Structured RNAs and synteny regions in the pig genome

BMC Genomics

Table 5 Synteny of the RNAs of the homology based pipeline

RNA class	# loci	hg19			RNAs conserved in N other organisms
RNA class	# loci	Syntenic	Conserved	Both	1	5	15
cisreg-elements	139	80	84	65	116	86	31
lncRNA-loci	58	57	53	53	58	57	7
miRNA	369	303	349	292	360	349	102
putative-miRNA	155	121	25	20	65	25	1
ribozyme	8	8	3	3	3	3	0
rRNA	185	143	0	0	6	1	0
snoRNA	638	473	266	221	400	282	43
snRNA	1,030	674	24	13	119	26	4
tRNA	810	549	274	199	389	284	14
other	153	111	10	10	17	11	0
Conflict	11	10	10	10	10	10	4
Sum	3,556	2,529	1,098	886	1,543	1,134	206

The columns are, RNA class, # RNA loci. # loci in human syntenic blocks, # loci conserved in human by 80% sequence identity. # loci both syntenic and conserved that is the number of ncRNAs in syntenic blocks where the ncRNA is actually conserved in human. # loci RNAs conserved in N other organisms, grouped by number of loci conserved in at least 1, 5, or 15 other organisms. Conservation is determined by the sequence identity in the pairwise alignments. The RNA loci are located in the pairwise alignments and the sequence identity is calculated when at least 80% of an RNA locus is covered. The RNA locus is counted as conserved in that organism if the locus has a sequence identity of at least 80%. In the table the number of RNAs conserved in at least N (N=1; N=5 or N=15) of the other genomes: bosTau5, canFam2, choHof1, danRer7, dasNov2, echTel1, equCab2, eriEur1, felCat4, galGal3, hg19, loxAfr3, mm9, monDom5, ornAna1, rn4, oryCun2, tarSyr1, turTru1, xenTro2.

ISSN: 1471-2164