Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_shortStem_5varHIGH_nonpairedHIGH (13 loci)

block1138079 [novel_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	0.840	no	no	0.50/0.50	20/22/1.00	2.0	3.0	2	0	2	0	4	12	5arm	1	nd	0.35	3	2	2	na	na

		reads	miRBase family seed
seed	-----CCUUGGA--------------------------------------------------------------------	1	novel
seed	---------GGACUGA----------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S1	T5S1
	--------TGGACTGAATCACACGGAGACA--------------------------------------------------	22	1	-
	----ACCTTGGACTGAATCACACG--------------------------------------------------------	20	-	1
rat	aagtACCTTGGACTGAATCACACGGAGACAgcattttgagccgaacgcaggctaaactcttgtaattactgtttatagct
	********************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000034425 ENSRNOG00000027002
rat	.(((....(((((..(((.(((.((((...........((((.......))))...))))))).)))...)))))..)))	0.550 -12.14

rat

chromosome:2:33815622:33815701:-1

Same_strand|Intronic_coding|ENSRNOT00000034425|ENSRNOG00000027002 ## ENSRNOG00000027002|protein_coding||

block1094297 [novel_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	0.083	no	no	0.50/0.53	19/24/0.75	2.0	0.0	4	0	2	0	4	6	3arm	1	nd	0.33	3	4	2	na	na

		reads	miRBase family seed
seed	---------------------------------------------CAGAGAU--------------------	2	novel
seed	--------------------------------------------------AUAAGCC---------------	1	novel
seed	------------------------------------------------AGAUAAG-----------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	--------------------------------------------TCAGAGATAAGCCACAAGAGGCAG----	24	1	1
	-----------------------------------------------GAGATAAGCCACAAGAGGCAG----	21	-	1
	-------------------------------------------------GATAAGCCACAAGAGGCAG----	19	-	1
rat	ctgtgcggcccactggggttgctcttgacgaaatttgcattttaTCAGAGATAAGCCACAAGAGGCAGcagc
	************************************************************************
rat	((((...(((..((..((((.(((.(((..((((....))))..))))))...))))...)).))).)))).	0.910 -22.00

rat

chromosome:20:5566206:5566277:1

intergenic

block1696117 [novel_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	0.382	no	no	0.37/0.45	19/20/0.75	2.5	2.2	4	0	2	0	0	10	3arm	2	nd	0.32	3	4	2	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------CCUCUUU------------	2	novel
seed	------------------------------------------------------------------------CUCCUCU--------------	1	novel
seed	----------------------------------------------------------------------CUCUCCU----------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	-------------------------------------------------------------------------TCCTCTTTTTCTTTCCTGCT	20	1	1
	-----------------------------------------------------------------------TCTCCTCTTTTTCTTTCCT---	19	1	-
	---------------------------------------------------------------------GCTCTCCTCTTTTTCTTTCC----	20	1	-
rat	ggctcccaagggctaagtcatatggagtcctggcccccatccattttcagctagctataggattggacaGCTCTCCTCTTTTTCTTTCCTGCT
	*********************************************************************************************
rat	(((....(((((..(((......((((..(((...((.((((.................)))).)).)))..)))).)))..)))))...)))	0.400 -19.13

rat

chromosome:4:164258653:164258745:1

intergenic

novel_Multihit_5varHIGH_loopOverlap_nonpairedHIGH (12 loci)

block353755 [novel_Multihit_5varHIGH_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	0.144	no	no	0.52/0.55	20/23/1.00	2.0	0.5	2	0	2	0	20	-2	3arm	29	nd	0.35	3	2	2	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------AGGAUGU--------------------------------	1	novel
seed	-----------------------------------------------------CUUGAGG------------------------------------	1	miR-327
		len	cloning frequencies
			T3S1	T4S1
	--------------------------------------------------------GAGGATGTTCCCCAACTCTG--------------------	20	-	1
	----------------------------------------------------CCTTGAGGATGTTCCCCAACTCT---------------------	23	1	-
rat	aaggctcctgcttgtaaggcctagtcttagaaggcacatctcaaacctacctCCTTGAGGATGTTCCCCAACTCTGcccacgactcaccaagcctt
	************************************************************************************************
rat	((((((..((.((((..(((..(((.......((.(((((((((..........))))).)))).))...)))..))).))))..))...))))))	0.460 -20.20

rat

chromosome:14:49231946:49232041:-1

intergenic

block353763 [novel_Multihit_5varHIGH_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	0.144	no	no	0.52/0.55	20/23/1.00	2.0	0.5	2	0	2	0	20	-2	3arm	29	nd	0.35	3	2	2	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------AGGAUGU--------------------------------	1	novel
seed	-----------------------------------------------------CUUGAGG------------------------------------	1	miR-327
		len	cloning frequencies
			T3S1	T4S1
	--------------------------------------------------------GAGGATGTTCCCCAACTCTG--------------------	20	-	1
	----------------------------------------------------CCTTGAGGATGTTCCCCAACTCT---------------------	23	1	-
rat	aaggctcctgcttgtaaggcctagtcttagaaggcacatctcaaacctacctCCTTGAGGATGTTCCCCAACTCTGcccacgactcaccaagcctt
	************************************************************************************************
rat	((((((..((.((((..(((..(((.......((.(((((((((..........))))).)))).))...)))..))).))))..))...))))))	0.460 -20.20

rat

chromosome:14:49238177:49238272:-1

intergenic

block354063 [novel_Multihit_5varHIGH_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	0.144	no	no	0.52/0.55	20/23/1.00	2.0	0.5	2	0	2	0	20	-2	3arm	29	nd	0.35	3	2	2	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------AGGAUGU--------------------------------	1	novel
seed	-----------------------------------------------------CUUGAGG------------------------------------	1	miR-327
		len	cloning frequencies
			T3S1	T4S1
	--------------------------------------------------------GAGGATGTTCCCCAACTCTG--------------------	20	-	1
	----------------------------------------------------CCTTGAGGATGTTCCCCAACTCT---------------------	23	1	-
rat	aaggctcctgcttgtaaggcctagtcttagaaggcacatctcaaacctacctCCTTGAGGATGTTCCCCAACTCTGcccacgactcaccaagcctt
	************************************************************************************************
	----------------------------------------------------------------------------------------------------------	ENSRNOT00000048005 ENSRNOG00000033205 LOC501255
	---------------------------------------------------------------------------------------------<<<<<<<<<<<<<	ENSRNOT00000043791 ENSRNOG00000032207 LOC690700
	----------------------------------------------------------------------------------------------------------	ENSRNOT00000050021 ENSRNOG00000032207 LOC690700
rat	((((((..((.((((..(((..(((.......((.(((((((((..........))))).)))).))...)))..))).))))..))...))))))	0.460 -20.20

rat

chromosome:14:49378672:49378767:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000045975|ENSRNOG00000032207 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000048005|ENSRNOG00000033205 ## Opposite_strand|Intronic_coding|ENSRNOT00000050021|ENSRNOG00000032207 ## ENSRNOG00000032207|protein_coding|LOC690700|LOC501224 protein. [Source:UniProtKB/TrEMBL;Acc:Q0P5Q7] ## ENSRNOG00000033205|protein_coding|LOC501255|

block354171 [novel_Multihit_5varHIGH_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	0.041	no	no	0.52/0.55	20/23/1.00	2.0	0.5	2	0	2	0	20	-2	3arm	29	nd	0.35	3	2	2	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------AGGAUGU--------------------------------	1	novel
seed	-----------------------------------------------------CUUGAGG------------------------------------	1	miR-327
		len	cloning frequencies
			T3S1	T4S1
	--------------------------------------------------------GAGGATGTTCCCCAACTCTG--------------------	20	-	1
	----------------------------------------------------CCTTGAGGATGTTCCCCAACTCT---------------------	23	1	-
rat	aaggctcctgcttgtaaggcctagtcttagaaggcacatctcaaacctacctCCTTGAGGATGTTCCCCAACTCTGcctacgactcaccaagcctt
	************************************************************************************************
	----------------------------------------------------------------------------------------------------------	ENSRNOT00000043791 ENSRNOG00000032207 LOC690700
	----------------------------------------------------------------------------------------------------------	ENSRNOT00000045975 ENSRNOG00000032207 LOC690700
	----------------------------------------------------------------------------------------------------------	ENSRNOT00000059076 ENSRNOG00000032207 LOC690700
	----------------------------------------------------------------------------------------------------------	ENSRNOT00000041734 ENSRNOG00000032207 LOC690700
rat	((((((..((.((((.((((..(((.......((.(((((((((..........))))).)))).))...)))..))))))))..))...))))))	0.860 -22.90

rat

chromosome:14:49554181:49554276:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000050021|ENSRNOG00000032207 ## Opposite_strand|Intronic_coding|ENSRNOT00000045975|ENSRNOG00000032207 ## ENSRNOG00000032207|protein_coding|LOC690700|LOC501224 protein. [Source:UniProtKB/TrEMBL;Acc:Q0P5Q7]

block354278 [novel_Multihit_5varHIGH_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	0.144	no	no	0.52/0.55	20/23/1.00	2.0	0.5	2	0	2	0	20	-2	3arm	29	nd	0.35	3	2	2	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------AGGAUGU--------------------------------	1	novel
seed	-----------------------------------------------------CUUGAGG------------------------------------	1	miR-327
		len	cloning frequencies
			T3S1	T4S1
	--------------------------------------------------------GAGGATGTTCCCCAACTCTG--------------------	20	-	1
	----------------------------------------------------CCTTGAGGATGTTCCCCAACTCT---------------------	23	1	-
rat	aaggctcctgcttgtaaggcctagtcttagaaggcacatctcaaacctacctCCTTGAGGATGTTCCCCAACTCTGcccacgactcaccaagcctt
	************************************************************************************************
	----------------------------------------------------------------------------------------------------------	ENSRNOT00000043791 ENSRNOG00000032207 LOC690700
	----------------------------------------------------------------------------------------------------------	ENSRNOT00000045975 ENSRNOG00000032207 LOC690700
	----------------------------------------------------------------------------------------------------------	ENSRNOT00000059076 ENSRNOG00000032207 LOC690700
	----------------------------------------------------------------------------------------------------------	ENSRNOT00000041734 ENSRNOG00000032207 LOC690700
rat	((((((..((.((((..(((..(((.......((.(((((((((..........))))).)))).))...)))..))).))))..))...))))))	0.460 -20.20

rat

chromosome:14:49606040:49606135:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000050021|ENSRNOG00000032207 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000043791|ENSRNOG00000032207 ## Opposite_strand|Intronic_coding|ENSRNOT00000045975|ENSRNOG00000032207 ## ENSRNOG00000032207|protein_coding|LOC690700|LOC501224 protein. [Source:UniProtKB/TrEMBL;Acc:Q0P5Q7]

block354339 [novel_Multihit_5varHIGH_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	0.144	no	no	0.52/0.55	20/23/1.00	2.0	0.5	2	0	2	0	20	-2	3arm	29	nd	0.35	3	2	2	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------AGGAUGU--------------------------------	1	novel
seed	-----------------------------------------------------CUUGAGG------------------------------------	1	miR-327
		len	cloning frequencies
			T3S1	T4S1
	--------------------------------------------------------GAGGATGTTCCCCAACTCTG--------------------	20	-	1
	----------------------------------------------------CCTTGAGGATGTTCCCCAACTCT---------------------	23	1	-
rat	aaggctcctgcttgtaaggcctagtcttagaaggcacatctcaaacctacctCCTTGAGGATGTTCCCCAACTCTGcccacgactcaccaagcctt
	************************************************************************************************
	----------------------------------------------------------------------------------------------------------	ENSRNOT00000043791 ENSRNOG00000032207 LOC690700
	----------------------------------------------------------------------------------------------------------	ENSRNOT00000045975 ENSRNOG00000032207 LOC690700
	----------------------------------------------------------------------------------------------------------	ENSRNOT00000059076 ENSRNOG00000032207 LOC690700
rat	((((((..((.((((..(((..(((.......((.(((((((((..........))))).)))).))...)))..))).))))..))...))))))	0.460 -20.20

rat

chromosome:14:49649447:49649542:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000050021|ENSRNOG00000032207 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000043791|ENSRNOG00000032207 ## Opposite_strand|Intronic_coding|ENSRNOT00000045975|ENSRNOG00000032207 ## ENSRNOG00000032207|protein_coding|LOC690700|LOC501224 protein. [Source:UniProtKB/TrEMBL;Acc:Q0P5Q7]

block354422 [novel_Multihit_5varHIGH_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	0.240	no	no	0.52/0.55	20/23/1.00	2.0	0.5	2	0	2	0	8	-2	3arm	29	nd	0.35	3	2	2	na	na

		reads	miRBase family seed
seed	----------------------------------------------AGGAUGU--------------------	1	novel
seed	------------------------------------------CUUGAGG------------------------	1	miR-327
		len	cloning frequencies
			T3S1	T4S1
	---------------------------------------------GAGGATGTTCCCCAACTCTG--------	20	-	1
	-----------------------------------------CCTTGAGGATGTTCCCCAACTCT---------	23	1	-
rat	ttgtaaggcctagtcttagaaggcacatctcaaacctacctCCTTGAGGATGTTCCCCAACTCTGcccacgac
	*************************************************************************
	-----------------------------------------------------------------------------------	ENSRNOT00000043791 ENSRNOG00000032207 LOC690700
	-----------------------------------------------------------------------------------	ENSRNOT00000045975 ENSRNOG00000032207 LOC690700
rat	((((..(((..(((.......((.(((((((((..........))))).)))).))...)))..))).)))).	0.750 -13.50

rat

chromosome:14:49705967:49706039:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000050021|ENSRNOG00000032207 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000043791|ENSRNOG00000032207 ## Opposite_strand|Intronic_coding|ENSRNOT00000045975|ENSRNOG00000032207 ## ENSRNOG00000032207|protein_coding|LOC690700|LOC501224 protein. [Source:UniProtKB/TrEMBL;Acc:Q0P5Q7]

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