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Table 1 The ncRNA classes used in the current study

From: Systematic classification of non-coding RNAs by epigenomic similarity

ncRNA abbreviation Parent family Source Description Function Counts Min length Mean length Max length
7SK Gene RFAM 7SK RNA Part of snRNP complex; involved in control of transcription elongation. 316 61 293 374
C/D box snoRNA RFAM CD-box RNA Localized to nucleolus, involved in methylation of rRNA. 509 30 99 238
H/ACA box snoRNA RFAM HACA-box Localized to nucleolus, involved in pseudouridylation of rRNA. 440 52 130 329
lncRNA Gene RFAM Long non-coding RNA A non protein-coding transcript with > 200 nt. 217 36 144 463
miRNA Gene miRbase micro RNA A short, hairpin-shaped RNA that usually suppresses translation of target mRNA by binding to 3' UTR. 2233 15 22 27
piRNA Gene UCSC piwi-interacting RNA A large class of 26-31 nt RNA suggested being involved in transposon silencing. 2152 20 47 8302
pri-miRNA Gene miRbase primary microRNA A transcript containing one or more microRNAs before processing by Drosha complex. 1595 41 83 180
rRNA Gene RFAM ribosomal RNA RNA which is directly incorporated into the ribosome (distinct from mRNA encoding ribosomal proteins). 611 34 119 1860
scaRNA snoRNA RFAM small Cajal body-specific RNA Located in the nucleolus, and involved in methylation and pseudouridylation of spliceosomal RNAs. 52 82 153 419
snoRNA snRNA RFAM small nucleolar RNA RNA located in the nucleolus, mostly involved in modification of other RNAs, such as rRNA or spliceosomal RNA. 1001 30 115 419
snRNA Gene RFAM small nuclear RNA Small RNA located in the nucleus, involved in the spliceosome, RNA modification, or other functions. 3024 30 109 419
spliceosomal snRNA RFAM spliceosomal RNA RNA forming part of the spliceosome complex. 1812 49 111 229
SRP-RNA Gene RFAM signal recognition particle RNA RNA forming part of the SRP complex. The SRP complex targets proteins to their proper subcellular localization by recognizing the signal recognition peptide tag on proteins. 941 201 286 361
tRNA Gene RFAM transfer RNA Transfer amino acids to the ribosome for protein construction. 905 59 72 107
Y-RNA Gene RFAM Y RNA Components of the Ro RNP complex; may repress Ro activity. As an independent function, is also required for DNA replication. 893 57 102 148
Total      16701