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Genome Example
Below is an example of the search results for 'EST2'. Clickable fields are linked to their help topics.


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
Position
Slippery Site
#Folds
1
Start Codon
72
AAAUUUA
14
448
Stop Codon


Green: 0 Frame Start Codon
Red: 0 Frame Stop Codon
Blue: Slippery Site
Orange: First -1 Frame Stop Codon

 

>SGDID:S0004310 | YLR318W EST2
1          ATG AAA ATC TTA TTC GAG TTC ATT CAA GAC AAG CTT GAC ATT     42
43     GAT CTA CAG ACC AAC AGT ACT TAC AAA GAA AAT TTA AAA TGT GGT     87
88     CAC TTC AAT GGC CTC GAT GAA ATT CTA ACT ACG TGT TTC GCA CTA    132
133    CCA AAT TCA AGA AAA ATA GCA TTA CCA TGC CTT CCT GGT GAC TTA    177
178    AGC CAC AAA GCA GTC ATT GAT CAC TGC ATC ATT TAC CTG TTG ACG    222
223    GGC GAA TTA TAC AAC AAC GTA CTA ACA TTT GGC TAT AAA ATA GCT    267
268    AGA AAT GAA GAT GTC AAC AAT AGT CTT TTT TGC CAT TCT GCA AAT    312
313    GTT AAC GTT ACG TTA CTG AAA GGC GCT GCT TGG AAA ATG TTC CAC    357
358    AGT TTG GTC GGT ACA TAC GCA TTC GTT GAT TTA TTG ATC AAT TAT    402
403    ACA GTA ATT CAA TTT AAT GGG CAG TTT TTC ACT CAA ATC GTG GGT    447
448    TAG

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.