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 ).

snoRNA Fournier Annot rRNA Methyl Site Functional Verfication Match/Mismatch snoRNA Score Genomic Placement Len Chr Start End Proximity
                       
U18 Info LSU-Am647 + (3) 15/0 (duplex) 34.96 intronic (EFB1) 102 1 142370 142471  
    LSU-Cm648 + (3) Slide --
snR56 Info SSU-Gm1425 + (2) gel 11/0 (duplex) 34.94 extragenic 88 2 88180 88267  
snR65 Info LSU-Um2345 + (2) gel 11/0 (duplex) 33.91 extragenic 100 3 175909 176008  
snR63 Info LSU-Am2254 + (2) gel 12/0 (duplex) 23.55 extragenic 255 4 323470 323216  
snR47 Info SSU-Am619 + (2) gel 11/0 (duplex) 27.88 extragenic 99 4 541739 541641 218171
  LSU-Am2218 + (2) gel 12/0 (duplex) 29.02
snR13 Info LSU-Am2278 + (2) gel 10/0 (duplex) 24.96 extragenic 124 4 1402956 1403079 861217
  LSU-Am2279 + (2) gel Slide --
snR67 Info LSU-Gm2616 + (2) gel 11/2 (duplex) 23.72 cluster 4 82 5 61352 61433  
LSU-Um2721 + (2) gel 11/0 (duplex) 26.39
snR53 Info SSU-Am796 + (2) gel 11/0 (duplex) 29.86 cluster 4 91 5 61699 61789 266
snR52 Info SSU-Am420 + (2) gel 13/0 (duplex) 27.84 extragenic 92 5 431217 431126 369337
LSU-Um2918 No (2) 11/1 (duplex) 32.44
LSU-Gm2919 No (2) Slide? --
snR39 Info LSU-Am805 + (3) 13/0 (duplex) 32.23 intronic (RPL7A) 89 7 365249 365161  
snR39b Info LSU-Gm803 + (2) gel 14/0 (duplex) 33.04 extragenic 96 7 366467 366372 1123
snR48 Info LSU-Gm2788 + (2) gel 17/1 (duplex) 20.56 extragenic 113 7 609578 609690 243111
LSU-Gm2790 + (2) gel 15/0 (duplex) 27.62
snR71 Info LSU-Am2943 + (2) gel 9/1 (duplex) 21.67 extragenic 90 8 411228 411317  
snR68 Info LSU-Am2637 + (2) gel 12/0 (duplex) 31.86 extragenic 136 9 97111 97246  
U14 Info SSU-Cm414 ND 13/1 (duplex) 31.7 cluster 5 128 10 139390 139263  
snR190 Info LSU-Gm2393 ?? No (2) 13/0 (duplex) 12.8 cluster 5 190 10 139648 139459 69
snR60 Info LSU-Am815 + (2) gel 10/0 (duplex) 31.52 extragenic 104 10 348928 348825 209435
LSU-Gm906 + (2) gel 19/0 (duplex) 35.49
snR64 Info LSU-Cm2335 + (2) gel 11/0 (duplex) 34.95 extragenic 101 11 38812 38912  
snR38 Info LSU-Gm2812 + (3) 13/0 (duplex) 43.55 intronic (TEF4) 95 11 282830 282924 243918
snR69 Info LSU-Cm2945 + (2) gel 18/3 (duplex) 29.17 extragenic 101 11 364418 364518 81494
snR79 (Z9) Info SSU-Cm1006 + (2) gel 16/1 (duplex) 31.27 extragenic 84 12 348510 348427  
snR61 Info LSU-Am1131 + (2) gel 11/0 (duplex) 33.76 cluster 2 90 12 794573 794484 445974
snR55 Info SSU-Um1265 + (2) gel 12/0 (duplex) 22.9 cluster 2 98 12 794792 794695 122
snR57 Info SSU-Gm1570 + (2) gel 15/0 (duplex) 21.93 cluster 2 88 12 795022 794935 143
snR54 Info SSU-Am973 + (2) gel 13/0 (duplex) 37.4 intronic (Hyp ORF) 86 13 163620 163535  
snR78 (Z8) Info LSU-Um2419 + (2) gel 12/0 (duplex) 27.39 cluster 1 80 13 297279 297358 133659
snR77 (Z7) Info SSU-Um578 + (2) gel 14/0 (duplex) 35.79 cluster 1 84 13 297506 297589 148
snR76 (Z6) Info LSU-Cm2195 + (2) gel 13/1 (duplex) 36.53 cluster 1 101 13 297727 297827 138
snR75 (Z5) Info LSU-Gm2286 + (2) gel 11/0 (duplex) 35.02 cluster 1 85 13 297915 297999 88
snR74 (Z4) Info SSU-Am28 + (2) gel 13/0 (duplex) 33.23 cluster 1 80 13 298138 298217 139
snR73 (Z3) Info LSU-Cm2956 + (2) gel 12/1 (duplex) 29.52 cluster 1 103 13 298306 298408 89
snR72 (Z2) Info LSU-Am874 + (2) gel 14/0 (duplex) 35.56 cluster 1 91 13 298554 298644 146
U24 Info LSU-Am1435 + (1) 14/0 29.82 intronic (ASC1) 89 13 500071 499983 201339
  LSU-Cm1447 + (1) 12/0 32.4
  LSU-Gm1448 + (1) Slide --
snR40 Info SSU-Gm1267 + (2) gel 11/1 (duplex) 25.91 extragenic 97 14 89208 89304  
  LSU-Um896 + (2) gel 12/0 (duplex) 28.23
snR66 Info LSU-Um2415 + (2) gel 12/0 (duplex) 36.63 extragenic 86 14 586086 586171 496782
snR58 Info LSU-Cm661 + (2) gel 13/0 (duplex) 37.69 extragenic 96 15 136182 136087  
snR50 Info LSU-Gm865 + (2) gel 12/0 (duplex) 31.25 extragenic 90 15 259488 259577 123306
snR62 Info LSU-Um1886 + (2) gel 14/0 (duplex) 35.89 extragenic 100 15 409862 409763 150186
snR59 Info LSU-Am805b + (3) 14/0 33.01 intronic (RPL7B) 78 16 173826 173903  
snR51 Info SSU-Am100 + (2) gel 16/1 (duplex) 33.76 cluster 3 107 16 718808 718702 544799
  LSU-Um2726 + (2) gel 14/1 (duplex) 23.02
snR70 Info SSU-Cm1637 + (2) gel 10/1 (duplex) 18.72 cluster 3 165 16 719053 718889 81
snR41 Info SSU-Am541 + (2) gel 11/1 (duplex) 29.76 cluster 3 110 16 719244 719135 82
  SSU-Gm1123 + (2) gel 20/1 (duplex) 33.83  

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)

snoRNA Fournier Annot Target 2'-O-Methyl Site Functional Verification Match/Mismatch snoRNA Score Genomic Placement Len Chr Start End
snR47 Info SSU-Am619 + (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 (SGD link)