Systematic classification of non-coding RNAs by epigenomic similarity

Dozmorov, Mikhail G; Giles, Cory B; Koelsch, Kristi A; Wren, Jonathan D

doi:10.1186/1471-2105-14-S14-S2

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

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