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CIS-REGULATION

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

Cis-regulatory Region

Name

Cirobu.REG.KH2012.S605:17448-17833_Cdx1-2Mut|βγ-crystallin

Short name

n/a

Region ID

REG00001401

Status

Curated

Origin

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

Type of Activity

inactive_region

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), is inactive cells. It contains 275bp upstream of the TSS and 110bp downstream. It contains 1 Sox, 1 Fox, 1 CREB and 1 Nkx/POU putative binding sites conserved with Ciona savigny. Compared to the -275bp/+110bp active enhancer, it lacks the two conserved Cdx binding sites and is not able to drive gene expression in pigment cells or in palps.

Hierarchy of Regulatory Regions

Modification of Cirobu.REG.KH2012.S605:17448-17833_Cdx1Mut|βγ-crystallin by substitution

Regulated gene(s)

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

Construct(s) made to test this region

CONS00001422: p.Cirobu.REG.KH2012.S605:17448-17833_Cdx1-2Mut>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 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: [17,448 / 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 two Cdx binding sites are mutated (mutated bases are shown in upper-case letters). AATTAT replaced by AGTCGT and ATTATC replaced by AGTCGC.

Show sequence

Length: 386


tttaattattaaaacaatcttgcttatcgtgctgtgttacgtcataatacatgcattagc
aattactttgttttgtcataatatgaGtCGtgtaaGtCGcgtgacgttgtttgttttaaa
aacccatttattattacgtcataatactttagatggttgtgtatgttacgtcataatgtt
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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