Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_Multihit_shortStem_loopOverlap_nonpairedHIGH (14 loci)

block400453 [novel_lenNOK_Multihit_shortStem_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	0.181	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	3	-4	3arm_loop	19	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	------------------------AAGCAGU-------------	1	novel
		len	cloning frequencies
			T1S2
	-----------------------AAAGCAGTGGCAGAAGGA---	18	1
rat	gccccccttccccctgtcctgggAAAGCAGTGGCAGAAGGAggc
	********************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000043791 ENSRNOG00000032207 LOC690700
	++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000045975 ENSRNOG00000032207 LOC690700
	++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000059076 ENSRNOG00000032207 LOC690700
	++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000041734 ENSRNOG00000032207 LOC690700
rat	......(((((..((((((((......))).)))))..))))).	0.870 -16.00

rat

chromosome:14:49591066:49591109:1

Same_strand|Boundary_non-coding|ENSRNOT00000050021|ENSRNOG00000032207 ## Same_strand|Intronic_coding|ENSRNOT00000045975|ENSRNOG00000032207 ## Same_strand|Intronic_non-coding|ENSRNOT00000041734|ENSRNOG00000032207 ## ENSRNOG00000032207|protein_coding|LOC690700|LOC501224 protein. [Source:UniProtKB/TrEMBL;Acc:Q0P5Q7]

novel_lenNOK_cloningOK_mirtron (14 loci)

block7120 [novel_lenNOK_cloningOK_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	0.269	no	no	0.63/0.67	18/22/0.60	0.0	0.9	7	0	3	0	25	3	3arm	1	0	0.27	3	10	3	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------CCCACUG---------------------------------------	8	novel
seed	----------------------------------------------------------------------CCACUGG--------------------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T4S1
	--------------------------------------------------------------------TCCCACTGGTCTCTCCCTGCAG-------------------------	22	5	-	-
	---------------------------------------------------------------------CCCACTGGTCTCTCCCTG----------------------------	18	-	1	1
	--------------------------------------------------------------------TCCCACTGGTCTCTCCCTG----------------------------	19	2	-	-
	--------------------------------------------------------------------TCCCACTGGTCTCTCCCTGC---------------------------	20	-	-	1
rat	ggcagcactgtgagtctccgaaggcaagctggccctctgggtgggacagggtgaggtggacttggaccTCCCACTGGTCTCTCCCTGCAGgagcgggccttcctcagcgtctcca
	*******************************************************************************************************************
	>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000048392 ENSRNOG00000033893 Cacna1h
	>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000043626 ENSRNOG00000033893 Cacna1h
rat	((.((.((..((((.....((((((..(((...(((..(((.(((((((((.(((((........))))))).))).)))).)))...))))))..))))))))))..)))))).	0.930 -47.70

rat

chromosome:10:14631260:14631374:-1

Same_strand|Intronic_coding|ENSRNOT00000048392|ENSRNOG00000033893 ## Same_strand|Boundary_non-coding|ENSRNOT00000060323|ENSRNOG00000033893 ## ENSRNOG00000033893|protein_coding|Cacna1h|Voltage-dependent T-type calcium channel subunit alpha-1H (Voltage- gated calcium channel subunit alpha Cav3.2). [Source:UniProtKB/Swiss-Prot;Acc:Q9EQ60]

block16173 [novel_lenNOK_cloningOK_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	0.084	no	no	0.53/0.56	18/19/0.00	0.0	0.0	7	0	8	0	7	27	5arm	3	2	0.22	2	14	8	na	na

		reads	miRBase family seed
seed	--------GAGUGUG-------------------------------------------------------------------------------------------------------	14	novel
		len	cloning frequencies
			T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-------TGAGTGTGTGTGTGGTCC---------------------------------------------------------------------------------------------	18	1	1	5	-	2	1	1	1
	-------TGAGTGTGTGTGTGGTCCA--------------------------------------------------------------------------------------------	19	-	-	-	1	-	1	-	-
rat	gaccgggTGAGTGTGTGTGTGGTCCagggccttgtgggaacacctcagagctaatgtgtgccagcttggaggagtgcaagtgtgagggcctgtgtcacaaacccatctctcctctgtc
	**********************************************************************************************************************
	>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>	ENSRNOT00000036789 ENSRNOG00000003475 MGC112682
rat	(((.(((.(((((.((.(((((..((((.(((..((...((.((((.(((((..........))))).)))).)).....))..))).))))..))))).)).)).))).)))..)))	0.960 -45.50

rat

chromosome:10:37145874:37145991:-1

Same_strand|Intronic_coding|ENSRNOT00000036789|ENSRNOG00000003475 ## ENSRNOG00000003475|protein_coding|MGC112682|similar to RIKEN cDNA 0610039K22 (MGC112682), mRNA [Source:RefSeq_dna;Acc:NM_001017473]

block645086 [novel_lenNOK_cloningOK_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	0.057	no	no	0.39/0.45	18/22/0.54	0.0	1.3	16	0	7	0	7	22	3arm	1	1	0.30	3	26	7	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------------GCAACUU---------------------	26	novel
		len	cloning frequencies
			T1S1	T1S2	T2S2	T3S1	T3S2	T5S1	T5S2
	--------------------------------------------------------------------------------------TGCAACTTTGGTTTTCCTG----------	19	4	-	2	1	-	1	1
	--------------------------------------------------------------------------------------TGCAACTTTGGTTTTCCTGCAA-------	22	1	2	-	2	-	1	-
	--------------------------------------------------------------------------------------TGCAACTTTGGTTTTCCTGCA--------	21	3	-	-	1	-	-	-
	--------------------------------------------------------------------------------------TGCAACTTTGGTTTTCCTGC---------	20	3	-	-	1	-	-	-
	--------------------------------------------------------------------------------------TGCAACTTTGGTTTTCCT-----------	18	-	-	1	-	1	1	-
rat	tagcggcctggagcggacgcctgtgagcagggctgaccttttgaaccaggcagggcaccatggagcaggctgtctggctcaccaccTGCAACTTTGGTTTTCCTGCAAgctgcta
	*******************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>	ENSRNOT00000051702 ENSRNOG00000011523 H2afy
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>	ENSRNOT00000015632 ENSRNOG00000011523 H2afy
rat	(((((((.((.((.(((.(((.((..(((((..........(((.((((((((.((........))...)))))))).)))...))))).))...))).))))).)).)))))))	0.850 -45.12

rat

chromosome:17:14489160:14489274:1

Same_strand|Intronic_coding|ENSRNOT00000015632|ENSRNOG00000011523 ## ENSRNOG00000011523|protein_coding|H2afy|Core histone macro-H2A.1 (Histone macroH2A1) (mH2A1) (H2A.y) (H2A/y). [Source:UniProtKB/Swiss-Prot;Acc:Q02874]

block838746 [novel_lenNOK_cloningOK_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	0.080	no	no	0.43/0.47	18/25/0.57	0.0	1.8	12	0	2	0	24	11	3arm	1	0	0.16	2	14	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------CACGGCU---------------------------------------	14	novel
		len	cloning frequencies
			T1S1	T1S2
	----------------------------------------------------------------------TCACGGCTTTCCCTTTTACTTAG------------------------	23	2	4
	----------------------------------------------------------------------TCACGGCTTTCCCTTTTAC----------------------------	19	2	2
	----------------------------------------------------------------------TCACGGCTTTCCCTTTTACT---------------------------	20	2	-
	----------------------------------------------------------------------TCACGGCTTTCCCTTTTA-----------------------------	18	-	1
	----------------------------------------------------------------------TCACGGCTTTCCCTTTTACTTAGAC----------------------	25	1	-
rat	gggaggcctctggctacagagagcagttagtaggagggagctggacgggggaaagcatgcttctgctcgcTCACGGCTTTCCCTTTTACTTAGacatggctggctaaggactgcccc
	*********************************************************************************************************************
	-------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000060560 ENSRNOG00000029049 Zdhhc14
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000060527 ENSRNOG00000017889 Serac1
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000024205 ENSRNOG00000017889 Serac1
rat	(((.(((((.(((((......(((.((((((((((((((((((((((((((.(((....))))).)))).)).))))..)))))))))))..)))...))))))))))).)).))).	0.710 -44.50

rat

chromosome:1:40831318:40831434:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000043521|ENSRNOG00000029049 ## Same_strand|Boundary_coding|ENSRNOT00000024205|ENSRNOG00000017889 ## Opposite_strand|Intronic_coding|ENSRNOT00000060560|ENSRNOG00000029049 ## ENSRNOG00000017889|protein_coding|Serac1|serine active site containing 1 Gene [Source:MGI (curated);Acc:Serac1-001] ## ENSRNOG00000029049|protein_coding|Zdhhc14|zinc finger, DHHC domain containing 14 Gene [Source:MGI Symbol;Acc:MGI:2653229]

block1489353 [novel_lenNOK_cloningOK_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	0.109	no	no	0.57/0.61	18/23/0.69	0.1	3.1	13	0	6	0	17	12	3arm	1	0	0.17	1	13	6	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------------------CCACCCA---------------------------------	12	novel
seed	-----------------------------------------------------------------------CACCCAC--------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T3S2	T4S2	T5S2
	---------------------------------------------------------------------CCCACCCACTTCATCGTCTCAC-------------------	22	2	1	-	-	1	-
	---------------------------------------------------------------------CCCACCCACTTCATCGTC-----------------------	18	1	-	1	2	-	-
	---------------------------------------------------------------------CCCACCCACTTCATCGTCTCACA------------------	23	-	-	2	-	1	-
	---------------------------------------------------------------------CCCACCCACTTCATCGTCTCA--------------------	21	-	1	-	-	-	-
	----------------------------------------------------------------------CCACCCACTTCATCGTCTCACAG-----------------	23	-	-	-	-	-	1
rat	ggcaagggccaggaggcacgagggtgatgaggtgagtgagcccaggaatgtgcagagctgggctggaggCCCACCCACTTCATCGTCTCACAGtgtttacagtgctgctg
	**************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000028821 ENSRNOG00000021222 Vps16
rat	(((.((.((....((((((..(((((((((((((.((((((((((............))))))).......))).)))))))))).)))...))))))...)).))))).	0.540 -42.61

rat

chromosome:3:118056652:118056761:1

Same_strand|Intronic_coding|ENSRNOT00000028821|ENSRNOG00000021222 ## ENSRNOG00000021222|protein_coding|Vps16|vacuolar protein sorting 16 [Source:RefSeq_peptide;Acc:NP_001005541]

block1503818 [novel_lenNOK_cloningOK_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	0.140	no	no	0.64/0.70	19/23/0.42	0.0	0.0	6	0	3	0	6	8	3arm	1	4	0.26	3	12	3	na	na

		reads	miRBase family seed
seed	-------------------------------------------ACCGCGU-----------------	10	novel
seed	--------------------------------------------CCGCGUC----------------	2	novel
		len	cloning frequencies
			T1S1	T3S1	T4S1
	------------------------------------------AACCGCGTCATGCCACGCC------	19	1	4	2
	------------------------------------------AACCGCGTCATGCCACGCCTCAG--	23	-	1	1
	-------------------------------------------ACCGCGTCATGCCACGCCTCAG--	22	-	-	1
	-------------------------------------------ACCGCGTCATGCCACGCCTC----	20	-	1	-
	------------------------------------------AACCGCGTCATGCCACGCCTCA---	22	-	1	-
rat	tctgggaggggtgggtgggcgtggccagagcctgctcttcctAACCGCGTCATGCCACGCCtcaggg
	*******************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>	ENSRNOT00000051014 ENSRNOG00000020246 Myl9_predicted
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>	ENSRNOT00000027445 ENSRNOG00000020246 Myl9_predicted
rat	.((..((((.((((...(((((((..((((....))))......)))))))...)))).)))).)).	0.720 -30.50

rat

chromosome:3:147193158:147193224:1

Same_strand|Intronic_coding|ENSRNOT00000027445|ENSRNOG00000020246 ## ENSRNOG00000020246|protein_coding|Myl9_predicted|Myosin regulatory light chain 2, smooth muscle isoform (Myosin RLC) (Myosin regulatory light chain 9). [Source:UniProtKB/Swiss-Prot;Acc:Q64122]

block1578746 [novel_lenNOK_cloningOK_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	0.013	no	no	0.55/0.59	18/22/0.50	0.0	1.9	10	0	3	0	20	5	3arm	1	2	0.00	0	10	3	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------ACCCAUC----------------------------------	10	novel
		len	cloning frequencies
			T1S1	T1S2	T5S2
	----------------------------------------------------------------------------TACCCATCCCTTCTGCCA------------------------	18	3	-	-
	----------------------------------------------------------------------------TACCCATCCCTTCTGCCACACC--------------------	22	3	-	-
	----------------------------------------------------------------------------TACCCATCCCTTCTGCCAC-----------------------	19	2	-	-
	----------------------------------------------------------------------------TACCCATCCCTTCTGCCACA----------------------	20	-	1	-
	----------------------------------------------------------------------------TACCCATCCCTTCTGCCACAC---------------------	21	-	-	1
rat	ccaggtgccggtgagtgttgctgttggaggtggctgggagggagaagtgggtggagcaagtggagcagtaaccactTACCCATCCCTTCTGCCACACCagcttgtgctgcaggcttgg
	**********************************************************************************************************************
	>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000022951 ENSRNOG00000017003 Plxna1
rat	(((...(((.((.(((...((.(((((..(((((.((((((((....((((((.....(((((........)))))))))))))))))))))))).)))))..))))))).))).)))	0.920 -49.90

rat

chromosome:4:123417719:123417836:-1

Same_strand|Intronic_coding|ENSRNOT00000022951|ENSRNOG00000017003 ## ENSRNOG00000017003|protein_coding|Plxna1|plexin A1 Gene [Source:MGI Symbol;Acc:MGI:107685]

block1870960 [novel_lenNOK_cloningOK_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	0.105	no	no	0.55/0.58	18/21/0.30	1.0	0.7	10	0	7	0	17	2	3arm	3	0	0.11	1	10	7	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------CACGCUC------------------------------	5	novel
seed	---------------------------------------------------------CGCUCUC----------------------------	5	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T4S1	T4S2	T5S1	T5S2
	--------------------------------------------------------ACGCTCTCTCCTTTCCCAG-----------------	19	3	1	-	-	-	-	-
	------------------------------------------------------TCACGCTCTCTCCTTTCCC-------------------	19	-	-	1	-	-	1	-
	------------------------------------------------------TCACGCTCTCTCCTTTCCCA------------------	20	-	-	-	-	1	-	1
	------------------------------------------------------TCACGCTCTCTCCTTTCCCAG-----------------	21	-	-	-	1	-	-	-
	--------------------------------------------------------ACGCTCTCTCCTTTCCCA------------------	18	-	1	-	-	-	-	-
rat	aggagctttgtgagcacgcatggggaatgagcagacgcctctgaggaactcaccTCACGCTCTCTCCTTTCCCAGgtactgtggatcattcc
	********************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000014091 ENSRNOG00000010512 Yipf1
rat	.(((.....((((.(((((.(((((((.(((.(((.((...(((((......))))).)))))))).))))))).))...)))..)))))))	0.860 -30.00

rat

chromosome:5:128447327:128447418:1

Same_strand|Intronic_coding|ENSRNOT00000014091|ENSRNOG00000010512 ## ENSRNOG00000010512|protein_coding|Yipf1|Protein YIPF1 (YIP1 family member 1). [Source:UniProtKB/Swiss-Prot;Acc:Q6P6G5]

block2076766 [novel_lenNOK_cloningOK_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	0.026	no	no	0.55/0.60	18/22/0.60	0.2	1.5	10	0	5	0	21	3	3arm	1	0	0.19	3	10	5	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------------UCUGCUU-----------------------------------	8	novel
seed	---------------------------------------------------------------UUCUGCU------------------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T4S1	T5S1
	---------------------------------------------------------------TTCTGCTTCTAACCCCCC-------------------------	18	3	-	-	-	-
	---------------------------------------------------------------TTCTGCTTCTAACCCCCCCAG----------------------	21	-	-	1	1	-
	--------------------------------------------------------------CTTCTGCTTCTAACCCCCCC------------------------	20	1	-	1	-	-
	---------------------------------------------------------------TTCTGCTTCTAACCCCCCCA-----------------------	20	-	1	-	-	-
	---------------------------------------------------------------TTCTGCTTCTAACCCCCCCAGA---------------------	22	-	-	-	-	1
	---------------------------------------------------------------TTCTGCTTCTAACCCCCCC------------------------	19	-	-	1	-	-
rat	ccaggagctaatgtgggcaggatctgaggggaaggtttgaagcttccaggagaacccgcttcCTTCTGCTTCTAACCCCCCCAGAcatgagtgacaagcggctgga
	**********************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000036373 ENSRNOG00000022943 Dgka
rat	((((..(((..(((...((...((((.((((..((((.(((((....(((((.......)))))...))))).))))))))))))..))....))))))..)))).	0.970 -39.40

rat

chromosome:7:2019809:2019914:-1

Same_strand|Boundary_coding|ENSRNOT00000036373|ENSRNOG00000022943 ## ENSRNOG00000022943|protein_coding|Dgka|Diacylglycerol kinase alpha (EC 2.7.1.107) (Diglyceride kinase alpha) (DGK-alpha) (DAG kinase alpha) (80 kDa diacylglycerol kinase). [Source:UniProtKB/Swiss-Prot;Acc:P51556]

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