Department of Cell Biology & Molecular Genetics
1. Find the sequence of the protein which this mRNA would produce?
-Go to a protein translation site at
http://alces.med.umn.edu/cuse.html.
Copy and paste the above sequence into the "raw sequence box" (you need to
scroll query type to be on "raw" and fill in genebank locus box with a name-
e.g. "cDNA1"). Leave all other settings at the default and hit submit button
at the bottom of the page. You will see output of the different open
reading frames. Which one is most likely to be the protein sequence
actually coded by the mRNA? Save this sequence for cutting and pasting
later.
2. Search a DNA sequence database with the mRNA sequence:
-Go to a Blast search at
http://www.ncbi.nlm.nih.gov/blast/blast.cgi and
perform a blast search. Select blastn in the program selection. Copy
and paste the protein sequence from your previous search onto the search
form. Fast A format requires a ">name" before the sequence. What
functions do you see appearing on the list of similar sequences?
3. What might be the function of this protein?
-Go to a Blast search at
http://www.ncbi.nlm.nih.gov/blast/blast.cgi and
perform a blast search . Select blastp in the program selection. Cut
and past the protein sequence from your previous search onto the search form.
Fast A format requires a ">name" as a separate line before the sequence,
but it also works without it. Does the list of similar sequences appear more
focused than the DNA based search?
4. Search a protein database for conserved sequence motifs:
-Cut and paste the protein or nucleotide sequence into the search form on
Blocks at
http://blocks.fhcrc.org/blocks/blocks_search.html.
You can use either the above mRNA sequence or the open reading frame
protein sequence you determined in #1 above. This search compares your sequence
to conserved mino acid motifs in known proteins. What conserved motifs
are seen in this protein?
-Alternately, you can use Prosites at:
http://www.expasy.ch/tools/scnpsit1.html.
Here, paste the protein sequence.
Last revised: Feb 16, 2000- Straney
Sequence of a cDNA you isolated from a cDNA library of rose:
attgtggaaa agaaaagaag tctaagaaaa aacccaaaag ctgcaactat ggcctatgaa aacaaaccca
acacggtcct ggacgctgat gcccaaagaa gattgggaag gggaaagatc gagatcaagc ggatcgaaaa
caccaccaat cgtcaagtca ccttctgcaa aaggcgcaat ggtttgctca agaaggccta tgagctctct
gtgctctgtg atgctgaggt tgctctcata gtcttctcta accgtggccg cctctatgag tattcaaaca
acagtgttag agaaacaatt gaacgataca agaaggcatg tgcagattct tcaaataatg gatctgtctc
tgaagctact actcagtact atcagcaaga agctgccaaa ctgcgtgccc agataaccac tttgcagaac
agtaacaggg gttatatggc tgagggtttg agcaatatgt ctatcaagga gctcaagggc gtggagacca
aacttgagaa agcaattagc agaattagat ccaagaagaa tgagctcttg tttgccgaaa ttgagtacat
gcagaaaagg gaacttgact tgcacaacaa taaccagctc ctccgagcaa agatagctga taatgagagg
caccagcaaa gcataaatgc cattgcaggt gggcatggaa gctacgagat catgcagccg actcagccat
ttcatgaggc tcgcaactat tttcaagtga atgctttgga acccaatatc catcagtact cgcgccatga
ccagatttcc cttcaattag tttgatatat gtatgcttgg cctggtttct gctgacttca tcttcaatgg
agggtgcata tgtgtaatgg caacagatga aagctagcta gctacaagta gcactttgtt aagtaggagt
taagcagaaa ccaacttcgc tttgtggtta attaattaaa aaacctctcc cacagttagt actggcatta
caccaagtac taaaagggga tatcttgttt gtataattat tactgaatgc tgcagcaata tgttctaaga
ttctgtgaga tacactttta acagttgaat tcatcattga tcttttataa aaaaaaaaaa aaaaaa
(alternate sequence- example from class)