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Various features of C/D and H/ACA snoRNAs |
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Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP, Ares M Jr. Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis. RNA. 2007 13(11):1923-39. |
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Small nucleolar RNAs (snoRNAs) are a class of small RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs. There are two main classes of snoRNA, the C/D box snoRNAs which are associated with methylation, and the H/ACA box snoRNAs which are associated with pseudouridylation. |
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Name |
snoRNA ID |
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Annotation |
Location |
Type |
Predicted modification sites |
Transcript |
Comments |
EC# |
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1686 |
snoR01 |
PF3D7_0219000 |
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intergenic |
C/D |
U: 3572 LSU, |
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2.7.11.13 |
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1694 |
snoR02 |
PF3D7_0309400 |
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small nucleolar RNA Me18S-Um1356 |
intergenic |
C/D |
G: 3315 LSU, |
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1695 |
snoR03 |
PF3D7_0307000 |
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small nucleolar RNA snoR03 |
intronic |
H/ACA |
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Predicted to guide modifications on 18S rRNA, |
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snoR04 |
PF3D7_0510900 |
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small nucleolar RNA snoR04 |
intergenic |
C/D |
C: 2950 LSU |
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snoR05 |
PF3D7_0826800 |
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small nucleolar RNA snoR05 |
Intronic |
C/D |
A: 3307 LSU |
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snoR06 |
PF3D7_0804100 |
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small nucleolar RNA snoR06 |
intronic |
C/D |
A: 744 LSU |
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1696 |
snoR07 |
PF3D7_1109000 |
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small nucleolar RNA snoR07 |
intergenic |
C/D |
C: 1936 SSU, |
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1697 |
snoR08 |
PF3D7_1109200 |
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conserved Plasmodium protein, unknown function |
intronic |
C/D |
A: 1264 LSU |
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1698 |
snoR09 |
PF3D7_1109500 |
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small nucleolar RNA snoR09 |
intronic |
C/D |
C: 3197 LSU, G: 3176 LSU, snR38 |
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1699 |
snoR10 |
PF3D7_1109200 |
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conserved Plasmodium protein, unknown function |
Intronic |
C/D |
G: 1037 LSU, G: 785 SSU, |
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1688 |
snoR11 |
PF3D7_1109700 |
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small nucleolar RNA snoR11 |
intronic |
H/ACA |
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Predicted to guide modifications on 18S rRNA, |
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1700 |
snoR12 |
PF3D7_1109400 |
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essential nuclear protein 1, putative |
intergenic |
C/D |
A: 28 SSU |
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1688 |
snoR12 |
PF3D7_1109800 |
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small nucleolar rna snor12 |
intergenic |
C/D |
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1701 |
snoR13 |
PF3D7_1130300 |
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small nucleolar RNA snoR13 |
intergenic |
C/D |
G: 95 SSU, C: 420 SSU U14 |
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1690 |
snoR14 |
PF3D7_1210800 |
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small nucleolar RNA snoR14 |
intergenic |
C/D |
A: 3417 LSU |
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snoR15 |
PF3D7_1222200 |
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small nucleolar RNA snoR15 |
intergenic |
C/D |
A: 66 |
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1702 |
snoR16 |
PF3D7_1304800 |
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small nucleolar RNA snoR16 |
intergenic |
C/D |
Single tRNA Ser (CGA) |
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1703 |
snoR17 |
PF3D7_1330900 |
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small nucleolar RNA snoR17 |
intronic |
C/D |
C: 1589 LSU |
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1704 |
snoR18 |
PF3D7_1331900 |
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small nucleolar RNA snoR18 |
intronic |
C/D |
A: 3248 LSU |
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1705 |
snoR19 |
PF3D7_1336500 |
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small nucleolar RNA snoR19 |
intronic |
C/D |
A:7 , G: 1277 LSU |
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snoR20 |
PF3D7_1341400 |
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small nucleolar RNA snoR20 |
intronic |
C/D |
C: 3320 LSU |
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1706 |
snoR21 |
PF3D7_1351500 |
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small nucleolar RNA snoR21 |
intronic |
C/D |
G: 2583 LSU, A: 2576 LSU |
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1707 |
snoR22 |
PF3D7_1402600 |
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small nucleolar RNA snoR22 |
intronic |
C/D |
C: 2632 LSU |
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1708 |
snoR22 |
PF3D7_1402600 |
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small nucleolar RNA snoR22 |
intronic |
C/D |
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1709 |
snoR23 |
PF3D7_1423900 |
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small nucleolar RNA snoR23 |
intergenic |
C/D |
A: 442 SSU |
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1710 |
snoR24 |
PF3D7_1424000 |
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small nucleolar RNA snoR24 |
intergenic |
C/D |
A: 442 SSU |
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1711 |
snoR25 |
PF3D7_1424200 |
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small nucleolar RNA snoR25 |
intronic |
C/D |
G: 1674 SSU |
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1712 |
snoR26 |
PF3D7_1424300 |
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small nucleolar RNA snoR26 |
intronic |
C/D |
G: 2172 LSU |
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1713 |
snoR27 |
PF3D7_1424500 |
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small nucleolar RNA snoR27 |
intergenic |
H/ACA |
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Targets 28S rRNA |
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1714 |
snoR28 |
PF3D7_1424600 |
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small nucleolar RNA snoR28 |
intergenic |
C/D |
C: 3248 LSU |
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1715 |
snoR29 |
PF3D7_1424700 |
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small nucleolar RNA snoR29 |
intergenic |
C/D |
G: 926 LSU |
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1716 |
snoR30 |
PF3D7_1424900 |
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small nucleolar RNA snoR30 |
intergenic |
C/D |
A: 728 LSU |
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1717 |
snoR31 |
PF3D7_1425100 |
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small nucleolar RNA snoR31 |
intergenic |
H/ACA |
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Predicted to guide modifications on 18S rRNA, |
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1718 |
snoR35 |
PF3D7_0626840 |
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small nucleolar rna snor35 |
intronic |
H/ACA |
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snoR36 |
PF3D7_0707420 |
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nucleolar rna snor36 |
intronic |
H/ACA |
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snoR37 |
PF3D7_0804000 |
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cactin homolog, putative |
intergenic |
C/D |
U124; RNase MRP snoRNA |
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snoR38 |
PF3D7_1421150 |
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C/D small nucleolar RNA |
intergenic |
C/D |
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snoR40 |
PF3D7_0804000 |
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cactin homolog, putative |
intronic |
H/ACA |
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snoR41 |
PF3D7_0218900 |
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small nucleolar rna snor41 |
CDS-hypprotein |
H/ACA |
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snoR42a |
PF3D7_0601800 |
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h/aca snorna |
intergenic |
H/ACA |
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snoR42b1 |
PF3D7_0800700 |
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surface-associated interspersed protein 8.3 (SURFIN 8.3) |
intergenic |
H/ACA |
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snoR43 |
PF3D7_1021800 |
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schizont egress antigen-1 |
intronic |
H/ACA |
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snoR44 |
PF3D7_0304300 |
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conserved Plasmodium protein, unknown function |
intronic |
H/ACA |
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snoRU14a |
PF3D7_1130310 |
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small nucleolar rna snor14a |
intergenic |
C/D |
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snoRNA |
PF3D7_1109600 |
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small nucleolar RNA SNORD127 |
intergenic |
C/D |
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snoRNA |
PF3D7_1109300 |
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small nucleolar RNA snR61/Z1/Z11 |
intronic |
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snoRNA |
PF3D7_0309400 |
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small nucleolar RNA Me18S-Um1356 |
intergenic |
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telomerase RNA |
PF3D7_0918500 |
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telomerase RNA |
intergenic |
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PfID |
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Length (Bp) |
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non-coding RNA |
PF3D7_0829900 |
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non-coding rna |
non-coding RNA |
3171 |
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1723 |
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PF3D7_0830100 |
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non-coding rna |
non-coding RNA |
2827 |
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PF3D7_1148100 |
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non-coding rna |
non-coding RNA |
1659 |
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PF3D7_1148200 |
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non-coding RNA |
non-coding RNA |
544 |
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PF3D7_1148500 |
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non-coding rna |
non-coding RNA |
273 |
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PF3D7_1229200 |
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non-coding rna |
non-coding RNA |
1171 |
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PF3D7_1309120 |
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non-coding rna |
non-coding RNA |
307 |
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PF3D7_1370800 |
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non-coding rna |
non-coding RNA |
1026 |
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PF3D7_1370900 |
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non-coding rna |
non-coding RNA |
597 |
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PF3D7_1421700 |
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non-coding rna |
non-coding RNA |
189 |
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PF3D7_1424800 |
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non-coding rna |
non-coding RNA |
118 |
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Genomic locations and properties of RNAs of unknown function (RUFs) |
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RNA |
PFID |
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Length (Bp) |
Comments |
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RUF1 |
PF3D7_1328700 |
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plasmodium rna of unknown function ruf1 |
222 |
Intergenic Upstream of PF13_0152, Sir2 homolog |
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RUF2 |
PF3D7_0218900 |
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small nucleolar rna snor41 |
160 |
Between snoR01 and RNAseP Conflict with gene prediction PFB0877c |
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RUF3 |
PF3D7_0804200 |
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plasmodium rna of unknown function ruf3 |
160 |
Intronic Intron of predicted gene Pf08_0124 |
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RUF4 |
PF3D7_1425000 |
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plasmodium rna of unknown function ruf4 |
172 |
Between snoR29 and snoR31 Possibly cotranscribed with other snoRNAs |
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RUF5 |
PF3D7_0110300 |
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lasmodium RNA of unknown function RUF5 |
275 |
Intergenic Not conserved, EST evidence |
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RUF6-1 |
PF3D7_0711600 |
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plasmodium RNA of unknown function RUF6 |
135 |
Intergenic, clustered |
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RUF6-2 |
PF3D7_0711800 |
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plasmodium rna of unknown function ruf6 |
135 |
Upstream of RIFIN, chr7 cluster 98.8% similar to RUF6-1 |
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RUF6-3 |
PF3D7_0412500 |
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plasmodium rna of unknown function ruf6 |
135 |
Upstream of RIFIN, chr4A cluster 97.4% similar to RUF6-1 |
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RUF6-4 |
PF3D7_0808500 |
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plasmodium rna of unknown function ruf6 |
135 |
Downstream from Asparagine-rich antigen, chr8 cluster 96.8% similar to RUF6-1 |
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RUF6-5 |
PF3D7_1240500 |
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plasmodium rna of unknown function ruf6 |
135 |
Upstream of PFL1975c, chr12 cluster 96.2% similar to RUF6-1 |
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RUF6-6 |
PF3D7_0420800 |
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plasmodium rna of unknown function ruf6 |
135 |
Upstream of RIFIN, chr4B cluster 96.8% similar to RUF6-1 |
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RUF6-7 |
PF3D7_0421000 |
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plasmodium rna of unknown function ruf6 |
135 |
Upstream of RIFIN, chr4B cluster 96.8% similar to RUF6-1 |
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RUF6-8 |
PF3D7_0413000 |
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plasmodium rna of unknown function ruf6 |
135 |
Upstream of RIFIN, chr4A cluster 94.9% similar to RUF6-1 |
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RUF6-9 |
PF3D7_0412800 |
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plasmodium rna of unknown function ruf6 |
135 |
Upstream of RIFIN, chr4A cluster 94.9% similar to RUF6-1 |
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RUF6-10 |
PF3D7_0809000 |
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plasmodium rna of unknown function ruf6 |
135 |
Downstream from Asparagine-rich antigen, chr8 cluster, 94.9% similar to RUF6-1 |
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RUF6-11 |
PF3D7_0421400 |
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plasmodium rna of unknown function ruf6 |
135 |
Downstream from RIFIN, chr4B cluster 94.9% similar to RUF6-1 |
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RUF6-12 |
PF3D7_0712100 |
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plasmodium RNA of unknown function RUF6 |
135 |
Upstream of RIFIN, chr7 cluster 94.2% similar to RUF6-1 |
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RUF6-13 |
PF3D7_0712700 |
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plasmodium RNA of unknown function RUF6 |
135 |
Upstream of RIFIN, chr7 cluster 94.2% similar to RUF6-1 |
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RUF6-14 |
PF3D7_1240800 |
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plasmodium rna of unknown function ruf6 |
135 |
Upstream of PFL1975c, chr12 cluster 93.6% similar to RUF6-1 |
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RUF6-15 |
PF3D7_1241000 |
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plasmodium rna of unknown function ruf6 |
135 |
Upstream of PFL1975c, chr12 cluster 92.1% similar to RUF6-1 |
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Many PfEMP1 loci are identified upstream of RUF6 copies on Chr4 and Chr12. a |
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Note that the origin and composition of the RUF6 Northern signal with respect to the 15 RUF6 genes is uncertain. |
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