Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_loopOverlap_nonpairedHIGH_bulgeHIGH (16144 loci)

block1869587 [novel_lenNOK_loopOverlap_nonpairedHIGH_bulgeHIGH]

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	0.110	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	21	-4	3arm_loop	1	nd	0.50	5	1	1	na	na

		reads	miRBase family seed
seed	----------------------------------------------AAUGGUU-------------------------------	1	novel
		len	cloning frequencies
			T2S1
	---------------------------------------------TAATGGTTCGGGGTTTCA---------------------	18	1
rat	ttatatatttatacttaacagtgacttatatccatacacctaactTAATGGTTCGGGGTTTCAaatggtatacatcatatgtaa
	************************************************************************************
	----------------------------------------------------------------------------------------------	ENSRNOT00000010680 ENSRNOG00000007706 Prkaa2
rat	.................(((((((..((((.((((((.(((((((....)))).))))).....))))))))..)))).)))..	0.580 -13.60

rat

chromosome:5:126032126:126032209:1

Opposite_strand|Intronic_coding|ENSRNOT00000010680|ENSRNOG00000007706 ## ENSRNOG00000007706|protein_coding|Prkaa2|5'-AMP-activated protein kinase catalytic subunit alpha-2 (EC 2.7.11.1) (AMPK alpha-2 chain). [Source:UniProtKB/Swiss-Prot;Acc:Q09137]

block1877532 [novel_lenNOK_loopOverlap_nonpairedHIGH_bulgeHIGH]

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	0.018	no	no	0.39/0.39	18/18/0.00	0.0	0.0	1	0	1	0	26	-1	3arm	1	nd	0.39	5	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------GGAGUGG------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	-------------------------------------------------GGGAGTGGATTTTGTTAT--------------------------	18	1
rat	tgtcctccaggaacgaagaagccccatcactcaacatccacgggctttgGGGAGTGGATTTTGTTATcattgtttttttttctgtggggataa
	*********************************************************************************************
rat	((((((((((((..((((((((.........(((.((((((...((....)).)))))).)))........))))))))))))).))))))).	0.470 -28.93

rat

chromosome:5:139047138:139047230:1

intergenic

block914162 [novel_lenNOK_loopOverlap_nonpairedHIGH_bulgeHIGH]

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	0.354	no	no	0.61/0.61	18/18/0.00	0.0	0.0	1	0	1	0	22	-4	5arm_loop	1	nd	0.50	5	1	1	na	na

		reads	miRBase family seed
seed	-----------------------UCGAAAC--------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	----------------------CTCGAAACCCAGCCACTG----------------------------------	18	1
rat	ggaagcctaaagtagtgtacatCTCGAAACCCAGCCACTGtggggctgtgggggttgtgctccgcatggccgcc
	**************************************************************************
rat	((..(((....((...(((((.(((....(((((((.......))))).))))).)))))...))..)))..))	0.480 -23.50

rat

chromosome:1:208430814:208430887:-1

intergenic

block1886759 [novel_lenNOK_loopOverlap_nonpairedHIGH_bulgeHIGH]

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	0.426	no	no	0.32/0.33	18/19/0.00	0.0	0.5	2	0	2	0	31	-1	3arm	1	nd	0.37	5	2	2	na	na

		reads	miRBase family seed
seed	------------------------------------------------------AGGAGUU------------------------------------------	2	novel
		len	cloning frequencies
			T3S1	T4S1
	-----------------------------------------------------TAGGAGTTAATGTGTTACT-------------------------------	19	-	1
	-----------------------------------------------------TAGGAGTTAATGTGTTAC--------------------------------	18	1	-
rat	ctgggtattttgcacaattttatagacttcttttttacatagccctttaaaaaTAGGAGTTAATGTGTTACTgtccgtgtagtgccaaggcaagggttttcag
	*******************************************************************************************************
rat	(((((..((((((...(((.((..(((........(((((((((((........))).)))).)))).....)))..)).)))......))))))...)))))	0.610 -19.32

rat

chromosome:5:151473090:151473192:1

intergenic

block1890265 [novel_lenNOK_loopOverlap_nonpairedHIGH_bulgeHIGH]

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	0.284	no	no	0.68/0.68	19/19/0.00	0.0	0.0	1	0	1	0	37	-3	5arm_loop	1	nd	0.58	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------UGGAACG-------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	-------------------------------------CTGGAACGGGAAGCCCCAC--------------------------------------------------------	19	1
rat	agggaccgcctcccaacccttggagtcaagctgcgagCTGGAACGGGAAGCCCCACagccgggaagccccacagccgccgtcttctcttccccactcccccaggtgcctccc
	****************************************************************************************************************
rat	.((((.(((((..........((((....((.(((.((((....(((...(((.......)))...)))..))))))).))...)))).............)))))..))))	0.650 -35.00

rat

chromosome:5:155027767:155027878:1

intergenic ## {Repeats: trf 22 34 0 class=trf}

block1930263 [novel_lenNOK_loopOverlap_nonpairedHIGH_bulgeHIGH]

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	0.329	no	no	0.39/0.39	18/18/0.00	0.0	0.0	1	0	1	0	24	-4	5arm_loop	1	nd	0.44	5	1	1	na	na

		reads	miRBase family seed
seed	-------------------------AACACAC------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	------------------------TAACACACAGGTAAAGTG--------------------------------------	18	1
rat	ccagaggagcttgatttccaaacaTAACACACAGGTAAAGTGtttccctgtaagtttatatgaaaatggggtagctttgc
	********************************************************************************
rat	.(((((..((((.((((.((.....(((..(((((.((.....)).)))))..)))....)).)))).))))..))))).	0.900 -16.10

rat

chromosome:6:45842424:45842503:-1

intergenic

block1931799 [novel_lenNOK_loopOverlap_nonpairedHIGH_bulgeHIGH]

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	0.594	no	no	0.32/0.33	18/19/0.00	0.3	0.0	3	0	2	0	18	-3	5arm_loop	1	nd	0.42	4	3	2	na	na

		reads	miRBase family seed
seed	--------------------CAAAAUA---------------------------------------------	2	novel
seed	-------------------CCAAAAU----------------------------------------------	1	novel
		len	cloning frequencies
			T4S1	T5S1
	-------------------CCAAAATAAACATGTCCT-----------------------------------	18	-	2
	------------------ACCAAAATAAACATGTCCT-----------------------------------	19	1	-
rat	ataccagggaatgaagatACCAAAATAAACATGTCCTaagtacttgtttactggttattctgagtgcgtatt
	************************************************************************
rat	((((((.((((((.....((((...((((((.((.......)).)))))).))))))))))...)).)))).	0.940 -10.30

rat

chromosome:6:49184990:49185061:-1

intergenic

novel_lenNOK_shortStem_nonpairedHIGH (12839 loci)

block916 [novel_lenNOK_shortStem_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	0.421	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	1	33	3arm	8	nd	0.37	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------------GGGACAC------------	1	novel
		len	cloning frequencies
			T2S1
	----------------------------------------------------------------------------------------------TGGGACACAGGTTACCTCA-	19	1
rat	ctgagcacagcatggtttgggaatggctaatcgggaagctgcatgcagggtattacagagatggggaggcctgctggactgaccagccagtaccTGGGACACAGGTTACCTCAg
	******************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000004384 ENSRNOG00000003285 Mpv17l
rat	(((((...(((.((.((..((..(((((..((((....((....(((((......((....))......))))).)).))))..)))))...))..))...)).)))..)))))	0.690 -32.90

rat

chromosome:10:1664905:1665018:-1

Opposite_strand|Intronic_coding|ENSRNOT00000004384|ENSRNOG00000003285 ## ENSRNOG00000003285|protein_coding|Mpv17l|Mpv17 transgene, kidney disease mutant-like Gene [Source:MGI Symbol;Acc:MGI:2135951]

block1033 [novel_lenNOK_shortStem_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	0.356	no	no	0.61/0.61	18/18/0.00	0.0	0.0	1	0	1	0	2	11	5arm	1	nd	0.44	3	1	1	na	na

		reads	miRBase family seed
seed	---CCUCUGU--------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	--GCCTCTGTCAGGTGGAGT----------------------------------------------------	18	1
rat	ggGCCTCTGTCAGGTGGAGTtcctatctgcaaccctgtcccttctgtctctccgctccttctcaaaagtcct
	************************************************************************
rat	((((...((...(((((((.........(((....)))...........)))))))......))...)))).	0.900 -13.05

rat

chromosome:10:1928742:1928813:-1

intergenic

block1259 [novel_lenNOK_shortStem_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	0.021	no	no	0.61/0.61	18/18/0.00	0.0	0.0	1	0	1	0	0	6	5arm	1	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	-GGGACAA------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	TGGGACAACAGGCCTGGT--------------------------------------------	18	1
rat	TGGGACAACAGGCCTGGTgcctggtgccttcctccaggcaccttatctatctggagactcct
	**************************************************************
rat	.((((...((((...(((((((((.........))))))))).......)))).....))))	0.780 -22.70

rat

chromosome:10:2498858:2498919:-1

intergenic

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