Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_multiarm_loopOverlap_bulgeHIGH (13 loci)

novel_shortStem_5varHIGH_nonpairedHIGH (13 loci)

block567319 [novel_shortStem_5varHIGH_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	0.326	no	no	0.23/0.30	22/23/1.00	2.5	3.0	2	0	2	0	1	20	5arm	7	nd	0.35	3	2	2	na	na

		reads	miRBase family seed
seed	--UAUUAUC----------------------------------------------------------------------------------------------------	1	novel
seed	-------UCUUUUC-----------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S1	T5S1
	-TTATTATCTTTTCAAATCCTCT--------------------------------------------------------------------------------------	22	1	-
	------ATCTTTTCAAATCCTCTTAGTTC--------------------------------------------------------------------------------	23	-	1
rat	gTTATTATCTTTTCAAATCCTCTTAGTTCttggccgagtcactgacagctgcctcgctctgtgaactggctgccttcgttctactacagcgatttgatcgatgngtngc
	*************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------	ENSRNOT00000049456 ENSRNOG00000025606 LOC685176
rat	((...((((...(((((((((..((((....(((((..((((....(((......)))..))))..)))))...........)))).)).)))))))..))))....))	0.640 -22.66

rat

chromosome:16:27389794:27389902:1

Opposite_strand|Intronic_coding|ENSRNOT00000049456|ENSRNOG00000025606 ## ENSRNOG00000025606|protein_coding|LOC685176|

block648476 [novel_shortStem_5varHIGH_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	0.936	no	no	0.43/0.47	19/23/0.80	3.6	2.4	5	0	1	0	2	3	3arm	1	nd	0.32	3	5	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------GUCAAAC----------------	3	novel
seed	--------------------------------------------AGCAGAG----------------------	2	novel
		len	cloning frequencies
			T5S1
	-------------------------------------------TAGCAGAGTCAAACCAAATGCAG-------	23	2
	-------------------------------------------------AGTCAAACCAAATGCAGCGAAG--	22	2
	-------------------------------------------------AGTCAAACCAAATGCAGCG-----	19	1
rat	tctacccctggattaggatgcatggccatgaggtaacctttctTAGCAGAGTCAAACCAAATGCAGCGAAGac
	*************************************************************************
rat	(((....(((.(((.((.....((((..(((((.......))))).....))))..)).))).)))...))).	0.410 -10.00

rat

chromosome:17:20760696:20760768:1

intergenic

block842339 [novel_shortStem_5varHIGH_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	0.588	no	no	0.50/0.52	20/21/1.00	2.5	2.0	2	0	1	0	2	16	5arm	3	nd	0.33	3	2	1	na	na

		reads	miRBase family seed
seed	--------GGAAGAU---------------------------------------------------------------------------------	1	novel
seed	---CCCCUGG--------------------------------------------------------------------------------------	1	miR-331
		len	cloning frequencies
			T5S1
	--TCCCCTGGAAGATTCCATGAG-------------------------------------------------------------------------	21	1
	-------TGGAAGATTCCATGAGCCCT---------------------------------------------------------------------	20	1
rat	taTCCCCTGGAAGATTCCATGAGCCCTtagtccaccagtcttcacctggtcggaggtgttgtgttttgggagaagttgaatccaggttaagggatg
	************************************************************************************************
rat	(((((((((((...(((.((...(((..((..((.((.(((((........))))))).))..))..)))....)).))))))))).....)))))	0.910 -25.10

rat

chromosome:1:48352648:48352743:-1

intergenic

block847623 [novel_shortStem_5varHIGH_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	0.266	no	no	0.39/0.42	18/24/0.80	1.6	1.2	5	0	1	0	4	13	5arm	3	nd	0.33	3	5	1	na	na

		reads	miRBase family seed
seed	---------GGACUUA--------------------------------------------------------------	3	novel
seed	-----AGCUGGA------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T5S1
	--------TGGACTTACACTTTTGCAGT--------------------------------------------------	20	3
	----TAGCTGGACTTACACTTTTGCAGT--------------------------------------------------	24	1
	----TAGCTGGACTTACACTTT--------------------------------------------------------	18	1
rat	actgTAGCTGGACTTACACTTTTGCAGTacctcaactgttgcaggaccaacaaggttgcaggacatagacccactcag
	******************************************************************************
	----------------------------------------------------------------------------------------	ENSRNOT00000041486 ENSRNOG00000033456 LOC308198
rat	.(((.((.(((..(((...(((((((..((((....(((((......))))))))))))))))..)))..))))))))	0.870 -17.50

rat

chromosome:1:52393829:52393906:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000044415|ENSRNOG00000033456 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000041486|ENSRNOG00000033456 ## ENSRNOG00000033456|protein_coding|LOC308198|

block958472 [novel_shortStem_5varHIGH_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	0.630	no	no	0.50/0.52	20/21/1.00	2.5	2.0	2	0	1	0	2	20	5arm	3	nd	0.33	3	2	1	na	na

		reads	miRBase family seed
seed	--------GGAAGAU---------------------------------------------------------------------------------	1	novel
seed	---CCCCUGG--------------------------------------------------------------------------------------	1	miR-331
		len	cloning frequencies
			T5S1
	--TCCCCTGGAAGATTCCATGAG-------------------------------------------------------------------------	21	1
	-------TGGAAGATTCCATGAGCCCT---------------------------------------------------------------------	20	1
rat	taTCCCCTGGAAGATTCCATGAGCCCTtagtccaccagtcttcacctggtcagaggtgttgtgttttgggagaagttgaatccaggttaagggatg
	************************************************************************************************
rat	(((((((((((...(((.((...(((..((..(((.......(((((......)))))..)))..)))))....)).))))))))).....)))))	0.880 -23.90

rat

chromosome:1:47731573:47731668:1

intergenic

block959035 [novel_shortStem_5varHIGH_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	0.588	no	no	0.50/0.52	20/21/1.00	2.5	2.0	2	0	1	0	2	16	5arm	3	nd	0.33	3	2	1	na	na

		reads	miRBase family seed
seed	--------GGAAGAU---------------------------------------------------------------------------------	1	novel
seed	---CCCCUGG--------------------------------------------------------------------------------------	1	miR-331
		len	cloning frequencies
			T5S1
	--TCCCCTGGAAGATTCCATGAG-------------------------------------------------------------------------	21	1
	-------TGGAAGATTCCATGAGCCCT---------------------------------------------------------------------	20	1
rat	taTCCCCTGGAAGATTCCATGAGCCCTtagtccaccagtcttcacctggtcggaggtgttgtgttttgggagaagttgaatccaggttaagggatg
	************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000043702 ENSRNOG00000034080 RGD1563490_predicted
rat	(((((((((((...(((.((...(((..((..((.((.(((((........))))))).))..))..)))....)).))))))))).....)))))	0.910 -25.10

rat

chromosome:1:47852194:47852289:1

Same_strand|Intronic_non-coding|ENSRNOT00000043702|ENSRNOG00000034080 ## ENSRNOG00000034080|protein_coding|RGD1563490_predicted|

block1060048 [novel_shortStem_5varHIGH_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	0.698	no	no	0.42/0.48	19/24/0.86	1.7	2.7	6	0	1	0	4	1	5arm	1	nd	0.33	3	7	1	na	na

		reads	miRBase family seed
seed	-----CAAAUGC------------------------------------------------------------	5	novel
seed	----------GCAAGAA-------------------------------------------------------	2	novel
		len	cloning frequencies
			T5S1
	----CCAAATGCAAGAAGCCTCAGA-----------------------------------------------	21	4
	---------TGCAAGAAGCCTCAGAATTCAAGA---------------------------------------	24	2
	----CCAAATGCAAGAAGCCTCA-------------------------------------------------	19	1
rat	gtggCCAAATGCAAGAAGCCTCAGAATTCAAGAtaaattcggtactgagtgggggtggggctctgagttcca
	************************************************************************
rat	.(((...(((...((.(((((((..(((((..((.......))..))))).....)))))))))..))))))	0.420 -14.40

rat

chromosome:20:5481217:5481288:-1

intergenic

block1300017 [novel_shortStem_5varHIGH_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	0.578	no	no	0.50/0.52	21/22/1.00	2.5	2.0	2	0	2	0	3	19	5arm	8	nd	0.33	3	2	2	na	na

		reads	miRBase family seed
seed	---------ACGGGAA-----------------------------------------------------------------------------------------------	1	novel
seed	----CAUCAAC----------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T4S2
	--------AACGGGAAACCCATCACCATC----------------------------------------------------------------------------------	21	-	1
	---TCATCAACGGGAAACCCATCAC--------------------------------------------------------------------------------------	22	1	-
rat	ttgTCATCAACGGGAAACCCATCACCATCttccaggagcgagatcccgctaacatcaaatggggtgacgctggtgctgagtatgtcgtggagtctcctagtgtcttcacaa
	***************************************************************************************************************
rat	.(((...((..((((.((((((.((...(((.((..((((..((((((...........))))))..))))..))..)))...)).)))).)).))))..)).....))).	0.530 -27.80

rat

chromosome:2:155700276:155700386:1

intergenic

block1308854 [novel_shortStem_5varHIGH_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	0.146	no	no	0.55/0.62	20/21/1.00	2.0	1.5	2	0	2	0	2	0	3arm	1	nd	0.33	3	2	2	na	na

		reads	miRBase family seed
seed	-----------------------------------GGUCUUC--------------	1	novel
seed	-------------------------------ACCCGGU------------------	1	novel
		len	cloning frequencies
			T2S1	T3S2
	------------------------------GACCCGGTCTTCGGCAATGCA-----	21	-	1
	----------------------------------CGGTCTTCGGCAATGCAATG--	20	1	-
rat	gcctcgcggcggagggaaggtgggtcacctGACCCGGTCTTCGGCAATGCAATGgc
	********************************************************
	........................................................>>>>>>>>>>	ENSRNOT00000057128 ENSRNOG00000037655 Pet112l_predicted
rat	(((..((.((.(((((....((((((....)))))).))))).))...))...)))	1.000 -23.50

rat

chromosome:2:177408058:177408113:1

Same_strand|Boundary_non-coding|ENSRNOT00000057128|ENSRNOG00000037655 ## ENSRNOG00000037655|protein_coding|Pet112l_predicted|

block1469514 [novel_shortStem_5varHIGH_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	0.186	no	no	0.40/0.47	19/24/0.75	1.8	2.0	4	0	1	0	3	2	3arm	1	nd	0.35	3	4	1	na	na

		reads	miRBase family seed
seed	------------------------------------AGAGCUC---------------------	2	novel
seed	-----------------------------------GAGAGCU----------------------	1	novel
seed	------------------------------------------CCUUUGA---------------	1	novel
		len	cloning frequencies
			T5S1
	-----------------------------------GAGAGCTCCTTTGAGAACAAGAGT-----	24	2
	-----------------------------------------TCCTTTGAGAACAAGAGTAC---	20	1
	----------------------------------TGAGAGCTCCTTTGAGAAC-----------	19	1
rat	ggtgatttctgtcttactttgggccagacacctcTGAGAGCTCCTTTGAGAACAAGAGTACgcc
	****************************************************************
rat	(((((((..(((((((....((((((((....))))...))))...))))).))..))).))))	0.990 -16.90

rat

chromosome:3:76943801:76943864:1

intergenic

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