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CIS-REGULATION

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  1. Clone 'cien203265' > 
  2. Transcript 'KH2012:KH.L171.13.v3...' > 
  3. Transcript 'KH2012:KH.C12.152.v1...' > 
  4. Region 'REG00001389'

Cis-regulatory Region

Name

Cirobu.REG.KH2012.S605:16609-17833|βγ-crystallin

Short name

n/a

Region ID

REG00001389

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Wei-Chung Chen (2018-05-25)

Annotator

Marion Gueroult-Bellone (2018-05-25)

Curator

Marion Gueroult-Bellone (2018-05-25)

View position in WashU

Description

This 1225bp sequence, coverinf the intergenic region upstream of βγ-crystallin (S605.3), drives reporter gene expression in palps and pigment cells. It contains 1115bp upstream of the TSS and 110bp downstream. It contains 1 Sox, 2 Cdx, 1 Fox, 1 CREB and 1 Nkx/POU putative binding sites conserved with Ciona savigny.

Hierarchy of Regulatory Regions

Regulated gene(s)

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

Construct(s) made to test this region

CONS00001419: p.Cirobu.REG.KH2012.S605:16609-17833>LacZ

CONS00001409: p.Cirobu.REG.KH2012.S605:16609-17833>GFP

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

16,60917,833

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 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.
6 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: [16,609 / 17,833] on scaffold KhS605

This sequence was retrieved using ANISEED Blast tool, thanks to the information provided in Fig1 of Chen et al. 2014.

Show sequence

Length: 1,225


attatggcgcacctgtgtcgtaaccacatctagatccttatcgttaatattcacccgccc
ctgtttagttttgaaagaaatattaaatcctccgccagcctcgaagaatagatgtccatt
gttcgtgtacattcgagatctaaagtatattattacgtcataataaacatttcaatgggt
taattcttactgttcggttgaaactcttgaatccactatgacgtcatcatcgtcgctaca
accgctataaacagcgagaaacaaaataaaaacaatcgacttcattacggaagagttggg
tcgaaagtggttgttgcatgaaatatatgtgtgttatatctcggtgctaagtggtacaac
aaacaaataaaacgtctggtttatgagatgctcgcgtggtacgggctatgtgatgtcata
atacctttgtctattatccttgttacgacataattaccatgaaacagcattgtgacgtca
cagtgctgtttgtgttggacaaacaacacgtggtttctacgagggggaatcccctctctg
tcattattacgtatgatgacgtataatatcgattattattcaccatccaaggttatatac
gatatctatttggttttatccgcttggtggcgacatcaatcctcaactacaattggtatt
atgacgtagttcgtagttacgtcacaagtcacacaacaaagaatttattatgagcaaata
aacgaactaatatgacgcaacaataactaacaatttatcacgtgatcgttttatttattt
tgtttgttatgtcataaccacttggtgcttaaaagggagcttatgacgtattaatgaact
ttaattattaaaacaatcttgcttatcgtgctgtgttacgtcataatacatgcattagca
attactttgttttgtcataatatgaattatgtaattatcgtgacgttgtttgttttaaaa
acccatttattattacgtcataatactttagatggttgtgtatgttacgtcataatgtta
attgttgaataaaaatgaagaaacaaagccatgaagaaggcggtttgttataaaacattg
ttgaagggatggaattaattatgttgttaacgtttgaattattgatgtaacaaggacgac
aagtgagcgcaaatcagatttcgtttactttccttctaaccctcctaaccactgcttatt
tcgcattttgtacaatcgaagtttc

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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