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CIS-REGULATION

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  1. Clone 'cima84458' > 
  2. Transcript 'KH2012:KH.C10.264.v2...' > 
  3. Region 'REG00001401' > 
  4. Region 'REG00000156' > 
  5. Region 'REG00001403'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.S605:17448-17833_CREBmut|βγ-crystallin

Short name

n/a

Region ID

REG00001403

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Wei-Chung Chen (2018-05-26)

Annotator

Marion Gueroult-Bellone (2018-05-26)

Curator

Marion Gueroult-Bellone (2018-05-26)

View position in WashU

Description

This 385bp sequence, located in the intergenic region upstream of βγ-crystallin (S605.3), drives reporter gene expression in palps. It contains 275bp upstream of the TSS and 110bp downstream. It contains 1 Sox, 2 Cdx, 1 Fox and 1 Nkx/POU putative binding sites conserved with Ciona savigny. Compared to the -275bp/+110bp enhancer, it lacks one conserved CREB binding site and is not able to drive strong reliable gene expression in pigment cells.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.S605:17448-17833|βγ-crystallin by substitution

Regulated gene(s)

KH2012:KH.S605.3 (CRYBB2; CRYGN; CRYGS)

Construct(s) made to test this region

CONS00001424: p.Cirobu.REG.KH2012.S605:17448-17833_CREBmut>GFP

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

17,44817,833

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 SOX n/a aacaat [17,460 / 17,466] This Sox binding site is located on the intergenic cis-regulatory region of βγ-crystallin (S605.3). It is conserved with Ciona savigny. Mutation of this binding site or deletion of the region containing this binding site inhibit enhancer activity in pigment cells.
2 Homeobox n/a aattat [17,533 / 17,539] This is the 1st of the 2 Cdx binding sites located on the cis-regulatory region of βγ-crystallin (S605.3). It is conserved with Ciona savigny. Mutation of this binding site inhibits enhancer activity in pigment cells. So does the deletion of the region containing this binding site and its upstream neighbours.
3 Homeobox n/a aattat [17,541 / 17,547] This is the 2nd of the 2 Cdx binding sites located on the cis-regulatory region of βγ-crystallin (S605.3). It is conserved with Ciona savigny. Mutation of both Cdx binding sites inhibits enhancer activity in pigment cells and palps. So does the deletion of the region containing this binding site and its upstream neighbours.
4 Fox n/a tgtttgt [17,555 / 17,562] This Fox binding site is located on the cis-regulatory region of βγ-crystallin (S605.3). It is conserved with Ciona savigny. Mutation of this Fox binding site inhibits enhancer activity in pigment cells and reduces enhancer activity in palps.
5 Homeobox n/a tgtta [17,624 / 17,629] This Nkx/POU binding site is located on the cis-regulatory region of βγ-crystallin (S605.3). It is conserved with Ciona savigny.

Sequence

Aniseed Coordinates: [17,448 / 17,833] on scaffold KhS605

This sequence was retrieved using ANISEED Blast tool, thanks to the information provided in Fig2C of Chen et al. 2014. In this construct the first Cdx binding site is mutated (mutated bases are shown in upper-case letters). TTACGTCATAA replaced by GTGAGTCATAA.

Show sequence

Length: 386


tttaattattaaaacaatcttgcttatcgtgctgtgttacgtcataatacatgcattagc
aattactttgttttgtcataatatgaattatgtaattatcgtgacgttgtttgttttaaa
aacccatttattattacgtcataatactttagatggttgtgtatgGtGAgtcataatgtt
aattgttgaataaaaatgaagaaacaaagccatgaagaaggcggtttgttataaaacatt
gttgaagggatggaattaattatgttgttaacgtttgaattattgatgtaacaaggacga
caagtgagcgcaaatcagatttcgtttactttccttctaaccctcctaaccactgcttat
ttcgcattttgtacaatcgaagtttc

Reference(s)

Chen et al. (2014). Dissection of a Ciona regulatory element reveals complexity of cross-species enhancer activity. Dev. Biol. 390(2):261-72

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