Supplemental Table 5B. Pyrococcus sRNA Annotation
Predicted methylation target sites for the Pyrococcus sRNAs is largely
conserved, so predictions for all three species are presented together
in this table.
Name |
Pho |
Pfu |
Pab |
Guide Box |
Target RNA |
Target Position |
Match/Mismatch |
sR1 |
+ |
+ |
+ |
D' |
23S |
G2252 |
9/0 |
|
+ |
+ |
+ |
D |
23S |
C2289 |
11/0 |
|
+ |
+ |
+ |
D |
23S |
C1105 |
11/0 |
sR2 |
+ |
+ |
+ |
D' |
23S |
A512 |
11/0 |
|
+ |
+ |
+ |
D |
23S |
U460 |
11/0, 11/0 12/0 |
sR3 |
+ |
+ |
+ |
D' |
23S |
C2612 |
9/0, 10/1, 11/1 |
|
+ |
+ |
+ |
D |
23S |
U2673 |
12/0, 13/0, 13/0 |
sR4 |
+ |
+ |
+ |
D' |
16S |
A361 |
9/1 |
|
+ |
+ |
+ |
D |
16S |
U52 |
11/0, 11/0, 10/0 |
sR5 |
+ |
+ |
+ |
D' |
23S |
G2396 |
11/1, 8/0, 12/1 |
|
+
|
+
|
+
|
D |
23S
|
G2429
|
12/0
|
sR6 |
+
|
+
|
+
|
D |
23S
|
G2062
|
10/0
|
|
+ |
+ |
+ |
D |
23S |
G2033 |
10/0 |
sR7 |
+ |
+
|
+
|
D' |
23S
|
G862
|
9/0, 13/1, 11/1
|
|
+ |
+ |
+ |
D |
23S |
A886 |
10/0 |
sR8 |
+ |
+ |
+ |
D' |
23S |
G861 |
10/0, 10/1, 11/1 |
|
+ |
+ |
+ |
D' |
16S |
G900 |
11/1 |
|
+ |
+ |
+ |
D' |
16S |
G644 |
10/0, 7/0, 10/0 |
|
+ |
+ |
+ |
D |
16S |
C1194 |
10/0, 11/0, 10/0 |
sR9 |
+ |
+ |
+ |
D' |
23S |
G220 |
11/0, 10/0, 10/0 |
|
+ |
+ |
+ |
D |
23S |
G61 |
12/0, 12/0, 11/0 |
sR10 |
+ |
+ |
+ |
D' |
23S |
G1413 |
11/0, 12/0, 11/0 |
|
+
|
+
|
+
|
D' |
16S
|
G627
|
10/0
|
|
+ |
+ |
+ |
D |
23S |
U2351 |
10/0 |
sR11 |
+ |
+ |
+ |
D' |
23S |
C1837 |
10/0, 12/0, 10/0 |
|
+ |
+ |
+ |
D |
23S |
C1919 |
10/0 |
sR12 |
+ |
+ |
+ |
D' |
23S |
G2027 |
11/0 |
|
+ |
+ |
+ |
D |
23S |
U1986 |
12/0, 12/0, 12/1 |
sR13 |
+ |
+ |
+ |
D' |
23S |
C2433 |
10/0 |
|
+ |
+ |
+ |
D |
23S |
U2406 |
10/0, 10/0, 11/0 |
sR14 |
+ |
+ |
+ |
D' |
16S |
U8 |
11/0 |
|
+
|
+
|
+
|
D' |
23S
|
U2976
|
9/0
|
|
+ |
+ |
+ |
D |
16S |
U775 |
9/0, 9/1, 10/1 |
sR15 |
+ |
+ |
+ |
D' |
23S |
G1539 |
10/0, 11/0, 8/0 |
|
+ |
+ |
+ |
D |
23S |
U1494 |
13/0, 13/0, 12/0 |
sR16 |
+ |
+ |
+ |
D' |
23S |
G2761 |
12/0, 11/0, 11/0 |
sR17 |
+ |
+ |
+ |
D' |
23S |
G893 |
13/0, 11/1, 12/0 |
|
|
|
+
|
D |
23S
|
G869
|
-, -, 9/1
|
|
+ |
|
+ |
D |
23S |
G3046 |
11/0, - , 11/1 |
sR18 |
+ |
+ |
+ |
D' |
16S |
C761 |
11/0, 11/0, 12/0 |
|
+ |
+ |
+ |
D |
16S |
G833 |
14/0, 12/0, 13/0 |
sR19 |
+ |
+ |
+ |
D' |
16S |
U818 |
11/0 |
|
+ |
+ |
+ |
D' |
16S |
U1469 |
14/1, 12/0, 14/1 |
|
+ |
+ |
+ |
D |
16S |
G763 |
13/0 |
sR20 |
+ |
+ |
+ |
D' |
23S |
U932 |
13/0, 12/0, 12/0 |
|
+ |
+ |
+ |
D |
23S |
G847 |
11/1 |
sR21 |
+ |
+ |
+ |
D' |
23S |
U1986 |
11/0, 9/1, 9/1 |
|
+ |
+ |
+ |
D |
23S |
C2012 |
9/0, 11/0, 10/0 |
sR22 |
+ |
+ |
+ |
D' |
23S |
U2559 |
10/0 |
|
+ |
+ |
+ |
D |
16S |
G415 |
12/1 |
|
+ |
+ |
+ |
D |
16S |
G697 |
10/1 |
sR23 |
+ |
+ |
+ |
D' |
23S |
C1285 |
9/1, 8/1, 8/1 |
|
+ |
+ |
+ |
D' |
tRNA Trp |
C32 |
11/1 |
|
|
+
|
|
D |
7S
|
G56
|
10/0
|
sR24 |
+ |
+ |
+ |
D' |
23S |
C1243 |
9/0 |
|
+ |
+ |
+ |
D |
23S |
C1221 |
14/0 |
sR25 |
+ |
+ |
+ |
D' |
23S |
G681 |
11/1 |
sR26 |
+ |
+ |
+ |
D' |
16S |
C1364 |
12/0 |
|
+ |
+ |
+ |
D |
16S |
C1490 |
9/0 |
sR27 |
+ |
+ |
+ |
D' |
tRNA Leu-TAA |
G47H |
11/1, 13/0, 10/0 |
sR28 |
+ |
+ |
+ |
D' |
23S |
G486 |
12/0, 10/2, 12/0 |
|
+ |
+ |
+ |
D' |
23S |
G814 |
14/0, 12/1, 12/0 |
|
+ |
+ |
+ |
D |
23S |
A946 |
10/0, 8/0, 10/0 |
sR29 |
+ |
+ |
+ |
D' |
16S |
G459 |
12/0, 13/0, 13/0 |
|
+ |
+ |
+ |
D |
16S |
U488 |
10/0 |
sR30 |
+ |
+ |
+ |
D |
16S |
G34 |
10/1, 9/2, 12/1 |
sR31 |
+ |
+ |
+ |
D |
tRNA Leu-CAA |
C34 |
11/0 |
sR32 |
+ |
+ |
+ |
D' |
tRNA Gln-YTG |
C16 |
13/0, 12/1, 13/0 |
|
+ |
+ |
+ |
D |
23S |
G648 |
10/1 |
sR33 |
+ |
X |
X |
D' |
23S |
C604 |
8/0 |
sR34 |
+ |
+ |
+ |
D' |
23S |
G2324 |
11/0 |
|
+ |
+ |
+ |
D |
23S |
C2050 |
11/0, 10/0, 11/0 |
sR35 |
+ |
X |
+ |
D' |
23S |
C1848 |
10/0 |
sR36 |
+ |
+ |
+ |
D' |
16S |
C117 |
12/1, 11/1, 12/1 |
|
+ |
+ |
+ |
D |
16S |
C238 |
11/1 |
sR37 |
+ |
+ |
+ |
D' |
16S |
G152 |
11/0 |
|
+ |
+ |
+ |
D |
16S |
G227 |
11/0 |
sR38 |
+ |
+ |
+ |
D' |
16S |
U425 |
13/0, 12/1, 13/0 |
|
+
|
+
|
+
|
D |
16S
|
G455
|
9/1
|
sR39 |
+ |
+ |
+ |
D' |
23S |
C2064 |
11/1 |
|
+
|
+
|
+
|
D |
23S
|
C2036
|
9/1
|
sR40 |
+ |
+ |
+ |
D' |
16S |
C1252 |
10/0 |
|
+ |
+ |
+ |
D' |
tRNA Trp |
C39 |
8/0 |
|
+ |
+ |
+ |
D |
tRNA Trp |
C34 |
12/0 |
sR41 |
|
|
|
|
?? |
|
|
sR42 |
+ |
+ |
+ |
D' |
23S |
C507 |
11/0 |
|
+ |
+ |
+ |
D' |
16S |
C1028 |
11/0 |
|
+ |
+ |
+ |
D |
16S |
G296 |
9/1 |
sR43 |
+ |
+ |
+ |
D' |
23S |
G1019 |
9/0 |
|
+ |
+ |
+ |
D' |
16S |
G1003 |
9/1 |
sR44 |
+ |
+ |
+ |
D' |
23S |
G488 |
10/0, 10/1, 10/0 |
|
+ |
+ |
+ |
D |
16S |
G507 |
13/0 |
sR45 |
+ |
+ |
+ |
D' |
23S |
C2124 |
9/1 |
|
+ |
+ |
+ |
D |
23S |
G2185 |
11/1 |
sR46 |
+ |
+ |
+ |
D' |
16S |
G922 |
10/0 |
|
+ |
+ |
+ |
D |
16S |
U1110 |
11/1 |
sR47 |
+ |
X |
+ |
D' |
23S |
C586 |
11/0 |
|
+
|
X
|
+
|
D' |
23S
|
C1951
|
10/0
|
|
+ |
X |
+ |
D |
23S |
G1909 |
9/0, - , 10/0 |
sR48 |
X |
+ |
+ |
D' |
23S |
G2664 |
12/0 |
sR49 |
+ |
X |
+ |
D' |
16S |
G329 |
10/1 |
|
+ |
X |
+ |
D' |
16S |
G1267 |
10/0 |
sR50
|
X
|
|
+ |
D' |
23S |
G1205
|
10/1
|
|
X
|
|
+
|
D' |
23S
|
G1604
|
10/0
|
|
X
|
+
|
+
|
D |
23S
|
G1246
|
10/0
|
sR51 |
X |
|
+ |
D' |
16S |
A1131 |
9/0 |
|
X
|
+
|
|
D' |
16S
|
G1059
|
10/0
|
|
X
|
+
|
+
|
D |
16S
|
U1165
|
12/0
|
sR52 |
X |
+ |
+ |
D |
23S |
G2113 |
-, 11/1, 12/1 |
sR53 |
+ |
+ |
+ |
D' |
16S |
U1218 |
10/1 |
|
+ |
|
+ |
D |
23S |
C2313 |
11/1 |
|
+ |
+ |
+ |
D |
16S |
C1351 |
10/1, 9/1, 10/1 |
sR54 |
+ |
+ |
+ |
D' |
23S |
C2511 |
9/0, 11/1, 11/2 |
|
+
|
+
|
+
|
D |
23S
|
C2562
|
11/1, 11/1, 10/1
|
sR55 |
+ |
+ |
+ |
D' |
23S |
A2545 |
11/0 |
|
+
|
+
|
+
|
D' |
23S
|
G2602
|
10/0, 11/0, 12/0
|
sR56 |
X |
+ |
+ |
D' |
16S |
G541 |
9/1 |
|
X
|
+
|
+
|
D |
16S
|
G504
|
-, 10/0, 9/0
|
sR57 |
X |
X |
|
|
?? |
|
|
None of the Pyrococcus predictions have been verified as RNA
transcripts by primer extension. Pho, Pfu, Pab Columns: "+"
in these columns indicate the target described in the row occurs in the
respective species. A blank indicates the target was not found, and an
"X" indicates the homologous sRNA was not found in the species. Guide
Box: the position of the guide within the sRNA (D or D' box associated).
A D'' box is noted for sR55, which appears to be a third guide region,
between the D' box and D box. This prediction is based on strong conservation
of the unusually long mid-sRNA linker region (see the Pyrococcus alignment). Target RNA: predicted target of methylation. Target
Position: predicted nucleotide postion of methylation. Nucleotide numbering
is identical for 16S rRNA for all three species. Pho rRNA
numbering is used for 23S rRNA target sites. See tables below for
nucleotide numbering adjustments for Pfu or Pab 23S rRNA
target sites. tRNA positions noted use canonical tRNA numbering (i.e.,
anticodon is always N34-N36). Match/Mismatch: the number of
Watson-Crick and G-U matches / mismatches within the sRNA-target RNA duplex.
"??" - no strong prediction found. When the three Pyrococcus sRNAs have
different Match/Mismatch values, all three are listed in the order of P.hori,
P.furi, P.abys.
23S rRNA Range |
Pfu 23S Numbering Adjustment |
1-12 |
0
|
13-1694 |
+1
|
1695-3056 |
+2
|
23S rRNA Range |
Pab 23S Numbering Adjustment |
1-163 |
0
|
164-761 |
+1
|
762-1467 |
+2
|
1468-2920 |
+3
|
2921-2942 |
+2
|
2943-3056 |
+3
|