Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_nonpairedHIGH (4445 loci)

block1790383 [novel_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	0.648	no	no	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	23	9	3arm	1	nd	0.38	3	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------------CGAUCCU------------------------------------	1	novel
		len	cloning frequencies
			T4S1
	-----------------------------------------------------------------------CCGATCCTCTGACTCTATAGC-----------------------	21	1
rat	gaccctggccaatgtcactgcagagctgaggcggccttgtcagggctaatgtgaaatctcttcccgtggcgCCGATCCTCTGACTCTATAGCgccagcttggacagattgaggtc
	*******************************************************************************************************************
rat	(((((((.((((.((...(((((((..((((((((...(((((((.................))).))))))))..))))...))))...)))...)))))).))).....))))	0.580 -32.83

rat

chromosome:5:151928080:151928194:-1

intergenic

block1793112 [novel_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	0.046	no	no	0.60/0.60	20/20/1.00	0.0	0.0	2	0	2	0	14	9	5arm	1	8	0.40	3	2	2	na	na

		reads	miRBase family seed
seed	---------------CCAUGGC--------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T2S1	T3S1
	--------------ACCATGGCGGTGAGTAGAGC--------------------------------------------------------------	20	1	1
rat	tcttcctgttctccACCATGGCGGTGAGTAGAGCaagagttgcttttgcctctctttcatccatctccatccgcggccggcggagcccacgagggc
	************************************************************************************************
	.....>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000030043 ENSRNOG00000026260 Rpl11
rat	(((((.((..((((.((...((((.(((..((..(((((..((....))..)))))...))...)))...))))....)).))))..)).))))).	0.960 -33.30

rat

chromosome:5:154830410:154830505:-1

Same_strand|Boundary_non-coding|ENSRNOT00000030043|ENSRNOG00000026260 ## ENSRNOG00000026260|protein_coding|Rpl11|60S ribosomal protein L11. [Source:UniProtKB/Swiss-Prot;Acc:P62914]

block914010 [novel_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	0.956	no	no	0.70/0.70	20/20/1.00	0.0	0.0	1	0	1	0	18	21	3arm	1	nd	0.40	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------GAGCUCC------------------------------	1	novel
		len	cloning frequencies
			T3S1
	----------------------------------------------------------------------------GGAGCTCCGACCAGCTCGAC------------------	20	1
rat	cgcccgccttcggacgcaggggtggaggggtggaggggtgggggtgcggctccaggaaacggcgcgctcgcaattcGGAGCTCCGACCAGCTCGACgcgccgcgacggcccggc
	******************************************************************************************************************
rat	.(((.((((((((.(((.(((.(((.(((((.(((..(((((.(((((..((...))..)).))).)))))..)))...)))))..))).)))...)))))).)).)))..)))	0.890 -48.90

rat

chromosome:1:208353663:208353776:-1

intergenic ## {SimpF: 1 Eponine}

block1820970 [novel_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	0.032	no	no	0.41/0.55	22/22/1.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	20 11	5 14	3arm 3arm	4 4	nd nd	0.36 0.36	3 4	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------AAGAAGU----------------------------------	1	novel
seed	-----------------------------------------------------------------CCAGAAG-------------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------------------------------------TAAGAAGTTCCCAGAAGTCTGT--------------------	22	1
	----------------------------------------------------------------CCCAGAAGTCTGTACCACAGTC-----------	22	1
rat	aggagggatctgggctggataagcttagtgggactgtaggaagacaccagtgctcTAAGAAGTTCCCAGAAGTCTGTACCACAGTCctaggcccacc
	*************************************************************************************************
rat	.((.(((.(((((((((.(((..(((..(((((((.(((..((.((....)))))))...))).)))).)))..)))....))).))))))))).))	0.980 -34.20

rat

chromosome:5:25626653:25626749:1

intergenic

block1848464 [novel_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	0.308	no	no	0.50/0.50	18/22/0.75	0.2	2.2	4	0	1	0	13	0	5arm	2	nd	0.35	3	4	1	na	na

		reads	miRBase family seed
seed	--------------GCCUGUG------------------------------------------------------	3	novel
seed	---------------CCUGUGU-----------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------TGCCTGTGTTTTGTGAGCTCTG----------------------------------------	22	1
	--------------GCCTGTGTTTTGTGAGCTCT-----------------------------------------	20	1
	-------------TGCCTGTGTTTTGTGAGC--------------------------------------------	18	1
	-------------TGCCTGTGTTTTGTGAGCTC------------------------------------------	20	1
rat	tcttcccagggccTGCCTGTGTTTTGTGAGCTCTGtccacagagagtgctgccatgcttctgccaagcaggagaa
	***************************************************************************
rat	(((((....(((..((.((.((...(((..(((((....)))))..))).)))).))....))).....))))).	0.590 -22.30

rat

chromosome:5:79244930:79245004:1

intergenic

block1879134 [novel_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	0.062	no	no	0.82/0.82	22/22/1.00	0.0	0.0	1	0	1	0	22	12	3arm	1	nd	0.32	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------GCCCUCA------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	-------------------------------------------------------------------------CGCCCTCACTGCCGGCCGCCAC----------------------	22	1
rat	cggcggcagggccgaccgaagtgcagcggcggccgcagagggaagtgagatctccgccagaggcgggaagcacCGCCCTCACTGCCGGCCGCCACctctctctccaccctcctcgcc
	*********************************************************************************************************************
rat	.(((((.((((..((..((........(((((((((((((((..(((...((.(((((...)))))))..)))..)))))..))).))))))).....))..))..))))..)))))	0.840 -53.62

rat

chromosome:5:141418295:141418411:1

intergenic

block1909828 [novel_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	0.330	no	no	0.40/0.40	20/20/1.00	0.0	0.0	1	0	1	0	9	30	3arm	2	nd	0.35	2	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------------------------------GAGUUCU---------------------	1	novel
		len	cloning frequencies
			T1S2
	-----------------------------------------------------------------------------------------TGAGTTCTTTGCTGACATTG---------	20	1
rat	agtcttcaaagccttataaagaacatacttggtgaggagtacacctatctgtggtgcacatcactgtctctagctgcttctgccagggcTGAGTTCTTTGCTGACATTGccctgactc
	**********************************************************************************************************************
rat	((((.....((..(((((((((((...((((((.(((((((.........(((((....)))))..........))))))))))))).....)))))))).)))..)).....)))).	0.620 -28.81

rat

chromosome:6:8897596:8897713:-1

intergenic

block603366 [novel_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	0.429	no	no	0.46/0.46	24/24/1.00	0.0	0.0	1	0	1	0	6	5	3arm	2	nd	0.33	2	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------GAUUGGU----------------------	1	novel
		len	cloning frequencies
			T5S1
	------------------------------------------TGATTGGTGTAGAGCTTGGGATGA------	24	1
rat	gtatttttccaaaggcctgtctcttgaaataaggaggtgtttTGATTGGTGTAGAGCTTGGGATGAtttgca
	************************************************************************
rat	(((..(((((..(((((((..((((((((((......))))))))..))..))).)))).))).))..))).	0.820 -13.20

rat

chromosome:17:20487290:20487361:-1

intergenic

novel_shortStem (3551 loci)

block502 [novel_shortStem]

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	0.238	no	no	0.61/0.61	23/23/1.00	0.0	0.0	1	0	1	0	2	18	5arm	1	nd	0.22	2	1	1	na	na

		reads	miRBase family seed
seed	---GCUGGGG---------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	--TGCTGGGGAGTCTCTGTCTTGCC------------------------------------------------------------------------------	23	1
rat	agTGCTGGGGAGTCTCTGTCTTGCCtgcctgtggatgacagccttcacggtcatgtttactttttatccttatggttagaatatgatgctgctccagtttgct
	*******************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000000029 ENSRNOG00000000028 Nde1
rat	(((((((((((((.((..(((.(((.......(((((((((((.....)))..))))........))))....))).)))....)).))).)))))))..)))	0.440 -26.30

rat

chromosome:10:807436:807538:-1

Same_strand|Intronic_coding|ENSRNOT00000000029|ENSRNOG00000000028 ## ENSRNOG00000000028|protein_coding|Nde1|Nuclear distribution protein nudE homolog 1 (NudE) (rNudE). [Source:UniProtKB/Swiss-Prot;Acc:Q9ES39]

block1663 [novel_shortStem]

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	0.50/0.50	20/20/1.00	0.0	0.0	1	0	1	0	2	23	3arm	1	nd	0.20	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------GGUACAG--------------	1	novel
		len	cloning frequencies
			T2S1
	----------------------------------------------------------------------AGGTACAGGACACATGAGTC--	20	1
rat	ctgcatacatccctttctgtgccaccctgacatgcccctagcccaacctagggcagatatccactgtgtcAGGTACAGGACACATGAGTCag
	********************************************************************************************
rat	(((.((.(((....(((((((((....(((((((.((((((......))))))))...........))))))))))))))...))).)))))	0.410 -26.00

rat

chromosome:10:3751185:3751276:-1

intergenic

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