C.elegans small RNAs

miR-Intess™

miR classification

miR expression

cel-mir-239b

cel-mir-239b

block7885 (miRBase cel-mir-239b) [miRNAknown_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-239b	0.001	no	no	0.32/0.32	22/22/1.00	nd	nd	0	0	0	0	15	6	5arm	1	nd	0.14	2	0	0	na	na

block7885 hairpin

		reads	miRBase family seed
seed	-------------------------------UUGUACU---------------------------------------------------------------------------------------------------	0	miR-239a
		len	cloning frequencies

cel-miR-239b	------------------------------TTTGTACT----------------------ACACAAAAGTACTG---------------------------------------------------------------	22
celegans	GCGAC---------------AGATGCAATTTTTGTACT----------------------ACACAAAAGTACTGGTCATTTAAGTTGAGGCTCAGCACT--TTTGTGGTGTGCAAAAATGGCAAGTTGCTTTTATCT
cbriggsae	------------------------------TTTGTACT----------------------GCACAAAAGTACTGACTATTT---------CTCAGCGCT--TTTGTCCAGTGCAAG---------------------
cjaponica	------------------------------TTTGTACT----------------------ACACATAGGTACTGGTGA----AAACGTGTTTAACCAGTGCCTGGTCTAGTGCAAG---------------------
cbrenneri	GCTGCCATTCCAAACTGACAAGTTGCAGTTTTTGTACT----------------------TCACAAGAGTACTGGCGGTTC-AGGTCCGGCTCAGAACT--TTTGTGGGGTGCAAGAACAGCAAAACTGTCA-----
ppacificus	------------------------------ATTGTACTAATTTATTTATTTATTTATTTAATAAAAAAATAAAAATAA---------------ATAAATAAATAATGTCATACAAG---------------------
cremanei	------------------------------TTTGTACT----------------------GCACAAAAGCTCTGACTGCTC-TGATATGGCTCAGCACT--TTTGTCT-GTGCAAA---------------------
	******* * * * * * * * ***
celegans	((((( ...(((.((((((((((. .(((((((((.((((((.((......))))).))).))) ))))))..)))))))))).))).)))))........	1.000 -37.50
cbriggsae	.((((((( (.(((((((..((((...... .))))..)) ))))).)))))))).	1.000 -24.20
cjaponica	.((((((( (.((.(((((((((((.. (((....))).))))))))))))).)))))))).	1.000 -28.40
cbrenneri	...............(((((..((((.((((((((((. .(((((((((.(((((((... ....)).)).))).))) ))))))..)))))))))).))))...)))))	0.972 -45.90
ppacificus	.(((((.....((((((((((((((((((.............)))))) )))))))))))).....))))).	0.999 -15.32
cremanei	.((((((. ..(((((((..((((..(((. ......)))))))..)) ))))).. )))))).	1.000 -17.90

celegans	chromosome:X:11791226:11791323:-1	intergenic ## {SimpF: WRM064aB01 -1 fosmid,WRM067bC07 -1 fosmid,WRM0624bH08 -1 fosmid,WRM068cE04 -1 fosmid,WRM0610bH05 -1 fosmid,WRM0632aD05 -1 fosmid,WRM0628bH10 -1 fosmid,WRM0621bA09 -1 fosmid,WRM0624aG10 -1 fosmid} ## {MIR: cel-mir-239b}
cbriggsae	chromosome:chrX:15174113:15174250:-1	Opposite_strand\|Intronic_coding\|NM_001099298 ## Same_strand\|Intronic_coding\|NM_077585 ## {MIR: cbr-mir-239b}
cjaponica	chromosome:chrUn:61791059:61791196:-1	intergenic
cbrenneri	chromosome:chrUn:34417669:34417775:1	intergenic
ppacificus	chromosome:chrUn:166913035:166913172:1	Opposite_strand\|Intronic_coding\|NM_145301 ## {Repeats: (TTTA)n 1 21 1 class=Simple_repeat,(TAAA)n 4 35 1 class=Simple_repeat}
cremanei	chromosome:chrUn:26918263:26918400:1	intergenic

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