCGTTGC

Reference(s)

Abitua et al. (2012). Identification of a rudimentary neural crest in a non-vertebrate chordate. Nature 492(7427):104-7

Russo et al. (2004). Regulatory elements controlling Ci-msxb tissue-specific expression during Ciona intestinalis embryonic development. Dev. Biol. 267(2):517-28

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