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CIS-REGULATION

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  1. Region 'REG00000314'

Cis-regulatory Region

Name

Cititf1 -2568/39

Short name

n/a

Region ID

REG00000314

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 (2007-12-10)

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 of this region in the paper : -2370bp/+238bp

Name of the construct in the paper : construct #7



Hierarchy of Regulatory Regions

Modification of Cititf1 -3698/39 by deletion

Regulated gene(s)

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

Construct(s) made to test this region

CONS00000299: pTitf1 -2568/39::LacZ

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

3,636,4203,639,026

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

Sequence

Aniseed Coordinates: [3,636,420 / 3,639,026] 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: 2,607

TAAAAACGCTACGCGGAATATATAGTAGAGTGGGGAAAGATGGGACACCTTTAACACATA
ATATCCAAATAGCCTGATCGTGTTTTAACAATTAACAACGGTATGTAGAACCGTGAATGT
CTTTTGTTTATTACCAAATGGAAAGAGAAAACTAAACGAAAAGGTGTCCCATCTTCCCCC
ACCCTACTATAGTATCAAATAAACCCATGCTATTCAATATGTATTCTGGTATCTTGAAAT
AATATAAAATTACCGAAAGGCTACAGTGAAGATATAAAATTAAAAAAGCATATCCCTTTT
TTACCAAATAAAATTTCCCTTGATTTTATACATACGAATTTAGTTTTATAAAGTCACTTC
AAGCACAAAATCAACAAAAAAATCACAAGAAAATATAAAATAAAATGATTAAACGAAAAA
CTATAATATAAATCTTTAATAAATTACTATACTACGAAGAACTTAATTTACCATACAGAT
GGTGTTATTGGTTGCTGGGGTAAGATCTTTCATGTTTTCATTCTCTTTTATCGTCCCATT
TGATAGAAAAGTTACAGGTTTTTTAACCGTACCCTCTGTTAATTGTAAATTCAAGGCAGA
TTTTGTATATTTTTTAACGATATTTATCTTACACCGCAGCACTATATTAGAACAACCTTG
TCACTTTTTACGATTAACGATTCCGCCATTTTGTTCACGATAATTTTCTTTCAATTCTGT
TCGTCTTTGCTAGTTCATGGTTAGCAATGACTCATGGCATGATACACAATAAGGGTCGTG
ATTCAGAATAATCAGTGACGTCATCTCTGACGTCATACGAGACAATGGTACTCCGGTGGC
GGCCGTCTAAAACCTCGATAAACCAAAATAACCACATTTTGCATGAGATTTTTTAAATCC
CGTTTTTGGTGTAATACCAAATAGATTGCTGTTATTCCATGAGCCAAGTCAGATTAGGGC
TTGTATCTTCTCTGTCGGTTTTTATGTAGTAGATTTAGGTAAGATCGCCGATGTTTTTAT
TAGAATTTATCGTCCCGTTTGGTGGTAAACAAAAAATACTTTCAGGAATGTGTAATCGTA
TCCTCACAACTCTAAAATAGCGTTGTTTTTTGGTAAAAACACGATTAGGAAACATGAGAT
ATTATCTGATCACGATATCCATCTTCACCCACAGTATTTTATATCGTTTAGGAGGTGTTA
GCATGGTGTTAGCGACACAACTTTCCAGTGCGCTAAAACATATTTTGGAACTTTACTTTC
AAATGATTGATTTTTTCGTAATGCGTGGCTGTGCTTTTATTTTGAAGTGTTGAAAGTATG
TGTGGCTTTGGGTCTTTTTTGTTTCTTTCTTTGTTCAGCGGCCTTACAATGACGCAAACC
TCAGTTTCGTTGCTAGAGAACGCTGTACACTGTTCACAAATTAGCACAAGCTAATTTAGT
TCGAATGCGGATCCAACATAGCGGCCTACGTCTCACAATAGCAGCCCGCGCTAATGCTAG
CTTCAGCTGCCGTTCAAGTGTCCCGTACTTTCGAGTGCCAACTCCAGTCGATATACTGAG
CACCCGGCCGTCGTCGTACCACCGCTCGATGGGGCTCAAGTGCTCTTCTCGCTGAACCCG
AGCCCGGGAACTGACGGAACATTTTCAAAGTTCTTCTGCGACAGATGATTTCGGGAATAA
TTGTTTGATAGTTCGCGGAATGCGAAGCTACAGCTGCCGCCGGATATTTTCCTAACTGTG
TTTGTTTTAAGCTCCCATTGCGAACAAAGCTTTAAGCCTTTCAGAATTCGCTCCTTTAAC
ACAAAAAATTATTTCCAGAACCAGAGCAGCTTCCGCATGCTGGAACTGAACTTCTTATTT
TCCAGAAGGAATGTCGTTATCCAGAATAAATTTGTTTTTTTTGAAATAGTCTATAGTTTT
CCAGATAAAATATCATTTTCCTCAACCAAAATGTCATTTTTCACAATAAAATGTCGTTTT
TTACGAATCAAATTTCCGTATACAATGCGTATACTCTATCCTGTGTGAGTTTGATGTCTA
TCTCTTCCTGGTTGTTTGTGTCTGCCAAGATACATCTGTCGAAAAAACTTCAAACGCTTA
TCAGCGCTAATGAGTTTGTAATGTCGCATTTAGTTTGGAACGGAAAGTTCCGATTCTTAT
TTGCATTTGATTTCCGTTCGTCGAACCGTTTCATTTCCCGCTCGATGTGGCTGTCGACCA
CAGTCTGTGAAGTCACAAGTTTAATTGTTCCGCGACTAAAATAAAGTTTAAAATATAGCA
GTTTAAGTATATGTTTTAACAGCAAATTTAACAAGTTTGGCCTGCAGGGTAAAATATAAA
CATTTAGTGCTAAGAATTTTAAAAATTCTGGAGTAAAGTTTCTTTCCGAGCATTATGTGT
TAGTATTTTTTAACTGTGACATCATAATAACCTGTTTGTTCACGATGGCATAGGGAAAGA
TAATCCGCGAATGGTTTTGTGCGGAACAATGAATATCTCTCTCCTATTTTCGGCGCGTAC
CTGCGCCTTTTTCTCCCCGCCTCTCTCGTTTTCCGGCGACCGAGATGGCCCGCAGACGCA
GGGAACCAGATCTTCAAATCGCTCTGA

Reference(s)

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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