wiki:PombeGeneLosses

Version 9 (modified by vw253, 6 years ago) (diff)

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Known pombe gene losses

Lipid metabolic process (mainly fatty acid oxidation?)

  • YAT1 YAR035W carnitine O-acetyltransferase (human, CPT2)
  • CAT2 YML042W (human CRAT)

  • DCI1 YOR180C (human PECI)
  • POT1 (FOX3) YIL160C
  • TES1 YJR019C (human ACOT8)
  • POX1 YGL205W (human candidates ACOX1 and 2)
  • FAA2 YER015W (human ACSL1,5,6 ?)
  • PXA2 YKL188C (possible human ABCD4)
  • EHT1 YBR177c
  • FAT1 YBR041W (from Compara) transporter

  • YDR287W (from Compara)
  • YDR294C (from Compara)
  • YHR046C (from Compara)
  • YJL153C (from Compara)
  • YLR118C (from Compara)
  • ECI1 YLR284C (human, PECI)

  • YMR210W similar to EEB1 and EHT1 medium-chain fatty acid metabolic process

TMA (translation machinery associated)

  • TMA64 YDR117C (human LGTN)
  • TMA7 YLR262C-A ribosome associated (human TMA7) ​http://pfam.xfam.org/family/PF09072?type=Family#tabview=tab7 (no pombe family member) could not find with tblastn
  • STF2 YGR008C TMA10 paralog ( human SERBP1) (not in compara list)
  • TMA10 YLR327C STF2 paralog ( conserved in human SERBP1) (not in compara list)
  • YER176W

Nucleobase containing small molecule met

  • YBR140C (from Compara)
  • YCR011C (from Compara)
  • YER155C (from Compara) check class
  • YIR027C (from Compara)
  • YKL088W (from Compara)
  • YKR072C (from Compara) CoA-synthesizing protein complex
  • YLR422W (from Compara)
  • YOL059W (from Compara)
  • YOL081W (from Compara)
  • YOR054C (from Compara)
  • YPL147W (from Compara)
  • YPR140W (from Compara)

Tryptophan degradation/ de novo NAD biosynthesis

  • BNA1 YJR025c tryptophan met 3-hydroxyanthranilate 3,4-dioxygenase activity (human HAAO)
  • BNA2 YJR078W tryptophan 2,3-dioxygenase activity (human IDO2)
  • BNA4 YBL098W tryptophan met kynurenine 3-monooxygenase (human KMO)
  • BNA5 YLR231C tryptophan met kynureninase (human KYNU)
  • BNA6 YFR047C biosynthesis of NAD from tryptophan via kynurenine (human QPRT) (missing from compara)

Other cellular amino acid/derivative metabolic process

  • YAL012W (from Compara)
  • YCL064C (from Compara)
  • YFL030W (from Compara)
  • YMR020W FMS1 (from Compara)
  • YNL040W possible FP (from Compara)
  • CYS4 YGR155W cystathionine beta-synthase (human CBS)

Urea metabolism

  • YBR208C (from Compara)

Carbohydrate metabolic process

  • YDL174C (from Compara)
  • YDR109C (from Compara)
  • YHL032C (from Compara)
  • YHR104W (from Compara)
  • YHR210C (from Compara)
  • YMR164C (from Compara)
  • YNR071C (from Compara)
  • YPR026W (from Compara)

Subset of carbohydrate , Glycogen metabolism

  • GLC3 YEL011W glycogen branching enzyme (human GBE1)
  • GSY1 YFR015C (human GYS1)
  • GLG2 YJL137C
  • GLG1 YKR058W
  • GSY2 YLR258W (human GYS1)
  • GPH1 YPR160W glycogen debranching enzyme (human PYGB)
  • GDB1 YPR184W glycogen debranching enzyme (human AGL)

Transmembrane Transporters

  • PFA4 YOL003C
  • AVT1 YJR001C
  • AVT2 YEL064C
  • FUN26 YAL022C (human SLC29A1,2,3,4)
  • YBR241C (from Compara)
  • YBR296C (from Compara)
  • YCR011C (from Compara)
  • YCR075C (from Compara)
  • YGL104C (from Compara)
  • YGR055W (from Compara)
  • YHL036W (from Compara)
  • YKL221W (from Compara)
  • YLR348C (from Compara)
  • YMR221C (from Compara)
  • YNL125C (from Compara)
  • YNL298W (from Compara) WHY IS THIS MAPPING HERE>=?
  • YOL119C (from Compara)
  • YOR079C (from Compara)
  • YOR306C (from Compara)
  • YPL147W (from Compara)
  • YPR021C (from Compara)
  • YPR192W AQY1 (from Compara)
  • YLL052C AQY2
  • YLL053C
  • YOL075C (from Compara) predict carnitine

transcription and chromatin remodelleing complexes CHRAC and isw1-2 complexes

  • ITC1 YGL133W CHRAC complex isw1-a complex (human BAZ1A,B) (no compara)
  • YPL216W ITC1 paralog (uncharacterised) (human BAZ1A,B) (no compara)
  • IOC3 YFR013W isw1-a (PWWP domain) (no compara REMOVE?)
  • IOC4 YMR044W isw1-b (PWWP domain) (no compara REMOVE?)
  • HHO1 YPL127C histone H1 (human H1F0)
  • YCL055W (from Compara)
  • YDR440W (from Compara)
  • YGL096W (from Compara)
  • YGL254W (from Compara)
  • YGR040W (from Compara)
  • YJL056C (from Compara)
  • YER040W (from Compara)
  • YKR034W (from Compara)
  • YKR099W (from Compara)
  • YMR164C (from Compara)
  • YNL239W (from Compara)
  • YPL177C (from Compara)

Chromosome organization

  • ISW1 YBR245C isw1-a/b complex amily confirmed by compara (FP?)
  • ISW2 YOR304W CHRAC complex family confirmed by compara (FP?)
  • YDR096W (from Compara)
  • HOS1 YPR068C (from Compara)

Nucleocytoplsmic transport

  • YKL068W (from Compara) (checked)
  • YMR047C (from Compara) (checked)
  • YNL298W (from Compara) (checked)

DNA recombination

  • YBR186W (from Compara)
  • YDL154W (from Compara)
  • YFL003C (from Compara)
  • YFR038W (from Compara)
  • YGL251C (from Compara)
  • YPL164C (from Compara)

DNA repair

  • YFL007W this isn't repair, cant figure why its mapping here
  • YOR386W (from Compara)
  • YDR054C (from Compara)
  • YGR109C (from Compara)
  • OGG1 YML060W "CBF3 complex" base excision repair protein (human OGG1)

DNA replication

  • YDL101C (from Compara)

Miitotoic cell cycle regulation === (does not map here)

  • YPR120C (from Compara)

tRNA metabolic process

  • TRM3 YDL112W (from Compara) checked
  • PUS6 YGR169C (from Compara) checked
  • RNY1 YPL123C (no compara)

Signalling

  • YBR164C (from Compara)
  • YBR264C (from Compara)
  • YDL159W (from Compara)
  • YDR006C (from Compara)
  • YDR294C (from Compara)
  • YDR466W (from Compara)
  • YPL051W (from Compara)
  • YOR212W (from Compara) not annotated to signalling
  • YGR152C (from Compara)
  • YKL092C (from Compara) not annotated to signalling
  • PDE2 YOR360C high affinity 3',5'-cAMP phosphodiesterase (family has human members, but no pombe member ​http://pfam.xfam.org/family/PF00233?type=Family#tabview=tab7)

Mitochondrial organization

Proteases

  • YCR045C (from Compara) (REMOVE?)
  • YCL057W (from Compara)
  • YFR006W (from Compara)
  • YOL057W

Proteasome assembly

  • YGL004C (from Compara)

Misc

  • move to above (in list)
  • YPC1 YBR183W paralog YDC1 (conserved in human ACER3) (no compara)
  • YDC1 YPL087W paralog YPC1 (conserved in human ACER3) (no compara)
  • SRN2 YLR119W Component of the ESCRT-I complex (no compara)
  • KXD1 YGL079W BLOC-1 complex (conserved in human KXD1)
  • SNN1 YNL086W BLOC-1 complex (conserved in human SNAPIN & BLOC1S6)
  • YKR013W (from Compara)

Unknown process

  • YGR001C
  • YHL021C
  • YJL078C
  • YJL079C
  • YMR114C
  • YMR110C

Compara false positive

to check:

  • YJR151C
  • YBL064C
    • YIL112W (should have pombe)