Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_Multihit_shortStem_5varHIGH (26 loci)

block846652 [novel_lenNOK_Multihit_shortStem_5varHIGH]

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	0.031	no	no	0.32/0.36	19/22/0.50	2.0	0.5	2	0	1	0	0	3	3arm	22	nd	0.27	3	2	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------CUUUCCA-----------	1	novel
seed	-----------------------------------------GCUUCUU---------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------------------------TGCTTCTTTCCATGCATTTTGA-	22	1
	--------------------------------------------TCTTTCCATGCATTTTGAT	19	1
rat	cattatatttgccatggtctggtctgggtggcatccttgcTGCTTCTTTCCATGCATTTTGAT
	***************************************************************
rat	.((((....((.(((((...((...(((..(((....)))..)))))..)))))))...))))	1.000 -15.60

rat

chromosome:1:51402082:51402144:-1

intergenic

block847601 [novel_lenNOK_Multihit_shortStem_5varHIGH]

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	0.095	no	no	0.32/0.36	19/22/0.50	2.0	0.5	2	0	1	0	1	3	3arm	22	nd	0.27	3	2	1	na	na

		reads	miRBase family seed
seed	----------------------------------------GCUUCUU----------------	1	novel
seed	--------------------------------------------CUUUCCA------------	1	novel
		len	cloning frequencies
			T5S1
	---------------------------------------TGCTTCTTTCCATGCATTTTGA--	22	1
	-------------------------------------------TCTTTCCATGCATTTTGAT-	19	1
rat	attatatttgctatggtctggtctggggggcatccttgcTGCTTCTTTCCATGCATTTTGATa
	***************************************************************
	-------------------------------------------------------------------------	ENSRNOT00000041486 ENSRNOG00000033456 LOC308198
rat	((((....(((.((((...((...(((.((((....)))).)))))..)))))))...)))).	1.000 -14.70

rat

chromosome:1:52392663:52392725:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000044415|ENSRNOG00000033456 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000041486|ENSRNOG00000033456 ## ENSRNOG00000033456|protein_coding|LOC308198|

block588892 [novel_lenNOK_Multihit_shortStem_5varHIGH]

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	0.149	no	no	0.56/0.68	19/25/0.50	2.2	1.3	6	0	3	0	0	4	3arm	54	nd	0.20	3	6	3	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------UGACAUG------------------	3	novel
seed	--------------------------------------------------------------CCGCCUG-----------	1	novel
seed	---------------------------------------------------GAUCUGA----------------------	1	novel
seed	-----------------------------------------------------UCUGACA--------------------	1	novel
		len	cloning frequencies
			T2S2	T4S1	T5S1
	------------------------------------------------------CTGACATGCCGCCTGGAGAAACC---	23	2	-	-
	-------------------------------------------------------------GCCGCCTGGAGAAACCTGC	19	-	-	1
	------------------------------------------------------CTGACATGCCGCCTGGAGAAACCTG-	25	1	-	-
	--------------------------------------------------GGATCTGACATGCCGCCTGGAGAA------	24	1	-	-
	----------------------------------------------------ATCTGACATGCCGCCTGGAGAAACC---	25	-	1	-
rat	cgcagactctccctgtgtgcatgaacttggggtcagaaaatgtgagttgtGGATCTGACATGCCGCCTGGAGAAACCTGC
	********************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000024334 ENSRNOG00000017671 Rasa3
rat	.((((..(((((..(((.(((((...((((..(((.((........)).)))..))))))))))))..)))))...))))	0.990 -24.90

rat

chromosome:16:80796322:80796401:1

Same_strand|Intronic_coding|ENSRNOT00000024334|ENSRNOG00000017671 ## ENSRNOG00000017671|protein_coding|Rasa3|Ras GTPase-activating protein 3 (GAP1(IP4BP)) (Ins P4-binding protein) (R-ras GAP). [Source:UniProtKB/Swiss-Prot;Acc:Q9QYJ2]

novel_lenNOK_Multihit_shortStem_randfoldOK_bulgeHIGH (26 loci)

block844686 [novel_lenNOK_Multihit_shortStem_randfoldOK_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	0.003	no	no	0.63/0.63	19/19/0.00	0.0	0.0	1	0	1	0	1	14	3arm	33	nd	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------UGCCUGC------------	1	novel
		len	cloning frequencies
			T2S2
	------------------------------------------------ATGCCTGCTGTGTGGGAGC-	19	1
rat	ggctcatccacagacatctcacactctccctgctgggagttaggttggATGCCTGCTGTGTGGGAGCt
	********************************************************************
rat	(((((.(((((((.(((((.((...(((((....)))))....)).)))))....))))).)))))))	1.000 -29.90

rat

chromosome:1:50309382:50309449:-1

intergenic

block847443 [novel_lenNOK_Multihit_shortStem_randfoldOK_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	0.008	no	no	0.63/0.63	19/19/0.00	0.0	0.0	1	0	1	0	1	14	3arm	33	nd	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------UGCCUGC------------	1	novel
		len	cloning frequencies
			T2S2
	------------------------------------------------ATGCCTGCTGTGTGGGAGC-	19	1
rat	ggctcatccacagacatctcacactctccctgctgggagttaggctggATGCCTGCTGTGTGGGAGCt
	********************************************************************
	------------------------------------------------------------------------------	ENSRNOT00000059925 ENSRNOG00000030145 LOC689315
rat	(((((.(((((((.((((.((..(((((((....)))))..))..))))))....))))).)))))))	0.410 -27.80

rat

chromosome:1:52325329:52325396:-1

Opposite_strand|Intronic_non-coding|ENSRNOT00000059925|ENSRNOG00000030145 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000041194|ENSRNOG00000030145 ## ENSRNOG00000030145|protein_coding|LOC689315|

block847466 [novel_lenNOK_Multihit_shortStem_randfoldOK_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	0.008	no	no	0.63/0.63	19/19/0.00	0.0	0.0	1	0	1	0	1	14	3arm	33	nd	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------UGCCUGC------------	1	novel
		len	cloning frequencies
			T2S2
	------------------------------------------------ATGCCTGCTGTGTGGGAGC-	19	1
rat	ggctcatccacagacatctcacactctccctgctgggagttaggctggATGCCTGCTGTGTGGGAGCt
	********************************************************************
rat	(((((.(((((((.((((.((..(((((((....)))))..))..))))))....))))).)))))))	0.410 -27.80

rat

chromosome:1:52344715:52344782:-1

intergenic

block847876 [novel_lenNOK_Multihit_shortStem_randfoldOK_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	0.008	no	no	0.63/0.63	19/19/0.00	0.0	0.0	1	0	1	0	1	14	3arm	33	nd	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------UGCCUGC------------	1	novel
		len	cloning frequencies
			T2S2
	------------------------------------------------ATGCCTGCTGTGTGGGAGC-	19	1
rat	ggctcatccacagacatctcacactctccctgctgggagttaggctggATGCCTGCTGTGTGGGAGCt
	********************************************************************
	------------------------------------------------------------------------------	ENSRNOT00000059913 ENSRNOG00000033456 LOC308198
rat	(((((.(((((((.((((.((..(((((((....)))))..))..))))))....))))).)))))))	0.410 -27.80

rat

chromosome:1:52547313:52547380:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000044415|ENSRNOG00000033456 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000059913|ENSRNOG00000033456 ## ENSRNOG00000033456|protein_coding|LOC308198|

block962588 [novel_lenNOK_Multihit_shortStem_randfoldOK_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	0.001	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	4	6	5arm	42	nd	0.28	4	1	1	na	na

		reads	miRBase family seed
seed	-----UUCACUG--------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	----CTTCACTGTCACAGAACC----------------------------------------------------	18	1
rat	ggatCTTCACTGTCACAGAACCggcactatttcagtgcctccactgtggcaggacctacctcttcacaggatct
	**************************************************************************
rat	((((((((.(((((((((....((((((.....))))))....)))))))))))..............))))))	0.520 -27.43

rat

chromosome:1:51486748:51486821:1

intergenic

block963185 [novel_lenNOK_Multihit_shortStem_randfoldOK_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	0.008	no	no	0.63/0.63	19/19/0.00	0.0	0.0	1	0	1	0	1	14	3arm	33	nd	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------UGCCUGC------------	1	novel
		len	cloning frequencies
			T2S2
	------------------------------------------------ATGCCTGCTGTGTGGGAGC-	19	1
rat	ggctcatccacagacatctcacactctccctgctgggagtnnggctggATGCCTGCTGTGTGGGAGCt
	********************************************************************
	------------------------------------------------------------------------------	ENSRNOT00000059938 ENSRNOG00000039174 RGD1563865_predicted
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000040973 ENSRNOG00000033340 RGD1561446_predicted
rat	(((((.(((((((.(((((......(((((....))))).......)))))....))))).)))))))	0.700 -27.02

rat

chromosome:1:51638790:51638857:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000059936|ENSRNOG00000039174 ## Same_strand|Boundary_non-coding|ENSRNOT00000048434|ENSRNOG00000033340 ## Same_strand|Intronic_non-coding|ENSRNOT00000040973|ENSRNOG00000033340 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000059938|ENSRNOG00000039174 ## ENSRNOG00000039174|protein_coding|RGD1563865_predicted| ## ENSRNOG00000033340|protein_coding|RGD1561446_predicted|

block963751 [novel_lenNOK_Multihit_shortStem_randfoldOK_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	0.008	no	no	0.63/0.63	19/19/0.00	0.0	0.0	1	0	1	0	1	14	3arm	33	nd	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------UGCCUGC------------	1	novel
		len	cloning frequencies
			T2S2
	------------------------------------------------ATGCCTGCTGTGTGGGAGC-	19	1
rat	ggctcatccacagacatctcacactctccctgctgggagttaggctggATGCCTGCTGTGTGGGAGCt
	********************************************************************
	------------------------------------------------------------------------------	ENSRNOT00000059938 ENSRNOG00000039174 RGD1563865_predicted
	------------------------------------------------------------------------------	ENSRNOT00000048246 ENSRNOG00000039174 RGD1563865_predicted
rat	(((((.(((((((.((((.((..(((((((....)))))..))..))))))....))))).)))))))	0.410 -27.80

rat

chromosome:1:51924539:51924606:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000059936|ENSRNOG00000039174 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000048246|ENSRNOG00000039174 ## ENSRNOG00000039174|protein_coding|RGD1563865_predicted|

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