Aniseed - Cis-regulation

Description

This region goes from 3,2Kb upstream the start of cDNA AF002987 to 1,3 kb downstream (corresponding to the middle of exon 2). It directs expression in a pattern that is virtually identical to the endogenous gene (Tail muscles, trunk mesenchyme, TVCs and CNS). Notochord expression is additionally detected.
This region was named -3200bp in the paper (Erives et al 1998) or 4.5kb Ci-sna in the paper from Erives et al in 2000.
Another study identifies between 2,8kb and 3,7kb upstream start of cDNA AF002987 a regulatory region that direct specific expression in the neural tube.

Hierarchy of Regulatory Regions

Ci-Sna -3200/codon 15 REG00000051 [ regulatory_region (extended_promoter) ]

Regulated gene(s)

KH2012:KH.C3.751 (SNAI1; SNAI2; SNAI3)

Construct(s) made to test this region

CONS00000035: pCi-Sna -3200/codon 15::GFP

CONS00000033: pCi-Sna -3200/codon 15::LacZ

Show in situ data

Overview of functional TF binding sites in this region

5,676,0835,680,582

	Motif Name	Binding Factor(s)	Sequence	Position in Region
1	bHLH	n/a	CAACTG	[5,678,683 / 5,678,688]
2	T-Box	n/a	GATCCCACCT	[5,678,737 / 5,678,746]
3	bHLH	n/a	CAACTG	[5,678,786 / 5,678,791]
4	T-Box	n/a	TTTGGCACCT	[5,678,873 / 5,678,882]
5	bHLH	n/a	CACCTG	[5,678,929 / 5,678,934]
6	bHLH	n/a	CATATG	[5,678,951 / 5,678,956]
7	bHLH	n/a	CATTTG	[5,679,045 / 5,679,050]
8	bHLH	n/a	CAAATG	[5,679,075 / 5,679,080]

Sequence

Aniseed Coordinates: [5,676,083 / 5,680,582] on scaffold KhC3

JGI v1.0 sequence for this region, as the sequence reported in the article is not available in Genbank. Note that the E5 sequence is absent from JGI assembly.

Show sequence

Length: 4,500

ATAATAAAATACGTAAAGGATTTTTTGATACGGACCAATTTGCGAATCCGCAAGGACTGT
AAAGTATAGGATAGAGGTTGATATATGAATAATAAGTGCTATTTTGTACACCTCATCAGA
GAAATGGCTAACTGTAACTTGCGATAAATTCTTTCGCAGTTTACGGTGTATCGTGGGCTT
TAATAAACAATGCACCTGTTTAAAACCGGCGTTCTGTATAGCGCCTATCACATTACCACG
CCTCGTGTGTCTTTACCCAAGAGACGTATATTTCAATCACTTAACGGCTTAATTCGAAAC
CGAGCAAGTGTTATGGTTAGATACGTCATGTTTCTAATGCAAGGGTATTTTAATCTATAT
CTCTATATACTATTAATAGACAATCATTATTCCTATGTAGTTAGAATTTCATCACATTCA
GTATTTTATTTGTATATAAGCCATCTTTGATTTTAAAATAATTTTATTGCCGCCTTAGCC
GAGAGCAAACTAATAACTGGACTTTAAACGATACGTCACTCGTTACGGATTTTTTCCAGA
CTATATTAAAGTGACGTCAGTGAAATGAATGCATGCGCGTGTCGCACTTTGTTATTTAAT
GACGTAATCTTGATGCGGCCACATAGATTAATGGGTGCACCGAGTACTTTCATCATACCA
GGCGTCCGGTGCCGAAGCAACAGGCGGCTAACCGAAATAGAACAACGACCAGCAGGAGCG
AGCCAACAACTGTTACCGAAGCGGTCCACTTAATCCCGGGACACGCGCGAACTGTACGCG
ACAAATATCAAAATATAAACAACGGCATTCAACTATTAATATTGCGCCTTTGGTTACGTT
CAACCGAGTTTTAAAAACCTGTCACATTTTTAAACTGAAGGCTGTCTGTATAGTCATCGA
AAGAATATCCCACGACCCAGCGTGCACACTTGGCCCGTATAACCTTCCGTTTGTGTTGGT
TTTTATTCCGAATACTCCAAATGATTGTAGCGCCGGGATACCTTAGTTGGCTTAGTACAC
CGATAGCAGACCGCCCCTCCACGAAATACAGACACTCTGTTTGTCACCAGTGTTCTATCA
ACTGTCTCGTTTAGCTACGGTGTACACATGCTTCTACATACGTTCCGCGGGTGTCTATTG
TTGCCCTTGTCCTTACAGTGCGTCTAGAGTAAACTAACCAAGATACGATTGCGTATACCG
GGACAATAGGATAACATTTGCACGGAGACACGTGGTCAACTATACGAGGCACGTAACCGC
AGGGCACTACCAAAGTCCGGTTATTTAAGTTTATATTTTTGCCTAGCCGTCGAAAAAACA
TGCATATATTAAAATTAATAAAACCGTTTATTCTCTATATCGTACATTGGTTATGAGCGC
TTTAGCACCAAAATATAACGAGTTCTATAAACGCAGTTAAATTCAATTGATTTTACCTTA
CCAGCAGGCAGTTTCTCTCCACAAACATTTAAGCCTCATTCCTAACGTGCGGGAATTCTC
CTCATCCGATAGAAACATATTAGTGTACGGACACTTCTCCATTCTTTGACAATGTGGTGA
CAGGGGAATATCATTTACGACAGTGCGAAGCGTCTCCTTTACCGAATAAACCTCATGATT
CTAACATTAAAGTCGTTGCAATAGGTACGGATATTCTAAAATTGAAACTATGCACAATCA
CGGGTATACCATATATATATATAGTAGGGTGGGAAAAATAGGACACCATTTTATTCTATT
TTCTCGTCCCATTTTGTAGAAAACAAGGAACATTTAAAGAATTATAAAACCGTATCCGTA
CGACTACCATAGACCGTTGTAAATTGTTTAAACACGATCAAGATATTTGGATATTATGTG
CTAACGGTGTCTCATCTACCCCCACCCTATTATAACACCGAACGTTAAAAATTCATTGCA
CCGAATGTTCCACCGTTTTAGTGTATTAGCGGATTCAGAATGTCGCACGCGTTCAAAGCG
ACCCAGTACCTATTGGTGTCAATTAACACCATTTTGGATCGAATTTTCGGATGAGCCTTT
GTGTGAAAATTAGCGGTTCACTCTGCCGGCCATCCTCAGGTTGAGATAACGCATCTATCG
CAAAGTAGCAGCTGAAGTGAAGACTTGCGATCGGAGAGAATTTAATTTCGATATTTTTAT
TTGCATTGATTTACAAAAATATTTATACAGTTTTTGATTTTGAAAACAATAGAGTAGGGT
GGGGGAAAATGGGATACCCTTTCATTCTATTTCCTTGTTCCATTTAGTAGTAAACAAAGA
CCTTTTCAGAGAATTATAAAACCGTATTCTCACGACTCCCACAGCCCTTTGTTAATTATT
TAAAACATGATTAGAATATTTAAATATAATGTCCCAAAGATGCCCCATCTTCCGCCACAG
TACTATACTTGAAAAATATATTGTTCTGCCCCTGAAATAGGAACTTTAGGGGGAGATTTT
TCTTACGCACATGATAAATTAATATGTTGTTACCGATAAATTGTAGATACTTAAAATGAA
AAGGTCGCAATTGTATTTACCATTATAAAACAGAAGATCGGTGTGTTTTGCTGGACAAAT
ATTGAGAAAATCTGTGGCGACAACTGTGGTCTGATTTACAGGCGAGTTGGACGGAGTTGA
CAGGTCGCGAAAGCGATCCCACCTTCGTGTCTGGGTTTCGAGGTGCCGCCCGTCGTGCAG
TAGCAACTGTGCGGTCAAGTTGAGAGCAAGAAGACACTACAGCGCGCTTTGAAGCGTCCA
AGCCGCCCGCTGAGCAGGGCGGATAGCTCGTTTGGCACCTCGTCTGGCATCGTCCGCACT
GTCAACCTTCTTCGTACAAACGTCCTCACCTGCCGCGCAGGATTGCTTCATATGGCAGAC
CGAGTTGAGTGGGAAATCATATTCTGGTTGCTTCGCTTATAGAGCTAGCTCACTAGAGAC
TAGAGTGTTGTGAATGATGAATCATTTGAATTAAGCATTTTGTTTAGTTGATCAAATGAG
TTTCAGTTTGATGTTCAGGACTGCTAAGTAATGCAGTGAAAGGAATTCTAAAGTGATTAT
ATTTAGAAATGGGCTATCAGTGCTTGATTACTGTTGCAGGGTTATTTAAAAATGCAGTCG
AACAGTCTAAGAAAGCTTAGCTATATTTGAAGGATTATGTATACTTATTTCATTAGAGCA
ATATTTTTTTTTTTATTTTAGACTTTTGGTACATATTCAAAATATCAAAATTCTCACTGT
GAAATATATTACTGTGATTACATCATGACCTCCGTCGAGCCCATGCTTTATCAAGGCAAG
CACGCCGTTCAGAAAAATGAAGGTATATATGCAGTCCTATTTATATTATAATTCATCGCG
GCAATTGTTTCTCTTATAAAAATCAAACGCGATCATTTTAAATGTTGTAAACAGAGCAGA
TGCCTTTGTAAATATGCATCATCTTGTACCGAGAATCCAGCAGAATTTTCCATGAGACTT
TCGTTCACGTAAAAGTTAAATTATTTTCGGAGGTTATTTGCGCACGGCGCGGTGTTGGAA
CTTTTCGCTAATCCGACTGTTTGTTTCCGCCTAAATTAATCACAAGTAACAGTTGCGATA
AAACAAGGAAACGACTGGATCTCCCGCTGTTATAGGATGCCACCTCGCACGTCAAACCCC
ACACATACCGTAACTTTTACCTAAATAATGGAAATGCAATTATTTAATTACCTGTGGAAG
AATCCGGACTAAGCCGAGATTGCCTAATATAGTTAGACAAGGTCCGGTCACTCGGGCTAA
ACATTCAAACAGGTGGTGCCTAAAATAGATGCGAGCTGGTACCAAGTGTTTTGCTCGCAC
CGTTCCTCCCATGGGTGACTGGCTGGCTTTAAGGATGGAACGCTACCGATATAAGTTTGA
CGTAATCTCGGTCTGGATGAAAGCGTTGACAGCACTACCTGTTTGCACACTCGGCACAAC
TGCTGCTTATGGAAGTGAACTGCGGTTTCCCGATATGGAAACCGTATGGCTCAATAACAA
ATTATTTACGGCCCTCAGGACAGCCCGCCATGCAGTCTGCACCATATTTTTAATCCTGGC
TTTTGCCAAGACCAAATATTACAAAGTTAAATCTTCTTTAGGCGAATCTACCCGTCCTTG
CACTTTGAGTGGAGATGACAGTTTTTACTGCAGCGGCGAATCAACAAATTCGACGTCATC
TCCCACGTCATCCATTACGTCATCGCGTTCATGTGGACCTGACAGCGACGAAGGTTTTCC
GAGACAGGATGACCTGGATTTGCGTGACAAAGCCAGCAAAAACTTGCAACATAGCGTTGA
GCTTTTTTGCCCTATTAAGAGCAAGTCAGTTGATCATGATAACGATTTAATGCCTATGGA
TCTCTCGTGCAAAAAGAGAACTTTCCCAAAACAAAATTGCAAAACTGCTAGCATGCCTAA
AACGAGCCCAACCATAAAATCAGAACCGATTGATGACTATCCAGCTTCACTTACACGCAA

Reference(s)

Erives et al. (2000). Characterization of a maternal T-Box gene in Ciona intestinalis. Dev. Biol. 225(1):169-78

Corbo et al. (1997). Dorsoventral patterning of the vertebrate neural tube is conserved in a protochordate. Development 124(12):2335-44

Erives et al. (1998). Lineage-specific regulation of the Ciona snail gene in the embryonic mesoderm and neuroectoderm. Dev. Biol. 194(2):213-25

Passamaneck et al. (2009). Direct activation of a notochord cis-regulatory module by Brachyury and FoxA in the ascidian Ciona intestinalis. Development 136(21):3679-89

Cis-regulatory Region

Name

Short name

Region ID

Status

Origin

Type of Activity

Author

Annotator

Curator

Show sequence