Table 1.
Novel snoRNAs and snoRNA gene variants
| SnoRNAa | Size (nt) | RNA class | Modification site | Rep. cloneb | Gene copy | Chrc | Yeast/humand | Organization | Orthologues—representative ESTs | |
|---|---|---|---|---|---|---|---|---|---|---|
| Novel box C/D snoRNAs | ||||||||||
| AtsnoR146 (U13) | 127 | capped C/D | Unknown | At304 | 1 | 1 | – | Single gene | ESTs: monkey flower | |
| AtsnoR147 | 83 | C/D | D 25S Cm1471 13bp | At502 | 1 | 1 | Not modified | Cluster: snoR163/snoR147/snoR95 | ESTs: tobacco, chicory, oat | |
| AtsnoR148 | 84 | C/D | D 25S Cm2673 18bp | At649 | 1 | 5 | Not modified | Single gene | Genomic: Poplar ESTs: tomato, Nicotiana benthamiana, Asparagus, etc. | |
| AtsnoR149 | 80 | C/D | Unknown | At870 | 1 | 2 | – | Cluster: snoR158a/snoR39BYa/snoR21a/snoR149 | ESTs: poplar, safflower, barley, cocoa | |
| AtsnoR116 | 84 | C/D | D’ 18S Um123 11bp | At938 | 1 | 1 | Mgh18S-121; Z17B | Cluster: snoR117/snoR116/snoR85a/snoR85b | ESTs: apple, Jerusalem artichoke, dandelion | |
| AtsnoR117 | 72 | C/D | D’ 25S Um2103 12bp | At359 | 1 | 1 | Not modified | Cluster: snoR117/snoR116/snoR85a/snoR85b | ESTs: lettuce, grape, cotton,etc. | |
| AtsnoR118 | 98 | C/D | D′ 25S Cm2187 12bp | Ath-19b— predicted | 1 | 3 | snR76(Y); HB-II 180A,B,C | Cluster: snoR161/snoR66/snoR118 | Genomic: poplar; ESTs: lettuce, Jerusalem artichoke | |
| AtsnoR120 | 72 | C/D | D 25S Um 44 12bp | At838; Ath-475 | 1 | 5 | Not modified | Cluster: snoR133/snoR120 | None found | |
| AtsnoR133 | 101 | C/D | Unknown | Predicted | 1 | 5 | – | Cluster: snoR133/snoR120 | ESTs: Columbine, rice, maize | |
| Novel box H/ACA snoRNAs | ||||||||||
| AtsnoR150 | 150 | H/ACA | P1:25S 2174 | At213 | 1 | 1 | Not modified | Cluster: snoR150/snoR138 | Genomic: poplar; ESTs: Poplar, Melon, Papaya, etc. | |
| AtsnoR151 | 151 | H/ACA | P1: 25S 973 | At549 | 1 | 4 | snR43(Y); ACA9 | Intronic snoRNA: in intron 2 of At4g17380.1 (RPL15B) | None found | |
| AtsnoR152a AtsnoR152b | 163 | H/ACA | P2: 18S 1531 | At675 | 2 | 2 | Target sequence not conserved | Cluster: snoR152a/snoR152b | Genomic: poplar; EST: poplar, cotton, orange, etc. | |
| AtsnoR153 | 155 | H/ACA | Unknown | At740 | 1 | 5 | – | Cluster: snoR153/snoR12-2/AtU24-2 | ESTs: cocoa, poplar, orange | |
| AtsnoR154 | 156 | H/ACA | P1: 18S 1479 | At696 | 1 | 4 | ACA54 | Cluster: AtU19-2/snoR154 | ESTs: orange, papaya | |
| AtsnoR155a AtsnoR155b AtsnoR155c | 95 | H/ACA | P1: 25S 397 P2: 18S 56 | At801 | 3 | 1 | PI: target sequence not conserved; P2: not modified | Intronic H/ACA cluster in intron 2 of At1g04480.1 (RPL23A): snoR155a/snoR155b/snoR155c | Genomic: poplar EST: orange, tobacco, apple, etc. | |
| AtsnoR156 | 156 | H/ACA | P1:25S 1465 | At1140 | 1 | 5 | Not modified (Y); C in human | Single gene | ESTs: globe artichoke, barnadesia, oil palm | |
| AtsnoR157 | 122 | H/ACA | Unknown | Predicted | 1 | 2 | – | Cluster: snoR157/snoR68/snoR159/snoR145/snoR135a/snoR135b | None found | |
| AtsnoR158a AtsnoR158b | 226 | H/ACA | Unknown | Ath-143— predicted | 2 | 2 | – | Clusters: snoR158a/snoR39BYa/snoR21a/snoR149; snoR158b/snoR39BY/snoR21b | ESTs: cow pea, red clover, asparagus | |
| AtsnoR159 | 225 | H/ACA | Unknown | Ath-319—predicted | 1 | 2 | – | Cluster: snoR157/son R68/snoR159/snoR145/snoR135a/snoR135b | ESTs: melon, American sweet flag, wild radish | |
| AtsnoR160 | 139 | H/ACA | P2: 18S 1306 | Ath-362—predicted | 1 | 1 | Not modified | Cluster: snoR160/snoR16-2/AtU43-2 | ESTs: orange, apple, wild radish | |
| AtsnoR161 | 155 | H/ACA | P2: 18S 1188 | At395; Ath-382 | 1 | 3 | snR36 (Y); ACA36; ACA36B | Cluster: snoR161/snoR66/snoR118 | ESTs: red sage, cowpea, runner bean | |
| AtsnoR162 | 146 | H/ACA | P1: 25S 654 | Ath-408—predicted | 1 | 1 | Not modified | Intron 6/exon 7 of AT1G30970 (Suppressor of FRIGIDA4) | Genomic: poplar; ESTs: eucalyptus, poplar, etc. | |
| AtsnoR163 | 194 | H/ACA | Unknown | Ath-424 | 1 | 1 | – | Cluster: snoR163/snoR147/snoR95 | ESTs: cowpea, orange, cassava | |
| AtsnoR164 | 142 | H/ACA | Unknown | Ath-601—predicted | 1 | 2 | – | Single gene in 3′UTR of At2g37250 Adenosine kinase | Genomic: poplar; ESTs: globe artichoke, Russian dandelion | |
| AtsnoR134-1 AtsnoR134-2 AtsnoR134-3 | 144 | H/ACA | P1: 18S 1104; P2: 18S 1192 | At511 | 3 | 1;1;4 | P1: not modified; P2: snR35(Y); ACA13 | Clusters: snoR134-1/AtU36-1/AtU38-1/snoR6-1/snoR97-1; snoR134-2/AtU36a-2/AtU38-2/snoR6-2/snoR97-2; snoR134-3/AtU36a-3/AtU38-3/snoR6-3 | Genomic: poplar; ESTs: poplar, tomato, morning glory, etc. | |
| AtsnoR139 | 152 | H/ACA | P1: 18S 762 | At654 | 1 | 5 | snR80 (Y); ACA28 | Cluster: snoR82/snoR139 | Genomic: poplar; ESTs: Aristolochia fimbriata | |
| AtsnoR138 | 116 | H/ACA | P1: 25S 2445 | Predicted | 1 | 1 | ACA3 | Cluster: snoR150/snoR138 | ESTs: apple, orange, papaya, Columbine | |
| AtsnoR137-1 AtsnoR137-2 | 158 | H/ACA | P1: 18S 1208 | At1253 | 2 | 3; 4 | Not modified | Single genes | Genomic: poplar; ESTs: Russian dandelion, papaya, Tomato, etc. | |
| AtsnoR136 | 128 | H/ACA | P2: 25S 2833 | Predicted | 1 | 3 | E3 | Cluster:snoR88-2/snoR19-1/snoR136/snoR64/snoR20-1/snoRY38Y-1 | ESTs: soya, tomato | |
| AtsnoR135a AtsnoR135b | 142 | H/ACA | P1: 25S 536 P2: 25S 2181 | Ath118a/b—predicted | 2 | 2 | P1: modified by unknown human snoRNA P2: snR30 (Y); unknown human snoRNA | Cluster: snoR157/snoR68/snoR159/snoR145/snoR135a/snoR135b | Genomic: poplar; ESTs: lettuce, watermelon | |
| AtsnoR145 | 145 | H/ACA | Unknown | At559; Ath-122 | 1 | 2 | – | Cluster: snoR157/snoR68/snoR159/snoR145/snoR135a/snoR135b | ESTs: cowpea | |
| Novel variants of known snoRNAs | ||||||||||
| Organization | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| AtsnoR79a AtsnoR79b AtsnoR79c | 199; 194; 195 | H/ACA | See ref. (21) | AtsnoR79c = At394 | 3 | 1 | Intronic cluster—Intron of At1g31860 (Histidine synthesis bifunctional protein) | ||
| AtsnoR80-1 AtsnoR80-2 AtsnoR80-3 | 141; 139; 139 | H/ACA | See ref. (21) | AtsnoR80-1 = At162 AtsnoR80-2 = At3103 | 3 | 3, 4 | Clusters: snoR37-1/snoR22-1/snoR23-1/snoR80-1; snoR37-2/snoR22-1/snoR23-1/snoR80-2; snoR37-1/snoR22-3a/snoR22-3b/snoR23-3/snoR80-3 | ||
| At snoR85a AtsnoR85b | 139; 140 | H/ACA | See ref. (21) | 2 | 1 | Cluster: snoR117/snoR116/snoR85a/snoR85b | |||
| AtsnoR86-1 AtsnoR86-2 | 139; 143 | H/ACA | See ref. (21) | AtsnoR86-1 = At378 AtsnoR86-2 = At3235 | 2 | 1, 3 | Cluster: snoR14-1/snoR15/snoR86-2; Single gene snoR86-1 | ||
| AtsnoR87-1 AtsnoR87-2a AtsnoR87-2b | 153; 155; 155 | H/ACA | See ref. (21) | AtsnoR87-1 = At589 | 3 | 3 | Intronic—intron 1 of At3g11400 (eIF3G); Intronic cluster—intron 1 of At5g06000 (eIF3G) | ||
| AtsnoR90a AtsnoR90b | 150; 151 | H/ACA | See ref. (21) | 2 | 2 | Intronic cluster: intron 3 of At2g33430 (plastid development protein) | |||
| AtsnoR97-1 AtsnoR97-2 | 134; 134 | H/ACA | See ref. (21) | AtsnoR97-1 = At815 AtsnoR97-2 = At552 | 2 | 3, 4 | Clusters: snoR134-1/U36a-1/U38-1/snoR6-1/snoR97-1; snoR134-2/U36a-2/U38-2/snoR6-2/snoR97-2 | ||
| AtsnoR100a AtsnoR100b AtsnoR100c | 154; 147; 159 | H/ACA | See ref. (21) | 3 | 5 | Intronic cluster—intron 2 of At5g08180 (RPL7Ae/RPL30e/RPS12e) | |||
| AtsnoR110-1 AtsnoR110-2a AtsnoR110-2b | 114; 138; 147 | H/ACA | See ref. (21) | AtsnoR110-1 = At1126 AtsnoR110-2b = At835 | 3 | 1 | Intronic—intron2 of At1g26880 (RPL34a); Intronic cluster—intron2 of At1g69620 (Rpl34B) | ||
asnoRNAs with numbers between 113 and 145 were also identified by Chen and Wu (35).
bRepresentative clone: clone numbers beginning with ‘At’ refer to clones obtained in this study; those beginning in ‘Ath’ refer to Marker et al. (21).
cChromosome location of genes.
dModification sites/snoRNA information from LMBE snoRNABase v3 (49). Not modified, sequence fully or partially conserved in yeast/human but no evidence of modification; Y, yeast snoRNAs.