C.elegans small RNAs

miR-Intess™

miR classification

miR expression

cel-mir-1823

cel-mir-1823

block1212 (miRBase cel-mir-1823) [miRNAknown_rep_randfoldOK]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
miRBase cel-mir-1823	0.004	no	Satellite	0.36/0.36	22/22/1.00	nd	nd	0	0	0	0	16	3	3arm	1	nd	0.27	2	0	0	na	na

block1212 hairpin

		reads	miRBase family seed
seed	--------------------------------------------------------------------------ACUGGAA---------------------------------------------	0	novel
		len	cloning frequencies

cel-miR-1823	-------------------------------------------------------------------------TACTGGAAGTGTTTAGG--AGTAA-----------------------------	22
celegans	TTTGACCTGAACGT-----CACCCCTAAC--CCTATGCAGTATTTGGAGCTCA---------------TAAAATACTGGAAGTGTTTAGG--AGTAATGCTCAGTTGTCAGAA-------------
cremanei	-----------TGCAGAAGCACTTGCAACAGTTACTGGAATTATTGAT-----------------------GGAACTGGAAGT-TGTGGATCTGCA------------------------------
cbriggsae	CAAAATAACGAAGTTTCTGAAACTCTAAA--TTCCTA-AATTTTTGATATTCAGAAGTTCGGAAATTCTGAAATACTGGAATTAAAAAATTCGGAAATTCGGAAATTTAGAAATTCTGGAATTCTG
cbrenneri	------------------GTTTTTCCAAA-----ATTGAGTTTTTGAT--------------------TAAAAAACTGGAATTTTGAGAG--AAAA------------------------------
ppacificus	------------------GCTCTCCTCAT--TTCCCATTGTCTCTCGT-----CAGTT---AGAGGTAAGTGACACTGGAAAAGAGAGGA--GGAA------------------------------
	* * * ******* *
celegans	((((((((((.((( .((.(((((( .((...((((((((........ ..))))))))..)).))).))) .)).))).))))..)))))).	1.000 -24.70
cremanei	.(((((..(((..((..(((((.(((..........) )))))))...)) .)))..))))).	0.994 -15.60
cbriggsae	((.(((..((.((((((((((..((..(( ((((.( (.((((((((.(((((...(((((.....)))))...))))))))))))).)).)))).))..))..)))))))))).))..))).))	0.980 -30.10
cbrenneri	.(((((((((( (((.(((((((... ..))))))).)).))))).))) ))).	1.000 -13.60
ppacificus	..(((((((.( ((.(((.((((.((..( (.... ...))..)).)))).))).)))..))))) ))..	1.000 -23.10

celegans	chromosome:I:12608609:12608697:1	intergenic ## {SimpF: WRM0635dA11 1 fosmid,WRM066cD10 1 fosmid,WRM0641dE06 1 fosmid,WRM0612aE11 1 fosmid,WRM0638dG06 1 fosmid} ## {MIR: cel-mir-1823}
cremanei	chromosome:chrUn:75746237:75746365:1	Same_strand\|Exonic_coding\|NM_069609 ## Same_strand\|Boundary_non-coding\|NM_207113 ## Same_strand\|Boundary_coding\|NM_001088723
cbriggsae	chromosome:chrII:4263615:4263737:-1	Opposite_strand\|Intronic_coding\|NM_140813 ## Same_strand\|Intronic_coding\|NM_006287 ## {Repeats: MINISAT4_CB 99 468 -1 class=Satellite}
cbrenneri	chromosome:chrUn:129274557:129274685:-1	Opposite_strand\|Intronic_coding\|NM_065052
ppacificus	chromosome:chrUn:25976493:25976621:-1	intergenic

©2008 InteRNA Genomics B.V.