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CIS-REGULATION

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  1. Region 'REG00000313'

Cis-regulatory Region

Name

Cititf1 -3698/39

Short name

n/a

Region ID

REG00000313

Status

Curated

Origin

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

Type of Activity

regulatory_region
(extended_promoter)

Author

Albertina Fanelli (2007-12-10)

Annotator

Jonathan Luchino (2007-12-11)

Curator

Delphine Dauga (2010-04-06)

View position in WashU

Description

Region from -553 bp to the +39 bp is the minimal enhancer which reproduces the spatial and temporal expression pattern of the endogenous gene Cititf1.


This region includes three distinct regions of regulation.

- a central region, involved in activation of the expression in the endoderm, is situated between -481 and -328 bp of the transcription start and contains cis-regulatory sequences associated with the endoderm-specific transcriptional activation.

- another region of control, required to achieve an efficient gene expression, lies between -553 and -581 bp.

- finally, the enhancer proximal region includes sequences relevant for the activation of expression in the mesenchyme cells, expression that is normally silenced by negative control elements between -481 and -433 bp


Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.

Coordinates in the two papers : -3500bp/+238bp

Name of the construct in Fanelli et al. : construct #1


Hierarchy of Regulatory Regions

Regulated gene(s)

KH2012:KH.C10.338 (NKX2-1; NKX2-2; NKX2-4)

Construct(s) made to test this region

CONS00000298: pTitf1 -3698/39::LacZ

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

3,636,4203,640,156

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

Sequence

Aniseed Coordinates: [3,636,420 / 3,640,156] on scaffold KhC10

This sequence was found using a blast on the JGI Version 1.0 with the sequence includes in the paper.

Show sequence

Length: 3,737

ACTTGAGCTGTTTAAACCCAGACTATCCACCATTTTCCATTTTAAGTTTAGCAAAAAAAT
GATTCAAATATTACACATGTGCACAGTACTGTTGCTGGGGAAGATGGATATCGTTGTGCC
ACATATTGGCCTATATTTTATAATCGTGTTTTTAACAAATAAAAACGCTAATTTAAAGTC
ATGAAGATACGGATATATAGTTCTAAAAAAATATGTTTACTATAAAATGGGACGATAAAA
GTGAATGAAAACATATACCATCTTACCCCAACCTACTATATTATAAAGTCGTACTGCTAG
TTTATTACAGACAGTTATTATACCGCGTGAAAAATGTATTTCTAAAAAGGACTTTTTAGG
TTTTGATTTCACATAAAAGACATTCACGTTAAAAGTAAAATGATGTTATATTGCATTTCT
TCGATTAATCAATTTTAAGAGTTTTTAAAATGAACTTAATTTAAATGTTCATTTATATCC
TAGAAAATAATAGCGAAGATCAAATTATTAAAACAAAGAACAGAAAGAAATTAGAAACAA
AATGGCATTAAAAACGTGCTGCAGGTGAATTCTATGAATAAAATGTCGAATAAAAGACGT
GACTTCTAAATCCTAATCAGCAGCAGACTTAAGCATTATTGGTCTTTAATGAAACTTGTT
AAAAAATTCAAGTCCGGATTTTGGTTTTGGTAATTTGTTCTACCAAAATATTACCAAAAA
ATAGACAAATAAATAAACAAAAGTAAAACATTTTTTTGGTAAATATCGTCACGCTGTGTG
AAATCTTGAAATCTTAGCAAACAAACGTTCTTGTGACGTCACAATACACAATCTTACGTC
ATGGCGTCGTGTGTACTTCTGGGTCAGCTTTGATTCGACCAAAGTATCCGTAACCAGTTA
AGTTGCGGAAAACTTGCATTGCCGCCAACGCGGCCCAAACTCAAGTGTTTGTTTTCATTT
CTCTCGTTTTGTTTTCGTCATTATTCTGATAGTTTACCTTTTTTCCTTTTCTATTTAAAA
AATGGTCAAAAGATATATTTATGTATTTTGACATTTATTTTCAGAAACATAACAATGTTA
AAGAGGTTCGACAAAAAGTATGTATAATAATACTTCAGCATTTTTTAGCATAAAAACGCT
ACGCGGAATATATAGTAGAGTGGGGAAAGATGGGACACCTTTAACACATAATATCCAAAT
AGCCTGATCGTGTTTTAACAATTAACAACGGTATGTAGAACCGTGAATGTCTTTTGTTTA
TTACCAAATGGAAAGAGAAAACTAAACGAAAAGGTGTCCCATCTTCCCCCACCCTACTAT
AGTATCAAATAAACCCATGCTATTCAATATGTATTCTGGTATCTTGAAATAATATAAAAT
TACCGAAAGGCTACAGTGAAGATATAAAATTAAAAAAGCATATCCCTTTTTTACCAAATA
AAATTTCCCTTGATTTTATACATACGAATTTAGTTTTATAAAGTCACTTCAAGCACAAAA
TCAACAAAAAAATCACAAGAAAATATAAAATAAAATGATTAAACGAAAAACTATAATATA
AATCTTTAATAAATTACTATACTACGAAGAACTTAATTTACCATACAGATGGTGTTATTG
GTTGCTGGGGTAAGATCTTTCATGTTTTCATTCTCTTTTATCGTCCCATTTGATAGAAAA
GTTACAGGTTTTTTAACCGTACCCTCTGTTAATTGTAAATTCAAGGCAGATTTTGTATAT
TTTTTAACGATATTTATCTTACACCGCAGCACTATATTAGAACAACCTTGTCACTTTTTA
CGATTAACGATTCCGCCATTTTGTTCACGATAATTTTCTTTCAATTCTGTTCGTCTTTGC
TAGTTCATGGTTAGCAATGACTCATGGCATGATACACAATAAGGGTCGTGATTCAGAATA
ATCAGTGACGTCATCTCTGACGTCATACGAGACAATGGTACTCCGGTGGCGGCCGTCTAA
AACCTCGATAAACCAAAATAACCACATTTTGCATGAGATTTTTTAAATCCCGTTTTTGGT
GTAATACCAAATAGATTGCTGTTATTCCATGAGCCAAGTCAGATTAGGGCTTGTATCTTC
TCTGTCGGTTTTTATGTAGTAGATTTAGGTAAGATCGCCGATGTTTTTATTAGAATTTAT
CGTCCCGTTTGGTGGTAAACAAAAAATACTTTCAGGAATGTGTAATCGTATCCTCACAAC
TCTAAAATAGCGTTGTTTTTTGGTAAAAACACGATTAGGAAACATGAGATATTATCTGAT
CACGATATCCATCTTCACCCACAGTATTTTATATCGTTTAGGAGGTGTTAGCATGGTGTT
AGCGACACAACTTTCCAGTGCGCTAAAACATATTTTGGAACTTTACTTTCAAATGATTGA
TTTTTTCGTAATGCGTGGCTGTGCTTTTATTTTGAAGTGTTGAAAGTATGTGTGGCTTTG
GGTCTTTTTTGTTTCTTTCTTTGTTCAGCGGCCTTACAATGACGCAAACCTCAGTTTCGT
TGCTAGAGAACGCTGTACACTGTTCACAAATTAGCACAAGCTAATTTAGTTCGAATGCGG
ATCCAACATAGCGGCCTACGTCTCACAATAGCAGCCCGCGCTAATGCTAGCTTCAGCTGC
CGTTCAAGTGTCCCGTACTTTCGAGTGCCAACTCCAGTCGATATACTGAGCACCCGGCCG
TCGTCGTACCACCGCTCGATGGGGCTCAAGTGCTCTTCTCGCTGAACCCGAGCCCGGGAA
CTGACGGAACATTTTCAAAGTTCTTCTGCGACAGATGATTTCGGGAATAATTGTTTGATA
GTTCGCGGAATGCGAAGCTACAGCTGCCGCCGGATATTTTCCTAACTGTGTTTGTTTTAA
GCTCCCATTGCGAACAAAGCTTTAAGCCTTTCAGAATTCGCTCCTTTAACACAAAAAATT
ATTTCCAGAACCAGAGCAGCTTCCGCATGCTGGAACTGAACTTCTTATTTTCCAGAAGGA
ATGTCGTTATCCAGAATAAATTTGTTTTTTTTGAAATAGTCTATAGTTTTCCAGATAAAA
TATCATTTTCCTCAACCAAAATGTCATTTTTCACAATAAAATGTCGTTTTTTACGAATCA
AATTTCCGTATACAATGCGTATACTCTATCCTGTGTGAGTTTGATGTCTATCTCTTCCTG
GTTGTTTGTGTCTGCCAAGATACATCTGTCGAAAAAACTTCAAACGCTTATCAGCGCTAA
TGAGTTTGTAATGTCGCATTTAGTTTGGAACGGAAAGTTCCGATTCTTATTTGCATTTGA
TTTCCGTTCGTCGAACCGTTTCATTTCCCGCTCGATGTGGCTGTCGACCACAGTCTGTGA
AGTCACAAGTTTAATTGTTCCGCGACTAAAATAAAGTTTAAAATATAGCAGTTTAAGTAT
ATGTTTTAACAGCAAATTTAACAAGTTTGGCCTGCAGGGTAAAATATAAACATTTAGTGC
TAAGAATTTTAAAAATTCTGGAGTAAAGTTTCTTTCCGAGCATTATGTGTTAGTATTTTT
TAACTGTGACATCATAATAACCTGTTTGTTCACGATGGCATAGGGAAAGATAATCCGCGA
ATGGTTTTGTGCGGAACAATGAATATCTCTCTCCTATTTTCGGCGCGTACCTGCGCCTTT
TTCTCCCCGCCTCTCTCGTTTTCCGGCGACCGAGATGGCCCGCAGACGCAGGGAACCAGA
TCTTCAAATCGCTCTGA

Reference(s)

Ristoratore et al. (1999). Expression and functional analysis of Cititf1, an ascidian NK-2 class gene, suggest its role in endoderm development. Development 126(22):5149-59

Fanelli et al. (2003). Interplay of negative and positive signals controls endoderm-specific expression of the ascidian Cititf1 gene promoter. Dev. Biol. 263(1):12-23

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