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CIS-REGULATION

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  1. Region 'REG00000158'

Cis-regulatory Region

Name

Ci-Hndx -2938/-56

Short name

Hand-r enhancer

Region ID

REG00000158

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Brad Davidson (2007-04-19)

Annotator

Jonathan Luchino (2007-04-19)

Curator

Delphine Dauga (2010-04-07)

View position in WashU

Description

This region drives the entire Ci-Hndx expression. Bioinformatics methods were used to identify putative Tinman- and GATA-bindings sites within the first 1kb of the Ci-Hndx 5 flanking region. Future study will determine whether these sites are essential for expression of Ci-Hndx. <br /> <br /> Be careful, coordinates in the paper may differ from ANISEED coordinates. We took the KH transcript model as reference. <br /> <br />

Hierarchy of Regulatory Regions

Regulated gene(s)

KH2012:KH.C1.1116 (HAND1; HAND2; SCX)

Construct(s) made to test this region

CONS00000152: pCi-Hndx -2938/-56 pfkh::LacZ

CONS00001273: p.Ci-Hndx -2938/-56>H2B:GFP

CONS00001287: p.Ci-Hndx -2938/-56>nsl:LacZ

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

7,466,2717,469,152

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

Sequence

Aniseed Coordinates: [7,466,271 / 7,469,152] on scaffold KhC1

This sequence was found scanning the v1.0 JGI assembly with the published primers: HndxF2955- <br />CGTTCTTGAAACTGGAGACATCCTG, and HndxB58- <br />GCCACGTGAAACTA

Show sequence

Length: 2,882

CGTTCTTGAAACTGGAGACATCCTGGAAAAGAACGCCGAAGTTGCCAAGGGTTTGACCAC
GTGACCTTGAACCAAGGTTACGTCATGTTCGAAAAATCGAAATTTCCCGAAGGAGGGACA
GCGGGGAAGTCCAAAGAAAGCAAACGATGAAGATTCGCTTTATCGTGACGTCACGGTCGC
ATTTATGACGTCACGATCGCGACCCTTCGAACTTTTTTGTTTAAGAACATCGTACTATAT
TCGATACAAAAGTACCATTGTGACGTCACACCATTACCGGCACTTTTATGTTCTCGTGAC
GTCACAATATTGTTCCGTGTGAAACGTTCAAATATTTTTTAAGACAAATTTCACTCAATT
TTGAGATTATTGGATCGATGTCGATACTCTGGCAATGCAGCCGCTGCTTCATATTAAATT
TGGCCCCATTTTTTAATCATATCTTGGCTGCTTCATACGCATTGTGTGAGCAACGAAAAA
TACTTCTGCGGCTTAACGAGTGCAGCGTCCGATTTTTCGCAGTTACACCGTGTGTAAGTT
TTTATTGTACGTCCATCAGCACTGTACACACTTTCACCGGTACCCCTTCAATTATTTATA
TTTACCGACGTAAATTTGCTGTGATTAACATGCGGTACCGTTGGCAATATATATTAGTTC
AATTTTCGAACTAATTTAAAAGTGTCTTGAGAGAATTCAGAAGAAGATAAAATATACAAT
ACAAGGTAGCGGAGCTATAATAAATAGACACGCAAAGTATAAAATCATAAAGAAAAACTT
ATTGTATACAGAGCAGAAATCATGTGTGTGTCACAGACTTTTTTTGCCGCCATGGACGTT
TCTAAAACCTCTTAGGTCAAAGTAATTTTTCTTACGTACATTTTTTGTCTGTCGTGGATA
TTTTAAGTCCGTCAAAGACACTCTATTTTCGTCACTTTAAATTTGTTACAGACAAATTAT
TATTATCCTTCTTAAAGTAGTAACCGGTTCGCTTATCGATATAATTTCGAATCTTTAGAG
AACAGTCCTTAAGATTCGTATAAACTCATCGCATCGTTTGTTTTGATAACGAGTGGCATA
GGCCTCATTACGTCATAATCAATTAGAACGACTTCCTTATTACGTAGGATCTGTGAACAA
TCAAAGGTTTGACTTTACACGGTTACAGTTTGACCTTATGGAATTCTGAGACACGAATAC
ACATAAAACAAACATACACTACAACTTGAACACCACAACCAATATTTAAAGTAAAAATTA
TTGGGAAAAACTTGTTGCAAAAAAAATAACTCGTTTCGTATTAAATATTTTTTAAACCAC
ACTTTACTGCATTTGTGTAATATTTAATTTAAAAAGTTTCCGTAGACATTTAAGTCTGCG
AAATTTTATTACGATTATTTTACATTTATGTTTATACAGCCAAGTTTTTGGCCAAGATAG
TTCAGTGTGTTAAAATCGACGCCGGTTTTGTATTATATTTAGCCCAGCTTTTACACCCGC
CACATAATAGTAAACCTTGCACCAACCTTCTATCCGTCCCATTCACCTGCCTTCATACCA
GCTATCATGGCGGGTTAAACGGCTCGCATTTAACCGCTGCCTCGTAAAATGTGACCTCGT
CAGTACTTCCGCATTAAAAGGGGCGAAAAGTTACCACCTCGTTAAGTAGGAACTGAAACT
AATATAACGTTTTGAATCAGACCCAGTGGTCTACTATTTAATGTCTAAATTGTCAGCCAT
ACATAACCAAAATTTTAAGAATTTCCACAAAGGTATATCAAGGTAACTCGTAAGCGGGCA
CATAGTGCATGAAACAGAAAACCCGTGTTTTAACCACTCTCATTGCCGCGCCAAGGCAGA
ATAAAGAGCTACAATTTATTACATTCATTTAAGTGTATACGATGAATAAACAACAGTTAA
AGTTACGAGAATTAACCTAAACTTTTAACGTCATACCAAACTGGAAAAAACGACCCTGGT
ATACGGCAACCCGTTAAAAACGTTTGACCTGATTTTTTTAATAGTAACAGTTATACGATT
AGGTTTAGGGCCGAAACAACTGTCTAAAAGGTTTGTTAGGTTTAAATTATATATTGCTAT
ATTCCAGGCGCTTGGAAACGGCATTCAAAGCTTTTAAGGGGTTTTATAAATCACTTAACA
GATATACTTATTTACGTATGCGAAAAAAATTGAAACCCTAAGACTTTACTAATAAACTTA
ATAGTTAGAAGCGCGAATTTATCCTAAAAAGAAAGCTGAAACTATGAAGGTTTTTTTCAT
ATTGATACATGATAGTCTTTACTGCATTTGGGATCGCCGTTAGGACGATAATCCTCCACA
GTTATCTAAACAAGTGTGTCTCCCCTGACGCACAATGGTTGCAACATATGTCAAAATTGA
GCATTACAGTAAAAGTTGTTTCAGTCATTTGTGTTATCTGCAGAACAGACTGCTCGGTGG
GGAATTAATATTAGCTTCTCACCGTCCTACTATGGGATTGCTTCTCTCGTCTCGAGATAC
TCTGTTTGCGGTGCACCTCGCACAAAAGAACGATTAATATAATGTAAATAGTAAGTAATT
CCAAACGCAAACCGAACAAGCGTCGCGTTAATTCTCGAAACGATACTGTGACGTCACAGA
AGCGTTTTCCTAATTAGTCGCATCGCCTTTTTTCAACGTCGGACGATCGCGTGAAACGGT
GTATATAAAACGAAGGCGCGTTTTAATTTATCTAAGCAGAGTTGTAGAGTCATGGTATAG
CATAGAGCCTAATTGGTATCTATATAGCCGTATGTGACAAATGCGTTAAGAAGCAGAAAA
AATACGTTTAGTGGCATTGTTTGGTGTGGTTAGCCGGGGACGCAGTTTTAGTTTCACGTG
GC

Reference(s)

Stolfi et al. (2014). Divergent mechanisms regulate conserved cardiopharyngeal development and gene expression in distantly related ascidians. Elife 3():e03728

Davidson et al. (2003). Evolutionary origins of the vertebrate heart: Specification of the cardiac lineage in Ciona intestinalis. Proc. Natl. Acad. Sci. U.S.A. 100(20):11469-73

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