DeathAndAptamers.gil

//This file should contain any source code related to the death receptor/aptamer subconstruct

import "ExpressionLocation"

using "regulation"

sequence construct
{
    silenced_DcR3
    E07
}

/*sequence Example_shRNA
{
    #region "Example shRNA"
    regulation:: .Gen_shRNASequence
    {
        'ATGAAAAAAATTTTTTTTTTTTTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCCC'
    }
    #endRegion
}
*/

sequence silenced_DcR3
{
    /* Death receptors are what allow for immune cells to bind to diseased/injured cells and allows for mediated apoptosis
       However, decoy receptors are able to similarly bind to the ligands of immune cells but they do not lead to the 
       expected apoptosis. Moreover, the decoy receptor appears to be overexpressed in cancer cells, therefore limiting its
       expression could make it easier for immune cells to kill cancer cells. 
    */
    ExpressionLocation:: .LocalExpressionInCells
    {
        DcR3_shRNA
    }
}

sequence E07
{
    ExpressionLocation:: .LocalExpressionInCells
    {
        E07_aptamer
    }
}

//shRNA for decoy receptor 3
sequence DcR3_shRNA
{
    #region "DcR3_shRNA"
    regulation:: .Gen_shRNASequence
    {
        //From https://www.ncbi.nlm.nih.gov/nuccore/AF104419.1?report=fasta 
        'TCCGCAGGCGGACCGGGGGCAAAGGAGGTGGCATGTCGGTCAGGCACAGCAGGGTCCTGTGTCCGCGCTG
        AGCCGCGCTCTCCCTGCTCCAGCAAGGACCATGAGGGCGCTGGAGGGGCCAGGCCTGTCGCTGCTGTGCC
        TGGTGTTGGCGCTGCCTGCCCTGCTGCCGGTGCCGGCTGTACGCGGAGTGGCAGAAACACCCACCTACCC
        CTGGCGGGACGCAGAGACAGGGGAGCGGCTGGTGTGCGCCCAGTGCCCCCCAGGCACCTTTGTGCAGCGG
        CCGTGCCGCCGAGACAGCCCCACGACGTGTGGCCCGTGTCCACCGCGCCACTACACGCAGTTCTGGAACT
        ACCTGGAGCGCTGCCGCTACTGCAACGTCCTCTGCGGGGAGCGTGAGGAGGAGGCACGGGCTTGCCACGC
        CACCCACAACCGTGCCTGCCGCTGCCGCACCGGCTTCTTCGCGCACGCTGGTTTCTGCTTGGAGCACGCA
        TCGTGTCCACCTGGTGCCGGCGTGATTGCCCCGGGCACCCCCAGCCAGAACACGCAGTGCCAGCCGTGCC
        CCCCAGGCACCTTCTCAGCCAGCAGCTCCAGCTCAGAGCAGTGCCAGCCCCACCGCAACTGCACGGCCCT
        GGGCCTGGCCCTCAATGTGCCAGGCTCTTCCTCCCATGACACCCTGTGCACCAGCTGCACTGGCTTCCCC
        CTCAGCACCAGGGTACCAGGAGCTGAGGAGTGTGAGCGTGCCGTCATCGACTTTGTGGCTTTCCAGGACA
        TCTCCATCAAGAGGCTGCAGCGGCTGCTGCAGGCCCTCGAGGCCCCGGAGGGCTGGGGTCCGACACCAAG
        GGCGGGCCGCGCGGCCTTGCAGCTGAAGCTGCGTCGGCGGCTCACGGAGCTCCTGGGGGCGCAGGACGGG
        GCGCTGCTGGTGCGGCTGCTGCAGGCGCTGCGCGTGGCCAGGATGCCCGGGCTGGAGCGGAGCGTCCGTG
        AGCGCTTCCTCCCTGTGCACTGATCCTGGCCCCCTCTTATTTATTCTACATCCTTGGCACCCCACTTGCA
        CTGAAAGAGGCTTTTTTTTAAATAGAAGAAATGAGGTTTCTTAAAAAAAAAAAAAAAAAAAAAA'
    }
}

//aptamer sequence complement that targets epidermal growth factor receptor
sequence E07_aptamer
{
    //From https://pubmed.ncbi.nlm.nih.gov/25242523/ 
    'ACGGCGATATTACGTGCCTAAATTAGCGGCATCTTTTCGTACAGTTTCGGC' 

}