{"id":329,"date":"2023-07-12T12:01:45","date_gmt":"2023-07-12T19:01:45","guid":{"rendered":"https:\/\/live-usc-dornsife.pantheonsite.io\/pombenet\/?page_id=329"},"modified":"2023-07-27T11:39:18","modified_gmt":"2023-07-27T18:39:18","slug":"almanac","status":"publish","type":"page","link":"https:\/\/dornsife.usc.edu\/pombenet\/almanac\/","title":{"rendered":"Almanac of fission yeast"},"content":{"rendered":"\n\n \n \n\n\n\n\n\n\n\n
\n\n \n \n
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Useful facts and figures, including ade6 alleles, restriction sites, and codon usage.<\/p>\n

 <\/p>\n

Cell Size & Growth<\/h3>\n\n\n\n\n\n\n
Doubling time<\/td>\nDepends on media: typically 2 to 5 hours<\/td>\n<\/tr>\n
haploid cell<\/td>\n12-15 \u00b5m at division, 3 – 4 \u00b5m width – constant<\/td>\n<\/tr>\n
diploid cell<\/td>\n20 – 25 \u00b5m length at division, 4 – 5 \u00b5m width – constant<\/td>\n<\/tr>\n
1 – 2 x 109 cells (haploid)<\/td>\n0.5 g wet weight<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

<\/h3>\n

Size of Genome<\/h3>\n\n\n\n\n\n\n\n
Total physical size<\/td>\n13.8 Megabase (Mb)<\/td>\n<\/tr>\n
Number of chromosomes<\/td>\n3<\/td>\n<\/tr>\n
Chromosome I<\/td>\n5.7 Mb<\/td>\n<\/tr>\n
Chromosome II<\/td>\n4.6 Mb<\/td>\n<\/tr>\n
Chromosome III<\/td>\n3.5 Mb<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

<\/h3>\n

Average Values for Haploid<\/h3>\n\n\n\n\n\n
2C DNA content<\/td>\n33.8 fg per cell<\/td>\n<\/tr>\n
RNA content<\/td>\n3 pg per cell (1 – 2% of which is polyA+)<\/td>\n<\/tr>\n
protein content<\/td>\n210 pg per cell<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

<\/h3>\n

Just where are all those ADE6 Alleles anyway?<\/h3>\n
\n

There are numerous\u00a0ade6<\/i>\u00a0alleles used for various reasons in various strains, which gets confusing for everyone. Here is a guide to some of them. We would like to be inclusive, so please send us references and info for any other alleles you know about! Enormous thanks to Juerg Kohli, who corrected what we had and provided much more. Also, thanks to John Armstrong, Ramsey MacFarlane, Greg Freyer, Jun Gao, Dan Pankratz and Katja Ludin for providing additional information.<\/p>\n<\/div>\n

<\/h3>\n

Alleles of ade6+<\/h3>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
allele<\/td>\nnt<\/td>\n<\/td>\n<\/td>\n<\/td>\n<\/tr>\n
(if A of ATG is 1)<\/td>\naa<\/td>\ncomments<\/td>\nReferences<\/td>\n<\/td>\n<\/tr>\n
M26<\/td>\nG135T<\/td>\nG46 to stop<\/td>\ndark pink on low ade. UGA codon, can suppress with sup3\/9\/12. Hyper-rec. Adjacent codon to M375<\/td>\nSzankasi et al 1988<\/td>\n<\/tr>\n
51<\/td>\nC1266T<\/td>\nH423Y<\/td>\n<\/td>\nSch\u00e4r et al 1993<\/td>\n<\/tr>\n
52<\/td>\nT955C<\/td>\nL319S<\/td>\nPale pink on low ade. Will complement with M210 (D. Pankratz).<\/td>\nSch\u00e4r et al 1993<\/td>\n<\/tr>\n
149<\/td>\nC1180T<\/td>\nS394L<\/td>\n<\/td>\nSch\u00e4r and Kohli 1993<\/td>\n<\/tr>\n
M210<\/td>\nC1466T<\/td>\nP489L<\/td>\ndark pink on low ade. Will complement with M216. Although most agree on this mutation, Greg Freyer reports his as a G1470A lesion, making a G491S mutation. In all cases, it destroys the Xho site.<\/td>\nMacfarlane and Wahls labs<\/td>\n<\/tr>\n
M216<\/td>\nG46A<\/td>\nG16D<\/td>\npale pink on low ade. Will complement with M210 and 149<\/td>\nSzankasi et al 1988<\/td>\n<\/tr>\n
M375<\/td>\nG132T<\/td>\nG45 to stop<\/td>\ndark pink on low ade. UGA codon; suppressed by sup3\/9\/12 Adjacent codon to M26.<\/td>\nSzankasi et al 1988<\/td>\n<\/tr>\n
M387<\/td>\nG1270C<\/td>\nR424P<\/td>\nG to C marker effect<\/td>\nSch\u00e4r et al 1993<\/td>\n<\/tr>\n
406<\/td>\nG2A<\/td>\nM1I<\/td>\n<\/td>\nSch\u00e4r and Kohli 1993<\/td>\n<\/tr>\n
421<\/td>\nG1176A<\/td>\nG393S<\/td>\n<\/td>\nSch\u00e4r and Kohli 1993<\/td>\n<\/tr>\n
424<\/td>\nC1261T<\/td>\nS421L<\/td>\n<\/td>\nSch\u00e4r and Kohli 1993<\/td>\n<\/tr>\n
424<\/td>\nT1222-T<\/td>\nFrameshift<\/td>\n<\/td>\nSch\u00e4r and Kohli 1993<\/td>\n<\/tr>\n
469<\/td>\n<\/td>\n<\/td>\n<\/td>\n<\/td>\n<\/tr>\n
=L469<\/td>\nC1468T<\/td>\nR490 to stop<\/td>\ndark pink on low ade. UGA codon; Can suppress with sup3\/9\/12. Destroys Xho site<\/td>\nSzankasi et al 1988<\/td>\n<\/tr>\n
485<\/td>\nC1244G<\/td>\nY415 to stop<\/td>\nG to C marker effect. UAG codon (not suppressible)<\/td>\nSch\u00e4r and Kohli 1993<\/td>\n<\/tr>\n
555<\/td>\nC124T<\/td>\n?<\/td>\n<\/td>\nLudin, MS thesis<\/td>\n<\/tr>\n
687<\/td>\nT341 +T<\/td>\nFrameshift (114)<\/td>\n<\/td>\nSch\u00e4r and Kohli 1993<\/td>\n<\/tr>\n
704<\/td>\nT645A<\/td>\nC215 to stop<\/td>\nv. dark pink on low ade. Can suppress with sup3. (Note conflict: reported by Sch\u00e4r and Kohli 1993 as C845A?; C282 to stop. It is possible there are two different UGA nonsense alleles both suppressible by sup3-5, and both are called 704)<\/td>\nPark JM, Intine RV, Maraia RJ. Gene Expr. 2007;14(2):71-81.<\/td>\n<\/tr>\n
706<\/td>\nC48T<\/td>\nR51 to stop<\/td>\nv. dark pink on low ade. UGA codon. Can suppress with sup3\/9\/12.<\/td>\nGrimm et al, 1994<\/td>\n<\/tr>\n
A1943<\/td>\nG1068A<\/td>\nG357R<\/td>\n<\/td>\nSch\u00e4r and Kohli 1993<\/td>\n<\/tr>\n
T1994<\/td>\nC1119T<\/td>\nQ374 to stop<\/td>\nUAG codon<\/td>\nSch\u00e4r and Kohli 1993<\/td>\n<\/tr>\n
A2097<\/td>\nT1222A<\/td>\nL408 to stop<\/td>\nUAA codon<\/td>\nSch\u00e4r and Kohli 1993<\/td>\n<\/tr>\n
A2196<\/td>\nT1321A<\/td>\nL441 to stop<\/td>\nUAG codon<\/td>\nSch\u00e4r and Kohli 1993<\/td>\n<\/tr>\n
A2244<\/td>\nT1369A<\/td>\nM487K<\/td>\n<\/td>\nSch\u00e4r and Kohli 1993<\/td>\n<\/tr>\n
T2291<\/td>\nG1416T<\/td>\nG473 to stop<\/td>\nUGA codon<\/td>\nSch\u00e4r and Kohli 1993<\/td>\n<\/tr>\n
N\/N<\/td>\ninternal deletion<\/td>\n<\/td>\nv. dark pink on low ade. Minigene.<\/td>\n?<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n
<\/div>\n
<\/div>\n
\n

Other Mutant Alleles<\/h3>\n<\/div>\n\n\n\n\n\n
allele<\/td>\nnt<\/td>\n<\/td>\n<\/td>\n<\/tr>\n
(if A of ATG is 1)<\/td>\naa<\/td>\ncomments<\/td>\nReferences<\/td>\n<\/tr>\n
his7-366<\/td>\nC868T<\/td>\nH290Y<\/td>\nHaochen Yu, pombelist<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

 <\/p>\n

\n

Restriction Site Usage<\/h3>\n
\n

This table was generated by A. John Callegari at Sloan Kettering (callegaa AT mskcc.org). Send questions or comments to John. Enzyme<\/p>\n<\/div>\n<\/div>\n

 <\/p>\n

Restriction site usage in S. pombe genome<\/h3>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Sites in Pombe Genome<\/td>\nRandom DNA Expect<\/td>\nAverage fragment size<\/td>\n<\/td>\n<\/tr>\n
PvuII<\/td>\n2,142<\/td>\n3,076<\/td>\n5,882<\/td>\n<\/tr>\n
PmlI<\/td>\n684<\/td>\n3,076<\/td>\n18,421<\/td>\n<\/tr>\n
AluI<\/td>\n47,242<\/td>\n49,218<\/td>\n266<\/td>\n<\/tr>\n
RsaI<\/td>\n29,655<\/td>\n49,218<\/td>\n424<\/td>\n<\/tr>\n
BsaBI<\/td>\n3,103<\/td>\n3,076<\/td>\n4060<\/td>\n<\/tr>\n
BsrBI<\/td>\n1,328<\/td>\n3,076<\/td>\n9487<\/td>\n<\/tr>\n
DraI<\/td>\n15,932<\/td>\n3,076<\/td>\n790<\/td>\n<\/tr>\n
EcoRV<\/td>\n4,965<\/td>\n3,076<\/td>\n2537<\/td>\n<\/tr>\n
HpaI<\/td>\n1,801<\/td>\n3,076<\/td>\n6,996<\/td>\n<\/tr>\n
NaeI<\/td>\n365<\/td>\n3,076<\/td>\n34,520<\/td>\n<\/tr>\n
StuI<\/td>\n911<\/td>\n3,076<\/td>\n13,830<\/td>\n<\/tr>\n
AscI<\/td>\n9<\/td>\n192<\/td>\n1,400,000<\/td>\n<\/tr>\n
NotI<\/td>\n13<\/td>\n192<\/td>\n969,230<\/td>\n<\/tr>\n
BamHI<\/td>\n1,460<\/td>\n3,076<\/td>\n8,630<\/td>\n<\/tr>\n
BglII<\/td>\n2,042<\/td>\n3,076<\/td>\n6,170<\/td>\n<\/tr>\n
EcoRI<\/td>\n4,180<\/td>\n3,076<\/td>\n3,014<\/td>\n<\/tr>\n
HindIII<\/td>\n6,457<\/td>\n3,076<\/td>\n1,951<\/td>\n<\/tr>\n
MluI<\/td>\n823<\/td>\n3,076<\/td>\n15,309<\/td>\n<\/tr>\n
PvuI<\/td>\n1,012<\/td>\n3,076<\/td>\n12,450<\/td>\n<\/tr>\n
KpnI<\/td>\n1,165<\/td>\n3,076<\/td>\n10,815<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n
\n
\n

Stats are based on the three chromosomes downloaded from genbank in August, 2006. There are 12.6 megabases in this sequence, suggesting that about 8.7% of the genome is missing (mostly likely repetitive DNA).Therefore, these stats must be viewed as approximations.<\/p>\n<\/div>\n<\/div>\n

\n

Codon Usage Table<\/h3>\n
\n

Created with the GCG CODONFREQUENCY program , using 153 fission yeast genes. Three highly expressed genes,\u00a0fyi1+\/spi1+, adh+,<\/i>and\u00a0tpi1+<\/i>, were also compared. Reference:\u00a0Forsburg, Yeast 10:1045, 1994<\/a><\/p>\n<\/div>\n<\/div>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Amino Acid<\/th>\nTriplet codon<\/th>\nTotal number<\/th>\nper 1000<\/th>\nFraction (153 genes)<\/th>\nFraction (High expr)<\/th>\n<\/tr>\n
Gly<\/td>\nGGG<\/td>\n281.00<\/td>\n3.62<\/td>\n0.07<\/td>\n0.00<\/td>\n<\/tr>\n
Gly<\/td>\nGGA<\/td>\n1204.00<\/td>\n15.52<\/td>\n0.29<\/td>\n0.00<\/td>\n<\/tr>\n
Gly<\/td>\nGGT<\/td>\n1942.00<\/td>\n25.04<\/td>\n0.47<\/td>\n0.86<\/td>\n<\/tr>\n
Gly<\/td>\nGGC<\/td>\n713.00<\/td>\n9.19<\/td>\n0.17<\/td>\n0.14<\/td>\n<\/tr>\n
Glu<\/td>\nGAG<\/td>\n1622.00<\/td>\n20.91<\/td>\n0.33<\/td>\n0.70<\/td>\n<\/tr>\n
Glu<\/td>\nGAA<\/td>\n3366.00<\/td>\n43.40<\/td>\n0.67<\/td>\n0.30<\/td>\n<\/tr>\n
Asp<\/td>\nGAT<\/td>\n2979.00<\/td>\n38.41<\/td>\n0.70<\/td>\n0.49<\/td>\n<\/tr>\n
Asp<\/td>\nGAC<\/td>\n1267.00<\/td>\n16.34<\/td>\n0.30<\/td>\n0.51<\/td>\n<\/tr>\n
Val<\/td>\nGTG<\/td>\n607.00<\/td>\n7.83<\/td>\n0.12<\/td>\n0.00<\/td>\n<\/tr>\n
Val<\/td>\nGTA<\/td>\n913.00<\/td>\n11.77<\/td>\n0.19<\/td>\n0.01<\/td>\n<\/tr>\n
Val<\/td>\nGTT<\/td>\n2385.00<\/td>\n30.75<\/td>\n0.49<\/td>\n0.47<\/td>\n<\/tr>\n
Val<\/td>\nGTC<\/td>\n979.00<\/td>\n12.62<\/td>\n0.20<\/td>\n0.51<\/td>\n<\/tr>\n
Ala<\/td>\nGCG<\/td>\n365.00<\/td>\n4.71<\/td>\n0.08<\/td>\n0.00<\/td>\n<\/tr>\n
Ala<\/td>\nGCA<\/td>\n1141.00<\/td>\n14.71<\/td>\n0.24<\/td>\n0.04<\/td>\n<\/tr>\n
Ala<\/td>\nGCT<\/td>\n2288.00<\/td>\n29.50<\/td>\n0.48<\/td>\n0.55<\/td>\n<\/tr>\n
Ala<\/td>\nGCC<\/td>\n1018.00<\/td>\n13.13<\/td>\n0.21<\/td>\n0.41<\/td>\n<\/tr>\n
Arg<\/td>\nAGG<\/td>\n356.00<\/td>\n4.59<\/td>\n0.09<\/td>\n0.00<\/td>\n<\/tr>\n
Arg<\/td>\nAGA<\/td>\n810.00<\/td>\n10.44<\/td>\n0.20<\/td>\n0.00<\/td>\n<\/tr>\n
Ser<\/td>\nAGT<\/td>\n1012.00<\/td>\n13.05<\/td>\n0.15<\/td>\n0.03<\/td>\n<\/tr>\n
Ser<\/td>\nAGC<\/td>\n701.00<\/td>\n9.04<\/td>\n0.10<\/td>\n0.03<\/td>\n<\/tr>\n
Lys<\/td>\nAAG<\/td>\n1993.00<\/td>\n25.70<\/td>\n0.40<\/td>\n0.90<\/td>\n<\/tr>\n
Lys<\/td>\nAAA<\/td>\n2979.00<\/td>\n38.41<\/td>\n0.60<\/td>\n0.10<\/td>\n<\/tr>\n
Asn<\/td>\nAAT<\/td>\n2561.00<\/td>\n33.02<\/td>\n0.64<\/td>\n0.20<\/td>\n<\/tr>\n
Asn<\/td>\nAAC<\/td>\n1416.00<\/td>\n18.26<\/td>\n0.36<\/td>\n0.80<\/td>\n<\/tr>\n
Met<\/td>\nATG<\/td>\n1692.00<\/td>\n21.82<\/td>\n1.00<\/td>\n1.00<\/td>\n<\/tr>\n
Ile<\/td>\nATA<\/td>\n847.00<\/td>\n10.92<\/td>\n0.18<\/td>\n0.00<\/td>\n<\/tr>\n
Ile<\/td>\nATT<\/td>\n2845.00<\/td>\n36.68<\/td>\n0.60<\/td>\n0.55<\/td>\n<\/tr>\n
Ile<\/td>\nATC<\/td>\n1079.00<\/td>\n13.91<\/td>\n0.23<\/td>\n0.45<\/td>\n<\/tr>\n
Thr<\/td>\nACG<\/td>\n461.00<\/td>\n5.94<\/td>\n0.11<\/td>\n0.02<\/td>\n<\/tr>\n
Thr<\/td>\nACA<\/td>\n1036.00<\/td>\n13.36<\/td>\n0.25<\/td>\n0.00<\/td>\n<\/tr>\n
Thr<\/td>\nACT<\/td>\n1808.00<\/td>\n23.31<\/td>\n0.43<\/td>\n0.42<\/td>\n<\/tr>\n
Thr<\/td>\nACC<\/td>\n909.00<\/td>\n11.72<\/td>\n0.22<\/td>\n0.56<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

 <\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Amino Acid<\/th>\nTriplet codon<\/th>\nTotal number<\/th>\nper 1000<\/th>\nFraction (153 genes)<\/th>\nFraction (High expr)<\/th>\n<\/tr>\n
Trp<\/td>\nTGG<\/td>\n695.00<\/td>\n8.96<\/td>\n1.00<\/td>\n1.00<\/td>\n<\/tr>\n
End<\/td>\nTGA<\/td>\n29.00<\/td>\n0.37<\/td>\n0.15<\/td>\n0.00<\/td>\n<\/tr>\n
Cys<\/td>\nTGT<\/td>\n710.00<\/td>\n9.15<\/td>\n0.61<\/td>\n0.18<\/td>\n<\/tr>\n
Cys<\/td>\nTGC<\/td>\n447.00<\/td>\n5.76<\/td>\n0.39<\/td>\n0.82<\/td>\n<\/tr>\n
End<\/td>\nTAG<\/td>\n47.00<\/td>\n0.61<\/td>\n0.24<\/td>\n0.00<\/td>\n<\/tr>\n
End<\/td>\nTAA<\/td>\n120.00<\/td>\n1.55<\/td>\n0.61<\/td>\n1.00<\/td>\n<\/tr>\n
Tyr<\/td>\nTAT<\/td>\n1667.00<\/td>\n21.49<\/td>\n0.64<\/td>\n0.25<\/td>\n<\/tr>\n
Tyr<\/td>\nTAC<\/td>\n957.00<\/td>\n12.34<\/td>\n0.36<\/td>\n0.75<\/td>\n<\/tr>\n
Leu<\/td>\nTTG<\/td>\n1865.00<\/td>\n24.05<\/td>\n0.25<\/td>\n0.32<\/td>\n<\/tr>\n
Leu<\/td>\nTTA<\/td>\n1942.00<\/td>\n25.04<\/td>\n0.26<\/td>\n0.10<\/td>\n<\/tr>\n
Phe<\/td>\nTTT<\/td>\n2285.00<\/td>\n29.46<\/td>\n0.70<\/td>\n0.38<\/td>\n<\/tr>\n
Phe<\/td>\nTTC<\/td>\n966.00<\/td>\n12.46<\/td>\n0.30<\/td>\n0.63<\/td>\n<\/tr>\n
Ser<\/td>\nTCG<\/td>\n561.00<\/td>\n7.23<\/td>\n0.08<\/td>\n0.03<\/td>\n<\/tr>\n
Ser<\/td>\nTCA<\/td>\n1309.00<\/td>\n16.88<\/td>\n0.19<\/td>\n0.00<\/td>\n<\/tr>\n
Ser<\/td>\nTCT<\/td>\n2350.00<\/td>\n30.30<\/td>\n0.34<\/td>\n0.35<\/td>\n<\/tr>\n
Ser<\/td>\nTCC<\/td>\n947.00<\/td>\n12.21<\/td>\n0.14<\/td>\n0.55<\/td>\n<\/tr>\n
Arg<\/td>\nCGG<\/td>\n247.00<\/td>\n3.18<\/td>\n0.06<\/td>\n0.00<\/td>\n<\/tr>\n
Arg<\/td>\nCGA<\/td>\n596.00<\/td>\n7.68<\/td>\n0.15<\/td>\n0.00<\/td>\n<\/tr>\n
Arg<\/td>\nCGT<\/td>\n1505.00<\/td>\n19.41<\/td>\n0.37<\/td>\n0.88<\/td>\n<\/tr>\n
Arg<\/td>\nCGC<\/td>\n502.00<\/td>\n6.47<\/td>\n0.13<\/td>\n0.12<\/td>\n<\/tr>\n
Gln<\/td>\nCAG<\/td>\n838.00<\/td>\n10.81<\/td>\n0.28<\/td>\n0.14<\/td>\n<\/tr>\n
Gln<\/td>\nCAA<\/td>\n2184.00<\/td>\n28.16<\/td>\n0.72<\/td>\n0.86<\/td>\n<\/tr>\n
His<\/td>\nCAT<\/td>\n1257.00<\/td>\n16.21<\/td>\n0.71<\/td>\n0.41<\/td>\n<\/tr>\n
His<\/td>\nCAC<\/td>\n517.00<\/td>\n6.67<\/td>\n0.29<\/td>\n0.59<\/td>\n<\/tr>\n
Leu<\/td>\nCTG<\/td>\n491.00<\/td>\n6.33<\/td>\n0.07<\/td>\n0.03<\/td>\n<\/tr>\n
Leu<\/td>\nCTA<\/td>\n599.00<\/td>\n7.72<\/td>\n0.08<\/td>\n0.00<\/td>\n<\/tr>\n
Leu<\/td>\nCTT<\/td>\n2051.00<\/td>\n26.45<\/td>\n0.27<\/td>\n0.40<\/td>\n<\/tr>\n
Leu<\/td>\nCTC<\/td>\n555.00<\/td>\n7.16<\/td>\n0.07<\/td>\n0.15<\/td>\n<\/tr>\n
Pro<\/td>\nCCG<\/td>\n331.00<\/td>\n4.27<\/td>\n0.09<\/td>\n0.00<\/td>\n<\/tr>\n
Pro<\/td>\nCCA<\/td>\n967.00<\/td>\n12.47<\/td>\n0.26<\/td>\n0.03<\/td>\n<\/tr>\n
Pro<\/td>\nCCT<\/td>\n1734.00<\/td>\n22.36<\/td>\n0.46<\/td>\n0.56<\/td>\n<\/tr>\n
Pro<\/td>\nCCC<\/td>\n710.00<\/td>\n9.15<\/td>\n0.19<\/td>\n0.42<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n
\n

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