Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_5varHIGH_loopOverlap (48 loci)

block881557 [novel_5varHIGH_loopOverlap]

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	0.150	no	no	0.48/0.48	21/23/1.00	2.5	1.5	2	0	1	0	14	-3	3arm	1	nd	0.19	2	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------GAACUUC---------------------------	1	novel
seed	---------------------------------------------------AUGGUGA--------------------------------	1	novel
		len	cloning frequencies
			T5S1
	--------------------------------------------------TATGGTGAACTTCAGGTTAGCCC-----------------	23	1
	-------------------------------------------------------TGAACTTCAGGTTAGCCCTGA--------------	21	1
rat	ttctgtatgtgtttggggccatgatacctgcttggcgaataaggtcacccTATGGTGAACTTCAGGTTAGCCCTGAtatttcactaagag
	******************************************************************************************
	----------------------------------------------------------------------------------------------------	ENSRNOT00000016427 ENSRNOG00000012031 St8sia2
rat	.(((....(((.(((((((......(((((..........(((.(((((....))))).))))))))..))))))).....)))..))).	0.540 -24.30

rat

chromosome:1:129022306:129022395:-1

Opposite_strand|Intronic_coding|ENSRNOT00000016427|ENSRNOG00000012031 ## ENSRNOG00000012031|protein_coding|St8sia2|Alpha-2,8-sialyltransferase 8B (EC 2.4.99.-) (ST8Sia II) (Sialyltransferase X) (STX). [Source:UniProtKB/Swiss-Prot;Acc:Q07977]

block1414023 [novel_5varHIGH_loopOverlap]

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	0.324	no	no	0.33/0.35	20/21/1.00	1.9	1.2	8	0	3	0	42	-4	3arm	1	nd	0.15	2	8	3	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------AGCUGUU------------------------------------------------------	5	novel
seed	--------------------------------------------------------GAUAGCU---------------------------------------------------------	3	novel
		len	cloning frequencies
			T1S1	T4S2	T5S1
	----------------------------------------------------------TAGCTGTTTGTTGTTTCATG------------------------------------------	20	1	1	3
	-------------------------------------------------------TGATAGCTGTTTGTTGTTTCA--------------------------------------------	21	-	-	3
rat	tcaagtaaactaggcaaacttaaggtgggaggagtaggaacagtagatcccttcaTGATAGCTGTTTGTTGTTTCATGcttggcactttgtatttcacagtttgatcctaattactggac
	************************************************************************************************************************
rat	((.(((((..(((((((((((((((((....(((((((((((((((((..((.......))..)))))))))))).)))))..)))))))........))))))..)))).))))).)).	0.730 -27.90

rat

chromosome:3:141687307:141687426:-1

intergenic

novel_lenNOK_cloningHIGH_shortStem_nonpairedHIGH (48 loci)

block7354 [novel_lenNOK_cloningHIGH_shortStem_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	0.298	no	no	0.44/0.47	18/19/0.00	0.0	0.0	37	0	9	0	2	7	3arm	1	nd	0.33	3	60	9	na	na

		reads	miRBase family seed
seed	--------------------------------------AAAGUGC------------	60	miR-106b/17/20a/20b/93
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-------------------------------------TAAAGTGCTGGTCTGTAC--	18	5	5	8	5	20	1	9	4	2
	-------------------------------------TAAAGTGCTGGTCTGTACG-	19	-	-	-	-	1	-	-	-	-
rat	tcttgcatgataccactacaccagcggcgctgttgagTAAAGTGCTGGTCTGTACga
	*********************************************************
rat	((.((((.(((..((((..(((((((....))))).))..))))...))))))).))	0.990 -14.00

rat

chromosome:10:15139508:15139564:-1

intergenic ## {SimpF: oe = 0.84 -1 CpG}

block17244 [novel_lenNOK_cloningHIGH_shortStem_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	0.599	no	no	0.67/0.72	18/21/0.03	0.0	0.2	65	0	10	0	2	16	5arm	1	nd	0.37	3	135	10	na	na

		reads	miRBase family seed
seed	---CCUAAGG-----------------------------------------------------------------------	128	novel
seed	----CUAAGGG----------------------------------------------------------------------	7	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--TCCTAAGGGGCTGGGGGAG------------------------------------------------------------	19	6	7	11	1	33	5	11	6	6	1
	--TCCTAAGGGGCTGGGGGA-------------------------------------------------------------	18	4	1	5	2	10	4	1	7	3	-
	---CCTAAGGGGCTGGGGGAG------------------------------------------------------------	18	1	-	-	1	1	1	-	2	1	-
	--TCCTAAGGGGCTGGGGGAGGG----------------------------------------------------------	21	-	1	1	-	2	-	-	-	-	-
rat	ccTCCTAAGGGGCTGGGGGAGgggagcaggtgtgggagagcttctgatctgccctactcgagagccataaccgtgatgggg
	*********************************************************************************
rat	.((((...((((((.(((...(((.((((((.(((((....)))))))))))))).)))...))))....)).....))))	0.880 -26.30

rat

chromosome:10:39067222:39067302:-1

intergenic

block30558 [novel_lenNOK_cloningHIGH_shortStem_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	0.552	no	no	0.33/0.33	18/18/0.00	0.0	0.0	59	0	6	0	2	5	5arm	2	nd	0.39	3	65	6	na	na

		reads	miRBase family seed
seed	---UUGGCAA-----------------------------------------------	65	miR-182
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T5S1	T5S2
	--TTTGGCAATGGTAGAAAT-------------------------------------	18	26	1	9	5	12	12
rat	acTTTGGCAATGGTAGAAATggggaccttggaataaattccctctttattgaacaag
	*********************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000056126 ENSRNOG00000022536 RGD1309650_predicted
rat	.(((...((((((.(((...(((((............))))))))))))))...)))	0.980 -8.60

rat

chromosome:10:66824783:66824839:-1

Same_strand|Boundary_non-coding|ENSRNOT00000031618|ENSRNOG00000022536 ## Same_strand|Intronic_non-coding|ENSRNOT00000056126|ENSRNOG00000022536 ## ENSRNOG00000022536|protein_coding|RGD1309650_predicted|

block81650 [novel_lenNOK_cloningHIGH_shortStem_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	0.051	no	no	0.47/0.55	18/22/0.47	0.0	0.9	1082	0	10	0	2	9	5arm	1	nd	0.33	3	1965	10	na	na

		reads	miRBase family seed
seed	---GUAAACA----------------------------------------------------------------------	1935	miR-30a/30b/30c/30d/30e/384
seed	----UAAACAU---------------------------------------------------------------------	30	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--TGTAAACATCCCCGGTCAA-----------------------------------------------------------	19	45	11	67	6	399	26	19	29	23	17
	--TGTAAACATCCCCGGTCAAGG---------------------------------------------------------	21	35	23	161	12	159	23	35	31	20	24
	--TGTAAACATCCCCGGTCA------------------------------------------------------------	18	28	6	51	8	215	25	9	15	15	13
	--TGTAAACATCCCCGGTCAAG----------------------------------------------------------	20	24	13	64	18	148	32	22	25	22	11
	---GTAAACATCCCCGGTCAAGG---------------------------------------------------------	20	1	1	4	1	-	1	3	2	2	-
	---GTAAACATCCCCGGTCAA-----------------------------------------------------------	18	2	1	1	-	4	-	-	2	-	-
	--TGTAAACATCCCCGGTCAAGGC--------------------------------------------------------	22	1	-	1	-	1	-	1	1	1	-
	---GTAAACATCCCCGGTCAAG----------------------------------------------------------	19	-	-	1	-	-	2	1	1	-	-
rat	acTGTAAACATCCCCGGTCAAGGccctggtggttcctgagttcacccagggctgtttattagcttgtcctgatgggcagc
	********************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000005406 ENSRNOG00000004041 Pps
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000048371 ENSRNOG00000004041 Pps
rat	.((((...((((...((.((((((((((((((.........))))).)))))..........)))).)).)))).)))).	0.690 -27.70

rat

chromosome:10:62960373:62960452:1

Same_strand|Intronic_coding|ENSRNOT00000005406|ENSRNOG00000004041 ## ENSRNOG00000004041|protein_coding|Pps|inositol polyphosphate 5-phosphatase K Gene [Source:MGI (curated);Acc:Pps-001]

block83828 [novel_lenNOK_cloningHIGH_shortStem_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	0.552	no	no	0.33/0.33	18/18/0.00	0.0	0.0	59	0	6	0	2	5	5arm	2	nd	0.39	3	65	6	na	na

		reads	miRBase family seed
seed	---UUGGCAA-----------------------------------------------	65	miR-182
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T5S1	T5S2
	--TTTGGCAATGGTAGAAAT-------------------------------------	18	26	1	9	5	12	12
rat	acTTTGGCAATGGTAGAAATggggaccttggaataaattccctctttattgaacaag
	*********************************************************
	-------------------------------------------------------------------	ENSRNOT00000056126 ENSRNOG00000022536 RGD1309650_predicted
rat	.(((...((((((.(((...(((((............))))))))))))))...)))	0.980 -8.60

rat

chromosome:10:66816241:66816297:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000031618|ENSRNOG00000022536 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000056126|ENSRNOG00000022536 ## ENSRNOG00000022536|protein_coding|RGD1309650_predicted|

block90812 [novel_lenNOK_cloningHIGH_shortStem_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	0.106	no	no	0.37/0.39	18/19/0.00	0.0	0.0	77	0	2	0	2	14	3arm	1	nd	0.33	3	79	2	na	na

		reads	miRBase family seed
seed	----------------------------------------------------GGAGUGU------------	78	miR-122
seed	-----------------------------------------------------GAGUGUG-----------	1	novel
		len	cloning frequencies
			T2S1	T2S2
	---------------------------------------------------TGGAGTGTGACAATATGT--	18	55	22
	----------------------------------------------------GGAGTGTGACAATATGTA-	18	-	1
	---------------------------------------------------TGGAGTGTGACAATATGTA-	19	-	1
rat	actatcagactgggcacagctggttgatatgtagaggacatatcaaacccaTGGAGTGTGACAATATGTag
	***********************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000050892 ENSRNOG00000002626 Car10
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000003553 ENSRNOG00000002626 Car10
rat	.(((.((...((..((((.(((((((((((((.....))))))))).))...))..)))).))...)))))	0.750 -16.90

rat

chromosome:10:81910814:81910884:1

Same_strand|Intronic_coding|ENSRNOT00000050892|ENSRNOG00000002626 ## ENSRNOG00000002626|protein_coding|Car10|carbonic anhydrase 10 Gene [Source:MGI (curated);Acc:Car10-001]

block92881 [novel_lenNOK_cloningHIGH_shortStem_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	0.020	no	no	0.42/0.44	18/19/0.00	0.0	0.0	38	0	10	0	4	26	3arm	1	nd	0.32	3	71	10	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------------UUUCCUG---------------	70	novel
seed	----------------------------------------------------------------------------------------UUCCUGG--------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--------------------------------------------------------------------------------------TTTTCCTGGGTTGAGGAAA----	19	14	6	6	4	1	4	2	4	5	7
	--------------------------------------------------------------------------------------TTTTCCTGGGTTGAGGAA-----	18	4	4	1	-	-	-	1	3	1	3
	---------------------------------------------------------------------------------------TTTCCTGGGTTGAGGAAA----	18	-	1	-	-	-	-	-	-	-	-
rat	tgtcacttttccatgcccaggttatcaggaagtccagctcaaagacacctctctctgtgcaggggaggaaagtcatgttccagtccTTTTCCTGGGTTGAGGAAAgaca
	*************************************************************************************************************
rat	.(((...(((((..(((((((.....((((.....(((.....(((.((((.((((....))))))))...)))..)))....))))...)))))))...)))))))).	0.650 -36.30

rat

chromosome:10:85722210:85722318:1

intergenic

block112095 [novel_lenNOK_cloningHIGH_shortStem_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	0.146	no	no	0.37/0.40	18/20/0.01	0.0	0.0	57	0	6	0	3	12	5arm	1	nd	0.44	3	70	6	na	na

		reads	miRBase family seed
seed	----AAGGGAA--------------------------------------------------------------	70	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T4S2	T5S1	T5S2
	---AAAGGGAATGGGGTTTTT----------------------------------------------------	18	38	19	6	2	1	1
	---AAAGGGAATGGGGTTTTTA---------------------------------------------------	19	1	1	-	-	-	-
	---AAAGGGAATGGGGTTTTTAC--------------------------------------------------	20	-	1	-	-	-	-
rat	tgcAAAGGGAATGGGGTTTTTacttctctactgagccttatccaggagggaagtacaattttgccataagcac
	*************************************************************************
rat	(((....((...((((((..(((((((((.(((.........))).))))))))).)))))).))....))).	0.950 -18.20

rat

chromosome:11:15921969:15922041:-1

intergenic

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