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