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CIS-REGULATION

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  1. Transcript 'Harore.CG.MTP2014.S1...' > 
  2. Transcript 'Harore.CG.MTP2014.S1...' > 
  3. Transcript 'KH2012:KH.C9.65.v3.A...' > 
  4. Region 'REG00001396'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.S605:17540-17833|βγ-crystallin

Short name

n/a

Region ID

REG00001396

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

n/a ()

Annotator

Marion Gueroult-Bellone (2018-05-25)

Curator

Marion Gueroult-Bellone (2018-05-25)

View position in WashU

Description

This 294bp sequence, located in the intergenic region upstream of βγ-crystallin (S605.3), drives reporter gene expression in palps. It contains 184bp upstream of the TSS and 110bp downstream. It contains 1 Cdx, 1 Fox, 1 CREB and 1 Nkx/POU putative binding sites conserved with Ciona savigny. Compared to the -275bp/+110bp enhancer, it lacks 1 Sox and 1 Cdx conserved binding sites and is not able to drive gene expression in pigment cells.

Hierarchy of Regulatory Regions

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

Regulated gene(s)

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

Construct(s) made to test this region

CONS00001416: p.Cirobu.REG.KH2012.S605:17540-17833>GFP

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

17,54017,833

Motif Name Binding Factor(s) Sequence Position in Region Comment
1 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.
2 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.
3 bZIP n/a gtcataa [17,617 / 17,624] This CREB binding site is located on the cis-regulatory region of βγ-crystallin (S605.3). It is conserved with Ciona savigny. Mutation of this CREB binding site inhibits enhancer activity in pigment cells.
4 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: [17,540 / 17,833] on scaffold KhS605

This sequence was retrieved using ANISEED Blast tool, thanks to the information provided in Fig2B of Chen et al. 2014.

Show sequence

Length: 294


taattatcgtgacgttgtttgttttaaaaacccatttattattacgtcataatactttag
atggttgtgtatgttacgtcataatgttaattgttgaataaaaatgaagaaacaaagcca
tgaagaaggcggtttgttataaaacattgttgaagggatggaattaattatgttgttaac
gtttgaattattgatgtaacaaggacgacaagtgagcgcaaatcagatttcgtttacttt
ccttctaaccctcctaaccactgcttatttcgcattttgtacaatcgaagtttc

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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