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CIS-REGULATION

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  1. Region 'REG00000486'

Cis-regulatory Region

Name

Ci-opsin3 -2399/-900

Short name

n/a

Region ID

REG00000486

Status

Curated

Origin

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

Type of Activity

regulatory_region
(complex_region)

Author

Kusakabe team (2009-12-09)

Annotator

Delphine Dauga (2010-01-14)

Curator

Delphine Dauga (2010-03-12)

View position in WashU

Description


Conversion to aniseed format of DBTGR database entry from Kusakabe team.


Transcription start site is based on the start of the first exon of the KH transcript model.

Hierarchy of Regulatory Regions

Regulated gene(s)

KH2012:KH.L57.28 (NPBWR1; RGR; RRH)

Construct(s) made to test this region

CONS00000455: pCi-opsin3 -2399/-900::EGFP

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

121,809123,308

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

Sequence

Aniseed Coordinates: [121,809 / 123,308] on scaffold KhL57

Sequence from JGI V1.0.

Show sequence

Length: 1,500

GCTGCTGGCTTCTTCACCAAGGGACCTCATAAGCACATCACACTCAGGTTCCAACCAAAG
GTTAGTATTTATTCAACTCAGGGTCTGTTTAATCTTGGTATGAAATATAAACTATTTATC
CTTGTGTGTCAGGAAAGTTACCCATTACCCCTAACACTACATATGTTGAAGTTAGAAACT
TTCATTTTAACTTTTTTAGTTGAAAAACATCGAACCTGAAACACCTCAAGTGTCTCTACT
AACCCTTCCAGTTACTTTGGTGATTGGACTTCTTGCTTACAACTATTTACAGGTTTGTTT
ATTAGATGTTGTTTGATTTGATTGTGCCCATAATTGGCTTCATTACCTAAAAATTTCAAG
GTTGTATGAATTGTGTTAGTGAGGTTACTTAATAAAGCAATTTAGTGAATTCAATGCGAC
AAAGAGTATTTTATGACACACCAGCAACTTTTCCTTCCCAGGTTTTCGAATTTCTTCAAA
AACTTTTCTCCATGATTGTCAGCAAGCTAGATAATCCTGAGGTTTCGACAAGGTCCACCA
GGAAGTCACGTAAATGATGACGTCACGGGGAATTCCCGGCGATATTTTATGCAGATTGAG
TTGGCAAGAGGTCATGAGAATACTTGGGTCAAATTCTATTTATGTTCACAACGATTGAGG
CAACCTATGCGATTTCTATGAACTATCTTTATGTTTGTTTAATTCTGTGTTGTTTGTACC
AATGTGAGAATAAACCGAATCAAAGTTATTCAATTTTTATCTTTAGGATAATGAAGTGAA
TTCATTGTGGCTTTATAATCGCGGGACGGTCGTTATAACACAGATGTTCTGCTTCATAAA
CCTCGTGTTCACTTGTTACCACGTATGTAACTTTGTGGGTGATTGCTTTTTTTGTTAACG
TAAAATCCTATAATTACATACATGGCAATTACAGCAAAATTTTTAATACCATATATTGGA
CCATCTTACCCCAACCTAATATACGTAAGATCTCCACATACATTCATTATGTGTGGAAAT
CCATCAACATTTTGTTCGTCATAAAACCGTAATTGCAGCGCCGGAACCAATTTTCGTCCT
AAATTGTTTCGTGTGTTTTATTAGCCATCTTTTAAACGTCTTGAGGGTAAAAACAGACAG
TGTTTTGGTTTTGGTTTCTAGTTTTGTTGAGGTTTGTTAAACATCTTAAGAAATCATCAA
CAAAGTTACATACGTGGTAACTCGTAAGTAGGCACCATGCATATAGTAGGGTGGGGGAAG
ATGGGACACTTTTAGCCCTGAATACCCAAATATCCTGATCGTGTTTTAAACAATTAACAA
CGGTCCATGGGAGTCGTGAGGATACGGTTTTATAATTCATTGACTATTCTTCGTTTACTG
CCATATAGGACGAGAAAATAGAATAAAAAGGTGTCCCATCTTCCTCCACCCTACTATATG
AAACAGAACACCTGTGTTATAACGACTGTTGATAACCCGCTGTAGCATTGACTGGGAAAA

Reference(s)

Kusakabe et al. (2004). Computational discovery of DNA motifs associated with cell type-specific gene expression in Ciona. Dev. Biol. 276(2):563-80

Sierro et al. (2006). DBTGR: a database of tunicate promoters and their regulatory elements. Nucleic Acids Res. 34(Database issue):D552-5

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