C.elegans small RNAs

miR-Intess™

miR classification

miR expression

cel-mir-254

cel-mir-254

block7874 (miRBase cel-mir-254) [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-254	0.001	no	no	0.48/0.48	23/23/1.00	nd	nd	0	0	0	0	19	7	3arm	1	nd	0.26	3	0	0	na	na

block7874 hairpin

		reads	miRBase family seed
seed	---------------------------------------------------------------------------GCAAAUC----------------------------------------------	0	miR-254
		len	cloning frequencies

cel-miR-254	--------------------------------------------------------------------------TGCAAATCTTTCGCGACTGTAGG-------------------------------	23
celegans	--------------ACTATGCATATTGCCGCCTACAGAAGCATAGATTTCCACAAACCA--TTCGAGGTGTTTGTGCAAATCTTTCGCGACTGTAGGCGGCGAACATGCAGTTTTT------------
cbriggsae	---AGCACCTCCACTCTATGCGGGTTGCCGTATACAGAAGCATCGATTTTCACACGCCA----TGATGCGCCTGTGCAAATCTTTTGCAACTGTATACGGCGATTTAGCA------------------
cjaponica	----------------------------CGCCTACAGAAGCATAGATTTCCACAAGTTAATTTTTAAGAGCCTGTGCAAATCTGTCGCATCTGTAAGCG-----------------------------
cbrenneri	GCATGATTCACTTAAAAATGCATATTGCCGCCTACAGAAGCATAGATTTTCACATACCGA-TCTGAAGAGTTTGTGCAAATCTGTCGCATCTGTAGGCGGCGATTATGCAGTCATTTGAGCACCTAGC
cremanei	GCATGATGAGCACTAGAATGCATATCGCCGCTTACAGAAGCGTGGATTTTCACATACCAA-TCGGAAGTGTCTGTGCAAATCTATCGCAACTGTACACGGCGATACTGCAGTTATT-GAACACCTTGC
	******* * *** ** * * * *********** * *
	+++++ +++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++	ZK455.2 ZK455.2 gcy-9
celegans	....(((((.(((((((((((((..((..((((((.((((((((. ......).))))))).))))))...))..)))))))))))))..)))))......	1.000 -46.90
cbriggsae	...............(((((((((((((((((((..(((..(((((.(((((((.. ....)))..)))).)))))...)))..)))))))))))))))).)))	0.853 -40.60
cjaponica	(((.((((((.((((((((((.((((.(((..........))).)))).)))))))).)).)))))).)))	1.000 -26.60
cbrenneri	..........((((((..((((((((((((((((((((.((((((((((.((((.((... ((....)))).)))).)))))))).)).))))))))))))))).)))))....))))))........	0.974 -53.00
cremanei	(((...((..((.((...((((((((((((..(((((..((((((((((.((((.((... ........)).)))).))))))).)))..)))))..)))))))).))))..)).) )..))...)))	0.971 -43.30

celegans	chromosome:X:11333459:11333558:-1	Same_strand\|Intronic_coding\|ZK455.2\|ZK455.2 ## ZK455.2\|protein_coding\|gcy-9\|gcy-9 encodes a membrane guanylyl cyclase. gcy-9 expression is reportedly weak and variable in non-neuronal tissues. [Source: WormBase] ## {SimpF: WRM067dB12 -1 fosmid,WRM0617bB05 -1 fosmid} ## {MIR: cel-mir-254}
cbriggsae	chromosome:chrX:5320049:5320151:1	Same_strand\|Intronic_coding\|NM_001105250 ## Opposite_strand\|Intronic_coding\|NM_072374 ## {MIR: cbr-mir-254}
cjaponica	chromosome:chrUn:593205:593275:-1	Same_strand\|Intronic_coding\|NM_001109695
cbrenneri	chromosome:chrUn:96346:96472:-1	Same_strand\|Intronic_coding\|NM_001109695
cremanei	chromosome:chrUn:33393203:33393328:-1	Same_strand\|Intronic_coding\|NM_001109695

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