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Genome Example Below is an example of the search results for 'EST2'. Clickable fields are linked to their help topics. |
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Gene Name:
YLR318W EST2, SGD Link Accession: SGDID:S0004310 Species: Saccharomyces cerevisiae Comments: Chr XII from 766542-769196 |
Run
Local Blast or
Remote Blast. Graph MFE minima or Download Sequence |
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1
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Start Codon
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AAAUUUA
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14
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448
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Stop Codon
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Green: 0 Frame Start Codon Red: 0 Frame Stop Codon Blue: Slippery Site Orange: First -1 Frame Stop Codon |
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>SGDID:S0004310 | YLR318W EST2 |
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Once a single gene is identified of interest, it may be examined
using the 'genome' interface. This page provides some general
information about the gene, its name, the number of foldings
completed in the PRFdb thus far, and the locations of in frame
slippery sites. There is a view of the sequence window showing the
start codon, stop codon, and potential prf signals.
It is possible from here to
blast the currently viewed gene
against all genes in the PRFdb or against the NCBI NR database. It
is also possible to look at the minimume free energy
landscape of the gene.
Gene name The gene name is provided by the SGD or NCBI. It is often but not always the short hand name for the gene. The comments field often proves more useful for actually learning what a given gene is.
Comments The comments field provides a bit more detail than the gene name. It will often provide the gene family, the source of the given sequence (mRNA/cDNA etc) and some information if you need to track down the actual experiment used to generate the sequence.
Link out Each gene comes with a link to its entry at yeastgenome.org or the NCBI. This should make it easier for one to learn more about what this gene is doing. For Homo sapiens sequences, this will also provide a link to the Online Mendelian Inheritance in Man database if one exists.
Position Each gene entry comes with a table sorted by position relative to the start of the mRNA sequence. As a point of reference, the start and stop codons are listed. There is a mild bias towards PRF signals which are 5' proximal, thus examining earlier PRF signals first is useful. Clicking on a position will take you to the detailed information for that particular putative PRF signal.
Slippery Site There are 24 canonical slippery sites following the motif: NNNWWWH. There is mild bias towards slippery sites consisting of all weak bases. Thus examining NNNNNNH PRF signals first is potentially useful.
Number of folds Not every putative PRF signal has been folded yet using pknots, nupack, or hotknots. Sequences which have greater numbers of folks have been folded with a larger number of sequence window sizes and so provide more information. Some sequences have more folds than others due to the way rnamotif was used to look for the potential for pseudoknot forming bases.
Highlighted codons When viewing the mRNA sequence of a particular gene, it is possible to see a few attributes at a glance. The start and stop codons are highlighted in green and red respectively. Each putative PRF signal is visible as a link to its detailed view. Following each PRF signal is its nearest -1 frame stop codon. This provides an easy way for those who wish to clone a given signal to see how far away trouble resides.