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BIO3350 Bioinformatics
Question:
Gene Structure
Dna
1.Use a BLAST search to discover the name of the gene.
2.Discover which human chromosome your gene is on and identify the genes directly upstream and downstream from your gene on the chromosome.
3.Hi-C Juicebox- Understand your gene in the context of genome organization. What other genes are physically near by? What domain is your gene found within? What epigenetic marks are associated with your gene?
4.Find the complete mRNA sequence (cDNA) including 5’ UTR, 3’UTR, Start codon, stop codon, and polyadenylation signal (if available).
5.Design PCR oligos to amplify and clone complete coding region including an appended C-terminal FLAG-tag. Use restriction sites that will allow you to clone your PCR fragment into the pcDNA3.1 cloning vector for expression in mammalian cells. Don’t forget a Kozak sequence for good expression!
-report oligo sequences and indicate regions of complementarity, start and stop codons, and restriction sites used.
6.Translate the protein.-show mRNA sequence (including FLAG tag) with associated protein translation
7.Perform protein blast search to find homologus proteins in 3 other organisms-show document of top hit in each of three organisms.
8.Note, you may have to enter your sequence data in FASTA It is very important to follow this format precisely or the program will get confused. There is an example of what your praline input should look like at the end of this document.
-show document of alignment with amino acid conservation.
Rna
1.How many exons and introns are in your gene? What percentage (rough guess) of basepairs in the gene fall within exons vs introns?
2.Find the 5’, branch point, and 3’ splice sites in the original sequence we gave you. If your sequence did not contain an intron, find these splice sites in the intron directly downstream from the exon you were given. Do these splice sites conform to the general rules?
3.Design 3 siRNAs to target the mRNA
-provide purchasing information for 3 siRNAs
4.Mutate your gene. Design mutagenic tools to mutate bases 100 – 103 from purines to pyrimidine’s or pyrimidine’s to purines (depending on
sequence) Ex. The sequence GAT could be mutated to CTA. Use at least two mutagenic tools.
5.Prepare one paragraph describing the known function of the protein. Prepare an endnote library or other referencing program (mendeley) for your references.
BIO3350 Bioinformatics
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Tellus molestie nunc non blandit massa enim nec dui. Tellus molestie nunc non blandit massa enim nec dui. Ac tortor vitae purus faucibus ornare suspendisse sed nisi. Pharetra et ultrices neque ornare aenean euismod. Pretium viverra suspendisse potenti nullam ac tortor vitae. Morbi quis commodo odio aenean sed. At consectetur lorem donec massa sapien faucibus et. Nisi quis eleifend quam adipiscing vitae proin sagittis nisl rhoncus. Duis at tellus at urna condimentum mattis pellentesque. Vivamus at augue eget arcu dictum varius duis at. Justo donec enim diam vulputate ut. Blandit libero volutpat sed cras ornare arcu. Ac felis donec et odio pellentesque diam volutpat commodo. Convallis a cras semper auctor neque. Tempus iaculis urna id volutpat lacus. Tortor consequat id porta nibh.
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Hac habitasse platea dictumst vestibulum rhoncus est pellentesque. Amet dictum sit amet justo donec enim diam vulputate ut. Neque convallis a cras semper auctor neque vitae. Elit at imperdiet dui accumsan. Nisl condimentum id venenatis a condimentum vitae sapien pellentesque. Imperdiet massa tincidunt nunc pulvinar sapien et ligula. Malesuada fames ac turpis egestas maecenas pharetra convallis posuere. Et ultrices neque ornare aenean euismod. Suscipit tellus mauris a diam maecenas sed enim. Potenti nullam ac tortor vitae purus faucibus ornare. Morbi tristique senectus et netus et malesuada. Morbi tristique senectus et netus et malesuada. Tellus pellentesque eu tincidunt tortor aliquam. Sit amet purus gravida quis blandit. Nec feugiat in fermentum posuere urna. Vel orci porta non pulvinar neque laoreet suspendisse interdum. Ultricies tristique nulla aliquet enim tortor at auctor urna. Orci sagittis eu volutpat odio facilisis mauris sit amet.
Tellus molestie nunc non blandit massa enim nec dui. Tellus molestie nunc non blandit massa enim nec dui. Ac tortor vitae purus faucibus ornare suspendisse sed nisi. Pharetra et ultrices neque ornare aenean euismod. Pretium viverra suspendisse potenti nullam ac tortor vitae. Morbi quis commodo odio aenean sed. At consectetur lorem donec massa sapien faucibus et. Nisi quis eleifend quam adipiscing vitae proin sagittis nisl rhoncus. Duis at tellus at urna condimentum mattis pellentesque. Vivamus at augue eget arcu dictum varius duis at. Justo donec enim diam vulputate ut. Blandit libero volutpat sed cras ornare arcu. Ac felis donec et odio pellentesque diam volutpat commodo. Convallis a cras semper auctor neque. Tempus iaculis urna id volutpat lacus. Tortor consequat id porta nibh.
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