Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_Multihit_shortStem_5varHIGH_nonpairedHIGH (12 loci)

block1444190 [novel_lenNOK_Multihit_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	0.208	no	no	0.17/0.25	18/23/0.60	1.6	2.8	5	0	3	0	0	17	5arm	11	nd	0.35	3	5	3	na	na

		reads	miRBase family seed
seed	----GUUCAAU-------------------------------------------------------------------------------------	2	novel
seed	-CAUGUUC----------------------------------------------------------------------------------------	2	novel
seed	------UCAAUAA-----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T3S2	T5S1
	---TGTTCAATAATAAATCTCAC-------------------------------------------------------------------------	20	2	-	-
	-----TTCAATAATAAATCTCACATCAA--------------------------------------------------------------------	23	-	1	-
	TCATGTTCAATAATAAAT------------------------------------------------------------------------------	18	-	-	1
	TCATGTTCAATAATAAATC-----------------------------------------------------------------------------	19	-	1	-
rat	TCATGTTCAATAATAAATCTCACATCAAatctgcttaaaaaaaagagtttctaaaacagctaagatgatgtagctgagaacagtttaggaaatgaa
	************************************************************************************************
rat	((((.(((...(((...((((((((((.....(((........((.....)).....))).....))))))....))))...)))...))))))).	0.520 -12.92

rat

chromosome:3:20720757:20720852:1

intergenic

block1687133 [novel_lenNOK_Multihit_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	0.470	no	no	0.42/0.45	19/22/0.25	1.2	0.5	4	0	2	0	4	14	5arm	26	nd	0.32	3	4	2	na	na

		reads	miRBase family seed
seed	----------GAUCUUU---------------------------------------------------------------------------	3	novel
seed	-----CCCUUGA--------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S2	T5S1
	---------TGATCTTTAGGTCTGTCCA----------------------------------------------------------------	19	3	-
	----TCCCTTGATCTTTAGGTCTGTC------------------------------------------------------------------	22	-	1
rat	agacTCCCTTGATCTTTAGGTCTGTCCAtaatcgagctgctgtcaaaccatcagccccatgtgagatgccaaggcagaaggtaaactgtcta
	********************************************************************************************
rat	((((..((((...((((.(((..(((((((.....((((.((......)).))))....)))).))))))))))...))))......)))).	0.700 -19.20

rat

chromosome:4:150766270:150766361:1

intergenic

block1934127 [novel_lenNOK_Multihit_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	0.238	no	no	0.55/0.58	19/22/0.50	1.5	0.0	2	0	2	0	2	2	3arm	129	nd	0.32	3	2	2	na	na

		reads	miRBase family seed
seed	--------------------------------ACGGCAC----------------	1	novel
seed	-----------------------------------GCACAGU-------------	1	novel
		len	cloning frequencies
			T3S1	T4S2
	----------------------------------GGCACAGTCAAGGCTGAGA--	19	1	-
	-------------------------------AACGGCACAGTCAAGGCTGAGA--	22	-	1
rat	gttccagtatgactctacccatggcaagttcAACGGCACAGTCAAGGCTGAGAat
	*******************************************************
rat	((((((((.(((((...((..(((.....)))..))...)))))..)))).))))	0.970 -12.10

rat

chromosome:6:54327057:54327111:-1

intergenic

block2147281 [novel_lenNOK_Multihit_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	0.449	no	no	0.55/0.58	19/22/0.50	1.5	0.0	2	0	2	0	2	2	3arm	129	nd	0.32	3	2	2	na	na

		reads	miRBase family seed
seed	--------------------------------ACGGCAC----------------	1	novel
seed	-----------------------------------GCACAGU-------------	1	novel
		len	cloning frequencies
			T3S1	T4S2
	----------------------------------GGCACAGTCAAGGCTGAGA--	19	1	-
	-------------------------------AACGGCACAGTCAAGGCTGAGA--	22	-	1
rat	gttccagtatggctctacccatggcaagttcAACGGCACAGTCAAGGCTGAGAat
	*******************************************************
rat	((((((((.(((((...((..(((.....)))..))...)))))..)))).))))	0.930 -11.50

rat

chromosome:7:108501064:108501118:-1

intergenic

block133093 [novel_lenNOK_Multihit_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	0.141	no	no	0.42/0.47	19/23/0.33	2.3	3.7	3	0	3	0	2	25	5arm	136	nd	0.37	3	3	3	na	na

		reads	miRBase family seed
seed	---CAUCCAU-------------------------------------------------------------------------------------------------------	2	novel
seed	----------GACAACU------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T3S1	T3S2
	--TCATCCATGACAACTTTGG--------------------------------------------------------------------------------------------	19	-	-	1
	--TCATCCATGACAACTTTGGCATC----------------------------------------------------------------------------------------	23	1	-	-
	---------TGACAACTTTGGCATCGTG-------------------------------------------------------------------------------------	19	-	1	-
rat	ggTCATCCATGACAACTTTGGCATCGTGgaagggctcatgaccacagtccatgtcatcactgccactcagaagactgtggatggcccctctggaaagctgtggcgtgatggcc
	*****************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000058917 ENSRNOG00000038610 Q8K4T8_RAT
rat	((((((.((((...((...(((.((.((((.((((.(((..((((((((..((..............))...))))))))))))))).))))))..)))))..))))))))))	0.740 -38.44

rat

chromosome:11:70680293:70680405:-1

Same_strand|Intronic_non-coding|ENSRNOT00000058917|ENSRNOG00000038610 ## ENSRNOG00000038610|protein_coding|Q8K4T8_RAT|Glyceraldehyde-3-phosphate-dehydrogenase (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q8K4T8]

block143653 [novel_lenNOK_Multihit_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	0.907	no	no	0.53/0.55	19/22/0.50	2.0	0.5	2	0	2	0	4	19	5arm	13	8	0.36	3	2	2	na	na

		reads	miRBase family seed
seed	-----GCUGGCC------------------------------------------------------------------------------------	1	novel
seed	---------GCCUCAA--------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1
	----TGCTGGCCTCAACGTACTTCGA----------------------------------------------------------------------	22	-	1
	--------GGCCTCAACGTACTTCGAA---------------------------------------------------------------------	19	1	-
rat	ctatTGCTGGCCTCAACGTACTTCGAAttatcaatgagccaactgctgctgctattgcctatgtcttagataagaaggtcggggctgaaaggaatg
	************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>++++++	ENSRNOT00000061950 ENSRNOG00000029311 Q7M081_RAT
rat	.((((.((((((((.((...((((...(((((....((.(((..((....))..))).))........))))))))))).))))))...)).))))	0.660 -18.50

rat

chromosome:11:5435024:5435119:1

Same_strand|Boundary_coding|ENSRNOT00000061950|ENSRNOG00000029311 ## ENSRNOG00000029311|protein_coding|Q7M081_RAT|DnaK-type molecular chaperone P72 (Fragments). [Source:UniProtKB/TrEMBL;Acc:Q7M081]

block706435 [novel_lenNOK_Multihit_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	0.049	no	no	0.53/0.55	19/22/0.50	2.0	0.5	2	0	2	0	4	19	5arm	13	8	0.32	3	2	2	na	na

		reads	miRBase family seed
seed	-----GCUGGCC------------------------------------------------------------------------------------	1	novel
seed	---------GCCUCAA--------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1
	----TGCTGGCCTCAACGTACTTCGA----------------------------------------------------------------------	22	-	1
	--------GGCCTCAACGTACTTCGAA---------------------------------------------------------------------	19	1	-
rat	ctatTGCTGGCCTCAACGTACTTCGAAttatcaatgagccaactgctgctgctattgcctatggcttagataagaaggttggggctgaaaggaatg
	************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>++++++	ENSRNOT00000052146 ENSRNOG00000031487 Q7M081_RAT
rat	.((((.(((((((((((...((((...(((((..(((((((...((..........))...)))))))))))))))))))))))))...)).))))	0.990 -29.40

rat

chromosome:18:49534213:49534308:-1

Same_strand|Boundary_coding|ENSRNOT00000052146|ENSRNOG00000031487 ## ENSRNOG00000031487|protein_coding|Q7M081_RAT|DnaK-type molecular chaperone P72 (Fragments). [Source:UniProtKB/TrEMBL;Acc:Q7M081]

novel_lenNOK_cloningHIGH_loopOverlap_randfoldOK_nonpairedHIGH (12 loci)

block282368 [novel_lenNOK_cloningHIGH_loopOverlap_randfoldOK_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	0.009	no	no	0.44/0.50	18/20/0.02	0.0	0.2	134	0	4	0	25	-2	3arm_loop	1	nd	0.32	2	151	4	na	na

		reads	miRBase family seed
seed	-------------------------------------------------UUCCGUG------------------------------------	151	novel
		len	cloning frequencies
			T1S1	T2S1	T4S1	T4S2
	------------------------------------------------TTTCCGTGCCCTAAAATG--------------------------	18	-	1	35	72
	------------------------------------------------TTTCCGTGCCCTAAAATGC-------------------------	19	1	-	12	27
	------------------------------------------------TTTCCGTGCCCTAAAATGCG------------------------	20	-	-	-	3
rat	tcattttgtttgctgttgaatcacagctctttagcaggaccccatacaTTTCCGTGCCCTAAAATGCgtgaaagactaaatgacaagatgaa
	********************************************************************************************
	------------------------------------------------------------------------------------------------------	ENSRNOT00000003489 ENSRNOG00000002593 Esrrg
rat	((((((((((....(((...((((.((..((((((((((...........))).)))..))))..))))))..))).....)))))))))).	0.970 -23.60

rat

chromosome:13:104369878:104369969:-1

Opposite_strand|Intronic_coding|ENSRNOT00000003489|ENSRNOG00000002593 ## ENSRNOG00000002593|protein_coding|Esrrg|Estrogen-related receptor gamma (Estrogen receptor-related protein 3) (Nuclear receptor subfamily 3 group B member 3). [Source:UniProtKB/Swiss-Prot;Acc:P62510]

block408406 [novel_lenNOK_cloningHIGH_loopOverlap_randfoldOK_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	0.001	no	no	0.35/0.39	18/22/0.04	0.0	0.3	187	0	7	0	7	-3	3arm_loop	1	nd	0.32	2	236	7	na	na

		reads	miRBase family seed
seed	------------------------UGUGCUU------------------	236	miR-218
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S1	T4S2	T5S1	T5S2
	-----------------------TTGTGCTTCTAGATTGGTA-------	19	71	37	1	1	2	6	22
	-----------------------TTGTGCTTCTAGATTGGT--------	18	35	22	1	1	-	12	16
	-----------------------TTGTGCTTCTAGATTGGTAA------	20	4	3	-	-	-	1	-
	-----------------------TTGTGCTTCTAGATTGGTAATG----	22	-	-	-	-	-	-	1
rat	tggcatcttcactctagtagcatTTGTGCTTCTAGATTGGTAatggcat
	*************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000007016 ENSRNOG00000005261 Fbxl5
rat	((.(((..(((.(((((.((((....)))).))))).)))..))).)).	1.000 -17.60

rat

chromosome:14:72488103:72488151:1

Same_strand|Intronic_coding|ENSRNOT00000007016|ENSRNOG00000005261 ## ENSRNOG00000005261|protein_coding|Fbxl5|F-box and leucine-rich repeat protein 5 Gene [Source:MGI (curated);Acc:Fbxl5-002]

block674120 [novel_lenNOK_cloningHIGH_loopOverlap_randfoldOK_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	0.006	no	no	0.47/0.50	18/21/0.03	0.0	0.0	161	0	10	0	24	-4	3arm_loop	1	nd	0.39	3	192	10	na	na

		reads	miRBase family seed
seed	---------------------------GCCUGUC----------------------------------	189	novel
seed	----------------------------CCUGUCU---------------------------------	3	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--------------------------TGCCTGTCTACACTTGCA------------------------	18	1	2	6	10	38	14	28	36	20	25
	--------------------------TGCCTGTCTACACTTGCAT-----------------------	19	1	1	-	-	1	-	-	1	-	-
	---------------------------GCCTGTCTACACTTGCAT-----------------------	18	-	-	-	-	-	-	1	-	-	2
	--------------------------TGCCTGTCTACACTTGCATGT---------------------	21	-	-	-	-	-	-	1	1	-	1
	--------------------------TGCCTGTCTACACTTGCATG----------------------	20	-	-	-	-	1	-	-	-	-	1
rat	gtgcacgcatgcacacacgtggtcaaTGCCTGTCTACACTTGCAtgtgctctcaaacacacctgcaca
	********************************************************************
rat	(((((((((((((.....((((.((.....)).))))...))))))))..............))))).	0.910 -19.43

rat

chromosome:17:76569956:76570023:1

intergenic

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