Almanac of fission yeast
Useful facts and figures, including ade6 alleles, restriction sites, and codon usage.
| Cell size and growth | |
|---|---|
| Doubling time | Depends on media: typically 2 to 5 hours |
| haploid cell | 12-15 µm at division, 3 - 4 µm width - constant |
| diploid cell | 20 - 25 µm length at division, 4 - 5 µm width - constant |
| 1 - 2 x 109 cells (haploid) | 0.5 g wet weight |
| Average Values for Haploid | |
|---|---|
| 2C DNA content | 33.8 fg per cell |
| RNA content | 3 pg per cell (1 - 2% of which is polyA+) |
| protein content | 210 pg per cell |
| Size of genome | |
|---|---|
| Total genetic size | 2100 centiMorgan |
| Total physical size | 13.8 Megabase (Mb) |
| Number of chromosomes | 3 |
| Chromosome I | 5.7 Mb |
| Chromosome II | 4.6 Mb |
| Chromosome III | 3.5 Mb |
Just where are all those ade6 alleles anyway?
There are numerous ade6 alleles 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.| Alleles of ade6+ | ||||
|---|---|---|---|---|
| allele | nt (if A of ATG is 1) | aa | comments | References |
| M26 | G135T | G46 to stop | dark pink on low ade. UGA codon, can suppress with sup3/9/12. Hyper-rec. Adjacent codon to M375 | Szankasi et al 1988 |
| 51 | C1266T | H423Y | Schär et al 1993 | |
| 52 | T955C | L319S | Pale pink on low ade. Will complement with M210 (D. Pankratz). | Schär et al 1993 |
| 149 | C1180T | S394L | Schär and Kohli 1993 | |
| M210 | C1466T | P489L | dark 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. | Macfarlane and Wahls labs |
| M216 | G46A | G16D | pale pink on low ade. Will complement with M210 and 149 | Szankasi et al 1988 |
| M375 | G132T | G45 to stop | dark pink on low ade. UGA codon; suppressed by sup3/9/12 Adjacent codon to M26. | Szankasi et al 1988 |
| M387 | G1270C | R424P | G to C marker effect | Schär et al 1993 |
| 406 | G2A | M1I | Schär and Kohli 1993 | |
| 421 | G1176A | G393S | Schär and Kohli 1993 | |
| 424 | C1261T | S421L | Schär and Kohli 1993 | |
| 424 | T1222-T | Frameshift | Schär and Kohli 1993 | |
| 469 =L469 | C1467T | R490 to stop | dark pink on low ade. UGA codon; Can suppress with sup3/9/12. Destroys Xho site | Szankasi et al 1988 |
| 485 | C1244G | Y415 to stop | G to C marker effect. UAG codon (not suppressible) | Schär and Kohli 1993 |
| 555 | C124T | ? | Ludin, MS thesis | |
| 687 | T341 +T | Frameshift (114) | Schär and Kohli 1993 | |
| 704 | T645A | C215 to stop | v. dark pink on low ade. Can suppress with sup3. (Note conflict: reported by Schär 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) | Park JM, Intine RV, Maraia RJ. Gene Expr. 2007;14(2):71-81. |
| 706 | C48T | R51 to stop | v. dark pink on low ade. UGA codon. Can suppress with sup3/9/12. | Grimm et al, 1994 |
| A1943 | G1068A | G357R | Schär and Kohli 1993 | |
| T1994 | C1119T | Q374 to stop | UAG codon | Schär and Kohli 1993 |
| A2097 | T1222A | L408 to stop | UAA codon | Schär and Kohli 1993 |
| A2196 | T1321A | L441 to stop | UAG codon | Schär and Kohli 1993 |
| A2244 | T1369A | M487K | Schär and Kohli 1993 | |
| T2291 | G1416T | G473 to stop | UGA codon | Schär and Kohli 1993 |
| N/N | internal deletion | v. dark pink on low ade. Minigene. | ? | |
Restriction site usage
This table was generated by A. John Callegari at Sloan Kettering (callegaa AT mskcc.org). Send questions or comments to John.| Restriction site usage in S. pombe genome | |||
|---|---|---|---|
| Sites in Pombe Genome | Random DNA Expect | Average fragment size | |
| PvuII | 2,142 | 3,076 | 5,882 |
| PmlI | 684 | 3,076 | 18,421 |
| AluI | 47,242 | 49,218 | 266 |
| RsaI | 29,655 | 49,218 | 424 |
| BsaBI | 3,103 | 3,076 | 4060 |
| BsrBI | 1,328 | 3,076 | 9487 |
| DraI | 15,932 | 3,076 | 790 |
| EcoRV | 4,965 | 3,076 | 2537 |
| HpaI | 1,801 | 3,076 | 6,996 |
| NaeI | 365 | 3,076 | 34,520 |
| StuI | 911 | 3,076 | 13,830 |
| AscI | 9 | 192 | 1,400,000 |
| NotI | 13 | 192 | 969,230 |
| BamHI | 1,460 | 3,076 | 8,630 |
| BglII | 2,042 | 3,076 | 6,170 |
| EcoRI | 4,180 | 3,076 | 3,014 |
| HindIII | 6,457 | 3,076 | 1,951 |
| MluI | 823 | 3,076 | 15,309 |
| PvuI | 1,012 | 3,076 | 12,450 |
| KpnI | 1,165 | 3,076 | 10,815 |
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.
Codon Usage Table
Created with the GCG CODONFREQUENCY program , using 153 fission yeast genes. Three highly expressed genes, fyi1+/spi1+, adh+, and tpi1+, were also compared. Reference: Forsburg, Yeast 10:1045, 1994| Amino Acid | Triplet codon | Total number | per 1000 | Fraction (153 genes) | Fraction (High expr) |
|---|---|---|---|---|---|
| Gly | GGG | 281.00 | 3.62 | 0.07 | 0.00 |
| Gly | GGA | 1204.00 | 15.52 | 0.29 | 0.00 |
| Gly | GGT | 1942.00 | 25.04 | 0.47 | 0.86 |
| Gly | GGC | 713.00 | 9.19 | 0.17 | 0.14 |
| Glu | GAG | 1622.00 | 20.91 | 0.33 | 0.70 |
| Glu | GAA | 3366.00 | 43.40 | 0.67 | 0.30 |
| Asp | GAT | 2979.00 | 38.41 | 0.70 | 0.49 |
| Asp | GAC | 1267.00 | 16.34 | 0.30 | 0.51 |
| Val | GTG | 607.00 | 7.83 | 0.12 | 0.00 |
| Val | GTA | 913.00 | 11.77 | 0.19 | 0.01 |
| Val | GTT | 2385.00 | 30.75 | 0.49 | 0.47 |
| Val | GTC | 979.00 | 12.62 | 0.20 | 0.51 |
| Ala | GCG | 365.00 | 4.71 | 0.08 | 0.00 |
| Ala | GCA | 1141.00 | 14.71 | 0.24 | 0.04 |
| Ala | GCT | 2288.00 | 29.50 | 0.48 | 0.55 |
| Ala | GCC | 1018.00 | 13.13 | 0.21 | 0.41 |
| Arg | AGG | 356.00 | 4.59 | 0.09 | 0.00 |
| Arg | AGA | 810.00 | 10.44 | 0.20 | 0.00 |
| Ser | AGT | 1012.00 | 13.05 | 0.15 | 0.03 |
| Ser | AGC | 701.00 | 9.04 | 0.10 | 0.03 |
| Lys | AAG | 1993.00 | 25.70 | 0.40 | 0.90 |
| Lys | AAA | 2979.00 | 38.41 | 0.60 | 0.10 |
| Asn | AAT | 2561.00 | 33.02 | 0.64 | 0.20 |
| Asn | AAC | 1416.00 | 18.26 | 0.36 | 0.80 |
| Met | ATG | 1692.00 | 21.82 | 1.00 | 1.00 |
| Ile | ATA | 847.00 | 10.92 | 0.18 | 0.00 |
| Ile | ATT | 2845.00 | 36.68 | 0.60 | 0.55 |
| Ile | ATC | 1079.00 | 13.91 | 0.23 | 0.45 |
| Thr | ACG | 461.00 | 5.94 | 0.11 | 0.02 |
| Thr | ACA | 1036.00 | 13.36 | 0.25 | 0.00 |
| Thr | ACT | 1808.00 | 23.31 | 0.43 | 0.42 |
| Thr | ACC | 909.00 | 11.72 | 0.22 | 0.56 |
| Amino Acid | Triplet codon | Total number | per 1000 | Fraction (153 genes) | Fraction (High expr) |
|---|---|---|---|---|---|
| Trp | TGG | 695.00 | 8.96 | 1.00 | 1.00 |
| End | TGA | 29.00 | 0.37 | 0.15 | 0.00 |
| Cys | TGT | 710.00 | 9.15 | 0.61 | 0.18 |
| Cys | TGC | 447.00 | 5.76 | 0.39 | 0.82 |
| End | TAG | 47.00 | 0.61 | 0.24 | 0.00 |
| End | TAA | 120.00 | 1.55 | 0.61 | 1.00 |
| Tyr | TAT | 1667.00 | 21.49 | 0.64 | 0.25 |
| Tyr | TAC | 957.00 | 12.34 | 0.36 | 0.75 |
| Leu | TTG | 1865.00 | 24.05 | 0.25 | 0.32 |
| Leu | TTA | 1942.00 | 25.04 | 0.26 | 0.10 |
| Phe | TTT | 2285.00 | 29.46 | 0.70 | 0.38 |
| Phe | TTC | 966.00 | 12.46 | 0.30 | 0.63 |
| Ser | TCG | 561.00 | 7.23 | 0.08 | 0.03 |
| Ser | TCA | 1309.00 | 16.88 | 0.19 | 0.00 |
| Ser | TCT | 2350.00 | 30.30 | 0.34 | 0.35 |
| Ser | TCC | 947.00 | 12.21 | 0.14 | 0.55 |
| Arg | CGG | 247.00 | 3.18 | 0.06 | 0.00 |
| Arg | CGA | 596.00 | 7.68 | 0.15 | 0.00 |
| Arg | CGT | 1505.00 | 19.41 | 0.37 | 0.88 |
| Arg | CGC | 502.00 | 6.47 | 0.13 | 0.12 |
| Gln | CAG | 838.00 | 10.81 | 0.28 | 0.14 |
| Gln | CAA | 2184.00 | 28.16 | 0.72 | 0.86 |
| His | CAT | 1257.00 | 16.21 | 0.71 | 0.41 |
| His | CAC | 517.00 | 6.67 | 0.29 | 0.59 |
| Leu | CTG | 491.00 | 6.33 | 0.07 | 0.03 |
| Leu | CTA | 599.00 | 7.72 | 0.08 | 0.00 |
| Leu | CTT | 2051.00 | 26.45 | 0.27 | 0.40 |
| Leu | CTC | 555.00 | 7.16 | 0.07 | 0.15 |
| Pro | CCG | 331.00 | 4.27 | 0.09 | 0.00 |
| Pro | CCA | 967.00 | 12.47 | 0.26 | 0.03 |
| Pro | CCT | 1734.00 | 22.36 | 0.46 | 0.56 |
| Pro | CCC | 710.00 | 9.15 | 0.19 | 0.42 |