Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_randfoldOK_nonpairedHIGH_bulgeHIGH (2552 loci)

block1607423 [novel_lenNOK_randfoldOK_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	0.004	no	no	0.33/0.33	18/18/0.00	0.0	0.0	1	0	1	0	17	19	3arm	1	nd	0.44	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------CCCUCUU---------------------------	1	novel
		len	cloning frequencies
			T4S2
	----------------------------------------------------------------------------------TCCCTCTTTGAAACTTAT-----------------	18	1
rat	gtgttctgttcacattaagattaaccttgaggaggtgaaagacctagtttagggcacagaaaacttactctgatggtcaaacTCCCTCTTTGAAACTTATctgtgaactcaaacata
	*********************************************************************************************************************
rat	(((((..(((((((.((((.((......((((..((....((((....((((((...((....))..)))))).))))..))..))))....)).))))..)))))))...))))).	0.880 -31.80

rat

chromosome:4:175525939:175526055:-1

intergenic

block839544 [novel_lenNOK_randfoldOK_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	0.002	no	no	0.39/0.39	18/18/0.00	0.0	0.0	1	0	1	0	34	2	5arm	1	nd	0.44	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------UGGUUGG------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	----------------------------------TTGGTTGGGATCTTTTGT--------------------------------------------------------------------	18	1
rat	gttcttgttgtgcttcagaattttcatcattattTTGGTTGGGATCTTTTGTctggaaattgagatgggggagggaaggaaggagggaggggaagagggtggggggagagggagagggag
	************************************************************************************************************************
rat	.(((((.((...((((...((((((.((.((.((((..((....((((..((((........))))..)))).....))..)))).))...)).))))))....))))...)).))))).	0.990 -22.80

rat

chromosome:1:42486461:42486580:-1

intergenic

block1683466 [novel_lenNOK_randfoldOK_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	0.002	no	no	0.72/0.72	18/18/0.00	0.0	0.0	2	0	1	0	16	17	5arm	4	nd	0.39	5	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------CCCUGAG---------------------------------------------------------	1	miR-125a/125b/351
seed	-----------------CCCUGAG---------------------------------------------------------------------------------------	1	miR-125a/125b/351
		len	cloning frequencies
			T1S1
	----------------------------------------------TCCCTGAGTGGGGGGAGG-----------------------------------------------	18	1
	----------------TCCCTGAGTGGGGGGAGG-----------------------------------------------------------------------------	18	1
rat	gaggaaggtgcatgcaTCCCTGAGTGGGGGGAGGaaggtgcatgcaTCCCTGAGTGGGGGGAGGaaggtgcaggcatccctgagtagggggaggaaggtgcatgcatccct
	***************************************************************************************************************
rat	.(((..((((((((((((((((..((((((.......((((.....(((((......))))).....)))).....))))))..)))))........))))))))))))))	0.820 -44.70

rat

chromosome:4:144080456:144080566:1

intergenic ## {Repeats: trf 470 488 0 class=trf}

block1683467 [novel_lenNOK_randfoldOK_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	0.002	no	no	0.72/0.72	18/18/0.00	0.0	0.0	2	0	1	0	16	17	5arm	4	nd	0.39	5	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------CCCUGAG---------------------------------------------------------	1	miR-125a/125b/351
seed	-----------------CCCUGAG---------------------------------------------------------------------------------------	1	miR-125a/125b/351
		len	cloning frequencies
			T1S1
	----------------------------------------------TCCCTGAGTGGGGGGAGG-----------------------------------------------	18	1
	----------------TCCCTGAGTGGGGGGAGG-----------------------------------------------------------------------------	18	1
rat	gaggaaggtgcatgcaTCCCTGAGTGGGGGGAGGaaggtgcatgcaTCCCTGAGTGGGGGGAGGaaggtgcaggcatccctgagtagggggaggaaggtgcatgcatccct
	***************************************************************************************************************
rat	.(((..((((((((((((((((..((((((.......((((.....(((((......))))).....)))).....))))))..)))))........))))))))))))))	0.820 -44.70

rat

chromosome:4:144080456:144080566:1

intergenic ## {Repeats: trf 440 458 0 class=trf}

block1736197 [novel_lenNOK_randfoldOK_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	0.005	no	no	0.28/0.28	18/18/0.00	0.0	0.0	1	0	1	0	14	5	5arm	1	nd	0.39	4	1	1	na	na

		reads	miRBase family seed
seed	---------------GCUUAUC----------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	--------------AGCTTATCACTTCAAAAA------------------------------------------------	18	1
rat	tttatagaaaaaagAGCTTATCACTTCAAAAActtctaaatccacaaaggaagtttcagaaatgcatgcttattctatga
	********************************************************************************
rat	.((((((((....((((....((.(((..((((((((...........))))))))..))).))...)))).))))))))	1.000 -17.40

rat

chromosome:5:52841643:52841722:-1

intergenic

block1801045 [novel_lenNOK_randfoldOK_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	0.008	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	15	22	3arm	3	nd	0.39	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------GACCUAG-------------------------	1	novel
		len	cloning frequencies
			T1S1
	-------------------------------------------------------------------------------------AGACCTAGAGGTACCTGA---------------	18	1
rat	agtgacaggaagttccgcccttcaaactttctccgtgtctttgctgcctccctttcaggaagtcctggtgggagactcgtcccggAGACCTAGAGGTACCTGAaaacttcctggagct
	**********************************************************************************************************************
rat	(((..(((((((((......((((.....((((...(((((((..(((((((..(((((....))))).)))))....))..)))))))...))))....)))))))))))))..)))	0.950 -43.20

rat

chromosome:5:164748461:164748578:-1

intergenic

block1801046 [novel_lenNOK_randfoldOK_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	0.010	no	no	0.61/0.70	18/20/0.50	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	30 27	6 11	3arm 3arm	3 3	nd nd	0.35 0.44	4 3	2	2	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------------------------CUCGUCC-------------------------------------	1	novel
seed	-----------------------------------------------------------------------GGAGACU------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T3S2
	----------------------------------------------------------------------GGGAGACTCGTCCCGGAGAC------------------------------	20	-	1
	---------------------------------------------------------------------------ACTCGTCCCGGAGACCTA---------------------------	18	1	-
rat	aagtgacaggaagttccgcccttcaaactttctccgtgtctttgctgcctccctttcaggaagtcctggtGGGAGACTCGTCCCGGAGACCTAgaggtacctgaaaacttcctggagctg
	************************************************************************************************************************
rat	.(((..(((((((((......((((.....((((...(((((((..(((((((..(((((....))))).)))))....))..)))))))...))))....)))))))))))))..))).	0.950 -44.20

rat

chromosome:5:164748460:164748579:-1

intergenic

block1848541 [novel_lenNOK_randfoldOK_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	0.008	no	no	0.57/0.63	19/21/0.14	0.1	0.4	7	0	3	0	15	0	3arm	1	nd	0.37	4	7	3	na	na

		reads	miRBase family seed
seed	---------------------------------------------UGCAUGG----------------------------	6	novel
seed	----------------------------------------------GCAUGGC---------------------------	1	novel
		len	cloning frequencies
			T2S2	T5S1	T5S2
	--------------------------------------------TTGCATGGCCGATTGTCCC-----------------	19	1	3	1
	---------------------------------------------TGCATGGCCGATTGTCCCC----------------	19	-	1	-
	--------------------------------------------TTGCATGGCCGATTGTCCCCT---------------	21	-	1	-
rat	agggactcgggagagtccctgagcaccgtggagcatgcaagcccTTGCATGGCCGATTGTCCCCTtgactctctgtcccc
	********************************************************************************
rat	.(((((...((((((((.....(((...(((..(((((((....))))))).)))..)))......))))))))))))).	0.980 -33.60

rat

chromosome:5:79247845:79247924:1

intergenic

block1881790 [novel_lenNOK_randfoldOK_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	0.001	no	no	0.42/0.42	19/19/0.00	0.0	0.0	1	0	1	0	19	17	5arm	1	nd	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------AAAGCAA------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S1
	-------------------CAAAGCAATTTGGGGTATC-------------------------------------------------------------------	19	1
rat	ggtctcagactccacctccCAAAGCAATTTGGGGTATCcctgtggagccaagaggatcccactggctgaaggagatcccctgtggggaatgggtgtcagagacca
	*********************************************************************************************************
rat	((((((.(((.((...((((...(((....((((.((((((....((((.((.((...)).))))))..))).)))))))))).))))...)).))).)))))).	0.490 -47.90

rat

chromosome:5:145152246:145152350:1

intergenic

novel_shortStem_nonpairedHIGH_bulgeHIGH (2382 loci)

block518 [novel_shortStem_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	0.476	no	no	0.55/0.55	22/22/1.00	0.0	0.0	1	0	1	0	2	6	3arm	1	nd	0.36	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------CAAAGUG----------------	1	novel
		len	cloning frequencies
			T3S2
	--------------------------------------------------CCAAAGTGGCTGCTAAGAGACC--	22	1
rat	cacgttcaagctataattacttggggaagcggctgaaattgaaactgcatCCAAAGTGGCTGCTAAGAGACCgt
	**************************************************************************
	------------------------------------------------------------------------------------	ENSRNOT00000003193 ENSRNOG00000002314 Lkap
rat	.(((.((.(((.....((((((..(((.((((............)))).))).))))))..)))....)).)))	0.800 -14.90

rat

chromosome:10:827276:827349:-1

Opposite_strand|Intronic_non-coding|ENSRNOT00000003193|ENSRNOG00000002314 ## ENSRNOG00000002314|protein_coding|Lkap|Limkain-b1. [Source:UniProtKB/Swiss-Prot;Acc:Q8VIG2]

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