Saccharomyces cerevisiae Methylation Guide snoRNAs

Several different numbering schemes for small subunit rRNA have been used in previous publications. Here is a table giving the mapping between these numbering schemes for the known 2'-O-methyls.

In addition to the text in this table, additional information is available via table entry links (see legend below ).

rRNA Methyl Site snoRNA Fournier Annot Functional Verfication rRNA Match/Mismatch snoRNA Score Genomic Placement Len Chr Start End
                     
SSU-Am28 snR74 (Z4) Info + (2) gel 13/0 (duplex) 33.23 cluster 1 80 13 298138 298217
SSU-Am100 snR51 Info + (2) gel 16/1 (duplex) 33.76 cluster 3 107 16 718808 718702
SSU-Cm414 U14 Info ND 13/1 (duplex) 31.7 cluster 5 128 10 139390 139263
SSU-Am420 snR52 Info + (2) gel 13/0 (duplex) 27.84 extragenic 92 5 431217 431126
SSU-Am541 snR41 Info + (2) gel 11/1 (duplex) 29.76 cluster 3 110 16 719244 719135
SSU-Um578 snR77 (Z7) Info + (2) gel 14/0 (duplex) 35.79 cluster 1 84 13 297506 297589
SSU-Am619 snR47 Info + (2) gel 11/0 (duplex) 27.88 extragenic 99 4 541739 541641
SSU-Am796 snR53 Info + (2) gel 11/0 (duplex) 29.86 cluster 4 91 5 61699 61789
SSU-Am973 snR54 Info + (2) gel 13/0 (duplex) 37.4 intronic (Hyp ORF) 86 13 163620 163535
SSU-Cm1006 snR79 (Z9) Info + (2) gel 16/1 (duplex) 31.27 extragenic 84 12 348510 348427
SSU-Gm1123 snR41 Info + (2) gel 20/1 (duplex) 33.83 cluster 3 110 16 719244 719135
SSU-Um1265 snR55 Info + (2) gel 12/0 (duplex) 22.9 cluster 2 98 12 794792 794695
SSU-Gm1267 snR40 Info + (2) gel 11/1 (duplex) 25.91 extragenic 97 14 89208 89304
SSU-Gm1425 snR56 Info + (2) gel 11/0 (duplex) 34.94 extragenic 88 2 88180 88267
SSU-Gm1570 snR57 Info + (2) gel 15/0 (duplex) 21.93 cluster 2 88 12 795022 794935
SSU-Cm1637 snR70 Info + (2) gel 10/1 (duplex) 18.72 cluster 3 165 16 719053 718889
                   
LSU-Am647 U18 Info + (3) 15/0 (duplex) 34.96 intronic (EFB1) 102 1 142370 142471
LSU-Cm648 U18 Info + (3) Slide -- intronic (EFB1) 102 1 142370 142471
LSU-Cm661 snR58 Info + (2) gel 13/0 (duplex) 37.69 extragenic 96 15 136182 136087
LSU-Gm803 snR39b Info + (2) gel 14/0 (duplex) 33.04 extragenic 96 7 366467 366372
LSU-Am805 snR39 Info + (3) 13/0 (duplex) 32.23 intronic (RPL7A) 89 7 365249 365161
LSU-Am805b snR59 Info + (3) 14/0 33.01 intronic (RPL7B) 78 16 173826 173903
LSU-Am815 snR60 Info + (2) gel 10/0 (duplex) 31.52 extragenic 104 10 348928 348825
LSU-Gm865 snR50 Info + (2) gel 12/0 (duplex) 31.25 extragenic 90 15 259488 259577
LSU-Am874 snR72 (Z2) Info + (2) gel 14/0 (duplex) 35.56 cluster 1 91 13 298554 298644
LSU-Um896 snR40 Info + (2) gel 12/0 (duplex) 28.23 extragenic 97 14 89208 89304
LSU-Gm906 snR60 Info + (2) gel 19/0 (duplex) 35.49 extragenic 104 10 348928 348825
LSU-Am1131 snR61 Info + (2) gel 11/0 (duplex) 33.76 cluster 2 90 12 794573 794484
LSU-Cm1435 U24 Info + (1) 14/0 (duplex) 29.82 intronic (ASC1) 89 13 500071 499983
LSU-Am1447 U24 Info + (1) 12/0 (duplex) 32.4 intronic (ASC1) 89 13 500071 499983
LSU-Gm1448 U24 Info + (1) Slide -- intronic (ASC1) 89 13 500071 499983
LSU-Um1886 snR62 Info + (2) gel 14/0 (duplex) 35.89 extragenic 100 15 409862 409763
LSU-Cm2195 snR76 (Z6) Info + (2) gel 13/1 (duplex) 36.53 cluster 1 101 13 297727 297827
LSU-Am2218 snR47 Info + (2) gel 12/0 (duplex) 29.02 extragenic 99 4 541739 541641
LSU-Am2254 snR63 Info + (2) gel 12/0 (duplex) 23.55 extragenic 255 4 323470 323216
LSU-Am2278 snR13 Info + (2) gel 10/0 (duplex) 24.96 extragenic 124 4 1402956 1403079
LSU-Am2279 snR13 Info + (2) gel Slide -- extragenic 124 4 1402956 1403079
LSU-Gm2286 snR75 (Z5) Info + (2) gel 11/0 (duplex) 35.02 cluster 1 85 13 297915 297999
LSU-Cm2335 snR64 Info + (2) gel 11/0 (duplex) 34.95 extragenic 101 11 38812 38912
LSU-Um2345 snR65 Info + (2) gel 11/0 (duplex) 33.91 extragenic 100 3 175909 176008
LSU-Gm2393 ?? snR190 Info No (2) 13/0 (duplex) 12.8 cluster 5 190 10 139648 139459
LSU-Um2415 snR66 Info + (2) gel 12/0 (duplex) 36.63 extragenic 86 14 586086 586171
LSU-Um2419 snR78 (Z8) Info + (2) gel 12/0 (duplex) 27.39 cluster 1 80 13 297279 297358
LSU-Gm2616 snR67 Info + (2) gel 11/2 (duplex) 23.72 cluster 4 82 5 61352 61433
LSU-Am2637 snR68 Info + (2) gel 12/0 (duplex) 31.86 extragenic 136 9 97111 97246
LSU-Um2721 snR67 Info + (2) gel 11/0 (duplex) 26.39 cluster 4 82 5 61352 61433
LSU-Um2726 snR51 Info + (2) gel 14/1 (duplex) 23.02 cluster 3 107 16 718808 718702
LSU-Gm2788 snR48 Info + (2) gel 17/1 (duplex) 20.56 extragenic 113 7 609578 609690
LSU-Gm2790 snR48 Info + (2) gel 15/0 (duplex) 27.62 extragenic 113 7 609578 609690
LSU-Gm2812 snR38 Info + (3) 13/0 (duplex) 43.55 intronic (TEF4) 95 11 282830 282924
LSU-Um2918 snR52 Info No (2) 11/1 (duplex) 32.44 extragenic 92 5 431217 431126
LSU-Gm2919 snR52 Info No (2) Slide? -- extragenic 92 5 431217 431126
LSU-Am2943 snR71 Info + (2) gel 9/1 (duplex) 21.67 extragenic 90 8 411228 411317
LSU-Cm2945 snR69 Info + (2) gel 18/3 (duplex) 29.17 extragenic 101 11 364418 364518
LSU-Cm2956 snR73 (Z3) Info + (2) gel 12/1 (duplex) 29.52 cluster 1 103 13 298306 298408

Functional Verification References:

  1. Kiss-Laszlo, Z., Henry, Y., Bachellerie, J.P., Caizergues-Ferrer, M., Kiss, T. (1996). Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell 85: 1077-1088.
  2. Lowe, T.M. and Eddy, S.R. (1999). A Computational Screen for Methylation Guide snoRNAs in Yeast. Science 283: 1168-1171.
  3. Ni, J. and Fournier, M.J. (unpublished)

Legend for additional information linked to table entries:

(snR47 is given as an example entry)

rRNA Methyl Site snoRNA Fournier Annot Functional Verfication rRNA Match/Mismatch snoRNA Score Genomic Placement Len Chr Start End
SSU-Am619 snR47 Info + (2) gel 11/0 (duplex) 27.88 extragenic 99 4 541739 541641
  Genbank entry for snoRNA (NCBI link) snoRNA entry in Fournier snoRNA database rRNA primer extension gel showing methyl loss in null mutant search program output for this snoRNA   neighboring genes