C.elegans small RNAs

miR-Intess™

miR classification

miR expression

cel-mir-359

cel-mir-359

Cloning frequencies
absolute	CE1
cel-mir-359 3arm	1
normalized	CE1
cel-mir-359 3arm	0.001

cel-mir-359 relative cloning frequencies

block8220 (miRBase cel-mir-359) [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-359	0.001	no	no	0.45/0.50	20/22/1.00	0.0	0.0	1	0	1	0	27	5	3arm	1	nd	0.18	1	1	1	na	na

Clusters
Located in cluster 9: cel-mir-359, cel-mir-785

block8220 hairpin

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------------------CACUGGU---------------------------------------------------------	1	miR-359
		len	cloning frequencies
			CE1
	--------------------------------------------------------------------------------------------TCACTGGTCTTTCTCTGACG---------------------------------------------	20	1
cel-miR-359	--------------------------------------------------------------------------------------------TCACTGGTCTTTCTCTGACGAA-------------------------------------------	22	-
celegans	---------AA--TGCTCCTTGAAA-----TT--------TCAATCGTTAGAGTAACACAC-------AGTTACACGACCTCATCAATCGTGTCACTGGTCTTTCTCTGACGAATTGAAGTTCTGGAGACAATTTTGGT--TG--------------
cbriggsae	----AAGATAAGTTACAAATCTAGACAAATCT--------TCATCCGTCAGAGCATATCTC-------AGTTACACAACTTCCTAAATAGTGTCACTGGTTATCCTCTGTCGAAATGAAGATGTCAAAAGTAGCTGTTTT-----------------
cjaponica	------------TTGCGCTG----------CC--------TCAATCATTGGAAAAATTCAC-------AGTAACAAGAGATTCCCAACT-TGCCACTGGTGTTTTTCTGATGAATTGAAGTCAGTGGCAA---------------------------
cbrenneri	---------CATTTGTATTCTGAAAAAAAACTCAAATCGTTCGATTGTCAGAGCAATCCTC-------AGTAACACGTACTCATTATTTGTGTCACTGGTTTTCTTCTGACGAATCGAAATGCTCGAGTTCTGGTTTGTTTTGCGAGAAAATGAATG
ppacificus	--------------------------------------------ATGTGAGAGTAGTGCACCACTTTGAATGATGGAAATGTATCA----TGACACTGGTTACCT--CGACAA--------------------------------------------
cremanei	GCAAAAGACTAATGGCCTCGATAAA-----CT--------TCATTGGTCAGAGCAACACGC-------AGTCACATAAGTTTCTGAAATGTGTCACTGGTTTTCCTCTGACTAATTGAAGATATCGAGTAAATTTTTTTGT----------------
	* ** * * * * * * * ***** * *
celegans	.. ((((((..(((. (( (((((((((((((.((.((.( (((.((((((.........)))))).)))))).)).)))))))).)))))))))).)))).))........ ..	1.000 -39.40
cbriggsae	(((((.((((((.......((((..((( ((((.((.(((((.(((..(( (((.((((.............)))).))))).))).))))).))..)))))))))))....)))))))))))	0.999 -33.62
cjaponica	.((((((( .( ((((((((..(((((((...( (((..((((..........)) ))..))))..)))))))..)))).))).)).))))).)).	1.000 -30.40
cbrenneri	(((((((.(((((((((.(((((....(((((((((((((((((.((...(( (((.(((((...........))))).)))))..)).))))))).))))))).....))).....))))).)))).)).))).)))))))	0.810 -35.60
ppacificus	.((((((.(((....((((......((((((......))))) ).....))))))))) ).))).	0.995 -12.90
cremanei	((((((((...((...(((((((.. (( (((((((((((((.((.((.( (((.(((((...........))))).)))))).)).))))))))))).)))).)))))))...))))))))))	0.997 -39.50

celegans	chromosome:X:3004283:3004392:1	intergenic ## {MIR: cel-mir-359}
cbriggsae	chromosome:chrX:7890588:7890708:1	Same_strand\|Intronic_coding\|NM_178660 ## Opposite_strand\|Intronic_coding\|NM_133381 ## {MIR: cbr-mir-359}
cjaponica	chromosome:chrUn:20284297:20284388:-1	intergenic
cbrenneri	chromosome:chrUn:1354700:1354840:1	intergenic
ppacificus	chromosome:chrUn:37820070:37820219:1	intergenic
cremanei	chromosome:chrUn:4288224:4288344:-1	intergenic

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