Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_shortStem_5varHIGH_nonpairedHIGH (61 loci)

block1043331 [novel_lenNOK_shortStem_5varHIGH_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	0.635	no	no	0.42/0.48	18/21/0.25	1.5	0.5	4	0	3	0	3	8	3arm	1	nd	0.37	3	4	3	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------AGCCAUG----------------	1	novel
seed	------------------------------------------------------GCCAUGA---------------	1	novel
seed	--------------------------------------------------------CAUGAUG-------------	1	novel
seed	-------------------------------------------------------CCAUGAU--------------	1	novel
		len	cloning frequencies
			T1S1	T2S2	T5S2
	------------------------------------------------------GCCATGATGGAAGTTTGA----	18	1	-	-
	-----------------------------------------------------AGCCATGATGGAAGTTTGA----	19	-	1	-
	----------------------------------------------------CAGCCATGATGGAAGTTTGAG---	21	-	-	1
	-------------------------------------------------------CCATGATGGAAGTTTGAG---	18	1	-	-
rat	gcgcttgggcgtcgggacgcggctgcgctcagctctctcctctcggaagctgCAGCCATGATGGAAGTTTGAGagt
	****************************************************************************
rat	((.((..(((.((....((.((((((....((((...(((....))))))))))))).))...)).)))..)).))	0.450 -24.10

rat

chromosome:1:236769828:236769903:1

intergenic ## {SimpF: oe = 0.76 0 CpG}

block6976 [novel_lenNOK_shortStem_5varHIGH_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	0.448	no	no	0.44/0.55	18/22/0.29	1.7 0.0	2.3 0.0	6 1	0 0	3 1	0 0	3 0	20 28	3arm 3arm	1 1	nd nd	0.36 0.47	3 3	7	3	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------CGGGCUA------------------	3	novel
seed	-------------------------------------------------------------------------------CUAAUUG--------------	2	novel
seed	-----------------------------------------------------------------------------GGCUAAU----------------	1	novel
seed	-----------------------------------------------------------------------------------UUGGAAG----------	1	novel
		len	cloning frequencies
			T2S1	T3S1	T4S2
	--------------------------------------------------------------------------GCGGGCTAATTGGAAGTGA-------	19	-	2	-
	------------------------------------------------------------------------------GCTAATTGGAAGTGAGACC---	19	-	1	1
	--------------------------------------------------------------------------GCGGGCTAATTGGAAGTGAGAC----	22	1	-	-
	----------------------------------------------------------------------------------ATTGGAAGTGAGACCGAT	18	-	-	1
	----------------------------------------------------------------------------GGGCTAATTGGAAGTGAGAC----	20	-	1	-
rat	tcgggccccgccctgatggcctggcgacttatggctttgtgtagttctcagtccctccacagagacctgagccaGCGGGCTAATTGGAAGTGAGACCGAT
	****************************************************************************************************
rat	((((....(((((...((((((.((..((((.(((((((((.((..........)).))))))).))))))...))))))))...))..)))...)))).	0.700 -32.20

rat

chromosome:10:14429767:14429866:-1

intergenic

block208958 [novel_lenNOK_shortStem_5varHIGH_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	0.768	no	no	0.46/0.50	18/24/0.50	2.5	0.5	2	0	1	0	2	6	5arm	1	nd	0.33	3	2	1	na	na

		reads	miRBase family seed
seed	--------AUGCGGC-----------------------------------------------------	1	novel
seed	---GAAGUAU----------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-------TATGCGGCATGGTATGAC-------------------------------------------	18	1
	--TGAAGTATGCGGCATGGTATGACT------------------------------------------	24	1
rat	caTGAAGTATGCGGCATGGTATGACTttctggccttccttgtccccaatctgccaaggtactctttgg
	********************************************************************
rat	((...(((((..(((((((...(((.....((....))..))).)))...))))...)))))...)).	0.780 -12.50

rat

chromosome:12:5611127:5611194:1

intergenic

block1093572 [novel_lenNOK_shortStem_5varHIGH_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	0.157	no	no	0.42/0.53	18/24/0.56	2.0	2.3	9	0	3	0	4	11	3arm	1	nd	0.32	3	9	3	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------CAGCAUA---------------------	3	novel
seed	----------------------------------------------------------UCAGCAU----------------------	3	novel
seed	-----------------------------------------------------------------ACAUGGC---------------	2	novel
seed	---------------------------------------------------------UUCAGCA-----------------------	1	novel
		len	cloning frequencies
			T1S1	T4S1	T5S1
	----------------------------------------------------------TCAGCATACATGGCTACAGACCTG-----	24	1	-	1
	----------------------------------------------------------------TACATGGCTACAGACCTGC----	19	-	-	2
	---------------------------------------------------------TTCAGCATACATGGCTACAGACC-------	23	-	-	2
	----------------------------------------------------------TCAGCATACATGGCTACAGAC--------	21	-	-	1
	--------------------------------------------------------TTTCAGCATACATGGCTAC------------	19	-	-	1
	---------------------------------------------------------TTCAGCATACATGGCTAC------------	18	-	1	-
rat	cacccgctcctggcagcgctgttttctgagacagctcctgactttgttggaggccaTTTCAGCATACATGGCTACAGACCTGCggtg
	***************************************************************************************
rat	...((((..(((..(((..(((...((((((..((..(((((...)))))..))..))))))...)))..))).)))....))))..	0.880 -27.60

rat

chromosome:20:5540781:5540867:1

intergenic

block1470217 [novel_lenNOK_shortStem_5varHIGH_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	0.463	no	no	0.45/0.59	19/25/0.50	2.1	1.1	8	0	3	0	1	27	3arm	1	nd	0.36	3	8	3	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------------CAGAUUG---------------------	5	novel
seed	-------------------------------------------------------------------------------------------GUCAUUC---------------	2	novel
seed	------------------------------------------------------------------------------------------UGUCAUU----------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T5S1
	------------------------------------------------------------------------------------TCAGATTGTCATTCGGAGACTCCCC----	25	-	-	3
	-----------------------------------------------------------------------------------------TTGTCATTCGGAGACTCCCC----	20	-	-	1
	------------------------------------------------------------------------------------------TGTCATTCGGAGACTCCCCGGT-	22	-	1	-
	------------------------------------------------------------------------------------TCAGATTGTCATTCGGAGAC---------	20	1	-	-
	------------------------------------------------------------------------------------------TGTCATTCGGAGACTCCCC----	19	-	1	-
	------------------------------------------------------------------------------------TCAGATTGTCATTCGGAGACTCCC-----	24	-	-	1
rat	actggtgtacttcctgtgtgttgaatgaatgaatgatccgtctggagaaaacagtctgttgtcttcctggccatgggatctttcTCAGATTGTCATTCGGAGACTCCCCGGTg
	*****************************************************************************************************************
rat	(((((.((.((((..(((.......(((..(((.((((((((.(((((.(((.....))).))).)).)))....))))).))))))......)))..))))))...))))).	0.510 -29.42

rat

chromosome:3:76971704:76971816:1

intergenic

block1606369 [novel_lenNOK_shortStem_5varHIGH_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	0.499	no	no	0.61/0.67	18/25/0.33	1.3	2.3	3	0	3	0	1	24	3arm	1	nd	0.33	3	3	3	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------AGGCCUU----------------	2	novel
seed	---------------------------------------------------------------------------------------CUAGGCC------------------	1	novel
		len	cloning frequencies
			T1S2	T3S1	T5S2
	----------------------------------------------------------------------------------------TAGGCCTTCTCCTTGGCC------	18	1	-	-
	--------------------------------------------------------------------------------------TCTAGGCCTTCTCCTTGGCCCCCTC-	25	-	1	-
	----------------------------------------------------------------------------------------TAGGCCTTCTCCTTGGCCCCC---	21	-	-	1
rat	ggtcacggctatggacgtggtgtatgcgctcaagcgccagggccgcacgctctatggcttcggcggctgagcggcgtcctcgtgtgTCTAGGCCTTCTCCTTGGCCCCCTCc
	****************************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>...............................................	ENSRNOT00000042564 ENSRNOG00000028928 RGD1562378_predicted
rat	((....(((((.(((...(((.((.((((....(((..((((.(((.(((((....((....))....))))))))))))))))))).)).)))...))).)))))....))	0.640 -46.00

rat

chromosome:4:173815333:173815444:-1

intergenic

block1696565 [novel_lenNOK_shortStem_5varHIGH_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	0.203	no	no	0.26/0.32	19/22/0.33	4.7	2.7	3	0	1	0	2	4	5arm	1	nd	0.42	3	3	1	na	na

		reads	miRBase family seed
seed	---------UUGCAAU----------------------------------------------------------	1	novel
seed	---AGUCUGU----------------------------------------------------------------	1	novel
seed	-----------GCAAUUA--------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----------TGCAATTAGATACATTACT---------------------------------------------	19	1
	--------GTTGCAATTAGATACATTA-----------------------------------------------	19	1
	--TAGTCTGTTGCAATTAGATACA--------------------------------------------------	22	1
rat	ttTAGTCTGTTGCAATTAGATACATTACTctgtgaaaggacaacagtgtcttgtatatattcttcaggtagaag
	**************************************************************************
rat	(((..((((....(((...(((((..((.((((.........)))).))..)))))..)))...))))..))).	0.950 -13.50

rat

chromosome:4:164281156:164281229:1

intergenic

novel_lenNOK_cloningHIGH_loopOverlap_nonpairedHIGH (60 loci)

block2838 [novel_lenNOK_cloningHIGH_loopOverlap_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	0.124	no	no	0.55/0.61	18/20/0.03	0.0	0.0	130	0	10	0	35	-2	5arm_loop	1	nd	0.33	3	157	10	na	na

		reads	miRBase family seed
seed	------------------------------------CCAUGUG---------------------------------------------------------	156	novel
seed	-----------------------------------CCCAUGU----------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-----------------------------------CCCATGTGGGCTCAGCAA-----------------------------------------------	18	2	2	4	3	23	7	21	38	21	27
	-----------------------------------CCCATGTGGGCTCAGCAAAT---------------------------------------------	20	-	-	-	-	1	-	-	1	1	1
	-----------------------------------CCCATGTGGGCTCAGCAAA----------------------------------------------	19	-	-	1	-	-	-	1	-	2	-
	----------------------------------TCCCATGTGGGCTCAGCAA-----------------------------------------------	19	-	-	-	-	-	-	1	-	-	-
rat	tcaaaggcaaaagaaacatctatagatttgaagttCCCATGTGGGCTCAGCAAatagtggcaggagtcatatgcaaagaatatggaatctgggctgggac
	****************************************************************************************************
	--------------------------------------------------------------------------------------------------------------	ENSRNOT00000044626 ENSRNOG00000033942 Grin2a
rat	((...(((...(((....((((((..((((.......(((((.(((((.((........))..))))))))))))))...)))))).)))..)))..)).	0.560 -21.81

rat

chromosome:10:5955322:5955421:-1

Opposite_strand|Intronic_coding|ENSRNOT00000044626|ENSRNOG00000033942 ## ENSRNOG00000033942|protein_coding|Grin2a|Glutamate [NMDA] receptor subunit epsilon-1 precursor (N-methyl D- aspartate receptor subtype 2A) (NR2A) (NMDAR2A). [Source:UniProtKB/Swiss-Prot;Acc:Q00959]

block13011 [novel_lenNOK_cloningHIGH_loopOverlap_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	0.385	no	no	0.44/0.50	18/20/0.01	0.0	0.0	114	0	9	0	12	-3	3arm_loop	1	nd	0.39	2	148	9	na	na

		reads	miRBase family seed
seed	-----------------------------------UGCAUGA----------------------	147	novel
seed	---------------------------------GAUGCAU------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1
	----------------------------------ATGCATGATGACCACATG------------	18	69	45	6	2	3	3	5	6	-
	----------------------------------ATGCATGATGACCACATGC-----------	19	3	3	-	-	-	-	-	1	-
	----------------------------------ATGCATGATGACCACATGCC----------	20	1	-	-	-	-	-	-	-	-
	--------------------------------AGATGCATGATGACCACA--------------	18	-	-	-	-	-	-	-	-	1
rat	tgtctgccacaggtacagaactgggaatgatgagATGCATGATGACCACATGccactgatagat
	****************************************************************
rat	.(((((.((..((((......(((..((.(((.....))).))..)))..))))..)).)))))	0.720 -13.10

rat

chromosome:10:29259456:29259519:-1

intergenic

block55522 [novel_lenNOK_cloningHIGH_loopOverlap_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	0.514	no	no	0.61/0.63	18/19/0.00	0.0	0.0	78	0	10	0	16	-1	3arm_loop	1	nd	0.33	3	117	10	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------CUUGACC--------------------------	117	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	----------------------------------------------------GCTTGACCCTCCCAGGAA----------------	18	13	15	4	5	2	6	12	28	4	10
	----------------------------------------------------GCTTGACCCTCCCAGGAAC---------------	19	3	-	-	2	-	2	1	7	1	2
rat	atccgttccttctgtgtacaaatatctgggctggcaagatgactgaacctgaGCTTGACCCTCCCAGGAActccatggttggagga
	**************************************************************************************
rat	.(((..(((..(((((........((((((..((((((...............)))).))..)))))).....)))))..))))))	0.430 -21.08

rat

chromosome:10:4345281:4345366:1

intergenic

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