Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_shortStem_loopOverlap (205 loci)

novel_lenNOK_cloningOK_shortStem_nonpairedHIGH_bulgeHIGH (199 loci)

block1226 [novel_lenNOK_cloningOK_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	0.131	no	no	0.50/0.53	18/19/0.00	0.0	0.0	10	0	4	0	0	15	5arm	1	nd	0.44	4	15	4	na	na

		reads	miRBase family seed
seed	-UGACCUA----------------------------------------------------------------	15	miR-192/215
		len	cloning frequencies
			T1S2	T2S1	T5S1	T5S2
	CTGACCTAACTTCACTGG------------------------------------------------------	18	1	10	2	1
	CTGACCTAACTTCACTGGC-----------------------------------------------------	19	-	1	-	-
rat	CTGACCTAACTTCACTGGcatcctttctgttgttttgtatacaatgaggaactcagagcagtgcacttcagc
	************************************************************************
rat	((((....(((...((((..(((((...(((((.......))))))))))..))))...))).....)))).	0.940 -14.40

rat

chromosome:10:2409202:2409273:-1

intergenic

block2263 [novel_lenNOK_cloningOK_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	0.120	no	no	0.67/0.74	18/19/0.00	0.0	0.2	15	0	8	0	3	28	5arm	1	nd	0.37	4	31	8	na	na

		reads	miRBase family seed
seed	----GGGAACC---------------------------------------------------------------------------------------------------------	23	novel
seed	---CGGGAAC----------------------------------------------------------------------------------------------------------	8	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S2	T5S1
	---CGGGAACCGGCACAAGGG-----------------------------------------------------------------------------------------------	18	9	3	2	-	1	-	2	1
	---CGGGAACCGGCACAAGGGG----------------------------------------------------------------------------------------------	19	3	-	2	-	-	-	-	-
	--TCGGGAACCGGCACAAGG------------------------------------------------------------------------------------------------	18	2	-	-	2	-	-	-	-
	--TCGGGAACCGGCACAAGGG-----------------------------------------------------------------------------------------------	19	2	-	-	-	-	1	-	1
rat	ggtCGGGAACCGGCACAAGGGGcagcactgaaaggctgcatttgggaaggacctgcccacaccaaatgctttgatggcggctggtttgctgctgccctaccctgccctgctctgcc
	********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000033122 ENSRNOG00000021902 RGD1563163_predicted
rat	(((.(((....((((...(((((((((..(((.((((((((((((...((......))...)))))))).........))))..)))..)))))))))....))))...))).)))	0.780 -46.20

rat

chromosome:10:4767939:4768054:-1

Same_strand|Intronic_coding|ENSRNOT00000033122|ENSRNOG00000021902 ## ENSRNOG00000021902|protein_coding|RGD1563163_predicted|

block4192 [novel_lenNOK_cloningOK_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	0.456	no	no	0.50/0.56	18/18/0.00	0.6	0.6	10	0	7	0	2	1	5arm	1	nd	0.33	4	10	7	na	na

		reads	miRBase family seed
seed	---GUCCCAC--------------------------------------------------------	5	novel
seed	----UCCCACU-------------------------------------------------------	4	novel
seed	-----CCCACUU------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T2S1	T2S2	T3S1	T3S2	T4S2	T5S1
	--TGTCCCACTTCTGACACC----------------------------------------------	18	-	1	1	-	1	1	1
	---GTCCCACTTCTGACACCT---------------------------------------------	18	2	-	-	2	-	-	-
	----TCCCACTTCTGACACCTT--------------------------------------------	18	-	-	1	-	-	-	-
rat	gaTGTCCCACTTCTGACACCTTaaagcagaaggaactaggggaaaagaaggattgatttggccatc
	******************************************************************
rat	((((.((..(((((....(((((.............)))))....))))).........)).))))	0.770 -11.72

rat

chromosome:10:9317256:9317321:-1

intergenic

block16677 [novel_lenNOK_cloningOK_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	0.152	no	no	0.56/0.58	18/19/0.00	0.0	0.1	14	0	7	0	3	11	3arm	1	nd	0.42	4	17	7	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------CUGGACU--------------	17	miR-378
		len	cloning frequencies
			T1S1	T2S1	T3S1	T3S2	T4S1	T4S2	T5S1
	------------------------------------------------------ACTGGACTTGGAGTGCCT----	18	2	-	1	1	4	4	2
	------------------------------------------------------ACTGGACTTGGAGTGCCTC---	19	-	1	2	-	-	-	-
rat	aaggagacttgatcccatgactcttctccctactgaaagcaacttctgggtgtcACTGGACTTGGAGTGCCTCctt
	****************************************************************************
rat	((((((((((..(((..((((......(((....(((......))).))).))))..)))....))))..))))))	0.920 -18.60

rat

chromosome:10:37943303:37943378:-1

intergenic

block23743 [novel_lenNOK_cloningOK_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	0.317	no	no	0.57/0.61	18/21/0.20	0.0	0.9	10	0	4	0	2	4	5arm	1	nd	0.38	5	10	4	na	na

		reads	miRBase family seed
seed	---GCCUGUG--------------------------------------------------------	10	novel
		len	cloning frequencies
			T1S2	T2S1	T3S1	T3S2
	--CGCCTGTGCACATGTCTG----------------------------------------------	18	1	3	-	-
	--CGCCTGTGCACATGTCTGT---------------------------------------------	19	1	1	1	1
	--CGCCTGTGCACATGTCTGTGT-------------------------------------------	21	-	1	-	-
	--CGCCTGTGCACATGTCTGTG--------------------------------------------	20	-	1	-	-
rat	ttCGCCTGTGCACATGTCTGTGTttgctcatgtaaacctcatgtccagttaacaatgcaatggaga
	******************************************************************
rat	.((.((..((((((((.....((((((....))))))..)))))............)))..)).))	0.790 -12.00

rat

chromosome:10:53860036:53860101:-1

intergenic

block48299 [novel_lenNOK_cloningOK_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	0.077	no	no	0.39/0.39	18/18/0.00	0.0	0.0	10	0	7	0	0	27	3arm	1	nd	0.35	4	10	7	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------AUUGAUG----------	10	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T4S1	T4S2	T5S1	T5S2
	----------------------------------------------------------------------------CATTGATGTAGCTGTGAA	18	3	1	1	2	1	1	1
rat	ttggggttacaagcctgtaccacattgagctccaaagggatgccatattggaaatcctattagcatagtggggtgaCATTGATGTAGCTGTGAA
	**********************************************************************************************
rat	(((.(((((((....((((((.(((((.(((..((.(((((.((.....))..))))).))))).))))).)))).))....))))))).))).	0.990 -26.50

rat

chromosome:10:101498065:101498158:-1

intergenic

block61853 [novel_lenNOK_cloningOK_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	0.122	no	no	0.47/0.47	19/19/0.00	0.0	0.0	21	0	5	0	1	6	3arm	3	nd	0.37	4	27	5	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------GACAUCA------------	27	novel
		len	cloning frequencies
			T1S1	T3S1	T4S1	T4S2	T5S1
	------------------------------------------------------------------------TGACATCATGGTGCCTACA-	19	2	1	2	1	21
rat	tgttttgcactagcagtctctggcatccattccccccccccccccccgcctcccatctcagcttatccagaaTGACATCATGGTGCCTACAc
	********************************************************************************************
rat	(((...((((((...((((((((...........................................)))))..)))....))))))..))).	0.900 -14.13

rat

chromosome:10:16947950:16948041:1

intergenic

block99114 [novel_lenNOK_cloningOK_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	0.265	no	no	0.53/0.57	18/21/0.05	0.0	0.0	13	0	8	0	4	13	5arm	2	nd	0.39	4	19	8	na	na

		reads	miRBase family seed
seed	-----GGAGACU------------------------------------------------------------	19	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S1	T4S1	T4S2	T5S1	T5S2
	----TGGAGACTGGACAGTCCT--------------------------------------------------	18	4	4	2	-	1	1	3	1
	----TGGAGACTGGACAGTCCTA-------------------------------------------------	19	-	-	-	-	-	1	-	1
	----TGGAGACTGGACAGTCCTAGC-----------------------------------------------	21	-	-	-	1	-	-	-	-
rat	tctgTGGAGACTGGACAGTCCTagcaggcctggtggaaacacttctcagagttgcaattgctttagttacag
	************************************************************************
	----------------------------------------------------------------------------------	ENSRNOT00000017371 ENSRNOG00000012864 RGD1559716_predicted
rat	.((((...(((((((((((....((((..((((((....)))....)))..)))).)))).)))))))))))	0.590 -18.90

rat

chromosome:10:95797469:95797540:1

Opposite_strand|Intronic_coding|ENSRNOT00000017371|ENSRNOG00000012864 ## ENSRNOG00000012864|protein_coding|RGD1559716_predicted|

block127842 [novel_lenNOK_cloningOK_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	0.041	no	no	0.42/0.45	18/20/0.18	0.0	0.6	11	0	6	0	0	35	3arm	1	nd	0.37	4	11	6	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------------AACAGCA------------	11	miR-21*
		len	cloning frequencies
			T2S1	T2S2	T3S1	T4S1	T5S1	T5S2
	-------------------------------------------------------------------------------------------TAACAGCACATCATGGTC--	18	-	-	3	2	1	-
	-------------------------------------------------------------------------------------------TAACAGCACATCATGGTCA-	19	2	-	1	-	-	-
	-------------------------------------------------------------------------------------------TAACAGCACATCATGGTCAC	20	-	1	-	-	-	1
rat	gtgcccttgtgcggtgaaattcaggcagtaaagctactaagtatccatgcgctacagcaactcacttcccaccattactgagaactgatacTAACAGCACATCATGGTCAC
	***************************************************************************************************************
rat	(((.((.(((((.((.....((((.((((((.......((((.....(((......)))....)))).......))))))....)))).....)).)))))....)).)))	0.600 -27.14

rat

chromosome:11:58987244:58987354:-1

intergenic

block128397 [novel_lenNOK_cloningOK_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	0.601	no	no	0.26/0.28	18/19/0.00	0.0	0.0	24	0	9	0	2	18	5arm	1	nd	0.44	4	30	9	na	na

		reads	miRBase family seed
seed	---AAAGGUU---------------------------------------------------------------	30	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--TAAAGGTTAATGGTGAAA-----------------------------------------------------	18	10	4	6	1	4	1	1	1	1
	--TAAAGGTTAATGGTGAAAT----------------------------------------------------	19	-	-	-	-	1	-	-	-	-
rat	caTAAAGGTTAATGGTGAAAtagatgacaagagaggtagctacagaaatgcttctaaataccacattttgatg
	*************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000047907 ENSRNOG00000031852 Lsamp
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042024 ENSRNOG00000031852 Lsamp
rat	(((.(((((...(((((..............(((((((..........)))))))...))))).))))).)))	0.680 -8.33

rat

chromosome:11:60431547:60431619:-1

Same_strand|Intronic_coding|ENSRNOT00000042024|ENSRNOG00000031852 ## ENSRNOG00000031852|protein_coding|Lsamp|Limbic system-associated membrane protein precursor (LSAMP). [Source:UniProtKB/Swiss-Prot;Acc:Q62813]

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