Table 2.
C/D box snoRNA candidates identified in T. rubrum
| |
|
Genome position |
Homologues |
|
|
||||
|---|---|---|---|---|---|---|---|---|---|
| Name | Len a | Chromosome | Start | End | Location | Accession 1 | Genes | Putative target(s) | Accession 2 |
| TRnc_1010 |
87 |
supercont2.10 |
749220 |
749306 |
3′UTR |
RF00477 |
snosnR66 |
|
KC353070 |
| TRnc_1157 |
95 |
supercont2.11 |
539262 |
539356 |
Intron |
RF00093 |
SNORD18, U18 |
25S: Am651, Gm654; 18S: Am1159 |
KC353075 |
| TRnc_1271 |
242 |
supercont2.12 |
280437 |
280196 |
Intron |
RF01152 |
sR1 |
25S: Am2268, Am3277,Cm964,Cm961;U5: Cm103; 18S: Am1540 |
KC353083 |
| TRnc_1272 |
265 |
supercont2.12 |
280712 |
280448 |
Intron |
RF01152 |
sR1 |
25S: Cm964, Cm961;18S: Um604; U5: Cm103 |
KC353084 |
| TRnc_1299 |
109 |
supercont2.13 |
24837 |
24729 |
Intron |
RF00593 |
snoU83B |
|
KC353086 |
| TRnc_1359 |
97 |
supercont2.14 |
159345 |
159441 |
Intron |
RF00475 |
snosnR69 |
25S: Cm3322 |
KC353090 |
| TRnc_1366 |
215 |
supercont2.14 |
179253 |
179467 |
3′UTR |
RF01152 |
sR1 |
|
KC353091 |
| TRnc_1449 |
234 |
supercont2.17 |
97081 |
97314 |
5′UTR |
RF01191 |
SNORD121A |
18S: Cm673, Gm234 |
KC353101 |
| TRnc_1560 |
77 |
supercont2.2 |
546818 |
546894 |
3′UTR |
RF01139 |
sR2 |
|
KC353110 |
| TRnc_1603 |
358 |
supercont2.2 |
766347 |
766704 |
3′UTR |
RF00345 |
snoR1 |
|
KC353115 |
| TRnc_1709 |
154 |
supercont2.2 |
1400380 |
1400533 |
5′UTR |
RF01193 |
snoR20a |
|
KC353124 |
| TRnc_1825 |
309 |
supercont2.2 |
1958330 |
1958022 |
3′UTR |
|
|
25S: Um2301; Um769 |
KC353137 |
| TRnc_1841 |
143 |
supercont2.2 |
2090171 |
2090313 |
3′UTR |
RF01144 |
sR17 |
|
KC353138 |
| TRnc_2011 |
127 |
supercont2.3 |
74633 |
74759 |
3′UTR |
RF00441 |
snoZ242 |
|
KC353147 |
| TRnc_2018 |
306 |
supercont2.3 |
117035 |
116730 |
3′UTR |
|
|
18S: Um628 |
KC353149 |
| TRnc_2027 |
96 |
supercont2.3 |
166668 |
166763 |
Intron |
RF01281 |
snoR35 |
|
KC353150 |
| TRnc_2179 |
431 |
supercont2.3 |
961995 |
961565 |
Intergenic |
|
|
25S: Um413 |
KC353160 |
| TRnc_2265 |
87 |
supercont2.3 |
1276133 |
1276219 |
Intron |
RF01197 |
snR39 |
25S: Gm808 |
KC353164 |
| TRnc_2283 |
233 |
supercont2.3 |
1301587 |
1301819 |
5′UTR |
|
|
18S: Am1105; 25S: Am499, Am1453 |
KC353165 |
| TRnc_2405 |
317 |
supercont2.3 |
1975149 |
1975465 |
3′UTR |
|
|
25S: Gm1738 |
KC353175 |
| TRnc_2419 |
204 |
supercont2.3 |
2045771 |
2045974 |
5′UTR |
RF01125 |
sR4 |
18S: Am350, Gm698, Cm701;25S: Gm215, Cm3127 |
KC353177 |
| TRnc_2421 |
182 |
supercont2.3 |
2046135 |
2046316 |
5′UTR |
RF00016 |
SNORD14, U14 |
18S: Um50, Cm379;25S: Cm2352 |
KC353178 |
| TRnc_2498 |
172 |
supercont2.3 |
2451919 |
2452090 |
5′UTR |
RF00527 |
|
|
KC353188 |
| TRnc_2545 |
119 |
supercont2.3 |
2657688 |
2657806 |
3′UTR |
RF01188 |
snR56 |
18S: Gm1389,Am385 |
KC353195 |
| TRnc_2569 |
192 |
supercont2.3 |
2759920 |
2759729 |
Intron |
RF01297 |
sR40 |
|
KC353197 |
| TRnc_2594 |
143 |
supercont2.3 |
2859175 |
2859033 |
Intron |
RF01305 |
sR51 |
|
KC353199 |
| TRnc_2691 |
158 |
supercont2.4 |
233433 |
233276 |
Intergenic |
|
|
5.8S: Gm87 |
KC353216 |
| TRnc_2782 |
128 |
supercont2.4 |
669565 |
669438 |
5′UTR |
RF00630 |
P26 |
18S: Cm534; 25S: Cm1583, Cm1196, Cm3233 |
KC353223 |
| TRnc_2936 |
246 |
supercont2.4 |
1403883 |
1403638 |
Intron |
RF00312 |
snoZ206 |
25S: Gm1378 |
KC353235 |
| TRnc_3227 |
139 |
supercont2.5 |
625518 |
625380 |
Intron |
RF00594 |
SNORD86, U86 |
KC353256 |
|
| TRnc_3297 |
138 |
supercont2.5 |
896392 |
896529 |
3′UTR |
RF00610 |
SNORD110 |
KC353262 |
|
| TRnc_338 |
135 |
supercont2.1 |
1643180 |
1643314 |
Intron |
RF01223 |
snR13 |
25S: Am2267 |
KC353022 |
| TRnc_3425 |
202 |
supercont2.6 |
22581 |
22782 |
3′UTR |
|
|
25S: Gm911 |
KC353267 |
| TRnc_3426 |
98 |
supercont2.6 |
23000 |
23097 |
3′UTR |
|
|
|
KC353268 |
| TRnc_3438 |
173 |
supercont2.6 |
91295 |
91467 |
5′UTR |
RF01291 |
snoU97, SNORD97 |
KC353269 |
|
| TRnc_3573 |
95 |
supercont2.6 |
964586 |
964680 |
Intron |
RF00530 |
snoMe28S-Cm2645 |
25S: Cm2324, Um2867; U2: Um43 |
KC353276 |
| TRnc_3654 |
191 |
supercont2.7 |
14823 |
15013 |
3′UTR |
RF01140 |
sR20 |
18S: Gm832 |
KC353284 |
| TRnc_3667 |
191 |
supercont2.7 |
59063 |
59253 |
3′UTR |
RF00529 |
snoMe28S-Am2589 |
KC353285 |
|
| TRnc_3778 |
101 |
supercont2.7 |
777627 |
777727 |
5′UTR |
RF00471 |
snosnR48, snr46 |
18S: Am721; 25S: Gm2780; Am2243 |
KC353293 |
| TRnc_3833 |
109 |
supercont2.7 |
1124537 |
1124429 |
3′UTR |
RF01273 |
sR34 |
|
KC353299 |
| TRnc_3855 |
288 |
supercont2.7 |
1281447 |
1281734 |
Intron |
RF01127 |
sR42 |
|
KC353305 |
| TRnc_3911 |
80 |
supercont2.8 |
194694 |
194773 |
Intron |
RF00213 |
snoR38 |
25S: Gm2799 |
KC353308 |
| TRnc_4113 |
681 |
supercont2.8 |
1152047 |
1152727 |
Intron |
RF01274 |
sR45 |
25S: Cm1856,Cm1673; 18S: Am833; U2: Am155 |
KC353324 |
| TRnc_415 |
103 |
supercont2.1 |
1918108 |
1918210 |
Intron |
RF01121 |
Sr38 |
|
KC353027 |
| TRnc_4250 |
192 |
supercont2.9 |
658585 |
658394 |
3′UTR |
|
|
18S: Cm373 |
KC353339 |
| TRnc_4259 |
104 |
supercont2.9 |
693331 |
693434 |
5′UTR |
RF00276 |
SNORD52, U52 |
25S: Um2408 |
KC353340 |
| TRnc_4260 |
95 |
supercont2.9 |
695194 |
695288 |
Intergenic |
RF01178 |
snoR77Y,snR77 |
18S: Um565, Am564 |
KC353341 |
| TRnc_4261 |
138 |
supercont2.9 |
695445 |
695582 |
Intergenic |
RF01209 |
snR76 |
18S: Cm1674;25S: Cm2184, Am2266, Cm3294, Cm1758 |
KC353342 |
| TRnc_4262 |
273 |
supercont2.9 |
695588 |
695860 |
Intergenic |
RF01185 |
snR75, U15 |
25S: Gm2275 |
KC353343 |
| TRnc_4263 |
157 |
supercont2.9 |
695917 |
696073 |
Intergenic |
RF00086 |
SNORD27, U27, snR74 |
25S: Cm1179 |
KC353344 |
| TRnc_4264 |
88 |
supercont2.9 |
696179 |
696266 |
5′UTR |
RF01207 |
snR73,U35 |
25S: Cm3333 |
KC353345 |
| TRnc_4267 |
100 |
supercont2.9 |
703004 |
703103 |
3′UTR |
|
|
18S: Um525, Gm527 |
KC353346 |
| TRnc_4316 |
97 |
supercont2.9 |
861468 |
861372 |
5′UTR |
RF01223 |
snR13 |
|
KC353347 |
| TRnc_4336 |
162 |
supercont2.9 |
996654 |
996493 |
Intron |
|
|
18S: Gm1089 |
KC353348 |
| TRnc_608 |
234 |
supercont2.1 |
2701229 |
2701462 |
3′UTR |
RF01202 |
sn2991 |
5.8S: Cm137 |
KC353041 |
| TRnc_640 |
129 |
supercont2.1 |
2869815 |
2869687 |
3′UTR |
RF00300 |
snoZ221 |
|
KC353043 |
| TRnc_801 |
488 |
supercont2.1 |
3681448 |
3681935 |
3′UTR |
RF00012 |
U3 |
18S: Um418; 25S: Cm1363, Cm1633, Cm1983, Cm3165; U1: Cm45 |
KC353053 |
| TRnc_821 |
210 |
supercont2.1 |
3768831 |
3768622 |
Intergenic |
|
|
18S: Cm1301,25S: Cm880 |
KC353055 |
| TRnc_985 | 153 | supercont2.10 | 686423 | 686575 | Intron | RF00494 | snoU2_19 | KC353066 | |
Name: the C/D box snoRNAs were numbered according to the order of identification. Lena: the cDNA length of the snoRNA. Homologues: homologues in Rfam or other organisms. Accession1 is the accession number in Rfam; Accession2 is the accession number in GenBank; Genes are homologous gene names in other organisms [19-22]. Putative target(s): the predicted modified nucleotides within rRNAs or snRNAs using the Snoscan package.