Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_loopOverlap_mirtron_nonpairedHIGH (38 loci)

novel_lenNOK_cloningOK_randfoldOK_nonpairedHIGH (37 loci)

block31372 [novel_lenNOK_cloningOK_randfoldOK_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	0.002	no	no	0.50/0.53	18/19/0.00	0.0	0.0	16	0	8	0	32	1	5arm	1	nd	0.33	3	20	8	na	na

		reads	miRBase family seed
seed	---------------------------------UACUGCC---------------------------------------------------------------	20	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T4S1	T4S2	T5S1	T5S2
	--------------------------------ATACTGCCACCAGGGATT-----------------------------------------------------	18	3	2	1	1	2	1	6	3
	--------------------------------ATACTGCCACCAGGGATTC----------------------------------------------------	19	-	1	-	-	-	-	-	-
rat	tcatacttatctcattccctaccttccaagtaATACTGCCACCAGGGATTctaccggaaactttttaggcagggtacttgatacagtgctagataagtatgaa
	*******************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------	ENSRNOT00000008083 ENSRNOG00000005538 Psmd11
rat	((((((((((((((((..........((((((...(((((...((((.(((.....))).))))...)))))..))))))....))))..)))))))))))).	0.940 -31.14

rat

chromosome:10:68669741:68669843:-1

Opposite_strand|Intronic_coding|ENSRNOT00000008083|ENSRNOG00000005538 ## ENSRNOG00000005538|protein_coding|Psmd11|proteasome (prosome, macropain) 26S subunit, non-ATPase, 11 Gene [Source:MGI (curated);Acc:Psmd11-001]

block60002 [novel_lenNOK_cloningOK_randfoldOK_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	0.007	no	no	0.50/0.62	18/21/0.14	0.0 0.0	0.0 0.3	1 18	0 0	1 2	0 0	35 29	5 10	3arm 3arm	1 1	11 5	0.44 0.32	3 3	22	2	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------------------AGACCUG----------------------------------------	20	novel
seed	-----------------------------------------------------------------CUCCUAG---------------------------------------------	1	novel
seed	-------------------------------------------------------------------------CCUGUCC-------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2
	---------------------------------------------------------------------TAGACCTGTCCTTCACCT------------------------------	18	5	7
	---------------------------------------------------------------------TAGACCTGTCCTTCACCTG-----------------------------	19	3	3
	---------------------------------------------------------------------TAGACCTGTCCTTCACCTGCC---------------------------	21	2	-
	----------------------------------------------------------------TCTCCTAGACCTGTCCTT-----------------------------------	18	1	-
	------------------------------------------------------------------------ACCTGTCCTTCACCTGCCCAG------------------------	21	1	-
rat	cagcttgggcaagggcagaaggaatggggtaggtaggccccagggaaggctgggccttggcttctctccTAGACCTGTCCTTCACCTGcccagcttctcagccctgcaccatgctgc
	*********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000004486 ENSRNOG00000003195 Caskin1
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000060705 ENSRNOG00000003195 Caskin1
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000043951 ENSRNOG00000003195 Caskin1
rat	((((.(((((.((((((((((.....(((((((((((...((((..(((..((((....))))....)))...)))).)))..))))))))..)))))..))))))).))).)))).	0.470 -54.40

rat

chromosome:10:13747835:13747951:1

Same_strand|Intronic_coding|ENSRNOT00000043951|ENSRNOG00000003195 ## ENSRNOG00000003195|protein_coding|Caskin1|Caskin-1 (CASK-interacting protein 1). [Source:UniProtKB/Swiss-Prot;Acc:Q8VHK2]

block68982 [novel_lenNOK_cloningOK_randfoldOK_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	0.005	no	no	0.55/0.61	18/20/0.08	0.0	0.2	12	0	7	0	10	27	5arm	1	nd	0.33	3	12	7	na	na

		reads	miRBase family seed
seed	-----------CUGAUGC----------------------------------------------------------------------------------------------------	12	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T3S2	T4S1	T4S2	T5S2
	----------CCTGATGCCCTTGATCCC------------------------------------------------------------------------------------------	18	2	2	2	2	1	1	1
	----------CCTGATGCCCTTGATCCCAA----------------------------------------------------------------------------------------	20	-	-	-	-	1	-	-
rat	ttctcttggcCCTGATGCCCTTGATCCCAAaccgagcttggataagacagggcaatccagttttgatacaattcctgtcctccaggccacagatcgggtttcagggcaccagtgagag
	**********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000004820 ENSRNOG00000003572 Adamts2
rat	.((((((((((((((.((((..((((.........(((((((...(((((((..(((.......))).....))))))).)))))))....)))))))).)))))))..))).)))).	0.900 -44.82

rat

chromosome:10:36361307:36361424:1

Same_strand|Intronic_coding|ENSRNOT00000004820|ENSRNOG00000003572 ## ENSRNOG00000003572|protein_coding|Adamts2|a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 2 Gene [Source:MGI (curated);Acc:Adamts2-001]

block133949 [novel_lenNOK_cloningOK_randfoldOK_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	0.005	no	no	0.63/0.67	18/19/0.00	0.0	0.4	19	0	9	0	19	16	5arm	1	nd	0.37	2	25	9	na	na

		reads	miRBase family seed
seed	--------------------CCCUGUC------------------------------------------------------------------------------------------	25	miR-339
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-------------------TCCCTGTCGGCCTGGAACT-------------------------------------------------------------------------------	19	2	3	4	-	-	-	1	1	2
	-------------------TCCCTGTCGGCCTGGAAC--------------------------------------------------------------------------------	18	1	2	1	3	1	1	3	-	-
rat	gcttcctaccatcaagtcaTCCCTGTCGGCCTGGAACTgggccaacagatgggcagctgcagaccagctgttggcctgagcaaaaccagcaagcgagagccatgacatggagaagca
	*********************************************************************************************************************
rat	(((((...((((...(((((..((.(((..((((..((((((((((((.(((((....))...))).)))))))))).)).....))))....))).))..))))))))).))))).	0.920 -46.10

rat

chromosome:11:72458368:72458484:-1

intergenic

block184156 [novel_lenNOK_cloningOK_randfoldOK_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	0.001	no	no	0.39/0.39	18/18/0.00	0.0	0.0	10	0	6	0	12	27	3arm	1	nd	0.33	2	14	6	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------CAUUUGG----------------------	14	novel
		len	cloning frequencies
			T1S1	T2S1	T3S1	T4S1	T4S2	T5S2
	----------------------------------------------------------------------------------------TCATTTGGCTTCTAGTCA------------	18	1	3	1	1	1	7
rat	gccaggggagggggtggagggagggttggtatagcataggctatggggcctcagtttacacaagcagggctccaaggcctagggggccTCATTTGGCTTCTAGTCAcatttccctggt
	**********************************************************************************************************************
rat	((((((((((.((.((((((..((((.(((......((((((.((((((((..((((....)))).)))))))).))))))....)))..))))..)))))).))...))))))))))	0.530 -54.80

rat

chromosome:12:13566036:13566153:-1

intergenic

block269218 [novel_lenNOK_cloningOK_randfoldOK_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	0.002	no	no	0.42/0.44	18/19/0.00	0.0	0.0	9	0	2	0	38	6	5arm	1	nd	0.44	3	13	2	na	na

		reads	miRBase family seed
seed	---------------------------------------CCUUACU------------------------------------------------------------------------	13	novel
		len	cloning frequencies
			T4S1	T4S2
	--------------------------------------TCCTTACTAAAGGGACAG--------------------------------------------------------------	18	2	9
	--------------------------------------TCCTTACTAAAGGGACAGA-------------------------------------------------------------	19	1	1
rat	ggtgagccttctctccttcctcccttccatctccctctTCCTTACTAAAGGGACAGagtcagagaattgacaatggttactttagtgtcctgaggggatgctagtcctggaagcacct
	**********************************************************************************************************************
rat	((((...........(((((...((..((((.(((((.....((((((((..((...(((((....)))))....))..))))))))....)))))))))..))....))))))))).	0.670 -39.10

rat

chromosome:13:74859797:74859914:-1

intergenic

block478129 [novel_lenNOK_cloningOK_randfoldOK_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	0.004	no	no	0.56/0.58	18/19/0.00	0.0	0.0	11	0	8	0	26	8	3arm	2	nd	0.33	3	18	8	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------GGGACAC------------------------------------	18	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T5S1	T5S2
	------------------------------------------------------------------TGGGACACTCACAGTGCA--------------------------	18	-	1	3	8	1	1	2	1
	------------------------------------------------------------------TGGGACACTCACAGTGCAC-------------------------	19	1	-	-	-	-	-	-	-
rat	gagagacagaaatcagatccctctgcctgacgtgctgcccacaagagaaagagagagcctcttctgTGGGACACTCACAGTGCAcgagacaatcaccttttcttctcttg
	**************************************************************************************************************
rat	((((((.(((((...(((..(((((((((..(((...(((((.(((...((((.....)))))))))))).)))...))).))).)))...)))....))))))))))).	1.000 -36.10

rat

chromosome:15:18129027:18129136:1

intergenic

block542060 [novel_lenNOK_cloningOK_randfoldOK_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	0.006	no	no	0.16/0.22	18/19/0.00	0.0 0.0	0.0 0.0	1 12	0 0	1 5	0 0	10 15	13 9	5arm 5arm	3 3	nd nd	0.53 0.33	7 3	16	6	na	na

		reads	miRBase family seed
seed	----------------AAAGGUU---------------------------------------------------------	15	novel
seed	-----------UUUUUAA--------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T4S2	T5S2
	---------------TAAAGGTTAAAAACAATG-----------------------------------------------	18	7	1	5	-	1	1
	----------TTTTTTAAAGGTTAAAAAC---------------------------------------------------	19	-	-	-	1	-	-
rat	aggggaattttttttTAAAGGTTAAAAACAATGctttagactctaaagtttagagaacagttgttgggcctaaagcctca
	********************************************************************************
rat	.((((..((.........(((((...((((((.(((((((((....)))))))))....)))))).)))))))..)))).	0.860 -21.50

rat

chromosome:16:59706046:59706125:-1

intergenic ## {Repeats: dust 59706110 59706116 0 class=dust}

block790439 [novel_lenNOK_cloningOK_randfoldOK_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	0.002	no	no	0.47/0.50	18/19/0.00	0.0	0.0	8	0	7	0	12	23	3arm	1	nd	0.33	3	14	7	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------AGACAAG----------------------	14	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T4S1	T4S2	T5S1
	----------------------------------------------------------------------------------TAGACAAGTTTGGGGCTG------------	18	4	2	1	1	1	1	2
	----------------------------------------------------------------------------------TAGACAAGTTTGGGGCTGA-----------	19	1	1	-	-	-	-	-
rat	gggatcctacagcctgaaaagacagcagagtcaagcaggcaaagtgggcaagcccggaaggaaggcctgctccaaggactgtTAGACAAGTTTGGGGCTGaaggaacagcct
	****************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000058080 ENSRNOG00000026791 NP_001099668.1
rat	(((.((((.((((((.(((..........(((.(((((....((..(((....((....))...)))..)).......))))).)))...))).)))))).))))....)))	0.440 -40.12

rat

chromosome:19:54570110:54570221:-1

Same_strand|Intronic_non-coding|ENSRNOT00000058080|ENSRNOG00000026791 ## Same_strand|Boundary_non-coding|ENSRNOT00000034335|ENSRNOG00000026791 ## ENSRNOG00000026791|protein_coding|NP_001099668.1|piggyBac transposable element derived 5 [Source:RefSeq_peptide;Acc:NP_001099668]

block808973 [novel_lenNOK_cloningOK_randfoldOK_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	0.004	no	no	0.61/0.61	18/18/0.00	0.0	0.0	9	0	4	0	14	18	5arm	3	nd	0.33	3	11	4	na	na

		reads	miRBase family seed
seed	---------------CUCCCAA----------------------------------------------------------------------------------	11	miR-150
		len	cloning frequencies
			T1S1	T2S1	T3S1	T5S1
	--------------TCTCCCAACCCCCACCTT------------------------------------------------------------------------	18	3	1	6	1
rat	gtagtccggcctatTCTCCCAACCCCCACCTTcagcctctactgctctctgcccagagagaacggaaagggtaggtactggggaggagtttgggcaaggaatgc
	********************************************************************************************************
	------------------------------------------------------------------------------------------------------------------	ENSRNOT00000020405 ENSRNOG00000015179 Tradd
rat	(((.(((.(((((..((((...((((.((((...((((...(((((((((....))))))..)))...))))))))...)))).))))..)))))..))).)))	1.000 -43.20

rat

chromosome:19:35074636:35074739:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000059696|ENSRNOG00000015179 ## Opposite_strand|Intronic_coding|ENSRNOT00000020405|ENSRNOG00000015179 ## ENSRNOG00000015179|protein_coding|Tradd|Tumor necrosis factor receptor type 1 associated death domain-like protein (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q8K3Z8]

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