Is there a complementary sequence within the 3' UTR of PC (Pyruvat Carboxylase) to postion 2-8 in the sequence of microRNA hsa-mir-182 or other microRNAs?
Use Targetscan to find out.
Examine the result and discuss the conservation in mammalian organisms.
Report the coordinates! Show the alignments!
List other miRNAs that have the Pyruvat Carboxylase as their target.
Finding splicing signals
Find the 5' and 3' splicing signals at the intron-exon borders of the Pyruvat Carboxylase gene
Hint: basic strategy to solve the task
Get sequences (+10bp/-10bp) around intron-exon borders and exon-intron borders
from pyruvate carboxylase using UCSC table browser or Ensembl
Use Notepad++ and regular expressions to format the obtained sequence files as follows:
3' splice sites file:
ccctccctagATGCTGAAGT
tgccctctagGTGAGATTGC
[...]
5' splice sites file:
GACGGCAGGAGgtgagtgtc
AAACACTAAGGgtaagtcct
[...]
Construct a sequence logo and a frequency plot for both cases using the http://icbi.at/logo/ service
Can you identify a sequence motif? Discuss and compare with splice signals from textbooks.