C.elegans small RNAs

miR-Intess™

miR classification

miR expression

cel-mir-38

cel-mir-38

Cloning frequencies
absolute	CE1
cel-mir-38 3arm	1
normalized	CE1
cel-mir-38 3arm	0.001

cel-mir-38 relative cloning frequencies

block2590 (miRBase cel-mir-38) [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-38	0.001	no	no	0.50/0.50	22/22/1.00	0.0	0.0	1	0	1	0	16	7	3arm	1	nd	0.14	2	1	1	na	na

Clusters
Located in cluster 1: cel-mir-35, cel-mir-36, cel-mir-37, cel-mir-38, cel-mir-39, cel-mir-40, cel-mir-41

Families
Member of family miR-35/36/38/39/40/41 (seed CACCGGG): cel-mir-40, cel-mir-35, cel-mir-36, cel-mir-37, cel-mir-39, cel-mir-41, cel-mir-38

block2590 hairpin

		reads	miRBase family seed
seed	----------------------------------------------------------------------------------------CACCGGG--------------------------------------------------	1	miR-35/36/38/39/40/41
		len	cloning frequencies
			CE1
cel-miR-38	---------------------------------------------------------------------------------------TCACCGGGAGAAAAACTGGAGT------------------------------------	22	1
celegans	-------TCTGT--------------GAGCCAGGTCCTGTTCCGGTTTTT-TCCGTG-GTGATAACGCATCCAAAA----GTCTCTATCACCGGGAGAAAAACTGGAGTAGGACCTGTGACTCAT--------------------
cbriggsae	------GTCCGATGGGTATTCATGTGGAGCCTGGACCTGTACCGGGTTCTCTTTGTG-GTGATATGACAACTCATAACCATTCCTTATCACCGGGAGACAACCTGGTATAGGTCCAGCGACTCTGCTGGATGGTCCCGTTGCCC-
cjaponica	GCAGTGGTCCCTCGGGGCAGAA----GAGCCAGGACCTACATCAGTTTCTTTCCGCG-GTAATAAATAATACATTA--------TTATCACCGGGAGAAAAACTGGAGTAGGACCTGCGACTCGACTCGACCTTTATTCCGCTGT
cbrenneri	-----GGTCTATTTCGTTTCCA----GAGCCAGGACCTGTTCCAGTTTTTTTCCGCG-GTAATAACGCGAGCAAGT-------CCTATCACCGGGAGAAAAACTGGAGTAGGTCCTGCGACTCTACAAGGATGTTCAGTAGTCT-
ppacificus	----------GTACCGTACCCA-------CCCCGTCCTGCATCGCGTATCGCCCGTGTGTGCTCGCATAAGAAGTA----------CTCACCGGGAGAAATGC-GATGTAGG-CCCGTGGCCTACCGTAC---------------
cremanei	--------------------------------------ATACCGGTTTAACTTCGTG-GTGATATGACACATATTA--CATTCTTTATCACCGGGAGTAAAACTGGTAT------------------------------------
	* * * * ** * ********** * * * *
	----- ----- ------------------------ ------ ------------------ --------------------------------------------- -----	Y62F5A.9 Y62F5A.9 Y62F5A.9
celegans	...(( (((((((((((((((((((((((( ..(.(( ((((((..((........ ))...)))))))).)..)))))))))))))))))))).).)))))	1.000 -50.10
cbriggsae	...(((((((((((((.((((((.((((((((((((((((((((((..((( (((((((((....)))))........)))))))..)))))..)))))))))))))))))...))))))))))))..)))))))...	0.997 -66.80
cjaponica	(((((((......((((..((. (((.((((.(((((..((((((.(((((.(( ((.((.(((((....))) )))).))))))))).))))))..))))).))))...)))...))..))))....)))))))	0.964 -51.50
cbrenneri	((.(((((.....(((( (((.((((((((((((((((((((((((.(( ((.(((..((......)) ..))).))))))))))))))))))))))))))))...))))....))).....))))).))	0.997 -55.90
ppacificus	((((.(((.((( (.....((((((((((((.((.((((((.((((((......)).))) ).))).))).)).)))) )))))))) ...))))..))).))))	1.000 -46.70
cremanei	((((((((((.(((((.(( ((((((............ .......))))))))))))).))))))))))	1.000 -26.31

celegans	chromosome:II:11537846:11537943:1	Opposite_strand\|Intronic_coding\|Y62F5A.9\|Y62F5A.9 ## Y62F5A.9\|protein_coding\|Y62F5A.9\|Y62F5A.9 [Source:RefSeq_peptide;Acc:NP_741048] ## {MIR: cel-mir-38}
cbriggsae	chromosome:chrII:7535848:7535984:1	Opposite_strand\|Intronic_coding\|NM_177732 ## Same_strand\|Intronic_coding\|NM_001101718 ## {MIR: cbr-mir-38}
cjaponica	chromosome:chrUn:117591702:117591833:-1	Opposite_strand\|Intronic_coding\|NM_171042
cbrenneri	chromosome:chrUn:41613392:41613518:-1	Same_strand\|Intronic_coding\|NM_001056672 ## Opposite_strand\|Intronic_coding\|NM_171042
ppacificus	chromosome:chrUn:118860534:118860634:1	Same_strand\|Intronic_coding\|NM_133957 ## {Repeats: (CCCTA)n 5 80 1 class=Simple_repeat}
cremanei	chromosome:chrUn:8778778:8778845:-1	Same_strand\|Intronic_coding\|NM_001011005 ## Opposite_strand\|Intronic_coding\|NM_171042

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