Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_Multihit_loopOverlap_nonpairedHIGH_bulgeHIGH (227 loci)

novel_loopOverlap_randfoldOK (224 loci)

block8540 [novel_loopOverlap_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	0.005	no	no	0.65/0.65	23/23/1.00	0.0	0.0	1	0	1	0	33	-2	3arm_loop	1	nd	0.26	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------AGCCAGU------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	-------------------------------------------------------------CAGCCAGTACGGGAGCCTGAGAC---------------------------------	23	1
rat	ttccttgactgagaacgctgggtggagacttgccacgcacagctcctgcactggtgggaatCAGCCAGTACGGGAGCCTGAGACggggtgcgccgagccagctcttggttttggagt
	*********************************************************************************************************************
rat	((((..(((..(((..(((((.(((......(((.((..(((((((((.((((((........)))))).))))))).))...)).)))...)))..))))))))..)))..)))).	0.600 -51.70

rat

chromosome:10:16872449:16872565:-1

intergenic

block9633 [novel_loopOverlap_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	0.010	no	no	0.50/0.50	20/20/1.00	0.0	0.0	1	0	1	0	21	-2	3arm_loop	1	7	0.30	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------CUUCUGA---------------------------------	1	novel
		len	cloning frequencies
			T3S1
	-------------------------------------------------------TCTTCTGACCTTGCGATGCT---------------------	20	1
rat	ccattagagagggctggaagagctggttggctctcagagttttcatttttcttttTCTTCTGACCTTGCGATGCTtttccagctaaagataaagga
	************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>	ENSRNOT00000009524 ENSRNOG00000006932 Q3MIE5_RAT
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>	ENSRNOT00000059810 ENSRNOG00000006932 Q3MIE5_RAT
rat	((.(((.....((((((((((((..((.((...((((((..................))))))))..))...)))))))))))).....))).)).	0.990 -28.77

rat

chromosome:10:19576589:19576684:-1

Same_strand|Intronic_coding|ENSRNOT00000009524|ENSRNOG00000006932 ## ENSRNOG00000006932|protein_coding|Q3MIE5_RAT|Dock2 protein. [Source:UniProtKB/TrEMBL;Acc:Q3MIE5]

block14339 [novel_loopOverlap_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	0.009	no	no	0.40/0.40	20/20/1.00	0.0	0.0	1	0	1	0	28	-2	5arm_loop	1	nd	0.15	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------CACCAUA----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	----------------------------ACACCATATCTACTACAGTG----------------------------------------------------------	20	1
rat	aggtatttggtagttcaataacaaacacACACCATATCTACTACAGTGttcttgtgggttttgggtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatactt
	**********************************************************************************************************
rat	((((((.........((...(((.((((((((((((((((((((((.....))))))....)))))))).))))))))...)))...))...........))))))	0.610 -30.25

rat

chromosome:10:32660112:32660217:-1

intergenic

block48985 [novel_loopOverlap_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	0.005	no	no	0.65/0.65	20/20/1.00	0.0	0.0	1	0	1	0	7	-2	3arm_loop	1	nd	0.30	2	1	1	na	na

		reads	miRBase family seed
seed	-------------------------UCCUGCU-------------------	1	novel
		len	cloning frequencies
			T2S2
	------------------------GTCCTGCTCTGTCCCCTCGA-------	20	1
rat	caggagtcaggggatttagtgggaGTCCTGCTCTGTCCCCTCGAtgctctg
	***************************************************
rat	((((.((((((((((..((..((...))..))..))))))).)))..))))	1.000 -24.00

rat

chromosome:10:103241519:103241569:-1

intergenic

block53130 [novel_loopOverlap_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	0.004	no	no	0.60/0.60	20/20/1.00	0.0	0.0	1	0	1	0	30	-3	3arm_loop	1	nd	0.25	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------UCACAUG------------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	----------------------------------------------GTCACATGGCCTGTAGCCTC------------------------------	20	1
rat	tcctcataggcggatgcccacccataagaggctacatccctttgtgGTCACATGGCCTGTAGCCTCttgctgacattgctggtgtcttctctgggg
	************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000054970 ENSRNOG00000036697 Mafg
rat	.(((((.(((.(((((((((..((((((((((((((..((..(((....))).))..)))))))))))).))....))..)))))))))).)))))	0.410 -36.90

rat

chromosome:10:110018644:110018739:-1

Same_strand|Intronic_non-coding|ENSRNOT00000054970|ENSRNOG00000036697 ## Same_strand|Boundary_non-coding|ENSRNOT00000051462|ENSRNOG00000036697 ## ENSRNOG00000036697|protein_coding|Mafg|v-maf musculoaponeurotic fibrosarcoma oncogene family, protein G [Source:RefSeq_peptide;Acc:NP_071781]

block68538 [novel_loopOverlap_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	0.006	no	no	0.60/0.60	20/20/1.00	0.0	0.0	1	0	1	0	37	-3	3arm_loop	1	nd	0.25	2	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------UCAAGCG-------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	-------------------------------------------------------------TTCAAGCGCAGGTCTGGAGG-------------------------------------	20	1
rat	ttgttggcttaattttcagccaaaagtggaatgactgccccttccaggtctgagttttcatTTCAAGCGCAGGTCTGGAGGgcagacatgtccagccagggtaggagcgcggcctcag
	**********************************************************************************************************************
rat	.((..((((....((((.(((.....(((((((.((((((..(((((..(((.((((.......)))).)))..))))))))))).))).)))).....))).))))...)))).)).	0.960 -46.80

rat

chromosome:10:35386080:35386197:1

intergenic

block73704 [novel_loopOverlap_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	0.001	no	no	0.29/0.29	21/21/1.00	0.0	0.0	1	0	1	0	15	-1	3arm	1	nd	0.05	1	1	1	na	na

		reads	miRBase family seed
seed	----------------------------------------GUAUCAU----------------------------	1	novel
		len	cloning frequencies
			T1S1
	---------------------------------------AGTATCATCATCATTATCATC---------------	21	1
rat	gaaggagagttgctgatgatgatcggtggtggcagcggcAGTATCATCATCATTATCATCgcagctgctctttta
	***************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000039444 ENSRNOG00000003226 MRIP_RAT
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000004357 ENSRNOG00000003226 MRIP_RAT
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000040865 ENSRNOG00000003226 MRIP_RAT
rat	(((((((((((((.(((((((((.((((((((..((....)).))))))))))))))))))))))).))))))).	1.000 -35.30

rat

chromosome:10:46036549:46036623:1

Same_strand|Boundary_non-coding|ENSRNOT00000004374|ENSRNOG00000003226 ## Same_strand|Intronic_coding|ENSRNOT00000039444|ENSRNOG00000003226 ## ENSRNOG00000003226|protein_coding|MRIP_RAT|Myosin phosphatase Rho-interacting protein (Rho-interacting protein 3) (p116Rip) (RIP3). [Source:UniProtKB/Swiss-Prot;Acc:Q9ERE6]

block73737 [novel_loopOverlap_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	0.001	no	no	0.54/0.54	24/24/1.00	0.0	0.0	1	0	1	0	12	-2	5arm_loop	1	nd	0.29	3	1	1	na	na

		reads	miRBase family seed
seed	-------------UCUCAGC----------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	------------CTCTCAGCTGATTGTCCTGCACCT------------------------------------	24	1
rat	gacagtaattacCTCTCAGCTGATTGTCCTGCACCTgcagtgcaggagggttagctgttcttgctatgctgt
	************************************************************************
rat	.((((((.........(((((((((.((((((((.....)))))))).))))))))).........))))))	1.000 -33.97

rat

chromosome:10:46093232:46093303:1

intergenic

block77932 [novel_loopOverlap_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	0.008	no	no	0.60/0.60	20/20/1.00	0.0	0.0	1	0	1	0	24	-2	3arm_loop	1	nd	0.25	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------ACCCCAA------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	--------------------------------------------------GACCCCAAAGTTGCCTCCTC------------------------	20	1
rat	gcacgacattatctgcaggtggtggggagcctgggcttttggggaactagGACCCCAAAGTTGCCTCCTCccagcccctctagtctagtttgct
	**********************************************************************************************
rat	(((.(((.....(((.(((.(((.(((((...((((.(((((((........)))))))...)))).))))).)))))).)))....)))))).	1.000 -38.90

rat

chromosome:10:55851097:55851190:1

intergenic

block118195 [novel_loopOverlap_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	0.004	no	no	0.60/0.60	20/20/1.00	0.0	0.0	1	0	1	0	6	-1	5arm_loop	1	nd	0.15	2	1	1	na	na

		reads	miRBase family seed
seed	-------CUUCCAU--------------------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	------CCTTCCATGGCACAAGCAGG--------------------------------------	20	1
rat	tggtgaCCTTCCATGGCACAAGCAGGtcttgcttgtctcgtatccacaggagcctggtcaccac
	****************************************************************
rat	((((((((((((((((.((((((((...)))))))).)))).......))))...)))))))).	0.490 -24.91

rat

chromosome:11:32569606:32569669:-1

intergenic

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