INTRON PCR PRIMERS AND THEIR GENOMIC COORDINATES

 

This table is supplemental to Davis et al. 2000.  These primers are available on request.
 
ORF NAME 5' Upstream primer 3' (+) Approx genomic coords 5' Downstream primer 3' (-) Approx genomic coords Comments???
YAL030W gcgagctcatgtcgtcatctactccct 87291 87306 chr1 cgggtacctttcacctctttctgctac 87563 87548 chr1  
YBL018C gcggatcctttacaagctttactgttcag 186514 186499 chr2 cgggtaccaaaataccataactacgtttc 186222 186237 chr2  
YBL026W gcgagctcttcaagactttagttgac 170606 170621 chr2 gccccgggcgtcttgtagcaaattcg 170964 170949 chr2  
YBL040C gcgagctcttcaaatttcgaggcagat 142913 142898 chr2 cgggtaccaaagaaataccttcaatg 142636 142651 chr2 +SAC -KPN
YBL050W cggagctcgataagaagtgggcagcac 124994 125009 chr2 gcggtaccatggtggctgcttggacac 125337 125322 chr2  
YBL059W gcggatccatcagtagtgaggaagtc 110705 110720 chr2 cgggtacctattgtctgcgtccg 110961 110946 chr2 Also named YBL050W-KPN
YBR057C gcgagctccgaatcactcgagaacgaa 352639 352624 chr2 gcggtacctaatcttaccaccattttg 352336 352351 chr2  Not previously annotated, no evidence for splicing
YBR078W gcgagctcatgcaattcaagaacgctt 393086 393101 chr2 gcggtaccaaccggagattttgtccaa 393557 393542 chr2  
YBR090C aka YBR089C-A gcggatccttcaggtgaaatgaaatag 426630 426615 chr2 cgggtacctgtctctgttttcattag 426321 426336 chr2 end named YBR090(+)BAM
YBR090C aka YBR089C-A gcgagctcgggtcacgtgcattcccc 427000 426985 chr2 cgggtaccagttaaggccttccacctc 426245 426260 chr2 3' primer named NHP6B(-)
YBR186W gcgagctctcaataaatatcaggacat 602019 602034 chr2 gcggtaccaagggcaatttccttattg 602213 602198 chr2  Not previously annotated, is spliced
YBR219C aka YBR220C gcggatccaatctcatatgtattgtagtc 663053 663038 chr2 cgggtacctaacactccctgcgccaattc 662464 662479 chr2  
YBR230C gcggatccgcatctcataatatgtctgca 680016 680001 chr2 cgggtaccttgaccaagacaacgaggttc 679689 679709 chr2  3' primer has errors, should end ggATTC, works.
YCR033W gcgagctcttcagcggcacctggaagc 185424 185439 chr3 cgggtacccctctggtttgtccaattt 186085 186070 chr3  
YDL012C gcggatccatgtcagctcaagattattac 431508 431493 chr4 cgggtacccttcatttccagaactggccg 431171 431186 chr4  
YDL064W cggagctcatgagtagtttgtgtctac 337489 337504 chr4 gcggtacctgggataccagcttcccat 337730 337715 chr4  
YDL079C gcgagctcgttgccaataagcacgaaa 314435 314420 chr4 gcggtaccacttctgccgtaggataac 313953 313968 chr4  
YDL115 gcgagctcgtaaagagaagaagggatg 255080 255065 chr4 ggcggtaccagctcacagtctttgata 254910 254925 chr4  Not previously annotated, is spliced
YDL125C gcgagctcatggagccattgatatcg 239603 239588 chr4 gccccgggggtaaggaattcgtccgg 239257 239272 chr4  
YDL189W gcggatccatacaactcgacaagttttgg 122020 122035 chr4 cgggtaccgctatttggtgcgatagaagc 122402 122387 chr4  
YDL219W gcggatccattgtcttacaaaaagtcagc 65254 65269 chr4 cgggtacccggtttagttcccttcttgg 65585 65570 chr4  
YDR092W gcggatcccaaaacacctctatagaga 629775 629790 chr4 cgggtaccacagaaatgatcactcgg 630606 630591 chr4  
YDR092 gcgagctccaaaacacctctatagag 629774 629789 chr4 gcgggcccccaacctatcaatattgg 630384 630369 chr4 Synthesized 9/3/98
YDR139C gcgagctcatgattgttaaagtgaag 733915 733900 chr4 gccccgggcctcttagtgttaatacc 733623 733638 chr4  
YDR305C gcgagctcatcttaagcaaaacaaag 1073474 1073459 chr4 gcgagctcaaaaccgtagttctcagtg 1073221 1073236 chr4  
YDR305C gcgagctcatggcagtttatatcttaa 1234023 1234008 chr4 1073748 1073733 chr4 gccccgggtcttgaaataatcttgag 1073173 1073188 chr4 end 47743 1/29/99 end 466649/25/98
YDR318 gcgagctctttacagcaggacattgaa 1103770 1103785 chr4 gcggtaccgattagcgctctcctcatt 1103959 1103944 chr4  Not previously annotated, no evidence for splicing
YDR367W gcggatccctgtgtaaagctgtataagtc 1212748 1212763 chr4 cgggtacccggatgacccgtgaacaatgc 1213076 1213061 chr4  5' primer has c instead of g at 3' end. Does NOT work
YDR367W gcgagctcctgtgtaaagctgtataa 1212745 1212760 chr4     This new 5' primer works
YDR397C cggagctcatgcagcatagcctgttca 1267172 1267157 chr4 gcggtacctatgccggagttgatgatt   This 3' primer is wrong last T doesn't match
YDR397C     gcggtacctatgccggagttgatgatg 1266673 1266688 chr4 New 3' Synthesized 9/10/99
YDR397-X cggagctcagttgtacctattaattaatt 1266904 1266889 chr4     New 5' primer
YEL003++ gcgagctcgtaaatgaacacacattat 147974 147989 chr5      Not previously annotated, no evidence for splicing
YEL003 gcgagctcattcatgagaagtggagaa 148146 148161 chr5 gcggtaccttgtcatgacctaattcta 148357 148342 chr5  
YEL076C-A  gcggatccaaaacactagatgccgtg   cggtcgaccagtgtgcagttggatgc    Repeated Y' element, see Table 2 for coordinates
YER007C-A gcggatccataaccttatgtaaaacc 166942 166927 chr5 cgggtaccttatcttcacatttaatc 166614 166629 chr5  
YER093C-A gcggatccaaggaacttaagaaacgcagg 348376 348361 chr5 cgggtacctatcaatgtgctgaacgtacc 348084 348099 chr5  
YER133W gcgagctcgacgttgataatatcatc 432512 432527 chr5 gccccgggtaatagacaaatagtctc 433332 433317 chr5  
YFL018C gcgagtcgaaatgaagaacagaggaat 103523 103508 chr6 cgggtaccgcctaatttgcctcttttt 102939 102954 chr6  
YFL035C aka YFL034C-A gcggatccatgtccttcttcaacttc 63991 63976 chr6 cgggtaccagatgtcaattgctgtgattg 63663 63678 chr6  
YFR024C gcggatccattaacaatcctattccaagg 203409 203394 chr6 cgggtaccggagctgaccaagtaccatcc 203087 203102 chr6  For some reason we ordered this exact 5' primer twice
YFR024C     cgggtaccgaaaacgacttaacagcatcc 202982 202997 chr6  
YGL033W gcggatcccaataagctatctatgtg 435164 435179 chr7 cgggtaccacagtttcaaaatcaaac 435984 435969 chr7  
YGL033W gcggagctcaacgtgaactgaccaggctc 435593 435608 chr7 cgcggtaccggttgctgttgtttttgtcac 435844 435829 chr7 Marc's HOP2 primers
YGL087C ccggtacccgtagaagaaagcagcgtt 346927 346912 chr7 gccccgggttctgttttcatgattac 346651 346666 chr7 5' primer named YGL087KDN (instead of KPN)
YGL087C+ gcgagctccctacacaatctctgctc 346991 346976 chr7      
YGL178W gcgagctcctcctctccaacacatag 167285 167300 chr7 gccccgggccaagggagattgtgtcg 168240 168225 chr7  
YGL232W gcggatccatgggtgaaaaacgtaac 62076 62091 chr7 cgggtacctctttgatatccccatag 62329 62314 chr7  
YGL251C gcggagctcggcgtcgtaaggatgaaaac 31644 31629 chr7 cgcggtacctactttaaaacttggttggcggc 31360 31375 chr7 Marc's MER3 (aka HFM1) primers
YGR001C gcggatcctacaataaaccactggac 497548 497533 chr7 cgggtacccgctaataaacactttgc 497334 497349 chr7  
YGR001++ gcgagctcccgaaagaatcactgataa 498046 498031 chr7 cgggtacctcaagggcagcgagggcat 497903 497918 chr7  Previously unannotated second intron in this gene
YGR225W ggaagagctcccacttatcaagctcaggcac 946292 946307 chr7 cgcggtaccgccgactgcaagcagg 946453 946438 chr7 Newly annotated, splices. Marc's SPO70 primers
YGR296W         Y' element annotated to have intron, see Table 2
YHL050C         Y' element annotated to have intron, see Table 2
YHR012W gcgagctctaaagatcataaaaatac 129381 129396 chr8 gccccgggtatattgttagatatctg 129763 129748 chr8  
YHR016C gcggatccgtaaaattttcaagagtagtg 138487 138472 chr8 cgggtaccgtaccgtcttttaacctggcc 138051 138066 chr8  
YHR039C cggagctcactgataggcattacaacg 186663 186648 chr8 gcggtacccctctcaatcttccttgaga 186326 186343 chr8  3' primer should end TTCTTGAGA, works, no evidence for splicing
YHR039C-B gcggatccatctctaaaagggagcgt 187768 187753 chr8 cggtcgacaacttatcttgtctgtac 187416 187431 chr8  
YHR041(+)  gcgagctcactgtagatgtcgccgcgt 190012 189992 chr8 gcccggggttcttgatagagcaccg 189612 189628 chr8 end Snthesized 9/23/98
YHR041C+SAC gcgagctcgtcgtgaactgtgatcgtg 190284 190269 chr8     end synthesized 12/15/98
YHR041C gcgagctcttagtatgccagtttcgc 189950 189935 chr8      
YHR041-X cggagctcagtagcaatccatcatgggaaaatc 189860 189845 chr8     New 5' primer
YHR097C gcggatcccaaacaggaaggaccataggc 298600 298585 chr8 gcgcgtctggagcttgctgtttcggtgtc 298248 298263 chr8  
YHR101C cggagtctagcttttgtgcttcggagg 315925 315910 chr8 gcggtacctcctcaggcctggttgatt 315634 315649 chr8 5' primer called SAL, but no Sal site!
YHR101C gcgagctctatttgttgcttattatg 315950 315935 chr8  gccccgggctgtaacgaaacaaactc 315589 315604 chr8 Synthesized 9/23/98
YHR123W gcgagctcatgggatattttgttccgg 354820 354835 chr8 gcggtaccttgggcgccatccacgtgg 355050 355035 chr8  
YHR124W gcgagctcctgcttcaggtgcggcttg 356291 356306 chr8 gcggtaccctgttctgtgcttaattcc 356640 356625 chr8  Not previously annotated, no evidence for splicing
YIL004C gcgagctcaaacaaacagtagttcac 348579 348564 chr9 gccccgggttgagattcaagagatgc 348203 348218 chr9  
YIL123W gcgagctccgtcacgaaaattgcggcg 127854 127869 chr9 cgggtacctgtacgcaacggccctctt 128265 128250 chr9  
YIL123-X cggagctcacatgcctttttttggcg 127909 127924 chr9     New 5' primer
YIL177C         Y' element annotated to have intron, see Table 2
YJL001W gcgagctcatgaatggaattcaagtgg 434854 434869 chr10 cgggtaccataattccaaatggtactg 435216 435201 chr10  
YJL024C gcgagctcggaacaatatcatttctg 396359 396344 chr10 gccccgggaaaatcgctattcctttg 396076 396091 chr10  
YJL024-X cggagctcacaatgattcatgcagttcta 396286 396271 chr10     New 5' primer
YJL041W cggagctcctctgatcgttttgaaaaa 365465 365480 chr10 gcggtaccgcaccagtagaggaattct 365692 365677 chr10  
YJL206C-A gcggatcccgcgggctctatttttcc 50538 50523 chr10 cgggtaccccagaaacttatatatac 50105 50120 chr10  
YJL225C gcggatccctataccacgaagtagcgcag   cgtagtcgacagtcgaggctccgatgaaccg   Repeated Y' element see Table 2 for coordinates
YJR079W gcgagctcgttgatgcagaagcctcg 579955 579970 chr10 cgggtacctcaaacatcgagaagacc 580925 580910 chr10  
YJR079-18 gcgagctcatacatgccaagagaacat 579525 579540 chr10      
YKL002W cggagctcatgagtttgtttgagtggg 437419 437434 chr11 gcggtacctttaatttctgatacaagt 437633 437618 chr11  
YKL006C-A gcgagctcatgtcaaattctaggtatt 430267 430252 chr11 gcggtaccgacagaactgtcagagacc 430001 430016 chr11  
YKL133C gcgagctcagaacgtaaaaacagcatt 193123 193108 chr11 gcggtacccaataaacccaccatatgt 192854 192869 chr11  Not previously annotated, no evidence for splicing
YKL157/8W gcgagctcaaggtacttaaaaacacag 154965 154985 chr11 cgggtaccgacggtgttcaatgttacc 155821 155801 chr11  
YKL186C gcgagctcatgcttctttgattggaca 93555 93540 chr11 cgggtaccagcattaaatattattctg 93136 93151 chr11 end 9/12/99
YLL050 gcgagctcacgtaaacttcagatttc 40463 40448 chr12 gcgggcccgaaggcatcgtaagatgg 40078 40093 chr12  
YLR078C gcgagctcctataatagacaggatcg 286652 286637 chr12 gccccgggttctgcatattgcttaac 286315 286330 chr12  
YLR093 gcgagctccagagtgaaaagcgacaat 327474 327459 chr12 gcggtaccgaagttattgtaccatagt 327172 327187 chr12  Not previously annotated, splices
YLR128W gcggatccaatgaacttacgcagtaa 398458 398473 chr12 cgggtaccttgagagcgtaattgatg 398765 398750 chr12  
YLR128-X cggagctcgagacgttcttgcattca 398511 398526 chr12     New 5' primer
YLR202C gcggatccatgcccaactttcatctt 550636 550621 chr12 cgggtaccgaatgatataaacgaaag 550242 550257 chr12  
YLR202C+SAC gcgagctctttggaaacagctccagtt 551184 551169 chr12      
YLR211 gcgagctcattcaacgacagttatact 564562 564547 chr12 gcggtacctgcatttgtaaaatctcct 564398 564413 chr12  Not previously annotated, splices
YLR275W gcgagctctcattcttaatagcaagc 694301 694316 chr12 gccccgggtgcctgtcgaaagctttc 694656 694641 chr12 Synthesized 9/23/98
YLR275W ccggtacctagaggagtattataaaac 694353 694368 chr12     Also named YLR275KPN 1/22/99
YLR275W gcgagctcttactacgggtaatactac 694226 694241 chr12 gcggtaccggaccatgtttgaattcaa 694553 694538 chr12 end 6/22/99 end 1/29/99
YLR426W gcggatccatagactgtttgtgtcgttgg 987067 987082 chr12 cgggtaccctccagtaataagaactatgc 987353 987338 chr12  
YLR464W         Y' element annotated to have intron, see Table 2
YML025C gcggatccaaagtataatacagaggttcc 225457 225442 chr13 cgggtaccggttctaatgatggaaaggag 225111 225126 chr13  
YML031 gcgagctcagattaattactctccaac 213767 213782 chr13 gcggtacccccttggcgtctgtatcat 214204 214189 chr13  Not previously annotated, no evidence for splicing
YML034C gcgagctccaaatttcatgcggtgacg 211274 211289 chr13 cgggtacctttcaaatcgacacttcat 211730 211715 chr13 Not previously annotated, alternative splicing
YML056C gcggatccaccactgttggtgaagttaag 163775 163760 chr13 cgggtaccacccttgatgccagtaactgg 163189 163204 chr13  
YML067C gcggatccatggcaggattgaagaca 140212 140197 chr13 cgggtacccgtgttgacgtatatatc 139899 139914 chr13  
YML094W ccggtaccacaagaaagagcactgtaa 82249 82264 chr13 gccccggggtataatgatgcagatgc 82574 82559 chr13 Also named YML094KPN 1/22/99
YML094W gcgagctcattttaaatagaaaagtg 82201 82216 chr13     Synthesized 9/23/98
YMR033W gcgagctcatctctaatagtaaactg 337698 337713 chr13 gccccgggatgatatgtgtaggaacc 338032 338017 chr13  
YMR033-X cggagctcacaactactatatgcattg 337768 337783 chr13     New 5' primer
YMR116C gcggatccggttcccgtgacaagacc 500313 500298 chr13 cgggtaccccacaacataatttcacc 499748 499763 chr13  
YMR201 gcgagctctgaaggtatcgaacgtaac 667062 667047 chr13 cgggtaccttggtcgctactcagtatt 666873 666888 chr13  
YMR201C gcgagctcgttgtagggagaaaagag 667141 667126 chr13 gccccgggttatcatcccgattgctg 666792 666807 chr13  
YMR292W gcggatcccttaagatgagttaaaaggcg 854703 854718 chr13 cgggtaccaaaacaaaatattgcccaagg 854995 854980 chr13  
YMR307W gcgagctctggcgtcgcaactgcggac 887056 887071 chr13 cgggtaccgccttaacatcatcatcac 887667 887652 chr13  
YMR307--     cgggtaccgttgcactgtaagactttg 888024 888009 chr13 Synthesized 5/3/99
YNL012 gcgagctcttattgacagtagtactag 609715 609730 chr14 gcggtaccaatcagtttattcttcgtt 609936 609921 chr14  Not previously annotated, splices
YNL012 (2) gcgagctccatggaaacgcatctaata 611437 611457 chr14 gcggtaccacagtagtctttaaagcat 611656 611636 chr14  
YNL044W gcgagctctcaaatacgcataaaataa 545231 545246 chr14 cgggtaccgaacttccccaaagttttg 545511 545496 chr14  
YNL049C++ gcgagctcatgtctcatcataagaaga 537904 537889 chr14 gcggtaccatagttgattgaccacttt 537697 537712 chr14 No evidence for splicing, 3' end named YNL049C--
YNL049C gcgagctctaaggctatgggtattaag 535374 535359 chr14 gcggtaccacataactctcacacgcaa 535155 535170 chr14  Not previously annotated, no evidence for splicing
YNL050C cgggtaccatgtctgaatttaag 534979 534964 chr14 cgggtaccgaaaataacgggaactcg 534642 534657 chr14  
YNL130C gcggatccatttatataggttaaagt 381254 381239 chr14 cgggtaccaacaaacctatagcatag 380470 380485 chr14  
YNL147W gcggatcccaattaagaatacgcatgtac 350842 350857 chr14 cgggtacccctataactaatttaccaccc 351176 351161 chr14  
YNL246W gcggatccctaatgattaggcgcttg 185406 185421 chr14 cgggtaccctgaagcccttatgtaattcg 185774 185759 chr14  
YNL247+SAC gcgagctccatatgttaagtgtttatc 184696 184711 chr14      Far upstream of 246 to look at upstream 5'ss
YNL265C gcggatccatggctccgtcaatgattccg 145275 145260 chr14 cgggtacctagctcaatatgaatatcgtc 144974 144989 chr14  
YNL339C  gcggatcccaagagaatatccacgaagcg   cgggtacctgttgattgttatgctttttg   Repeated Y' element see below for coordinates
YNR053C gcgagctcagggatccattgggtacc 722413 722398 chr14 cggtcgacaccagtgtttggatagcc 721599 721614 chr14  Original 5' had error, new one is shown
YOL047C gcggatccaggctccgatagttcgat 242601 242586 chr15 cgggtaccccttcaccatagaattac 242219 242234 chr15  
YOR074C gcggatccatcaaacaataaagtatc 467637 467622 chr15 cgggtaccattgatcaataccttgtc 467165 467180 chr15  
YOR074C gcgagctcactatagcatagctgtaat 467687 467672 chr15     Synthesized 5/6/99
YOR074C+BAM gcggatcctacgggtgatttcccagca 468183 468168 chr15      
YOR180 gcgagctctcttcaggacataaagcag 674551 674536 chr15 gcggtacctatgttaaaatcctatctc 674320 674335 chr15 Not previously annotated, no evidence for splicing
YOR195 gcgagctcaaaaggatagagatgatga 715007 715022 chr15 gcggtaccaacaattatggcatggtcc 715558 715543 chr15  3' primer should end ggacc, works, no evidence for splicing
YOR221C gcgggatccatgcttgtcttgagaaag 757827 757812 chr15  cgggtaccagtcatattttttggtgc 757301 757316 chr15 Synthesized 7/16/98
YOR221C gcgagctccatgttagaaatgcacaag 758043 758028 chr15     Synthesized 5/6/99
YOR234C gcggatccattatagcagataaaggtccg 779480 779465 chr15 cgggtacccttggaagctctgtaaacgta 778711 778726 chr15  
YOR318C gcggatcccgttttgaaagaaaagcc 912521 912506 chr15 cgggtacctcaatctcgcatagactg 911953 911968 chr15  
YOR336W gcgagctcatgagactacttgcgttgg 949767 949782 chr15 cgggtaccatcgttgtctgctccaacc 950528 950513 chr15  
YPL129W gcgagctcagtattacacgtcaaggc 305199 305214 chr16 gccccgggtcttttccttcatcatcc 305533 305518 chr16  
YPL129-X cggagctcgactgatattagataactaat 305280 305295 chr16     New 5' primer
YPL175W gcgagctcaaacttatgcaaaaatac 218562 218577 chr16 gccccgggttggtaagatgtcgtacg 218890 218875 chr16  
YPL175W-X cggagctcattatataaaacaatgggcttc 218622 218637 chr16     New 5' primer
YPL175W-Kpn gcggtaccttggtaagatgtcgtacgc 218889 218874 chr16     New synthesized 6/22/99
YPL208 gcgagctctttaccagaacttcatcta 159545 159560 chr16 gcggtaccgcatcgcagctccatggcg 159743 159728 chr16 Not previously annotated, no evidence for splicing
YPL283C         Y' element annotated to have intron, see Table 2
YPR028W gcggatcctaaaaaacattcccttgaagc 623427 623442 chr16 cgggtacctcaaaaggagataagcgaaac 623800 623785 chr16  
YPR063C gcggatccagcttgagcagaatgggcatg 678395 678380 chr16 cgggtacccaagaaaatagcggccatagg 678097 678112 chr16  
YPR187W gcgagctcaagaatatcattcaaagg 911157 911172 chr16 gccccggggttgaaaatcttctgggc 911503 911488 chr16  
YPR202W gcggatccatggaaattgaaaacgaa   cgggtaccatagtatgttgattgttatgc   Repeated Y' element, see Table 2
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