Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_nonpairedHIGH_bulgeHIGH (5657 loci)

block1893020 [novel_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	0.069	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	8	22	3arm	1	nd	0.50	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------CCGCAGU--------------------	1	novel
		len	cloning frequencies
			T1S2
	------------------------------------------------------------------------GCCGCAGTAGTACGACGAAA--------	20	1
rat	acgcgcacgagtgcgtcacttccgctccctcccgggaggcggcgctgggccggtggcaagcccccggagggaGCCGCAGTAGTACGACGAAAgatggcga
	****************************************************************************************************
	..................................................................................................>>>>>>>>>>>>	ENSRNOT00000039663 ENSRNOG00000018183 Rbaf600
rat	.(((.((((.((((...(((...(((((((.(((((.(((..(((((...)))))....)))))))))))))))...))).))))..)).....))))).	0.670 -44.20

rat

chromosome:5:158181926:158182025:1

intergenic

block914227 [novel_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	0.118	no	no	0.50/0.50	22/22/1.00	0.0	0.0	1	0	1	0	22	14	3arm	1	nd	0.41	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------UCUCAGG------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------------------------------------------------------TTCTCAGGAATCCCTGTGTGTC----------------------	22	1
rat	gctgcctaagttgatgtctgcacagtgaattccagaggcttaggaagctctgcgctgccgcgtgtccaggcctTTCTCAGGAATCCCTGTGTGTCgaaggccatcgtttaagtcagc
	*********************************************************************************************************************
rat	((((.((.((.((((((((((((((.((.((((((((((((.(((......((((....)))).)))))))))))....)))))).)))))).....)))).)))).)).)).))))	0.990 -40.00

rat

chromosome:1:208478593:208478709:-1

intergenic

block1913299 [novel_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	0.29/0.29	21/21/1.00	0.0	0.0	1	0	1	0	15	8	3arm	1	nd	0.43	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------AAACCUU----------------------------	1	novel
		len	cloning frequencies
			T3S1
	--------------------------------------------------------TAAACCTTTCTCTTTCCAAAA---------------	21	1
rat	tagtatctgtatgaaaggtgtgaattagaaggtgaaacatatacctaagtatcataTAAACCTTTCTCTTTCCAAAAtattcatatttctat
	********************************************************************************************
rat	(((.....(((((((...((.(((..(((((((.......((((....)))).......))))).))..))))).....)))))))..))).	1.000 -15.64

rat

chromosome:6:14049909:14050000:-1

intergenic

novel_nonpairedHIGH (4445 loci)

block774 [novel_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	0.116	no	no	0.48/0.48	21/21/1.00	0.0	0.0	1	0	1	0	17	5	3arm	3	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------AGGAGAC------------------------------	1	novel
		len	cloning frequencies
			T4S2
	-----------------------------------------------------CAGGAGACCTACAGAAGGATA-----------------	21	1
rat	tgaattcctagtggggatacctttgaggggatacctttgagacacacacttatCAGGAGACCTACAGAAGGATAtcacgggttgaattcac
	*******************************************************************************************
rat	(((((((((.((((..((.(((((...(((...(((.((((.......))))..)))...)))...))))))).)))).))..))))))).	0.980 -23.20

rat

chromosome:10:1447912:1448002:-1

intergenic

block822 [novel_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	0.596	no	no	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	15	5	3arm	1	nd	0.33	2	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------GGCUGGG----------------------------	1	novel
		len	cloning frequencies
			T5S2
	-------------------------------------------------------GGGCTGGGGGTATATCTTACA---------------	21	1
rat	agttcatgtgatttactgttataaaatattcctttcatttcttctgaagacataaGGGCTGGGGGTATATCTTACAaataggcacttgtct
	*******************************************************************************************
	-----------------------------------------------------------------------------------------------------	ENSRNOT00000047367 ENSRNOG00000003326 RGD1305001_predicted
	-----------------------------------------------------------------------------------------------------	ENSRNOT00000004429 ENSRNOG00000003326 RGD1305001_predicted
rat	....((.(((.....(((((.(((.((((..((..((.(((((.((....)).))))).))..)).)))).)))..))))).))).))...	0.920 -14.40

rat

chromosome:10:1535106:1535196:-1

Opposite_strand|Intronic_non-coding|ENSRNOT00000047367|ENSRNOG00000003326 ## Opposite_strand|Intronic_coding|ENSRNOT00000004429|ENSRNOG00000003326 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000004459|ENSRNOG00000003326 ## ENSRNOG00000003326|protein_coding|RGD1305001_predicted|

block1270 [novel_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	0.123	no	no	0.41/0.41	22/22/1.00	0.0	0.0	1	0	1	0	8	14	3arm	1	nd	0.32	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------GUUCUUG----------------------	1	novel
		len	cloning frequencies
			T4S2
	------------------------------------------------------------------GGTTCTTGTACTTCGAAATCAG--------	22	1
rat	tattgtgcagattacaaggttgttggaattttctgttaggcctatacaatctggccccacaatgatGGTTCTTGTACTTCGAAATCAGcttccaat
	************************************************************************************************
rat	.((((.((.((((...((((....(((((..(((((..((((..........))))..)))..))..)))))...))))...)))).))...))))	0.920 -20.40

rat

chromosome:10:2547374:2547469:-1

intergenic

block1750 [novel_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	0.174	no	no	0.50/0.50	20/20/1.00	0.0	0.0	1	0	1	0	9	26	3arm	1	nd	0.35	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------------UCCUCUG---------------------	1	novel
		len	cloning frequencies
			T4S1
	-------------------------------------------------------------------------------------------ATCCTCTGTGTCTGACCTGA---------	20	1
rat	ctagcaggctggggcaggggcattataaggttgaagctagcctgggccacttctctgctcaaactgagctcagtctcccacatcctagagcATCCTCTGTGTCTGACCTGAtcctgatgg
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000003150 ENSRNOG00000002294 LOC687335
rat	(((.((((...(((((((.(((.....(((.((...((((..((((..(((.....((((.....))))..)))..))))....))))..)).))).))).)))).)))...)))).)))	0.930 -36.80

rat

chromosome:10:3935894:3936013:-1

Same_strand|Intronic_coding|ENSRNOT00000003150|ENSRNOG00000002294 ## ENSRNOG00000002294|protein_coding|LOC687335|similar to kinesin-like motor protein C20orf23 (LOC689142), mRNA [Source:RefSeq_dna;Acc:NM_001109526]

block2232 [novel_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	0.518	no	no	0.54/0.54	24/24/1.00	0.0	0.0	1	0	1	0	7	4	5arm	1	nd	0.33	2	1	1	na	na

		reads	miRBase family seed
seed	--------GUUCGGU------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	-------GGTTCGGTTTCCCCTTAGACATGC--------------------------------------------	24	1
rat	ggcgttcGGTTCGGTTTCCCCTTAGACATGCgcaggattttactggccagcatctggaggaactgctgtcagccc
	***************************************************************************
rat	(((...((((..((((((.((..(((..(((.(((.......)))....)))))))).))))))))))...))).	1.000 -21.90

rat

chromosome:10:4702923:4702997:-1

intergenic

block2849 [novel_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	0.864	no	no	0.67/0.70	21/23/1.00	0.0	0.7	3	0	1	0	5	8	3arm	1	nd	0.43	3	3	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------CAGCCAC--------------------	3	novel
		len	cloning frequencies
			T2S2
	----------------------------------------------------GCAGCCACAGGCAGTGAGGAC-------	21	2
	----------------------------------------------------GCAGCCACAGGCAGTGAGGACCC-----	23	1
rat	gcccgtaagccacagtgtctccagctcctccatctcacctgcacagaacacaGCAGCCACAGGCAGTGAGGACCCaagcg
	********************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<-----------------------------------------------	ENSRNOT00000044626 ENSRNOG00000033942 Grin2a
rat	((.......((.((.(((((...(((.((...(((.........)))....)).)))...))))).)).))......)).	0.790 -14.42

rat

chromosome:10:5996454:5996533:-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]

block3349 [novel_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	0.273	no	no	0.48/0.48	23/23/1.00	0.0	0.0	1	0	1	0	17	0	5arm	1	nd	0.35	3	1	1	na	na

		reads	miRBase family seed
seed	------------------ACAGAAA------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	-----------------TACAGAAACCCAAAGCAGTCCCT---------------------------------------------------------------------	23	1
rat	agctggaagctccagatTACAGAAACCCAAAGCAGTCCCTtccaataacatcatcccgcagggcaggccaaggggacttctgttctccaccaaaccgagctgaactgct
	*************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------	ENSRNOT00000003514 ENSRNOG00000002610 Carhsp1
rat	(((....(((((..((..((((((.(((...((...((((...................))))...))...)))...))))))..)).........))))).....)))	0.780 -24.51

rat

chromosome:10:6988397:6988505:-1

Opposite_strand|Intronic_non-coding|ENSRNOT00000003514|ENSRNOG00000002610 ## ENSRNOG00000002610|protein_coding|Carhsp1|Calcium-regulated heat stable protein 1 (Calcium-regulated heat-stable protein of 24 kDa) (CRHSP-24). [Source:UniProtKB/Swiss-Prot;Acc:Q9WU49]

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