Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_cloningOK_nonpairedHIGH_bulgeHIGH (533 loci)

block1751059 [novel_lenNOK_cloningOK_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	0.863	no	no	0.58/0.70	19/24/0.20	0.3	0.3	7	0	3	0	32	5	3arm	2	nd	0.47	5	10	3	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------CAACAGU-------------------------------------------	6	novel
seed	------------------------------------------------------------------UCAACAG--------------------------------------------	3	novel
seed	--------------------------------------------------------------GCCUUCA------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S2	T5S1
	------------------------------------------------------------------TCAACAGTCGGGGCGATCC--------------------------------	19	-	1	5
	-----------------------------------------------------------------TTCAACAGTCGGGGCGATC---------------------------------	19	-	-	2
	-------------------------------------------------------------GGCCTTCAACAGTCGGGGCG------------------------------------	20	-	-	1
	-----------------------------------------------------------------TTCAACAGTCGGGGCGATCCGTTG----------------------------	24	1	-	-
rat	gatgcccagatgatgcagacagccccacctcagccagtccttccttttccaggctcctgtgggccTTCAACAGTCGGGGCGATCCgttgggtcggtcgtcgccacttcggaggaatc
	*********************************************************************************************************************
rat	(((.((..((....((.(((.(((..(((.((((..(((((..((.((..((((((....))))))..)).))..))))).....))))))).))).)))))....))...)).)))	0.420 -34.80

rat

chromosome:5:79240233:79240349:-1

intergenic

block1766909 [novel_lenNOK_cloningOK_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	0.688	no	no	0.37/0.40	19/20/0.18	0.0	0.0	11	0	3	0	5	25	3arm	1	nd	0.42	4	17	3	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------UCCAUGC----------------	13	novel
seed	----------------------------------------------------------------------------CCAUGCC---------------	4	novel
		len	cloning frequencies
			T1S2	T4S2	T5S1
	--------------------------------------------------------------------------TTCCATGCCTTAGAAACTT-----	19	1	1	11
	---------------------------------------------------------------------------TCCATGCCTTAGAAACTTAG---	20	-	1	2
	---------------------------------------------------------------------------TCCATGCCTTAGAAACTTA----	19	-	-	1
rat	tttcacgtgtttcgagtattgactgaaaaatatagctaatttctgtttacagaatttacttctggtgatgtcacTTCCATGCCTTAGAAACTTagagg
	**************************************************************************************************
rat	.(((....(((((..((((.((.(((......(((.(((.(((((....))))).)))...)))......)))..)).))))....)))))...))).	0.470 -15.30

rat

chromosome:5:114552245:114552342:-1

intergenic

block1820479 [novel_lenNOK_cloningOK_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	0.870	no	no	0.79/0.85	18/20/0.12	0.6	1.1	16	0	7	0	15	5	5arm	1	nd	0.42	4	16	7	na	na

		reads	miRBase family seed
seed	----------------CCGCCAG------------------------------------------------------------------	13	novel
seed	--------------------CAGGGCA--------------------------------------------------------------	2	novel
seed	-----------------CGCCAGG-----------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S1	T3S2	T4S1	T5S2
	---------------GCCGCCAGGGCAGCGACC--------------------------------------------------------	18	1	1	1	1	-	1	1
	---------------GCCGCCAGGGCAGCGACCG-------------------------------------------------------	19	1	1	-	-	2	1	-
	---------------GCCGCCAGGGCAGCGACCGC------------------------------------------------------	20	1	-	-	-	1	-	-
	-------------------CCAGGGCAGCGACCGCAGC---------------------------------------------------	19	-	-	-	-	-	2	-
	----------------CCGCCAGGGCAGCGACCGC------------------------------------------------------	19	-	-	-	1	-	-	-
rat	ccggacgggccggcgGCCGCCAGGGCAGCGACCGCAGCgcaggagcccggcccgccgcagctacctcagcgcccgccgcgccgctcggc
	*****************************************************************************************
rat	(((..((.((((((((.(((..(((.(((....((.(((..((.......))))).)).))).)))..))).)))))).))))..))).	0.450 -43.40

rat

chromosome:5:25000396:25000484:1

intergenic ## {SimpF: 1 Eponine, -1 Eponine}

block1848457 [novel_lenNOK_cloningOK_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	0.863	no	no	0.58/0.70	19/24/0.20	0.3	0.3	7	0	3	0	32	5	3arm	2	nd	0.47	5	10	3	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------CAACAGU-------------------------------------------	6	novel
seed	------------------------------------------------------------------UCAACAG--------------------------------------------	3	novel
seed	--------------------------------------------------------------GCCUUCA------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S2	T5S1
	------------------------------------------------------------------TCAACAGTCGGGGCGATCC--------------------------------	19	-	1	5
	-----------------------------------------------------------------TTCAACAGTCGGGGCGATC---------------------------------	19	-	-	2
	-------------------------------------------------------------GGCCTTCAACAGTCGGGGCG------------------------------------	20	-	-	1
	-----------------------------------------------------------------TTCAACAGTCGGGGCGATCCGTTG----------------------------	24	1	-	-
rat	gatgcccagatgatgcagacagccccacctcagccagtccttccttttccaggctcctgtgggccTTCAACAGTCGGGGCGATCCgttgggtcggtcgtcgccacttcggaggaatc
	*********************************************************************************************************************
rat	(((.((..((....((.(((.(((..(((.((((..(((((..((.((..((((((....))))))..)).))..))))).....))))))).))).)))))....))...)).)))	0.420 -34.80

rat

chromosome:5:79242729:79242845:1

intergenic

block1414090 [novel_lenNOK_cloningOK_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	0.470	no	no	0.47/0.50	18/19/0.00	0.0	0.0	7	0	3	0	14	8	3arm	2	nd	0.42	4	10	3	na	na

		reads	miRBase family seed
seed	------------------------------------------------------UCGCAUU-------------------------	8	novel
seed	-------------------------------------------------------CGCAUUC------------------------	2	novel
		len	cloning frequencies
			T1S1	T2S1	T5S1
	-----------------------------------------------------TTCGCATTCTTAGAGCCAG--------------	19	1	-	7
	------------------------------------------------------TCGCATTCTTAGAGCCAG--------------	18	-	1	1
rat	gcttccccacagaggaatggtggagtgaaacactcagggaggacaccttgcttTTCGCATTCTTAGAGCCAGctctggacacatgc
	**************************************************************************************
rat	((.......(((((...((((((((((.......(((((......))))).......))))))....)))).))))).......))	0.630 -22.68

rat

chromosome:3:141689385:141689470:-1

intergenic

novel_lenNOK_cloningOK_nonpairedHIGH (528 loci)

block4041 [novel_lenNOK_cloningOK_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	0.470	no	no	0.28/0.32	18/19/0.00	0.0	0.0	23	0	3	0	35	2	3arm	1	nd	0.33	3	26	3	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------CCUUACA---------------------------------------------	26	novel
		len	cloning frequencies
			T1S1	T4S1	T4S2
	-------------------------------------------------------------------TCCTTACATTTCTTTATG-----------------------------------	18	-	11	12
	-------------------------------------------------------------------TCCTTACATTTCTTTATGG----------------------------------	19	1	-	2
rat	acatggtttttttctgattgtttaggaatccccactgtggctctaagacatgctgggaaagcaaagcTCCTTACATTTCTTTATGgcctgggatcactctcatggagatttggctgggtt
	************************************************************************************************************************
rat	((..((((..(((((...((...((..(((((......((((..((((.(((..((((..((...))))))..))).))))...)))).)))))..))..)).)))))...))))..)).	0.510 -28.50

rat

chromosome:10:8829772:8829891:-1

intergenic

block6603 [novel_lenNOK_cloningOK_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	0.311	no	no	0.50/0.50	18/18/0.00	0.0	0.0	13	0	7	0	19	6	5arm	1	14	0.33	2	17	7	na	na

		reads	miRBase family seed
seed	--------------------GCACCAU----------------------------------------------------------------------------	17	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T4S1	T4S2
	-------------------AGCACCATCTGATCGCTA------------------------------------------------------------------	18	1	1	1	1	3	3	7
rat	gcacggatcctggtggccgAGCACCATCTGATCGCTAgcccccacctgcaggggtctggtccttcctgtggttcgtaggcttctgtttcctcaccaatcagtg
	*******************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000017833 ENSRNOG00000012620 NP_001100455.1
rat	.(((.(((..((((((((....(((((..((..(((((.((((.......)))).)))))...))..))))).....)))...........)))))))).)))	0.570 -32.10

rat

chromosome:10:13939925:13940027:-1

Same_strand|Intronic_coding|ENSRNOT00000017833|ENSRNOG00000012620 ## ENSRNOG00000012620|protein_coding|NP_001100455.1|synaptogyrin 3 [Source:RefSeq_peptide;Acc:NP_001100455]

block7068 [novel_lenNOK_cloningOK_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	0.067	no	no	0.42/0.44	18/19/0.00	0.0	0.2	17	0	6	0	18	1	5arm	1	nd	0.32	3	18	6	na	na

		reads	miRBase family seed
seed	-------------------GACUCAU----------------------------------------------------	18	novel
		len	cloning frequencies
			T1S1	T2S1	T2S2	T4S1	T4S2	T5S1
	------------------TGACTCATTTCACTGAGCT-----------------------------------------	19	2	1	2	2	5	2
	------------------TGACTCATTTCACTGAGC------------------------------------------	18	-	-	-	2	2	-
rat	ttcttgtcagtttatgacTGACTCATTTCACTGAGCTagatcagcagtagcaccagtgacagggagggagggacaaga
	******************************************************************************
rat	.(((((((.........((..(((...((((((.((((.........))))..))))))....)))..)).)))))))	0.840 -22.60

rat

chromosome:10:14539192:14539269:-1

intergenic

block8147 [novel_lenNOK_cloningOK_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	0.011	no	no	0.60/0.67	18/20/0.09	0.0	0.0	22	0	9	0	19	21	5arm	2	nd	0.33	3	35	9	na	na

		reads	miRBase family seed
seed	--------------------GCAGCAA------------------------------------------------------------------------------------------	35	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S2	T4S1	T4S2	T5S1	T5S2
	-------------------AGCAGCAAACCCCAGGGG--------------------------------------------------------------------------------	18	7	8	1	1	1	1	4	3	2
	-------------------AGCAGCAAACCCCAGGGGT-------------------------------------------------------------------------------	19	2	1	-	-	-	1	-	-	-
	-------------------AGCAGCAAACCCCAGGGGTT------------------------------------------------------------------------------	20	-	-	-	-	-	-	1	1	1
rat	gctgagggcctcagaacaaAGCAGCAAACCCCAGGGGttcctccaactggcacctgtacttcctgcttaagagcctagctaagagtcacccagggtctgctttgtcagcccagcagc
	*********************************************************************************************************************
rat	((((.((((....((.((((((((...((((...((((..(((...(((((....(((.....)))......))).))....)))..)))).)))))))))))))).))))..))))	0.930 -42.20

rat

chromosome:10:16188928:16189044:-1

intergenic

block9952 [novel_lenNOK_cloningOK_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	0.042	no	no	0.50/0.50	18/18/0.00	0.0	0.0	10	0	3	0	5	1	3arm	1	nd	0.33	3	11	3	na	na

		reads	miRBase family seed
seed	------------------------------UUCACGU---------------	11	novel
		len	cloning frequencies
			T3S1	T3S2	T4S1
	-----------------------------CTTCACGTCAGATCAGGA-----	18	1	5	5
rat	ccagcgtaaggatgctgactaagcttcagCTTCACGTCAGATCAGGAtctgg
	****************************************************
	--------------------------------------------------------------	ENSRNOT00000009714 ENSRNOG00000007377 Slit3
rat	((((.((...(((.(((((.((((....))))...))))))))...))))))	0.930 -16.10

rat

chromosome:10:20299089:20299140:-1

Opposite_strand|Intronic_coding|ENSRNOT00000009714|ENSRNOG00000007377 ## ENSRNOG00000007377|protein_coding|Slit3|Slit homolog 3 protein precursor (Slit-3) (Multiple epidermal growth factor-like domains 5). [Source:UniProtKB/Swiss-Prot;Acc:O88280]

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