Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_mirtron_nonpairedHIGH_bulgeHIGH (99 loci)

block2585116 [novel_lenNOK_mirtron_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	0.070	no	no	0.63/0.63	19/19/0.00	0.0	0.0	2	0	1	0	10	27	5arm	1	2	0.42	4	2	1	na	na

		reads	miRBase family seed
seed	-----------GUCAGCU------------------------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T2S2
	----------TGTCAGCTCTGCTCTCCCC-------------------------------------------------------------------------------------	19	2
rat	ctagtctcccTGTCAGCTCTGCTCTCCCCagccgcagggtgcctcagaacttcagcagatggagcttgaagggacgccatcttgtacctgggaagtgggaacggcgggattaga
	******************************************************************************************************************
	++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000018935 ENSRNOG00000014035 LOC301334
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000059983 ENSRNOG00000014035 LOC301334
rat	((((((((.((((...(((....((.(((((..(((((((((.((....(((((((.......))).)))).)).)).)))))))..))))).)).))).)))).)))))))).	1.000 -43.90

rat

chromosome:9:33463696:33463809:1

Same_strand|Intronic_coding|ENSRNOT00000059983|ENSRNOG00000014035 ## Same_strand|Intronic_non-coding|ENSRNOT00000018935|ENSRNOG00000014035 ## ENSRNOG00000014035|protein_coding|LOC301334|

block2708959 [novel_lenNOK_mirtron_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	0.794	no	no	0.47/0.47	19/19/0.00	0.0	0.0	1	0	1	0	8	9	5arm	1	1	0.37	4	1	1	na	na

		reads	miRBase family seed
seed	---------UAAGCAG----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	--------GTAAGCAGCCCTCTCTATA-----------------------------------------------------------	19	1
rat	tcgtaaagGTAAGCAGCCCTCTCTATAtccagtcattgctttctatgtgacctccagagtgaacaaggacagctgagcctccaaga
	**************************************************************************************
	>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000008938 ENSRNOG00000006632 RGD1563860_predicted
rat	((....((((...(((((((((((.......(((((..........)))))....))))......)))...)))).))))....))	0.780 -14.70

rat

chromosome:X:56724123:56724208:-1

Same_strand|Boundary_coding|ENSRNOT00000008938|ENSRNOG00000006632 ## ENSRNOG00000006632|protein_coding|RGD1563860_predicted|

block2954686 [novel_lenNOK_mirtron_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	0.109	no	no	0.58/0.62	19/21/0.50	0.0	1.0	2	0	1	0	11	7	3arm	5	0	0.38	4	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------AGGACAG------------------------	2	novel
		len	cloning frequencies
			T5S1
	----------------------------------------------------CAGGACAGGTACAGCACAG-------------	19	1
	----------------------------------------------------CAGGACAGGTACAGCACAGGC-----------	21	1
rat	gcatgcttactagcccaagccctccagttctccagtcatctttgcaggtgatCAGGACAGGTACAGCACAGGCagtacctgtgc
	************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>	ENSRNOT00000050969 ENSRNOG00000019487
rat	(((((..((((.(((...((...((.(((((...(((((((....))))))).))))).))....))...)))))))..)))))	0.500 -25.00

rat

chromosome:X:29767353:29767436:1

Same_strand|Boundary_coding|ENSRNOT00000050969|ENSRNOG00000019487 ## ENSRNOG00000019487|protein_coding||

block2271250 [novel_lenNOK_mirtron_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	0.669	no	no	0.67/0.67	18/18/0.00	0.0	0.0	1	0	1	0	20	17	3arm	1	1	0.44	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------GGUGAGU------------------------------	1	novel
		len	cloning frequencies
			T3S2
	----------------------------------------------------------------------------------AGGTGAGTGAGCGGCCGA--------------------	18	1
rat	gcccgtcgcgcccgctataatcacgtgattgcctcatccgggtcctttgcgttctctctccctctcccaacatggcggcctcAGGTGAGTGAGCGGCCGAgcgtggccaaagaccaggct
	************************************************************************************************************************
	..............................................................>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000014033 ENSRNOG00000010103 Eif4b
rat	(((.((((((((((((....((((.(((..(((((((..(((.......................)))...)))).))).))).))))...)))))....))))))).........))).	0.550 -38.40

rat

chromosome:7:140814606:140814725:1

Same_strand|Boundary_non-coding|ENSRNOT00000014033|ENSRNOG00000010103 ## ENSRNOG00000010103|protein_coding|Eif4b|eukaryotic translation initiation factor 4B [Source:RefSeq_peptide;Acc:NP_001008325]

block527321 [novel_lenNOK_mirtron_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	0.158	no	no	0.61/0.63	18/19/0.00	0.0	0.5	2	0	1	0	7	20	3arm	1	4	0.33	4	2	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------CCGGGUA------------------	2	novel
		len	cloning frequencies
			T3S2
	------------------------------------------------------------------------ACCGGGTAAGCAGAGCTC--------	18	1
	------------------------------------------------------------------------ACCGGGTAAGCAGAGCTCC-------	19	1
rat	agctcttcctctgcagacttcggctgggagtggacagcctcccaccagcttcctggtctcaggccctgctacACCGGGTAAGCAGAGCTCCccggctg
	**************************************************************************************************
	..........................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++	ENSRNOT00000044198 ENSRNOG00000014055 Nat2
	.......................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++	ENSRNOT00000018854 ENSRNOG00000014055 Nat2
rat	((((....((((((..((.((((.((..(((((...((((...(((((....)))))...)))).))))).))))))))..))))))......)))).	0.540 -35.60

rat

chromosome:16:23876468:23876565:-1

Same_strand|Boundary_non-coding|ENSRNOT00000044198|ENSRNOG00000014055 ## ENSRNOG00000014055|protein_coding|Nat2|Arylamine N-acetyltransferase 1 (EC 2.3.1.5) (Arylamide acetylase 1) (N-acetyltransferase type 1) (NAT-1) (AT-1). [Source:UniProtKB/Swiss-Prot;Acc:P50297]

block789741 [novel_lenNOK_mirtron_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	0.274	no	no	0.61/0.61	18/18/0.00	0.0	0.0	1	0	1	0	10	1	5arm	1	1	0.33	4	1	1	na	na

		reads	miRBase family seed
seed	-----------GCGGAAG------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----------AGCGGAAGATGGAGCAGC--------------------------------------	18	1
rat	ccgtagctgcAGCGGAAGATGGAGCAGCgccgcctgcgacttcaggaggctgccaacaggtatggc
	******************************************************************
	++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++	ENSRNOT00000051945 ENSRNOG00000028904 1300018I17Rik
rat	(((((.(((..((((....(((((..(((.....)))..))))).....))))...))).))))).	0.710 -23.00

rat

chromosome:19:53566607:53566672:-1

Same_strand|Boundary_coding|ENSRNOT00000051945|ENSRNOG00000028904 ## ENSRNOG00000028904|protein_coding|1300018I17Rik|RIKEN cDNA 1300018I17 gene Gene [Source:MGI Symbol;Acc:MGI:1914143]

novel_loopOverlap_randfoldOK_nonpairedHIGH (98 loci)

block4640 [novel_loopOverlap_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	0.009	no	no	0.61/0.61	23/23/1.00	0.0	0.0	2	0	1	0	17	-4	3arm_loop	1	11	0.35	3	2	1	na	na

		reads	miRBase family seed
seed	---------------------------------------UCCAGCC--------------------------------	2	novel
		len	cloning frequencies
			T3S2
	--------------------------------------CTCCAGCCACCATGTCTCACAGC-----------------	23	2
rat	gcaagcaggcaggtgcagccggggacaggtggctcaccCTCCAGCCACCATGTCTCACAGCccagcgccagcagcagc
	******************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000037926 ENSRNOG00000002917 RGD1564638_predicted
	----------------------------------------------------------------------------------------	ENSRNOT00000004026 ENSRNOG00000002930 NP_001100446.1
rat	....((..((.(((((.((..(((((((((((((........))))))).))))))...))...))))).)).))...	0.980 -35.60

rat

chromosome:10:10567332:10567409:-1

Opposite_strand|Intronic_coding|ENSRNOT00000004026|ENSRNOG00000002930 ## Same_strand|Boundary_non-coding|ENSRNOT00000061253|ENSRNOG00000002917 ## Same_strand|Intronic_non-coding|ENSRNOT00000037926|ENSRNOG00000002917 ## ENSRNOG00000002917|protein_coding|RGD1564638_predicted| ## ENSRNOG00000002930|protein_coding|NP_001100446.1|periplakin [Source:RefSeq_peptide;Acc:NP_001100446]

block7626 [novel_loopOverlap_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	0.008	no	no	0.42/0.42	24/24/1.00	0.0	0.0	1	0	1	0	8	-4	3arm_loop	1	nd	0.42	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------UUUUAUC------------------------	1	novel
		len	cloning frequencies
			T1S1
	----------------------------------------------CTTTTATCTTGGCTCTGAGTCAGT--------	24	1
rat	ttttgggtagcaacattcttggagccagaatgtgccttctctgaccCTTTTATCTTGGCTCTGAGTCAGTtgcctgga
	******************************************************************************
	----------------------------------------------------------------------------------------	ENSRNOT00000048663 ENSRNOG00000020414 Axin1
	----------------------------------------------------------------------------------------	ENSRNOT00000027705 ENSRNOG00000020414 Axin1
rat	.((..((((((......((..((((((..(((..................)))..))))))..))...))))))..))	0.970 -25.27

rat

chromosome:10:15458219:15458296:-1

Opposite_strand|Intronic_coding|ENSRNOT00000048663|ENSRNOG00000020414 ## ENSRNOG00000020414|protein_coding|Axin1|Axin-1 (Axis inhibition protein 1) (rAxin). [Source:UniProtKB/Swiss-Prot;Acc:O70239]

block36307 [novel_loopOverlap_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	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	20	-1	5arm_loop	1	nd	0.35	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------GGGGGUG----------------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	--------------------TGGGGGTGTTGTGGTTTTGG----------------------------------	20	1
rat	agagaaatgagagatgaagtTGGGGGTGTTGTGGTTTTGGaaacaggcacagggtttcaaatttttctttttct
	**************************************************************************
rat	(((((((.(((((((.......((((..(((((..((((....)))))))))..))))..))))))))))))))	1.000 -18.40

rat

chromosome:10:78435583:78435656:-1

intergenic

block62213 [novel_loopOverlap_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	0.003	no	no	0.45/0.45	20/20/1.00	0.0	0.0	1	0	1	0	28	-1	5arm_loop	1	10	0.35	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------CACUCUC--------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	----------------------------TCACTCTCACAGCTTTCTGT--------------------------------------------------	20	1
rat	cgagcccacattcacctttccctggcgtTCACTCTCACAGCTTTCTGTtctcttccagagtctgggatgtgaacacgggggaagttctcaacacactc
	**************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000005874 ENSRNOG00000004395 Fbxw11
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000006078 ENSRNOG00000004395 Fbxw11
rat	.(((...........(((((((((..((((((..((.(((..(((((........))))).)))))..)))))).)))))))))...........)))	0.810 -31.25

rat

chromosome:10:17591287:17591384:1

Same_strand|Intronic_coding|ENSRNOT00000005874|ENSRNOG00000004395 ## ENSRNOG00000004395|protein_coding|Fbxw11|F-box and WD-40 domain protein 11 Gene [Source:MGI (curated);Acc:Fbxw11-002]

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