ORF numbers
francis at NCBI.NLM.NIH.GOV
francis at NCBI.NLM.NIH.GOV
Mon Jul 10 23:59:53 EST 1995
> From: cgdn at uhura.cc.rochester.edu (Craig Duncan)
> Subject: ORF numbers
> Yeast open reading frames have been assigned numbers, for example
> YKL203C for the TOR2 gene on chromosome 11. My question is this:
> how do I find out which number has been assigned to a given gene?
> Is there some kind of central database which stores this information?
> I have looked at the SGD. It contains a few of these numbers, but
> not for most genes.
Dear Craig,
I think you will find all numbers/names in the SGD, but a nice table
that I like to consult ids the one maintained by Amos Bairoch, at the
Universite de Geneve (home of Swiss-Prot, the protein database).
Go and have a look at:
http://expasy.hcuge.ch/sprot/sp-docu.html
where you will find:
Yeast Chromosome I entries
Yeast Chromosome II entries
Yeast Chromosome III entries
Yeast Chromosome V entries
Yeast Chromosome VIII entries
Yeast Chromosome IX entries
Yeast Chromosome XI entries
I append the text version (WWW has links to Swiss-Prot) of
the Yeast Chromosome XI.
regards,
francis
--
| B.F. Francis Ouellette
| GenBank
|
| francis at ncbi.nlm.nih.gov
------------------------------------------------------------------------------
SWISS-PROT Protein Sequence Data Bank.
Release 32.0, June 1995
------------------------------------------------------------------------------
Yeast Chromosome XI entries
------------------------------------------------------------------------------
Amos Bairoch Email: bairoch at cmu.unige.ch
Medical Biochemistry Department
University of Geneva
Switzerland
------------------------------------------------------------------------------
Document name: YEAST11.TXT
------------------------------------------------------------------------------
=======================================
Yeast chromosome XI open reading frames
=======================================
The complete DNA sequence of chromosome XI of the yeast S.cerevisiae has been
determined in the framework of the European Uninion genome sequencing
programmes.
See: Dujon B., et al.
Nature 369:371-378(1994).
Correspondence concerning the molecular biology of the work presented:
Bernard Dujon
Unite de Genetique moleculaire des levures
Departement de Biologie moleculaire
Institut Pasteur 25 rue du Dr. Roux
F-75724 PARIS-CEDEX 15, France.
Tel. : +33-1-45 68 84 82 or +33-1-45 68 84 78
FAX : +33-1-40 61 30 60
E-Mail: bdujon at mendel.sis.pasteur.fr
Size of CHRXI: 666 Kb
Total number of ORFs currently in SWISS-PROT: 332
======================
ORF codes nomenclature
======================
YX[L|R]ddd[w|c]
Y = Yeast
X = Letter representing the chromosome (in this case X is 'K' for CHRXI)
L | R = 'L' is for Left arm; 'R' is for Right arm
ddd = ORF number on the left or right arm
c | w = 'c' is for complementary strand; 'w' is for Watson strand
==================
Categories of ORFs
==================
1: genetically and biochemically characterized
2: genetically characterized, but exact function not known
3: high similarity to a protein of characterized function
4: high similarity to a protein of uncharacterized function
5: low similarity to an existing protein
6: no known similarity (temporary assignment)
7: probable non-expressed ORF
---------- ---------- ------ ---- ------------------- --------------- ----
ORF SWISS-PROT S-PROT Size Gene name and ORF code Cat.
code entry name AC a.a. synonyms synonyms
---------- ---------- ------ ---- ------------------- --------------- ----
YKL225w YKW5_YEAST P36030 115 6
YKL224c YKW4_YEAST P35994 123 4
YKL223w YKW3_YEAST P36031 110 4
YKL222c YKW2_YEAST P35995 705 3
YKL221w YKW1_YEAST P36032 473 3
YKL220c YKW0_YEAST P36033 711 3
YKL219w YKV9_YEAST P36034 407 4
YKL218c YKV8_YEAST P36007 326 3
YKL217w YKV7_YEAST P36035 616 3
YKL216w PYRD_YEAST P28272 314 URA1 1
YKL215c YKV5_YEAST P28273 1286 3
YKL214c YKV4_YEAST P36036 203 5
YKL213c YKV3_YEAST P36037 715 3
YKL212w RSD1_YEAST P32368 623 RSD1; SAC1 1
YKL211c TRPG_YEAST P00937 484 TRP3 1
YKL210w UBA1_YEAST P22515 1024 UBA1 1
YKL209c STE6_YEAST P12866 1290 STE6 1
YKL208w YKU8_YEAST P36038 271 6
YKL207w YKU7_YEAST P36039 260 6
YKL206c YKU6_YEAST P36040 267 5
YKL205w LOS1_YEAST P33418 1100 LOS1 1
YKL204w YKU4_YEAST P36041 632 5
YKL203c TOR2_YEAST P32600 2473 TOR2; DRR2 1
YKL202w YKU2_YEAST P36042 193 6
YKL201c YKU1_YEAST P36043 539 4
YKL200c YKU0_YEAST P36044 398 4
YKL199c YKT9_YEAST P36045 187 6
YKL198c KKT8_YEAST P36002 560 3
YKL197c PAS1_YEAST P24004 1043 PAS1 2
YKL196c YKT6_YEAST P36015 200 3
YKL195w YKT5_YEAST P36046 427 5
YKL194c SYTM_YEAST P07236 462 MST1 1
YKL193c YKT3_YEAST P36047 338 3
YKL192c ACP_YEAST P32463 125 3
YKL191w DPH2_YEAST P32461 534 DPH2 2
YKL190w CALB_YEAST P25296 174 CNB1; YCNB; YCN2 1
YKL189w YKS9_YEAST P32464 399 4
YKL188c YKS8_YEAST P34230 853 YKL741 3
YKL187c YKS7_YEAST P34231 750 5
YKL186c YKS6_YEAST P34232 184 6
YKL185w YKS5_YEAST P34233 588 5
YKL184w DCOR_YEAST P08432 466 ORD1 1
YKL183w YKS3_YEAST P34234 306 6
YKL182w FAS1_YEAST P07149 2051 FAS1 1
YKL181w KPR1_YEAST P32895 427 PRS1; PRPS; PRP1 1
YKL180w RL17_YEAST P05740 183 RPL17 1
YKL179c YKR9_YEAST P34237 679 5
YKL178c STE3_YEAST P06783 470 STE3 1
YKL177w YKR7_YEAST P34238 112 6
YKL176c YKR6_YEAST P34239 828 YKL642 6
YKL175w YKR5_YEAST P34240 503 YKL640 6
YKL174c YKR4_YEAST P36029 618 YKL639 3
YKL173w GI10_YEAST P36048 1008 GIN10 YKL637 1
YKL172w YKR2_YEAST P36049 427 YKL636 6
YKL171w KKR1_YEAST P36003 928 YKL635 3
YKL170w RM38_YEAST P35996 138 MRPL38 YKL634 1
YKL169c YKQ9_YEAST P36050 127 YKL633 6
YKL168c KKQ8_YEAST P36004 734 YKL632 3
YKL167c RM49_YEAST P32388 137 MRP49 YKL631 1
YKL166c KAPC_YEAST P05986 398 TPK3; PKA3 YKL630 1
YKL165c YKQ5_YEAST P36051 919 YKL619 5
YKL164c PIR1_YEAST Q03178 341 PIR1 YKL618 2
YKL163w PIR3_YEAST Q03180 361 PIR3 YKL617 2
YKL162c YKQ2_YEAST P36052 402 YKL616 6
YKL161c KKQ1_YEAST P36005 433 YKL615 3
YKL160w YKQ0_YEAST P36053 145 YKL614 6
YKL159c YKP9_YEAST P36054 211 YKL613 6
YKL158w YKP8_YEAST P36055 100 YKL612 6
YKL157w APE2_YEAST P32454 844 APE2; LAP1 YKL611 1
YKL156w R271_YEAST P35997 82 3
YKL155c YKP5_YEAST P36056 628 YKL610 6
YKL154w YKP4_YEAST P36057 244 YKL609 3
YKL153w YKP3_YEAST P36058 169 YKL608 7
YKL152c PMGY_YEAST P00950 246 GPM1; GPM YKL607 1
YKL151c YKP1_YEAST P36059 337 YKL606 4
YKL150w YKP0_YEAST P36060 302 YKL605 3
YKL149c DBR1_YEAST P24309 405 DBR1; PRP26 YKL604 1
YKL148c DHSA_YEAST Q00711 640 SDHA; SDH1 YKL602 1
YKL147c YKO7_YEAST P36061 205 YKL601 6
YKL146w YKO6_YEAST P36062 692 YKL600 6
YKL145w TBP3_YEAST P33299 467 YTA3; CIM5 1
YKL144c YKO4_YEAST P35718 212 YKL1; UNF1 3
YKL143w LTV1_YEAST P34078 463 LTV1 YKL2 2
YKL142w RT08_YEAST P35719 219 MRP8 YKL3 1
YKL141w SDH3_YEAST P33421 198 SDH3; CYB3 YKL4 1
YKL140w TGL1_YEAST P34163 548 TGL1 YKL5 2
YKL139w CTK1_YEAST Q03957 528 CTK1 1
YKL138c RM31_YEAST P14063 131 MRPL31 1
YKL137w YKN7_YEAST P36064 103 6
YKL136w YKN6_YEAST P36065 132 7
YKL135c ADB2_YEAST P36000 726 APL2 1
YKL134c YKN4_YEAST P35999 770 3
YKL133c YKN3_YEAST P36066 463 5
YKL132c FOLC_YEAST P36001 430 3
YKL131w YKN1_YEAST P36067 173 6
YKL130c YKN0_YEAST P36068 246 6
YKL129c YKM9_YEAST P36006 1271 3
YKL128c YKM8_YEAST P36069 295 6
YKL127w PGMU_YEAST P33401 570 PGM1 1
YKL126w YPK1_YEAST P12688 680 YPK1 1
YKL125w YKM5_YEAST P36070 627 6
YKL124w YKM4_YEAST P32343 579 YKL529 6
YKL123w YKM3_YEAST P36071 126 6
YKL122c SR21_YEAST P32342 167 SRP21 YKL527 6
YKL121w YKM1_YEAST P32330 852 YKL525 4
YKL120w PMT_YEAST P32332 324 PMT; PMT1 YKL522 2
YKL119c VM12_YEAST P32341 215 VMA12, VPH2; CLS10 YKL520 2
YKL118w YKL8_YEAST P36072 103 7
YKL117w YKL7_YEAST P28707 216 YKL518 6
YKL116c KKL6_YEAST P28708 518 YKL516 3
YKL115c YKL5_YEAST P36073 130 6
YKL114c APN1_YEAST P22936 366 APN1 YKL513 1
YKL113c YKL3_YEAST P26793 382 YKL510 3
YKL112w BAF1_YEAST P14164 731 BAF1; ABF1; OBF1 YKL505 1
YKL111c YKL1_YEAST P36074 111 7
YKL110c KT12_YEAST P34253 313 KTI12 YKL500; YKL446 2
YKL109w HAP4_YEAST P14064 554 HAP4 YKL465 1
YKL108w YKK8_YEAST P34252 453 YKL463 6
YKL107w YKK7_YEAST P34251 309 YKL462 6
YKL106w AATM_YEAST Q01802 451 AAT1 YKL461 1
YKL105c YKK5_YEAST P34250 1132 YKL459 6
YKL104c GFA1_YEAST P14742 717 GFA1 YKL457 1
YKL103c AMPL_YEAST P14904 514 APE1; LAP4 YKL455 1
YKL102c YKK2_YEAST P34249 101 YKL454 6
YKL101w KKK1_YEAST P34244 1518 YKL453 3
YKL100c YKK0_YEAST P34248 587 YKL450 6
YKL099c YKJ9_YEAST P34247 256 YKL449 6
YKL098w YKJ8_YEAST P34246 357 YKL448 6
YKL097c YKJ7_YEAST P34245 136 YKL445 6
YKL096w CWP1_YEAST P28319 239 CWP1 YKL443; YJU1 2
YKL095w YKJ5_YEAST P28320 278 YKL442; YJU2 2
YKL094w YKJ4_YEAST P28321 313 YKL441; YJU3 5
YKL093w MBR1_YEAST P23493 339 MBR1 YKL440 2
YKL092c BUD2_YEAST P33314 1104 BUD2; CLA2; ERC25 YKL424 1
YKL091c YKJ1_YEAST P33324 310 3
YKL090w YKJ0_YEAST P36075 443 6
YKL089w MIF2_YEAST P35201 549 MIF2 1
YKL088w YKI8_YEAST P36076 571 4
YKL087c CYT2_YEAST Q00873 224 CYT2 1
YKL086w YKI6_YEAST P36077 127 6
YKL085w MDHM_YEAST P17505 334 MDH1 1
YKL084w YKI4_YEAST P36078 116 6
YKL083w YKI3_YEAST P36079 204 7
YKL082c YKI2_YEAST P36080 434 6
YKL081w EF1H_YEAST P36008 412 TEF4 1
YKL080w VATC_YEAST P31412 392 VMA5; VAT3; VATC YKL410 1
YKL079w SMY1_YEAST P32364 656 SMY1 YKL409 2
YKL078w YKH8_YEAST P36009 735 YKL408 3
YKL077w YKH7_YEAST P36081 392 6
YKL076c YKH6_YEAST P36082 127 6
YKL075c YKH5_YEAST P36083 450 6
YKL074c YKH4_YEAST P36084 527 YKL358 6
YKL073w YKH3_YEAST P36016 881 YKL355 3
YKL072w YKH2_YEAST P36085 766 YKL352 6
YKL071w YKH1_YEAST P36086 256 4
YKL070w YKH0_YEAST P36087 169 YKL343 5
YKL069w YKG9_YEAST P36088 180 YKL340 6
YKL068w N100_YEAST Q02629 959 NSP100; NUP100 YKL336 1
YKL067w NDK_YEAST P36010 153 NDK1; YNK1; YNK YKL333 3
YKL066w YKG6_YEAST P36089 147 YKL332 6
YKL065c YKG5_YEAST P35723 206 YKL331 6
YKL064w YKG4_YEAST P35724 969 6
YKL063c YKG3_YEAST P35725 167 YKL327 6
YKL062w MSN4_YEAST P33749 630 MSN4 2
YKL061w YKG1_YEAST P35727 113 YKL321 6
YKL060c ALF_YEAST P14540 358 FBA1 YKL320 1
YKL059c YKF9_YEAST P35728 441 YKL316 6
YKL058w TOA2_YEAST P32774 122 TOA2 1
YKL057c YKF7_YEAST P35729 1037 YKL314; YKL313 6
YKL056c TCTP_YEAST P35691 167 YKL312 2
YKL055c YKF5_YEAST P35731 278 3
YKL054c YKF4_YEAST P35732 738 YKL308 6
YKL053w YKF3_YEAST P35733 124 YKL307 6
YKL052c YKF2_YEAST P35734 292 YKL306 6
YKL051w YKF1_YEAST P35735 353 YKL303 6
YKL050c YKF0_YEAST P35736 922 YKL301; YKL263 6
YKL049c CSE4_YEAST P36012 229 CSE4 YKL262 1
YKL048c ELM1_YEAST P32801 640 ELM1 YKL261 1
YKL047w YKE7_YEAST P36090 516 YKL260 6
YKL046c YKE6_YEAST P36091 449 YKL259 6
YKL045w PRI2_YEAST P20457 528 PRI2 YKL258 1
YKL044w YKE4_YEAST P36092 106 YKL257 6
YKL043w PHD1_YEAST P36093 366 PHD1 YKL256 1
YKL042w YKE2_YEAST P36094 363 YKL255 6
YKL041w YKE1_YEAST P36095 224 YKL254 6
YKL040c YKE0_YEAST P32860 256 YKL253 4
YKL039w PTM1_YEAST P32857 531 PTM1 YKL252 2
YKL038w YKD8_YEAST P32862 1170 YKL251 3
YKL037w YKD7_YEAST P32858 118 YKL250 6
YKL036c YKD6_YEAST P32859 130 YKL249 6
YKL035w UDPG_YEAST P32861 499 YKL248 3
YKL034w YKD4_YEAST P36096 758 YKL247 5
YKL033w YKD3_YEAST P36097 1038 YKL246 6
YKL032c IXR1_YEAST P33417 597 IXR1 YKL245 1
YKL031w YKD1_YEAST P36098 137 YKL244 7
YKL030w YKD0_YEAST P36099 201 YKL243 6
YKL029c MAOX_YEAST P36013 669 3
YKL028w T2EA_YEAST P36100 482 TFA1 1
YKL027w YKC7_YEAST P36101 447 4
YKL026c GSHH_YEAST P36014 167 3
YKL025c YKC5_YEAST P36102 679 5
YKL024c UMPK_YEAST P15700 204 URA6; SOC8 1
YKL023w YKC3_YEAST P36103 277 6
YKL022c CC16_YEAST P09798 840 CDC16 2
YKL021c MK11_YEAST P20484 468 MAK11 2
YKL020c SP23_YEAST P35210 1082 SPT23 2
YKL019w RAM2_YEAST P29703 316 RAM2 1
YKL018w YKB8_YEAST P36104 329 5
YKL017c YKB7_YEAST P34243 683 5
YKL016c ATP7_YEAST P30902 173 ATP7 1
YKL015w PUT3_YEAST P25502 979 PUT3 1
YKL014c YKB4_YEAST P34241 1764 6
YKL013c YKB3_YEAST P33204 171 YKL166 6
YKL012w YKB2_YEAST P33203 583 YKL165 5
YKL011c CCE1_YEAST Q03702 353 CCE1 YKL164 1
YKL010c YKB0_YEAST P33202 1483 YKL162 4
YKL009w YKA9_YEAST P33201 236 YKL160 5
YKL008c YKA8_YEAST P28496 418 YKL156 3
YKL007w CAPA_YEAST P28495 268 CAP1 YKL155 1
YKL006w R14A_YEAST P36105 138 RPL14A YKL153 1
YKL005c YKA5_YEAST P36106 594 YKL150 5
YKL004w YKA4_YEAST P36107 401 6
YKL003c RT17_YEAST P28778 131 MRP17 1
YKL002w YKA2_YEAST P36108 151 6
YKL001c KAPS_YEAST Q02196 202 MET14 1
YKR001c VPS1_YEAST P21576 704 VPS1; SPO15; LAM1 2
YKR002w PAP_YEAST P29468 568 PAP1 1
YKR003w YKY3_YEAST Q02201 448 YK102 4
YKR004c YKY4_YEAST Q02202 292 YK103 6
YKR005c YKY5_YEAST Q02203 447 YK104 6
YKR006c RM13_YEAST Q02204 275 MRPL13 YK105 1
YKR007w YKY7_YEAST Q02205 184 YK106 6
YKR008w YKY8_YEAST Q02206 625 YK107 4
YKR009c FOX2_YEAST Q02207 900 FOX2 YK108 1
YKR010c YKY0_YEAST Q02208 771 YK109 6
YKR011c YKZ1_YEAST Q02209 353 YK110 6
YKR012c YKZ2_YEAST P36109 125 6
YKR013w YKZ3_YEAST P36110 329 YK111 4
YKR014c YP52_YEAST P36018 234 YPT52 YK112 2
YKR015c YKZ5_YEAST P36111 568 6
YKR016w YKZ6_YEAST P36112 540 6
YKR017c YKZ7_YEAST P36113 551 3
YKR018c YKZ8_YEAST P36114 725 6
YKR019c YKZ9_YEAST P36115 615 6
YKR020w YK00_YEAST P36116 164 6
YKR021w YK01_YEAST P36117 915 6
YKR022c YK02_YEAST P36118 322 6
YKR023w YK03_YEAST P36119 530 6
YKR024c YK04_YEAST P36120 742 5
YKR025w YK05_YEAST P36121 282 6
YKR026c E2BA_YEAST P14741 305 GCN3; AAS2 1
YKR027w YK07_YEAST P36122 765 4
YKR028w YK08_YEAST P36123 1098 4
YKR029c YK09_YEAST P36124 751 4
YKR030w YK10_YEAST P36125 273 6
YKR031c YK11_YEAST P36126 1683 6
YKR032w YK12_YEAST P36127 104 6
YKR033c YK13_YEAST P36128 141 7
YKR034w DA80_YEAST P26343 269 DAL80; UGA43 1
YKR035c YK15_YEAST P36129 213 6
YKR036c YK16_YEAST P36130 659 4
YKR037c YK17_YEAST P36131 295 6
YKR038c YK18_YEAST P36132 421 3
YKR039w GAP1_YEAST P19145 602 GAP1 1
YKR040c YK20_YEAST P36133 167 6
YKR041w YK21_YEAST P36134 250 6
YKR042w YK22_YEAST P36135 450 4
YKR043c YK23_YEAST P36136 271 6
YKR044w YK24_YEAST P36137 443 6
YKR045c YK25_YEAST P36138 191 6
YKR046c YK26_YEAST P36139 283 6
YKR047w YK27_YEAST P36140 101 6
YKR048c NAP1_YEAST P25293 417 NAP1 1
YKR049c YK29_YEAST P36141 133 6
YKR050w TRK2_YEAST P28584 889 TRK2 1
YKR051w YK31_YEAST P36142 418 6
YKR052c MRS4_YEAST P23500 304 MRS4 2
YKR053c YK33_YEAST P23501 404 6
YKR054c DYHC_YEAST P36022 4092 DYN1; DHC1 1
YKR055w RHO4_YEAST Q00246 291 RHO4 1
YKR056w RNC1_YEAST P33753 617 RNC1; NUD1 1
YKR057w RS21_YEAST P05760 87 RPS25 1
YKR058w YK38_YEAST P36143 480 6
YKR059w IF4A_YEAST P10081 395 TIF1 1
YKR060w YK40_YEAST P36144 274 6
YKR061w KTR2_YEAST P33550 425 KTR2 2
YKR062w T2EB_YEAST P36145 328 TFA2 1
YKR063c LAS1_YEAST P36146 502 LAS1 2
YKR064w YK44_YEAST P36023 863 3
YKR065c YK45_YEAST P36147 197 6
YKR066c CCPR_YEAST P00431 361 CCP1; CCP; CPO 1
YKR067w YK47_YEAST P36148 743 4
YKR068c YK48_YEAST P36149 193 6
YKR069w SUMT_YEAST P36150 593 3
YKR070w YK50_YEAST P36151 352 5
YKR071c YK51_YEAST P36152 348 6
YKR072c SIS2_YEAST P36024 562 SIS2 2
YKR073c YK53_YEAST P36153 106 7
YKR074w YK54_YEAST P36154 155 6
YKR075c YK55_YEAST P36155 307 4
YKR076w YK56_YEAST P36156 370 4
YKR077w YK57_YEAST P36157 363 6
YKR078w YK58_YEAST P36158 585 6
YKR079c YK59_YEAST P36159 838 6
YKR080w MTD1_YEAST Q02046 320 MTD1 YKR400 1
YKR081c YK61_YEAST P36160 344 YKR401 6
YKR082w N133_YEAST P36161 1157 NUP133 YKR402 1
YKR083c YK63_YEAST P36162 133 YKR403 6
YKR084c HBS1_YEAST P32769 611 HBS1 YKR404 2
YKR085c RM20_YEAST P22354 195 MRPL20 YKR405 1
YKR086w PR16_YEAST P15938 1071 PRP16 YKR406 1
YKR087c YK67_YEAST P36163 314 YKR407 6
YKR088c YK68_YEAST P36164 337 YKR408 6
YKR089c YK69_YEAST P36165 910 YKR409 6
YKR090w YK70_YEAST P36166 706 4
YKR091w YK71_YEAST P36167 152 YKR411 6
YKR092c SR40_YEAST P32583 406 SRP40 YKR412A 2
YKR093w PTR2_YEAST P32901 601 PTR2 YKR413 1
YKR094c UBIQ_YEAST P04838 76 UBI2 1
RLUB_YEAST P14796 52 UBI2 1
YKR095w MLP1_YEAST Q02455 1875 MLP1 YKR415 2
YKR096w YK76_YEAST P36168 1195 4
YKR097w PPCK_YEAST P10963 549 PCK1; PPC1; PEPC 1
YKR098c UBPX_YEAST P36026 717 3
YKR099w BAS1_YEAST P22035 811 BAS1 1
YKR100c YK80_YEAST P36169 241 4
YKR101w SIR1_YEAST P21691 678 SIR1 2
YKR102w YK82_YEAST P36170 1169 4
YKR103w YK83_YEAST P36028 1218 3
YKR104w YK84_YEAST P36171 306 3
YKR105c YK85_YEAST P36172 582 4
YKR106w YK86_YEAST P36173 615 4
More information about the Yeast
mailing list