Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_shortStem_5varHIGH_loopOverlap_nonpairedHIGH (11 loci)

block843142 [novel_lenNOK_shortStem_5varHIGH_loopOverlap_nonpairedHIGH]

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
no	0.139	no	no	0.37/0.42	18/24/0.67	6.0	2.5	6	0	2	0	2	-3	5arm_loop	7	nd	0.33	3	6	2	na	na

		reads	miRBase family seed
seed	-----------GAAUCCU--------------------------------------------------	3	novel
seed	---------CUGAAUC----------------------------------------------------	2	novel
seed	---GUUCUUC----------------------------------------------------------	1	miR-22*
		len	cloning frequencies
			T1S2	T5S1
	--------TCTGAATCCTCTATGACTAGA---------------------------------------	21	-	1
	--------TCTGAATCCTCTATGACTAG----------------------------------------	20	-	1
	----------TGAATCCTCTATGACTAG----------------------------------------	18	-	1
	----------TGAATCCTCTATGACTAGA---------------------------------------	19	-	1
	--GGTTCTTCTGAATCCTCTATGACT------------------------------------------	24	-	1
	----------TGAATCCTCTATGACTAGACA-------------------------------------	21	1	-
rat	gtGGTTCTTCTGAATCCTCTATGACTAGACAtaggcataaactaggccatggggaatgacaagtccca
	********************************************************************
rat	.(((..(((.....(((.(((((.((((.............))))..)))))))).....)))..)))	0.870 -15.62

rat

chromosome:1:49040412:49040479:-1

intergenic

block948773 [novel_lenNOK_shortStem_5varHIGH_loopOverlap_nonpairedHIGH]

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
no	0.286	no	no	0.42/0.50	18/24/0.40	2.4	4.2	5	0	4	0	4	-4	3arm	4	nd	0.39	3	5	4	na	na

		reads	miRBase family seed
seed	-----------------------------ACUACUG-------------------------	3	novel
seed	------------------------------------GAACUUC------------------	1	novel
seed	----------------------------------UGGAACU--------------------	1	novel
		len	cloning frequencies
			T2S2	T3S2	T4S1	T5S1
	----------------------------CACTACTGGAACTTCACAA--------------	19	-	-	-	2
	----------------------------CACTACTGGAACTTCACAAACTGG---------	24	1	-	-	-
	-----------------------------------GGAACTTCACAAACTGGC--------	18	-	1	-	-
	---------------------------------CTGGAACTTCACAAACTGGCTACT----	24	-	-	1	-
rat	ctgcacttggaaaagagtgtgattcagtCACTACTGGAACTTCACAAACTGGCTACTgaca
	*************************************************************
rat	.......(((...((..(((((((((((....))))))...)))))..))..)))......	0.530 -11.90

rat

chromosome:1:24186238:24186298:1

intergenic

block1057713 [novel_lenNOK_shortStem_5varHIGH_loopOverlap_nonpairedHIGH]

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
no	0.064	no	no	0.48/0.58	19/25/0.00	4.0	1.0	2	0	2	0	4	-4	5arm_loop	10	nd	0.40	3	2	2	na	na

		reads	miRBase family seed
seed	-------------CAUCUUG----------------------------------------------	1	novel
seed	-----AAGUAAA------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T5S2
	----CAAGTAAACCATCTTGTGCACCCAC-------------------------------------	25	-	1
	------------CCATCTTGTGCACCCACGA-----------------------------------	19	1	-
rat	ggtcCAAGTAAACCATCTTGTGCACCCACGAagccttcgggagcagaagtaagggatgctgaagcc
	******************************************************************
	----------------------------------------------------------------------------	ENSRNOT00000061299 ENSRNOG00000000777 RT1-S3
rat	(((...((((..((..(((.(((.(((...........))).))).)))...))..))))...)))	1.000 -20.70

rat

chromosome:20:2850371:2850436:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000061293|ENSRNOG00000000777 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000061299|ENSRNOG00000000777 ## ENSRNOG00000000777|protein_coding|RT1-S3|RT1-149 protein [Source:RefSeq_peptide;Acc:NP_001008826]

block1060556 [novel_lenNOK_shortStem_5varHIGH_loopOverlap_nonpairedHIGH]

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
no	0.114	no	no	0.39/0.45	18/24/0.43	1.3	3.6	7	0	4	0	4	-12	5arm_loop	1	nd	0.39	3	7	4	na	na

		reads	miRBase family seed
seed	-----GGUCCUC-----------------------------------------	4	novel
seed	---------CUCUCUU-------------------------------------	2	novel
seed	------GUCCUCU----------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S2	T4S2	T5S1
	----TGGTCCTCTCTTTTTCTA-------------------------------	18	-	2	-	-
	----TGGTCCTCTCTTTTTCTAC------------------------------	19	2	-	-	-
	--------CCTCTCTTTTTCTACCTAGACTGA---------------------	24	-	-	-	2
	-----GGTCCTCTCTTTTTCTACCT----------------------------	20	-	-	1	-
rat	tggtTGGTCCTCTCTTTTTCTACCTAGACTGAtgacagggaagggacacaccc
	*****************************************************
rat	.(((..((((..(((((.((.............)).)))))..))))..))).	0.970 -14.52

rat

chromosome:20:5508999:5509051:-1

intergenic

block1093618 [novel_lenNOK_shortStem_5varHIGH_loopOverlap_nonpairedHIGH]

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
no	0.851	no	no	0.47/0.53	18/23/0.33	0.0 2.0	0.0 1.6	1 5	0 0	1 1	0 0	0 4	9 -4	5arm 5arm_loop	1 1	nd nd	0.39 0.32	5 3	6	1	na	na

		reads	miRBase family seed
seed	-----------GAUACUU-----------------------------------------------	3	novel
seed	-----CUUGGUG-----------------------------------------------------	1	novel
seed	-------UGGUGAU---------------------------------------------------	1	novel
seed	-GCGUCUU---------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----------TGATACTTCCTCCCGGGAA------------------------------------	19	2
	CGCGTCTTGGTGATACTT-----------------------------------------------	18	1
	------TTGGTGATACTTCCTCCCGGGAA------------------------------------	23	1
	----------TGATACTTCCTCCCGGGAATG----------------------------------	21	1
	----TCTTGGTGATACTTCCTCC------------------------------------------	19	1
rat	CGCGTCTTGGTGATACTTCCTCCCGGGAATGgccctggggtagcagaagagggctcacgctccgc
	*****************************************************************
rat	.(((.....((((..((((.(((((((......)))))))........))))..))))....)))	0.510 -19.10

rat

chromosome:20:5542315:5542379:1

intergenic

block1107937 [novel_lenNOK_shortStem_5varHIGH_loopOverlap_nonpairedHIGH]

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
no	0.116	no	no	0.48/0.58	19/25/0.00	4.0	1.0	2	0	2	0	3	-1	5arm_loop	10	nd	0.32	2	2	2	na	na

		reads	miRBase family seed
seed	------------CAUCUUG----------------------------------------------------	1	novel
seed	----AAGUAAA------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T5S2
	---CAAGTAAACCATCTTGTGCACCCAC-------------------------------------------	25	-	1
	-----------CCATCTTGTGCACCCACGA-----------------------------------------	19	1	-
rat	gtcCAAGTAAACCATCTTGTGCACCCACGAagcctgcgggagcagaagtaagggatgctgaagcccgggac
	***********************************************************************
rat	((((.((((..((..(((.(((.(((.((.....)).))).))).)))...))..))))........))))	0.910 -23.00

rat

chromosome:20:28516931:28517001:1

intergenic

block234809 [novel_lenNOK_shortStem_5varHIGH_loopOverlap_nonpairedHIGH]

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
no	0.501	no	no	0.47/0.59	19/26/0.29	5.1	4.0	7	0	4	0	4	-4	5arm_loop	1	nd	0.47	3	7	4	na	na

		reads	miRBase family seed
seed	---------------CACCAGU----------------------------------------------------	2	novel
seed	-------GAGAGCU------------------------------------------------------------	2	novel
seed	--------------UCACCAG-----------------------------------------------------	1	novel
seed	--------AGAGCUU-----------------------------------------------------------	1	novel
seed	-----GAGAGAG--------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T4S1	T5S1	T5S2
	----TGAGAGAGCTTCACCAGTCTTCCCC---------------------------------------------	25	-	-	1	-
	-------GAGAGCTTCACCAGTCTTCCCC---------------------------------------------	22	-	-	1	-
	------AGAGAGCTTCACCAGTCTTCCCC---------------------------------------------	23	-	-	1	-
	-------------TTCACCAGTCTTCCCCTTCCCTACC------------------------------------	25	-	1	-	-
	--------------TCACCAGTCTTCCCCTTCCCTACCTC----------------------------------	26	-	-	1	-
	--------------TCACCAGTCTTCCCCTTCC-----------------------------------------	19	-	-	-	1
	------AGAGAGCTTCACCAGTCTT-------------------------------------------------	19	1	-	-	-
rat	tcttTGAGAGAGCTTCACCAGTCTTCCCCTTCCCTACCTCataggcttggaaacctatgtcccccttcctttga
	**************************************************************************
rat	((...(((..((...((..((..((((.....((((.....))))...))))..)).)).....))..))).))	0.750 -8.60

rat

chromosome:12:44302357:44302430:1

intergenic

novel_lenNOK_shortStem_mirtron_randfoldOK (11 loci)

block5255 [novel_lenNOK_shortStem_mirtron_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
no	0.007	no	no	0.44/0.45	18/22/0.67	0.3	3.0	3	0	2	0	3	12	3arm	1	0	0.06	1	3	2	na	na

		reads	miRBase family seed
seed	-------------------------------------------------AAUCUGG------------------	2	novel
seed	--------------------------------------------------AUCUGGU-----------------	1	novel
		len	cloning frequencies
			T1S1	T1S2
	------------------------------------------------GAATCTGGTTTTTCCTCCTCCA----	22	1	-
	------------------------------------------------GAATCTGGTTTTTCCTCC--------	18	-	1
	-------------------------------------------------AATCTGGTTTTTCCTCCTCCAG---	22	-	1
rat	ttcacacagtggggaagaatcagatcatccactaaaggtcatcattctGAATCTGGTTTTTCCTCCTCCAGgaa
	**************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>	ENSRNOT00000009409 ENSRNOG00000007117 LOC363544
rat	.((....((.(((((((((((((((((.((......)).........))).))))))))))))))))....)).	0.700 -20.80

rat

chromosome:10:11865461:11865534:-1

Same_strand|Intronic_coding|ENSRNOT00000009409|ENSRNOG00000007117 ## ENSRNOG00000007117|protein_coding|LOC363544|Clusterin-associated protein 1. [Source:UniProtKB/Swiss-Prot;Acc:Q6AYJ5]

block6543 [novel_lenNOK_shortStem_mirtron_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
no	0.003	no	no	0.61/0.61	18/18/0.00	0.0	0.0	1	0	1	0	2	19	3arm	1	0	0.17	3	1	1	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------------------CCGUGGC------------	1	novel
		len	cloning frequencies
			T4S2
	---------------------------------------------------------------------TCCGTGGCCCTGTTTCAG--	18	1
rat	tctgagacagggcaggaggcaggatactctcctcttctgtgagagcaaagcacagacggtcctctctgcTCCGTGGCCCTGTTTCAGgc
	*****************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>	ENSRNOT00000016221 ENSRNOG00000011375 Tsc2_v2
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>	ENSRNOT00000052138 ENSRNOG00000011375 Tsc2_v2
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>	ENSRNOT00000030886 ENSRNOG00000011375 Tsc2_v2
rat	(((((((((((((.(((.((((((......((...((((((.........)))))).))...)).)))))))...))))))))))))).	0.950 -41.20

rat

chromosome:10:13872371:13872459:-1

Same_strand|Intronic_coding|ENSRNOT00000030886|ENSRNOG00000011375 ## ENSRNOG00000011375|protein_coding|Tsc2_v2|Tuberin (Tuberous sclerosis 2 homolog protein). [Source:UniProtKB/Swiss-Prot;Acc:P49816]

block33262 [novel_lenNOK_shortStem_mirtron_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
no	0.003	no	no	0.39/0.39	18/18/0.00	0.0	0.0	1	0	1	0	0	1	5arm	1	4	0.17	2	1	1	na	na

		reads	miRBase family seed
seed	-CUUCAUU-------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	CCTTCATTCCGTAGATTA---------------------------	18	1
rat	CCTTCATTCCGTAGATTAccagagtgagtactacggtcctggagg
	*********************************************
	+++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000003799 ENSRNOG00000002812 Lhx1
rat	((((((..((((((.((((....))))...))))))...))))))	1.000 -16.90

rat

chromosome:10:72800929:72800973:-1

Same_strand|Boundary_coding|ENSRNOT00000003799|ENSRNOG00000002812 ## ENSRNOG00000002812|protein_coding|Lhx1|LIM/homeobox protein Lhx1 (LIM homeobox protein 1) (Homeobox protein Lim-1) (Rlim). [Source:UniProtKB/Swiss-Prot;Acc:P63007]

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