C.briggsae small RNAs

miR-Intess™

miR classification

miR expression

cel-mir-36

cel-mir-36

Cloning frequencies
absolute	AF16
cel-mir-36 3arm	8.500
normalized	AF16
cel-mir-36 3arm	0.022

cel-mir-36 relative cloning frequencies

block5130 (miRBaseHomolog cel-mir-36) [miRBaseHomolog_cloningOK_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
miRBaseHomolog cel-mir-36	0.001	no	no	0.47/0.48	19/21/0.94	0.0	0.0	16	0	1	0	11	5	3arm	2	nd	0.19	2	17	1	na	na

Clusters
Located in cluster 14: block5129_cand, cel-mir-36

Families
Member of family miR-35/36/38/39/40/41 (seed CACCGGG): cel-mir-35, cel-mir-35, cel-mir-36, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cbr-mir-39, cbr-mir-35, cbr-mir-36, cbr-mir-40, cbr-mir-41, cbr-mir-38, block969_novel, block5129_cand

block5130 hairpin

		reads	miRBase family seed
seed	--------------------------------------------------------------CACCGGG-------------------------------------	17	miR-35/36/38/39/40/41
		len	cloning frequencies
			AF16
	-------------------------------------------------------------TCACCGGGTGAA---AA-TTGGTAC--------------------	21	16
	-------------------------------------------------------------TCACCGGGTGAA---AA-TTGGT----------------------	19	1
cbriggsae	------GACTCGGTCCTGCGCCACTTT-CCACCGCGGTGATATTCCAAGCAAAACGG-TTATCACCGGGTGAA---AA-TTGGTACAGGTC---CGATCC------
cremanei	TCGGTCGGATCGGACCTACACTGGTTT-TCGCTGCGGTGATACTTCGAG---AATGA-TTATCACCGGGTGAA---AA-TCAGGGCAGGTC---CGATTCCACCGA
celegans	-CCGCTGTCGGGGAACCGCGCCAATTT-TCGCTTCAGTGCTAGACCATCCAAAGTGT-CTATCACCGGGTGAA---AA-TTCGCATGGGTCCC-CGACGCGG----
cbrenneri	-----------------GTGCTGATTT-TTGCCGCTGTGATATTTCTAA-GCCATGA-TTATCACCGGGCGAA---AATTTGGCAC--------------------
cjaponica	-----GAGCCAGGACCTACATCAGTTTCTTTCCGCGGTAATAAATAATA---CATTA-TTATCACCGGGAGAA---AAACTGGAGTAGGACCTGCGACTC------
ppacificus	------TCTGAGTCCCTTCGATCGCCTCTGATCACTACGATGAAACTGAGATAACGAGTTTTCACCGGGTGAACAGAAGCTGTTGAAGATATCGGA----------
	* * * * ****** * **
cbriggsae	((.((((.((((..(((.((( .((((.((((((((..((.........)) .)))))))))))).) )) .)))..)))).) ))))).	1.000 -41.40
cremanei	(((((.(((((((((((...((((((( (((((.((((((((..((... ...)) .)))))))))))))) )) ))))...))))) )))))).)))))	1.000 -55.10
celegans	((((.((((((((.(((.((.((((( ((((((..(((.((((.(((.....)))) ))).))).))))))) )) )).)).))).)))) ))))))))	1.000 -47.90
cbrenneri	(((((((((( (((((...((((((..((... .....)) .))))))..)))))) )))).)))))	1.000 -23.10
cjaponica	(((.((((.(((((..((((((.(((((.((((.((.(((((.. ..))) )))).))))))))). ))))))..))))).))))...)))	1.000 -35.20
ppacificus	(((((....(((((((.((.((((.(((((.((.(((((((.........))))).)).))))))).)))).)).)))))))...)))))	1.000 -30.60

cbriggsae	chromosome:chrX:15337746:15337830:1	{Repeats: no}
cremanei	chromosome:chrUn:26787656:26787749:-1	intergenic
celegans	chromosome:chrII:11537631:11537724:1	Opposite_strand\|Intronic_coding\|Y62F5A.9 ## {MIR: cel-mir-36}
cbrenneri	chromosome:chrUn:47821542:47821666:-1	intergenic ## {SimpF: trf}
cjaponica	chromosome:chrUn:117591724:117591811:-1	Opposite_strand\|Intronic_coding\|NM_171042
ppacificus	chromosome:chrUn:171595123:171595212:-1	intergenic ## {Repeats: (GA)n 2 38 -1 class=Simple_repeat} ## {SimpF: trf}

©2008 InteRNA Genomics B.V.