I'm trying to determine if the UAS-driven protein construct I am using in Drosophila possesses the native 5'UTR, or if the process of generating the flies swaps out the 5'UTR for another.
The flies were generated from full length cDNA from the drosophila genomics resource center, and I can access the nucleotide sequence. The cDNA clearly has some sort of upstream nucleotide sequence, but I can't figure out more than that.
The cDNA were ligated into pENTR/D-TOPO using topoisomerase-mediated cloning and then recombined into the pTRW plasmid. The plasmid seems to have the SV40 3'UTR, but makes no mention of the 5'.
this link is useful
http://www.microbiologyresearch.org/docserver/fulltext/jgv/76/5/JV0760051189.pdf?expires=1521735035&id=id&accname=guest&checksum=2D11B5B817563FEE7E42B80FC94D0520
regards
Hello Michael.
Hit your 5-UTR including the first exon 1 sequence together in FASTA whether it has Kozac seuence and initiation codon element. Beside the elements 5-UTR also has other cis-acting elements within 70~100 bp, thus affecting translation of the transcripts within the cells.
You could use any analysis tools for UTR sequence databases. Try the links.
http://mblab.wustl.edu/software.html (for transcription factor networks)
http://utrsite.ba.itb.cnr.it/ (for 5'- or 3'-UTR sequence motifs)
http://regrna2.mbc.nctu.edu.tw/detection.html (for an integrated web server for identifying functional RNA motifs and sites)
Best wishes.
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