Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_multiarm_DicerNOK_loopOverlap_mirtron (4 loci)

sblock6516 [novel_lenNOK_multiarm_DicerNOK_loopOverlap_mirtron]

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	0.044	no	no	0.33/0.61	18/19/0.00	0.0 0.0 0.0	0.0 0.0 0.0	1 1 1	0 0 0	1 1 1	0 0 0	0 26 16	9 -16 9	5arm 5arm_loop_3arm 3arm	1 1 2	1 25 41	0.21 0.44 0.67	2 5 11	3	2	0	0

		reads	miRBase family seed
seed	-GGUAUCC--------------------------------------------------------------------	1	novel
seed	-------------------------------------------ACUAAGU--------------------------	1	novel
seed	---------------------------UGCCCUG------------------------------------------	1	miR-874
		len	cloning frequencies
			T2S1	T2S2
	AGGTATCCACGCTTAACTC---------------------------------------------------------	19	1	-
	--------------------------TTGCCCTGACCCCCTAGA--------------------------------	18	-	1
	------------------------------------------GACTAAGTTAACCATTTC----------------	18	1	-
rat	AGGTATCCACGCTTAACTCtgggaagTTGCCCTGACCCCCTAGACTAAGTTAACCATTTCtgcaaagtgcttacca
	****************************************************************************
	>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000012192 ENSRNOG00000024848 Fga
rat	.((((..((((((((..((((((..(((.....)))..)))))).)))))................)))..)))).	0.560 -17.89

rat

chromosome:2:174752225:174752300:1

Same_strand|Boundary_coding|ENSRNOT00000012192|ENSRNOG00000024848 ## Same_strand|Intronic_coding|ENSRNOT00000012192|ENSRNOG00000024848 ## ENSRNOG00000024848|protein_coding|Fga|Fibrinogen alpha chain precursor [Contains: Fibrinopeptide A]. [Source:UniProtKB/Swiss-Prot;Acc:P06399]

novel_lenNOK_multiarm_DicerNOK_mirtron_nonpairedHIGH_bulgeHIGH (4 loci)

sblock3814 [novel_lenNOK_multiarm_DicerNOK_mirtron_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	0.650	no	no	0.53/0.63	19/21/0.40	0.0 0.0 0.0	0.0 0.0 0.0	1 2 2	0 0 0	1 1 1	0 0 0	8 18 5	6 0 11	5arm 3arm 3arm	1 1 1	37 4 9	0.58 0.58 0.52	4 5 5	5	2	-6	-6

		reads	miRBase family seed
seed	------------------------------------------UGACCAG-----------------------------	2	novel
seed	-----------------------------------------------------GACUCAC------------------	2	novel
seed	---------GGAAUCA--------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T2S2
	-----------------------------------------GTGACCAGGGAGGACTCAC------------------	19	2	-
	----------------------------------------------------GGACTCACGGAGCCTACACTT-----	21	-	2
	--------AGGAATCACACTCAGCCAC---------------------------------------------------	19	-	1
rat	ggtttggtAGGAATCACACTCAGCCACtctcacttcgtgctGTGACCAGGGAGGACTCACGGAGCCTACACTTagccc
	******************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000029777 ENSRNOG00000003515 Ephx1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>	ENSRNOT00000004780 ENSRNOG00000003515 Ephx1
rat	((((..(((((..((....((..((....((((........))))....))..)).....))..)))))....)))).	0.820 -19.00

rat

chromosome:13:96740221:96740298:-1

Same_strand|Intronic_non-coding|ENSRNOT00000004780|ENSRNOG00000003515 ## Same_strand|Boundary_non-coding|ENSRNOT00000004780|ENSRNOG00000003515 ## ENSRNOG00000003515|protein_coding|Ephx1|Epoxide hydrolase 1 (EC 3.3.2.9) (Microsomal epoxide hydrolase) (Epoxide hydratase). [Source:UniProtKB/Swiss-Prot;Acc:P07687]

sblock4720 [novel_lenNOK_multiarm_DicerNOK_mirtron_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	0.055	no	no	0.58/0.70	19/22/0.38	0.0 0.0	0.0 0.0	1 4	0 0	1 2	0 0	12 9	5 5	5arm 3arm	1 1	37 3	0.32 0.32	4 4	8	2	0	-3

		reads	miRBase family seed
seed	-----------------------------------------------CAUCUCC--------------------	7	novel
seed	-------------CUGGUGG------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2
	----------------------------------------------GCATCTCCCCTGTCCCACC---------	19	-	4
	----------------------------------------------GCATCTCCCCTGTCCCACCCAG------	22	1	-
	----------------------------------------------GCATCTCCCCTGTCCCACCC--------	20	1	-
	------------CCTGGTGGGAGGAGAAGAA-------------------------------------------	19	1	-
	----------------------------------------------GCATCTCCCCTGTCCCACCCA-------	21	1	-
rat	actgaggttgttcctggtgggaggagaagaacctagctcatctcagGCATCTCCCCTGTCCCACCcaggctcgg
	**************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>	ENSRNOT00000025162 ENSRNOG00000018452 Unc13a
rat	.(((((.(((.....((((((((((((....(((((.....)).)))..)))))....)))))))))).)))))	0.960 -27.10

rat

chromosome:16:18829220:18829293:-1

Same_strand|Intronic_coding|ENSRNOT00000025162|ENSRNOG00000018452 ## ENSRNOG00000018452|protein_coding|Unc13a|unc-13 homolog A (C. elegans) Gene [Source:MGI Symbol;Acc:MGI:3051532]

sblock5195 [novel_lenNOK_multiarm_DicerNOK_mirtron_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	0.386	no	no	0.62/0.67	18/21/0.67	0.0 0.0	0.0 0.0	2 1	0 0	1 1	0 0	16 0	3 26	5arm 3arm	1 1	60 4	0.38 0.59	4 7	3	1	0	-12

		reads	miRBase family seed
seed	-----------------UGCCAUG------------------------------------------------------------------	2	novel
seed	-------------------------------------------------------------------------GCGGGUG----------	1	novel
		len	cloning frequencies
			T3S1
	----------------ATGCCATGTGGCGCTTCAGCG-----------------------------------------------------	21	2
	------------------------------------------------------------------------AGCGGGTGAGCCACTCCT	18	1
rat	gccccacgctggtcacATGCCATGTGGCGCTTCAGCGgtcggcggggactgtgcgctgtacagcgactgagcAGCGGGTGAGCCACTCCT
	******************************************************************************************
	..........................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++	ENSRNOT00000022356 ENSRNOG00000016511 Pitrm1
rat	((.((.(((((.(((..(((..((..((((....((((((......))))))))))..))..)))..))).)))))))...)).......	0.590 -35.80

rat

chromosome:17:74856709:74856798:-1

Same_strand|Boundary_coding|ENSRNOT00000022356|ENSRNOG00000016511 ## Same_strand|Boundary_non-coding|ENSRNOT00000022356|ENSRNOG00000016511 ## ENSRNOG00000016511|protein_coding|Pitrm1|pitrilysin metallepetidase 1 Gene [Source:MGI Symbol;Acc:MGI:1916867]

sblock5511 [novel_lenNOK_multiarm_DicerNOK_mirtron_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	0.997	no	no	0.63/0.67	18/19/0.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	0 9	18 9	5arm 3arm	1 1	4 47	0.32 0.33	4 2	2	2	-5	-5

		reads	miRBase family seed
seed	----------------------------------------------------GGCCGCG-------------------	1	novel
seed	-CCGCGUA----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T3S1
	---------------------------------------------------AGGCCGCGGGTTCAAGTC---------	18	-	1
	GCCGCGTAAGTTGGGTTGC-----------------------------------------------------------	19	1	-
rat	GCCGCGTAAGTTGGGTTGCgtctgtgttcgggaacgtgaggagcgtcagggAGGCCGCGGGTTCAAGTCgcaagggcc
	******************************************************************************
	>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000059188 ENSRNOG00000018053 NP_001101904.1
	>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000024328 ENSRNOG00000018053 NP_001101904.1
rat	((((((....(((..(((((...((.(((..((.(((.....)))))..))).))))).))..)))..)))...))).	0.460 -20.50

rat

chromosome:18:60708182:60708259:-1

Same_strand|Boundary_coding|ENSRNOT00000059188|ENSRNOG00000018053 ## Same_strand|Intronic_coding|ENSRNOT00000024328|ENSRNOG00000018053 ## ENSRNOG00000018053|protein_coding|NP_001101904.1|ferrochelatase [Source:RefSeq_peptide;Acc:NP_001101904]

novel_lenNOK_multiarm_DicerNOK_shortStem_5varHIGH_nonpairedHIGH (4 loci)

sblock10955 [novel_lenNOK_multiarm_DicerNOK_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	0.206	no	no	0.56/0.80	18/20/0.33	0.0 0.0 1.2	0.0 0.0 1.2	1 1 4	0 0 0	1 1 2	0 0 0	18 21 4	-2 2 13	5arm_loop 3arm 3arm	1 1 1	nd nd nd	0.32 0.44 0.37	3 5 4	6	3	15	17

		reads	miRBase family seed
seed	--------------------------------------------------------CCGGCGC-----------------	2	novel
seed	----------------------------------------------------------GGCGCGG---------------	1	novel
seed	------------------------------------------CAGUAAA-------------------------------	1	novel
seed	-------------------GGCUCUC------------------------------------------------------	1	novel
seed	-----------------------------------------------------UAGCCGG--------------------	1	novel
		len	cloning frequencies
			T1S1	T3S1	T3S2
	-------------------------------------------------------GCCGGCGCGGTGCAGCATGG-----	20	2	-	-
	------------------AGGCTCTCCCGCTGCCGGA-------------------------------------------	19	1	-	-
	---------------------------------------------------------CGGCGCGGTGCAGCATGGC----	19	-	-	1
	-----------------------------------------GCAGTAAATCGGTAGCCG---------------------	18	-	1	-
	----------------------------------------------------GTAGCCGGCGCGGTGCAGC---------	19	-	-	1
rat	cctgactgagggcacacgAGGCTCTCCCGCTGCCGGAagcgGCAGTAAATCGGTAGCCGGCGCGGTGCAGCATGGCgggg
	********************************************************************************
	.....................................................................>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000025134 ENSRNOG00000021773 Bop1
	............................................................................>>>>>>>>>>>>>>	ENSRNOT00000056365 ENSRNOG00000021773 Bop1
rat	((((..((...((((.((.((((..((.(((((((....))))))).....)).))))....))))))..))...)))).	0.990 -35.10

rat

chromosome:7:114524015:114524094:-1

Same_strand|Boundary_non-coding|ENSRNOT00000025134|ENSRNOG00000021773 ## intergenic ## ENSRNOG00000021773|protein_coding|Bop1|block of proliferation 1 [Source:RefSeq_peptide;Acc:NP_001019421]

sblock11779 [novel_lenNOK_multiarm_DicerNOK_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	0.115	no	no	0.42/0.52	19/21/0.50	0.0 1.2	0.0 0.6	1 5	0 0	1 2	0 0	0 0	16 30	5arm 3arm	1 1	nd nd	0.33 0.65	3 13	6	2	9	3

		reads	miRBase family seed
seed	------------------------------------------------------------------------------------------------CACUGCC-----------	3	miR-324
seed	----------------------------------------------------------------------------------------------CUCACUG-------------	2	novel
seed	-UGUUAGU----------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T5S1
	-----------------------------------------------------------------------------------------------TCACTGCCTATTGTCACTT	19	1	2
	---------------------------------------------------------------------------------------------TCTCACTGCCTATTGTCACT-	20	-	2
	GTGTTAGTGAGGTCCTCTACC---------------------------------------------------------------------------------------------	21	-	1
rat	GTGTTAGTGAGGTCCTCTACCgtgatttttttaaaaaatactttacatattcatactattctgtttttgaaaactttaaggtaactttggtatTCTCACTGCCTATTGTCACTT
	******************************************************************************************************************
rat	....((((((((.((..((((.(((..((((((((((..........................))))))))))..))).)))).....))...)))))))).............	0.860 -19.17

rat

chromosome:8:72066638:72066751:-1

intergenic

sblock7295 [novel_lenNOK_multiarm_DicerNOK_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	0.904	no	no	0.33/0.56	18/22/0.33	0.0 3.8	0.0 1.2	1 5	0 0	1 3	0 0	4 3	16 12	5arm 3arm	1 3	nd nd	0.44 0.39	3 2	6	3	-5	0

		reads	miRBase family seed
seed	----------------------------------------------------------AGAGCCA---------------	2	novel
seed	------------------------------------------------------------AGCCAGU-------------	1	novel
seed	------------------------------------------------------AGACAGA-------------------	1	novel
seed	-----------------------------------------------------------GAGCCAG--------------	1	novel
seed	-----UUUCAAC--------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T5S1	T5S2
	----------------------------------------------------------AGAGCCAGTGAGGAAGAT----	18	1	-	-
	----TTTTCAACAACAGGAAGT----------------------------------------------------------	18	1	-	-
	---------------------------------------------------------CAGAGCCAGTGAGGAAGATG---	20	1	-	-
	-----------------------------------------------------CAGACAGAGCCAGTGAGGAAGA-----	22	-	-	1
	---------------------------------------------------------CAGAGCCAGTGAGGAAGAT----	19	1	-	-
	-----------------------------------------------------------GAGCCAGTGAGGAAGATG---	18	-	1	-
rat	ctttTTTTCAACAACAGGAAGTgaagcgggctcccagcaaggcaggcagctccCAGACAGAGCCAGTGAGGAAGATGaag
	********************************************************************************
rat	(((((((((..((...((...((....(((((.((.((...)).)).))))).....))...))..))..))))).))))	0.520 -15.30

rat

chromosome:20:25379791:25379870:1

intergenic

sblock8079 [novel_lenNOK_multiarm_DicerNOK_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	0.082	no	no	0.39/0.67	19/25/0.50	2.2 0.0	5.2 0.0	5 1	0 0	1 1	0 0	0 15	3 0	5arm 3arm	1 1	nd nd	0.37 0.33	2 3	6	1	-11	-13

		reads	miRBase family seed
seed	-GAGCUGA---------------------------------------------------------------------	3	novel
seed	------------------------------------------CCAGGCA----------------------------	1	novel
seed	-----------GAUGAUC-----------------------------------------------------------	1	novel
seed	--AGCUGAA--------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	TGAGCTGAATTGATGATCC----------------------------------------------------------	19	2
	TGAGCTGAATTGATGATCCTTTG------------------------------------------------------	23	1
	----------TGATGATCCTTTGTGTTGGCTGAG-------------------------------------------	24	1
	-----------------------------------------TCCAGGCAGTGGGCTGGGTCT---------------	21	1
	-GAGCTGAATTGATGATCCTTTGTGT---------------------------------------------------	25	1
rat	TGAGCTGAATTGATGATCCTTTGTGTTGGCTGAGggagggcTCCAGGCAGTGGGCTGGGTCTtagggcaaggtagtg
	*****************************************************************************
rat	...((((..(((..(((((.....(((.((((..(((....)))...)))).))).)))))......)))..)))).	0.990 -23.60

rat

chromosome:3:76975263:76975339:1

intergenic

novel_lenNOK_multiarm_DicerNOK_shortStem_5varHIGH_nonpairedHIGH_bulgeHIGH (4 loci)

sblock10386 [novel_lenNOK_multiarm_DicerNOK_shortStem_5varHIGH_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	0.256	no	no	0.35/0.48	19/23/0.67	3.6 0.0	1.6 0.0	5 1	0 0	2 1	0 0	0 8	26 17	5arm 3arm	1 1	nd nd	0.37 0.35	4 6	6	2	-12	-8

		reads	miRBase family seed
seed	-------GUCCCUU------------------------------------------------------------------------------------------	2	novel
seed	----GCUGUCC---------------------------------------------------------------------------------------------	2	novel
seed	-UCUGCUG------------------------------------------------------------------------------------------------	1	novel
seed	--------------------------------------------------------------------------GGGAAUG-----------------------	1	novel
		len	cloning frequencies
			T1S2	T5S1
	---TGCTGTCCCTTCTTTTGTT----------------------------------------------------------------------------------	19	1	1
	------TGTCCCTTCTTTTGTTAAAG------------------------------------------------------------------------------	20	1	1
	-------------------------------------------------------------------------TGGGAATGTTTACACAAGCCAGG--------	23	-	1
	TTCTGCTGTCCCTTCTTTTGTT----------------------------------------------------------------------------------	22	-	1
rat	TTCTGCTGTCCCTTCTTTTGTTAAAGccaacattcagcagggcattctctgggtaatcaggctggaatggcatTGGGAATGTTTACACAAGCCAGGaaggtgaa
	********************************************************************************************************
	------------------------------------------------------------------------------------------------------------------	ENSRNOT00000005175 ENSRNOG00000003813 Kcnk10
rat	........(((((((((..(((......(((((((..(((.(((((((((((....))))...))))).)).))).)))))))......))).))))))).)).	0.510 -25.70

rat

chromosome:6:122603394:122603497:1

Opposite_strand|Intronic_coding|ENSRNOT00000005175|ENSRNOG00000003813 ## ENSRNOG00000003813|protein_coding|Kcnk10|Potassium channel subfamily K member 10 (Outward rectifying potassium channel protein TREK-2) (TREK-2 K(+) channel subunit). [Source:UniProtKB/Swiss-Prot;Acc:Q9JIS4]

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