Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_nonpairedHIGH_bulgeHIGH (37545 loci)

block1929301 [novel_lenNOK_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	0.168	no	no	0.56/0.56	18/18/0.00	0.0	0.0	1	0	1	0	12	15	5arm	1	nd	0.39	4	1	1	na	na

		reads	miRBase family seed
seed	-------------UCAGUAA--------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	------------CTCAGTAACGGTCCTCAG----------------------------------------------------------------------	18	1
rat	ttaagtgcagaaCTCAGTAACGGTCCTCAGatgacagctttcagagatctctaccaaggaagaaaacaagcagcggccgcagctagtcacatgcacttgc
	****************************************************************************************************
rat	.((((((((..(((.(((..(((((((....((....((((((((....))).....)))))....))...)).)))))..))))))....)))))))).	0.840 -24.70

rat

chromosome:6:43548420:43548519:-1

intergenic

block1929477 [novel_lenNOK_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	0.442	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	10	13	5arm	1	nd	0.50	4	1	1	na	na

		reads	miRBase family seed
seed	-----------ACACCAG--------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----------AACACCAGCAAGATCACG----------------------------------------------------	18	1
rat	tccctatagaAACACCAGCAAGATCACGttgaaatatatacacttgtgtgttttccctgtgggagcccgtttagtagagg
	********************************************************************************
rat	.((((((..((((....((....(((((..((((.((((((....))))))))))..)))))..))..)))).)))).))	0.500 -16.30

rat

chromosome:6:43955203:43955282:-1

intergenic

block1930593 [novel_lenNOK_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	0.099	no	no	0.68/0.68	19/19/0.00	0.0	0.0	1	0	1	0	34	2	5arm	1	nd	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------CCCCUGA---------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	----------------------------------GCCCCTGAGACTGAGGTGC----------------------------------------------------------------	19	1
rat	tcttcagtttctcaaatgtcagtggagatggtagGCCCCTGAGACTGAGGTGCttcccagctgccaagtgcctagtccaatcccagcacatcaaaacggatttggaaacgggaggaa
	*********************************************************************************************************************
rat	(((((.(((((.(((..(((.((...((((((.((....((.((((.(((..(((..........)))..)))))))))...)).)).))))...)).)))))))))))..))))).	0.980 -35.60

rat

chromosome:6:46528382:46528498:-1

intergenic

block1941501 [novel_lenNOK_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	0.335	no	no	0.17/0.17	18/18/0.00	0.0	0.0	1	0	1	0	8	19	3arm	1	nd	0.39	5	1	1	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------------------------AAAAAUU------------------	1	novel
		len	cloning frequencies
			T4S2
	---------------------------------------------------------------------------TAAAAATTACCTAAAACT--------	18	1
rat	cagcccagtacttagtcagtgttttgcctgttatttgttgttatttagtacccaggggtgtgactaaatggaaagTAAAAATTACCTAAAACTaggggttg
	*****************************************************************************************************
rat	((((((.....((((..(((.((((((...(((((((..(((((.....(((....)))))))))))))))...)))))))))..))))......))))))	0.620 -22.00

rat

chromosome:6:69320380:69320480:-1

intergenic

block1943366 [novel_lenNOK_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	0.130	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	8	15	5arm	1	nd	0.39	4	1	1	na	na

		reads	miRBase family seed
seed	---------GGAAUGG-----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	--------TGGAATGGCCCTATCACT-------------------------------------------------------------	18	1
rat	ggagcaggTGGAATGGCCCTATCACTgggaatacaccctccttctggaatattctgtccttggtggttccttgcttgacaccttctt
	***************************************************************************************
rat	.(((.(((((....(((...((((((((((........(((....)))........)))).)))))).....)))...))))).)))	0.850 -24.29

rat

chromosome:6:72592984:72593070:-1

intergenic ## {Repeats: trf 1 13 0 class=trf}

novel_lenNOK_nonpairedHIGH (36989 loci)

block492 [novel_lenNOK_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	0.414	no	no	0.33/0.33	18/18/0.00	0.0	0.0	1	0	1	0	8	29	3arm	1	nd	0.44	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------------GAGAACU------------------	1	miR-146a/146b
		len	cloning frequencies
			T1S1
	----------------------------------------------------------------------------------------------AGAGAACTAGATATAGAC--------	18	1
rat	ctaggcaagcactgtgccactgagctaaatccccaaccctgttaaacagttttaaagtgagtgggcattggtagatatgtggtcatggaaggggAGAGAACTAGATATAGACaggcctgt
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000000029 ENSRNOG00000000028 Nde1
rat	.(((((.....(((((...(((..((...(((((..((.((....(((..((((.((((......))))..))))..)))...)).))..))))).))...))).)))))....))))).	0.540 -29.60

rat

chromosome:10:786687:786806:-1

Same_strand|Intronic_coding|ENSRNOT00000000029|ENSRNOG00000000028 ## ENSRNOG00000000028|protein_coding|Nde1|Nuclear distribution protein nudE homolog 1 (NudE) (rNudE). [Source:UniProtKB/Swiss-Prot;Acc:Q9ES39]

block501 [novel_lenNOK_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	0.565	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	6	4	3arm	2	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------GGAUGCA----------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------------------------TGGATGCACACTGTTTAC------	18	1
rat	ggttagaatatgatgctgctccagtttgcttttcttcacaTGGATGCACACTGTTTACtcaact
	****************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000000029 ENSRNOG00000000028 Nde1
rat	((((((...((..((.(((((((...((........))..)))).)))))..))...)).))))	0.840 -9.20

rat

chromosome:10:807402:807465:-1

Same_strand|Intronic_coding|ENSRNOT00000000029|ENSRNOG00000000028 ## ENSRNOG00000000028|protein_coding|Nde1|Nuclear distribution protein nudE homolog 1 (NudE) (rNudE). [Source:UniProtKB/Swiss-Prot;Acc:Q9ES39]

block623 [novel_lenNOK_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	0.214	no	no	0.58/0.58	19/19/0.00	0.0	0.0	1	0	1	0	22	0	3arm	1	nd	0.37	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------CAGCCAA---------------------------------	1	novel
		len	cloning frequencies
			T1S1
	------------------------------------------GCAGCCAAGTGCACTGAAC----------------------	19	1
rat	taatgtatggaattcacttgctgagtgtgaggggatgctacaGCAGCCAAGTGCACTGAACaatctgttattttatgatttta
	***********************************************************************************
rat	.....((((((((.((.(((...((((((...((.(((....))).))...))))))...)))..))..))))))))......	0.790 -16.30

rat

chromosome:10:1098432:1098514:-1

intergenic

block650 [novel_lenNOK_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	0.310	no	no	0.56/0.56	18/18/0.00	0.0	0.0	1	0	1	0	9	20	5arm	3	nd	0.39	3	1	1	na	na

		reads	miRBase family seed
seed	----------GGGACUC------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S1
	---------TGGGACTCTGGGAAAGAG--------------------------------------------------------------------------------	18	1
rat	gctccaccaTGGGACTCTGGGAAAGAGtggctcacaagtcaaggcacaacttctgcagtaccatcctagtgagtcacacatcgccttcgaggagcatcttaggagtc
	***********************************************************************************************************
rat	(((((...(((...(((.(((...(((((((((((.((....((.((..........)).))...)).)))))))))...)).)))..)))...)))....))))).	0.470 -29.20

rat

chromosome:10:1140828:1140934:-1

intergenic

block683 [novel_lenNOK_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	0.566	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	5	3	5arm	1	nd	0.37	3	1	1	na	na

		reads	miRBase family seed
seed	------GGGAACA----------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	-----TGGGAACATGAGTGTCTGG-----------------------------------------------------	19	1
rat	gccacTGGGAACATGAGTGTCTGGaccacaagggggcaggctgagggagtgacagagagcatgggtcttgaatggcc
	*****************************************************************************
	---------------------------------------------------------------------------------------	ENSRNOT00000061723 ENSRNOG00000029076 LOC688631
rat	((((..(((..((((...(((((..((.....))..)))))..................))))..)))....)))).	0.510 -19.60

rat

chromosome:10:1208500:1208576:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000047701|ENSRNOG00000029076 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000061723|ENSRNOG00000029076 ## ENSRNOG00000029076|protein_coding|LOC688631|

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