Aniseed - Cis-regulation

Cis-regulatory Region

Name

Ci-tensin 4620/6022

Short name

n/a

Region ID

REG00000838

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Hiroki Takahashi (2010-07-07)

Annotator

Clara Degos (2010-07-07)

Curator

Delphine Dauga (2010-07-26)

View position in WashU

Description

Region of Ci-tensin from +4620 to +6022bp. This region drives notochord expression.

The corresponding construct is named p(-1.5k)tensin/lacZ in the paper.

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

Hierarchy of Regulatory Regions

Modification of Ci-tensin 3974/6022 by deletion

Ci-tensin 2942/6022 REG00000835 [ regulatory_region (extended_promoter) ]
- Ci-tensin 3545/6022 REG00000836 [ regulatory_region (extended_promoter) ]
  - Ci-tensin 3974/6022 REG00000837 [ regulatory_region (extended_promoter) ]
    - Ci-tensin 4620/6022 REG00000838 [ regulatory_region (extended_promoter) ]
      - Ci-tensin 5581/6022 REG00000839 [ regulatory_region (extended_promoter) ]

Regulated gene(s)

KH2012:KH.C9.28 (TNS1; TNS2; TNS3)

Construct(s) made to test this region

CONS00000801: pCi-tensin 4620/6022::LacZ

Show in situ data

Overview of functional TF binding sites in this region

4,280,3614,281,762

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

Sequence

Aniseed Coordinates: [4,280,361 / 4,281,762] on scaffold KhC9

Show sequence

Length: 1,402

GCATGCGCACTAATCGTATTATGACGATATGGCGGTATTCCTTTCACGGTAATTGAATTG
GAAAATGAATAACTCGGTATGACCAATGCTTGTAAAGTTGCGATTATAGCGCGCAACGGT
CAGCGATAGTCGAGTAATGTTTGCCTAAGATTTTCACTTCGGTGTGTTTTCTAGTTTACT
GGGAAATGCGAAGTTACGAGGACAGCATTCGAGTGACTTTGTTTACTCTGGAAATCTGTT
GTTTGCTTCGCAACTATTCAGCTTGCTCGACCGCTTGTTCAAGGCAGAGATTGGCTCGCT
AATTAATGTTTACCCGCCTGGGCGATGCCTGCCTTTCTCGGGCCGACGGATGGCGTATGA
GTGCGAATCGGCGATTGAAGATCACCGGCCGTCATGTAGGAGTCCAGATCGCCCGCAGAA
GTTCGGTCGCAGGTTCGGCTGTAGGTCAGCGTCGCTGGCGGGTTTACGACCTAGTGTAAA
AGCGGTGCATACGGTCTCGTTGGCCGGACGACTGTAAAACCGCAGCAGTTTAATAAGTTA
CTACTATACTGGCGTCGTATTGCAAGGTTTCCGTCTCTGCGGTTTCAAGGCGAAGAATAA
TGCGGGTTTTAGTGTACCCATAGACAGTAAGATCAATTTTGCGGGGTTATAACTGTTTAC
ATAAGCAGGGCAGGATAGGAAAGTAATTTAATCAATCGCTTAAAAAAAGCAATGCAAAAG
AATTTACCAACTATTCGTTTGCTTGGATTAGCTGGTTATTTATTACTTTCTATACGGGCA
GCGTATGCGAGAAACGATGTTGTCTATCAGTGGAAATGCCGGGGAGCCGCGCATGAGGTC
ACATACCCCCATTGACAATGCTCGGGAATTCCTACTTTGCCGTGGAATTCGGTGTCTTTC
AAGACGCTTTTTACTCGTGTATGTTTAGTATTTGAATTATTTGGGATGGAGTTAAAGCGA
TCTGCAGCGTCCATTACAAAGGCTGTATTTCTAGGCGTAAAAAGCCACATAGATCGTCCG
CGAATCCCCGCTACCGGTTAATGTAAAAAACGCCCAGATCTTGGCGTCAGAAGTCCGAAC
TTTATATCGCATTTAGCTGCGAAACTACCAGCAATAGTGGATGACAGGAGACGACAGCTT
TAGTGCGATTATAAAAAGCAAATGATTTAAATATCAAATCGCGGCAGAGGGCATTCAAAA
TCATCGCCTTAATTTATACAGCGCCTAGAGTCCGAAAGATCAGAATTTTGTTATTAAAGT
TGTCATTACTTGGATGAGAGCCTAAATTACCACTTGTTGGTTTACAGGTCAGGTCGTTTG
TTGAAAAAGAGCTGTTCTACCATTTGTATTGTTAAAGATCAACGGAAATACGGAATATTT
TAACACAGAGCAATGAGAGAAG

Reference(s)

Takahashi et al. (2010). Regulation of notochord-specific expression of Ci-Bra downstream genes in Ciona intestinalis embryos. Zool. Sci. 27(2):110-8