User:Ilya/Yeast/Miscellaneous

• Yeast cells are approximately round and have a diameter of about 2 to 10 µm on average.
• Petite-negative: a mutation of yeast that produces small (petite) anaerobic-like colonies.

Abbreviations

• AKR - ankyrin repeat-containing protein
• BEM - bud emergence mediator
• CAP - Catabolite Activator Protein, aka CRP for cAMP Receptor Protein is a transcription promoter that binds at more than 100 sites within the E. coli genome.
• ERK - extracellular signal-regulated kinase
• GAP - GTPas-activating protein
• GDI - guanine nucleotide dissociation inhibitor
• GEF - guanine nucleotide exchange factor (dissociation stimulator)
• HOG - high-osmolarity glycerol
• JIP - JNK-interacting protein
• KSR - Kinase Suppressor of Ras
• MP1 - MEK Partner 1
• MTL - mating type-like locus
• RGS - regulator of G protein signaling
• RHO - Ras homolog

SGD

ORF naming convention

• How do I interpret the chromosomal coordinates of a gene?

The start and stop coordinates refer to the entire chromosome, where position 1 is the first nucleotide of the left arm of the chromosome. The Watson strand is defined as running 5' to 3' from the left to right telomere, and the Crick strand is complementary to it.

• What is the significance of the systematic names assigned to the open reading frames?

The first letter of each name is 'Y', denoting 'yeast'. The second letter denotes chromosome number (I=A, II=B, etc.). The third letter denotes the chromosomal arm where each locus resides: L for left and R for right. Numbers were assigned to open reading frames sequentially from the centromeres out towards each telomere. The final 'W' or 'C' in the systematic name refers to location on the Watson or Crick strand. So, for example, YNR045W is the 45th open reading frame from the centromere on the right arm of chromosome XIV.

• How are newly identified open reading frames named?

When additional open reading frames are identified between genes, '-A' is appended to the systematic name of the adjacent gene closest to the centromere, e.g. an open reading frame on the Watson strand between YNR045W and YNR046W would be named YNR045W-A. If a second open reading frame were identified on the Watson strand in this region, it would be named YNR045W-B. A new open reading frame on the Crick strand would be YNR045C-A.

• An ORF (Open Reading Frame) corresponds to a stretch of DNA that could potentially be translated into a polypeptide or RNA; i.e., it begins with an ATG "start" codon and terminates with one of the 3 "stop" codons. For an ORF to be considered as a good candidate for coding a bona fide cellular protein, a minimum size requirement is often set, e.g., many of the systematic sequencing groups define an ORF as a stretch of DNA that would code for a protein of 100 amino acids or more. An ORF is not usually considered equivalent to a gene or locus until there has been shown to be a phenotype associated with a mutation in the ORF, and/or an mRNA transcript or a gene product generated from the ORF's DNA has been detected.