Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_randfoldOK_nonpairedHIGH (2321 loci)

block1885882 [novel_lenNOK_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	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	8	13	5arm	3	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	---------AGCCAAG-------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	--------TAGCCAAGGCTAGGATGT---------------------------------------------------------------	18	1
rat	ctaggatgTAGCCAAGGCTAGGATGTagccaaggctgggatgtgtagcccagtgatggaacatatacaggcactggtttggatccttag
	*****************************************************************************************
rat	..(((((.((((((..(((...((((..(((..((((((........))))))..))).)))).....)))..)))).)).)))))...	0.910 -31.10

rat

chromosome:5:150385155:150385243:1

intergenic ## {Repeats: trf 18 36 0 class=trf}

block1928468 [novel_lenNOK_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	0.50/0.58	18/19/0.00	1.0	0.5	2	0	2	0	10	25	5arm	1	nd	0.33	3	2	2	na	na

		reads	miRBase family seed
seed	-----------CAAUACA------------------------------------------------------------------------------------------------	1	novel
seed	-------------AUACAGG----------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T3S1
	------------AATACAGGACCGAGACCA------------------------------------------------------------------------------------	18	-	1
	----------GCAATACAGGACCGAGACC-------------------------------------------------------------------------------------	19	1	-
rat	ctgcaagcagGCAATACAGGACCGAGACCAggccccagagacagagctcagacctacacgggttttctggaattttgtttctgtagctgtggctgtcctggaattctgctcagg
	******************************************************************************************************************
rat	(((..((((((.....((((((..((.((((((..(((((((((((.((((((((....))))))....)).)))))))))))..))).)))))))))))....))))))))).	1.000 -45.20

rat

chromosome:6:42127058:42127171:-1

intergenic

novel_lenNOK_shortStem_bulgeHIGH (2306 loci)

block40 [novel_lenNOK_shortStem_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	0.081	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	2	32	3arm	1	nd	0.22	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------------------GACCUUA------------	1	novel
		len	cloning frequencies
			T1S1
	-------------------------------------------------------------------------------------------------TGACCTTAATCCCTTCTC--	18	1
rat	tgagacataaagacaaataaggtttccaggaagcttggaatttccggaaagagaaaagactgtaggtcctactcgtaccttgacccgtcttccatggTGACCTTAATCCCTTCTCat
	*********************************************************************************************************************
	-------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000004346 ENSRNOG00000003198 RGD1305733
rat	(((((.....((.....(((((((.((((((((..(((.......((...(((....(((.....)))...)))...)).....))).))))).))).)))))))....))))))).	0.860 -28.90

rat

chromosome:10:73355:73471:-1

Opposite_strand|Intronic_coding|ENSRNOT00000004346|ENSRNOG00000003198 ## ENSRNOG00000003198|protein_coding|RGD1305733|Uncharacterized protein C16orf45 homolog. [Source:UniProtKB/Swiss-Prot;Acc:Q5FVJ5]

block994 [novel_lenNOK_shortStem_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	0.597	no	no	0.39/0.39	18/18/0.00	0.0	0.0	1	0	1	0	4	16	3arm	1	nd	0.28	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------CCUGAAA--------------	1	novel
		len	cloning frequencies
			T1S2
	--------------------------------------------------------CCCTGAAAATGGGAATTT----	18	1
rat	ctgtcttatttctcagttctatccacataagaccttaaaatatgcgataacaaaggCCCTGAAAATGGGAATTTcagt
	******************************************************************************
	----------------------------------------------------------------------------------------	ENSRNOT00000003927 ENSRNOG00000002912 RGD1565449_predicted
	----------------------------------------------------------------------------------------	ENSRNOT00000061645 ENSRNOG00000002912 RGD1565449_predicted
	----------------------------------------------------------------------------------------	ENSRNOT00000061644 ENSRNOG00000002912 RGD1565449_predicted
rat	(((((((((((.((((..(((((..((((...........)))).)))......))..))))))))))))....))).	0.600 -9.50

rat

chromosome:10:1835375:1835452:-1

Opposite_strand|Intronic_coding|ENSRNOT00000003927|ENSRNOG00000002912 ## ENSRNOG00000002912|protein_coding|RGD1565449_predicted|

block2867 [novel_lenNOK_shortStem_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	0.077	no	no	0.60/0.61	18/20/0.50	0.0	1.0	2	0	2	0	0	33	3arm	2	nd	0.28	4	2	2	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------------------------GGAGACC------------	2	novel
		len	cloning frequencies
			T4S2	T5S2
	--------------------------------------------------------------------------------------------------TGGAGACCCTCACAGGGA--	18	1	-
	--------------------------------------------------------------------------------------------------TGGAGACCCTCACAGGGACA	20	-	1
rat	gtctaagggcagagcaggttcttggttacacataagcgttatgtgtttgcagaacagaaggggagtctgtgtctgtgacaaagtgataggatgcgtgaTGGAGACCCTCACAGGGACA
	**********************************************************************************************************************
rat	((((.......(((..((.((((.(((((.(((....(((((....((((((((((((.......))))).)))))))....)))))...))).))))).)))))))))....)))).	0.720 -33.70

rat

chromosome:10:6042617:6042734:-1

intergenic

block4691 [novel_lenNOK_shortStem_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	0.108	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	0	37	3arm	1	nd	0.29	4	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------------------------------------AUGACAG----------	1	novel
		len	cloning frequencies
			T5S1
	-----------------------------------------------------------------------------------------------GATGACAGTAACAGAGTC	18	1
rat	ggctcttttgtttctcttgcaggaaaagcccaagggtgtggataacttggccctggaaccttaacgctagcttgcccttggcatgggtcctgctgGATGACAGTAACAGAGTC
	*****************************************************************************************************************
rat	((((((.(((((..(((.((((((.....((((((((((.........((........)).........))..))))))))......)))))).))).)))))....))))))	0.530 -37.07

rat

chromosome:10:10688664:10688776:-1

intergenic

block4765 [novel_lenNOK_shortStem_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	0.504	no	no	0.74/0.74	19/19/0.00	0.0	0.0	2	0	1	0	0	13	5arm	1	nd	0.21	4	2	1	na	na

		reads	miRBase family seed
seed	-GGCCGCG------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T5S2
	AGGCCGCGGGAGCAGACTG-------------------------------------------------------	19	2
rat	AGGCCGCGGGAGCAGACTGcgggctacttagacgtcgttttaatacacctgatcgcttgttccctgctaggacc
	**************************************************************************
rat	.((((((((((((((....((((....(((((......)))))....))))....)).)))))).))..)).))	0.970 -20.70

rat

chromosome:10:10812115:10812188:-1

intergenic

block5272 [novel_lenNOK_shortStem_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	0.828	no	no	0.57/0.58	19/21/0.67	0.0	0.7	3	0	2	0	2	13	5arm	1	nd	0.24	4	3	2	na	na

		reads	miRBase family seed
seed	---AGAGCUA---------------------------------------------------------------------------	3	novel
		len	cloning frequencies
			T2S1	T5S1
	--GAGAGCTAGGCCTGAGAACTC--------------------------------------------------------------	21	-	2
	--GAGAGCTAGGCCTGAGAAC----------------------------------------------------------------	19	1	-
rat	gcGAGAGCTAGGCCTGAGAACTCtaaagagacgagcagcgacgcctcagtggactcttggggaccacagcgccatgtctttccgc
	*************************************************************************************
	..............................................................................>>>>>>>>>>>>>>>>>	ENSRNOT00000009409 ENSRNOG00000007117 LOC363544
rat	(((((((.((((((((....((((.(((((((((((......)).)).))...)))))))))....))).))).)).))))).))	0.560 -22.40

rat

chromosome:10:11885896:11885980:-1

intergenic

block9080 [novel_lenNOK_shortStem_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	0.513	no	no	0.22/0.22	18/18/0.00	0.0	0.0	1	0	1	0	4	16	3arm	1	nd	0.28	4	1	1	na	na

		reads	miRBase family seed
seed	----------------------------------------------------GGUUACA--------------	1	novel
		len	cloning frequencies
			T4S2
	---------------------------------------------------TGGTTACATTTATTCATA----	18	1
rat	tactgaacttaaggtaactgttcaaagcaaaattggtcttgatgtatttatTGGTTACATTTATTCATAgtag
	*************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000006591 ENSRNOG00000004616 Npm1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000059926 ENSRNOG00000004616 Npm1
rat	(((((....(((((((((((.((((.((.......)).)))).........))))))).))))....))))).	0.850 -9.60

rat

chromosome:10:18059218:18059290:-1

Same_strand|Intronic_coding|ENSRNOT00000006591|ENSRNOG00000004616 ## ENSRNOG00000004616|protein_coding|Npm1|Nucleophosmin (NPM) (Nucleolar phosphoprotein B23) (Numatrin) (Nucleolar protein NO38). [Source:UniProtKB/Swiss-Prot;Acc:P13084]

block9666 [novel_lenNOK_shortStem_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	0.224	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	2	18	5arm	1	nd	0.28	4	1	1	na	na

		reads	miRBase family seed
seed	---GCCUUUG--------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	--TGCCTTTGAGGATGCAGA----------------------------------------------------------------------------	18	1
rat	ccTGCCTTTGAGGATGCAGAccagtaataaatctctggacaaggttacaaatatcccacagttactactaatcccgtttctcaggttggggcaggt
	************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000009524 ENSRNOG00000006932 Q3MIE5_RAT
rat	((((((((((((((....((..((((.(((..((.(((.................))).))))).))))..))....)))))))....))))))).	0.590 -22.93

rat

chromosome:10:19650865:19650960:-1

Same_strand|Boundary_non-coding|ENSRNOT00000059810|ENSRNOG00000006932 ## Same_strand|Intronic_non-coding|ENSRNOT00000009524|ENSRNOG00000006932 ## ENSRNOG00000006932|protein_coding|Q3MIE5_RAT|Dock2 protein. [Source:UniProtKB/TrEMBL;Acc:Q3MIE5]

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