Closed ValWood closed 2 months ago
kimrutherford
commented
2 months ago do you know why a query on dev intersecting the transit peptides with mitochondrion included bot1
Do you mean on my desktop version? dev won't have the transit peptides until tomorrow morning.
Can you add a link to the query results?
kimrutherford
commented
2 months ago The version shown on my desktop version doesn't include all the input data so might not include GOA for example. I stopped the local load as soon as the transit peptide data was in Chado because that's what I was testing.
kimrutherford
commented
2 months ago so might not include GOA
It doesn't include Canto data either because that takes an hour or two to load.
kimrutherford
commented
2 months ago I uploaded the list of mitochondrion downloaded from the main server: https://desktop.kmr.nz/results/from/id/3fd1fed4-d5ff-4ada-8eaa-a315ca39875e
There are 4 genes that have a transit peptide not annotated to mitochondrion: https://desktop.kmr.nz/results/from/id/1eb723a5-5093-4d55-8c95-4ecebfcdd7b0
ValWood
commented
2 months ago Its OK I did the same!
ValWood
commented
2 months ago Well I got one more
| Systematic ID | Gene name | Product description |
|---|---|---|
| SPBC56F2.09c | arg5 | arginine specific carbamoyl-phosphate synthase subunit Arg5 |
| SPBC17D11.02c | hrd1 | Hrd1 ubiquitin ligase complex E3 subunit Hrd1 |
| SPCC4G3.13c | cue1 | Hrd1 ubiquitin ligase complex, CUE domain protein Cue1 |
| SPCC548.06c | ght8 | plasma membrane hexose:proton symporter, unknown specificity Ght8 |
| SPBC1677.03c | tda1 | threonine ammonia-lyase Tda1 |
Tda1- problem with the legacy file annotation, now fixed
SPBC17D11.02c | hrd1 | Hrd1 ubiquitin ligase complex E3 subunit Hrd1 SPCC4G3.13c | cue1 | Hrd1 ubiquitin ligase complex, CUE domain protein Cue1 SPCC548.06c | ght8 | plasma membrane hexose:proton symporter, unknown specificity Ght8 look like False positives, so the false positive rate is really low, but these
[ ] could also be incorrect translation sites. It will be interesting to see if hrd1 and cue1 also have signal peptides (they should be ER), but odd that both subunits get a transit peptide.
[x] arg5, should be mitochondrial. I will make an IC to the complex GO annotation
ValWood
commented
2 months ago only these don't have a mitochondrial annotation now, so these are FP. It shouldn't be so misleading because we know what they are.
It's possible the ligase might have a mitochondrial role, unlikely for ght8
Systematic ID Gene name Product descriptionSorted by: Product description SPBC56F2.09c arg5 arginine specific carbamoyl-phosphate synthase subunit Arg5 SPAC25G10.02 cce1 cruciform-cutting endonuclease Cce1 SPCC18.18c fum1 fumarate hydratase Fum1 SPCC4G3.13c cue1 Hrd1 ubiquitin ligase complex, CUE domain protein Cue1 SPBC3D6.03c trz2 mitochondrial 3'-tRNA processing endonuclease tRNAse Z, Trz2 SPBC1718.06 msp1 mitochondrial dynamin family fusion GTPase Msp1 SPAC17C9.08 pnu1 mitochondrial endodeoxyribonuclease Pnu1 SPBC14C8.16c bot1 mitochondrial ribosomal protein subunit S45 SPBC800.07c tsf1 mitochondrial translation elongation factor EF-Ts Tsf1 SPCC548.06c ght8 plasma membrane hexose:proton symporter, unknown specificity Ght8 SPAC140.01 sdh2 succinate dehydrogenase (ubiquinone) iron-sulfur protein subunit SPBC1677.03c tda1 threonine ammonia-lyase Tda1