Department of Cell Biology & Molecular Genetics
alternate sequence- example from class
Sequence of a cDNA you isolated from a cDNA library of soybean:
tgtcttgacg cacaacccaa agaaaaggtc tattggtgag gtcaattcca agagctagtt
cattgaattg gttttgatca aaatgagtga aactaccaaa ggcaacatac aagacagaac
catgaggttg ttggtcgagc caactcatac aagagagatc ttcttcccag tattgtccga
ttgattttgc agttgcaatt gtgtcaccat aacttctcaa caatggacca attggcacaa
gattaggaat agaggataat ggcccaggtt caagttcatt tgtggtgttg caaagccacc
attcagtcag attcaaactt cgtgtacact gaatcaaata tntaattact attttaccg
Sequence of a cDNA you isolated from a cDNA library of rice:
atggccgcgg ccaccatggc gctctcctcc ccggtgatgg cccgcgcggc gccgtcgacc
tcctccgcgc tcttcggcga ggcgcggatc accatgcgca agaccgccgc gaagcccaag
ccggcggcgt cgtcggggag cccgtggtac ggcgccgacc gcgtcctcta cctcggcccg
ctctccggcg agccgccgag ctacctcacc ggcgagttcc cgggcgacta cgggtgggac
accgcggggc tctccgccga cccggagacg ttcgccaaga accgggagct ggagctgatc
cactcccgat gggcgatgct gggcgcgctc ggctgcgtct tcccggagct cctcgcccgg
aacggcgtca agttcggcga ggccgtgtgg ttcaaggcgg gctcgcagat cttcagcgag
ggcgggctcg actacctcgg caacccgagc ctgatccacg cgcagagcat cctcgccatc
tgggcggtgc aggtggtgct catgggcgcc gtcgaggggt accgcatcgc cggcgggccg
ctcggcgagg tcgtcgaccc gctctacccc ggcggcgcct tcgacccgct cggcctcgcc
gatgaccccg aggcgttcgc ggagctcaag gtgaaggaga tcaagaaagg ccgcctcgcc
atgttctcca tgttcggctt cttcgtccag gccatcgtca ccggcaaggg ccccctcgag
aacctcgccg accacctcgc cgaccccgtc aacaacaacg cctgggcgta cgccaccaac
ttcgtccccg gcaagtga
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