Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_multiarm_DicerNOK_loopOverlap_bulgeHIGH (9 loci)

sblock1836 [novel_multiarm_DicerNOK_loopOverlap_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	0.026	no	no	0.36/0.65	19/23/0.80	0.0 0.0 0.0 0.0	0.0 0.0 0.0 0.0	2 1 1 1	0 0 0 0	1 1 1 1	0 0 0 0	16 51 25 20	18 -13 1 8	5arm 5arm_loop_3arm 3arm 3arm	1 2 2 4	nd nd nd nd	0.39 0.58 0.32 0.30	7 6 6 4	5	2	-17	-18

		reads	miRBase family seed
seed	-----------------CCCCAGC---------------------------------------------------------------------------------------	2	novel
seed	----------------------------------------------------UGCAUCU----------------------------------------------------	1	novel
seed	------------------------------------------------------------------------UUGACCA--------------------------------	1	novel
seed	-----------------------------------------------------------------GUUCUAU---------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T5S1
	----------------TCCCCAGCTCCACAGTCCCTGAG------------------------------------------------------------------------	23	2	-
	----------------------------------------------------------------TGTTCTATTTGACCAAACTCAG-------------------------	22	1	-
	---------------------------------------------------GTGCATCTCCATATGTTCT-----------------------------------------	19	-	1
	-----------------------------------------------------------------------TTTGACCAAACTCAGGGCCA--------------------	20	-	1
rat	atgtccagaaaatcccTCCCCAGCTCCACAGTCCCTGAGtgcctgagtcatGTGCATCTCCATATGTTCTATTTGACCAAACTCAGGGCCAttcaagcttggtgtgacatt
	***************************************************************************************************************
rat	(((((((...........((.((((.......((((((((...((.((((...((((......))))......)))))).)))))))).......)))).)))).))))).	0.800 -28.94

rat

chromosome:1:102763291:102763401:1

intergenic

sblock3085 [novel_multiarm_DicerNOK_loopOverlap_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	0.542	no	no	0.60/0.67	18/23/0.83	0.0 0.0	2.4 0.0	5 1	0 0	4 1	0 0	37 19	-7 18	5arm_loop_3arm 3arm	1 1	35 0	0.26 0.35	4 3	6	5	15	17

		reads	miRBase family seed
seed	--------------------------------------CCGGGAG---------------------------------------------------------------------	5	novel
seed	----------------------------------------------------------------------------GUCUCCU-------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T3S2	T4S1
	-------------------------------------ACCGGGAGAGACCTGGGATG---------------------------------------------------------	20	-	-	1	-	1
	-------------------------------------ACCGGGAGAGACCTGGGATGT--------------------------------------------------------	21	-	-	-	1	-
	---------------------------------------------------------------------------TGTCTCCTCCCTCTCCCTAG-------------------	20	1	-	-	-	-
	-------------------------------------ACCGGGAGAGACCTGGGATGTCA------------------------------------------------------	23	-	-	-	1	-
	-------------------------------------ACCGGGAGAGACCTGGGA-----------------------------------------------------------	18	-	1	-	-	-
rat	gggcagtgtgtaaaagatgcaggtgaggttggaagtgACCGGGAGAGACCTGGGATGTCAgggtcactcacttgcTGTCTCCTCCCTCTCCCTAGgaatctcagcagatgcttg
	******************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000002747 ENSRNOG00000002001 Itsn1
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000047843 ENSRNOG00000002001 Itsn1
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000042750 ENSRNOG00000002001 Itsn1
rat	(((((...(((...((((..(((.((((..(((...(((((((.(((.(((((....)))))....))).))))..))))))..))))..)))....))))..)))..))))).	0.610 -33.70

rat

chromosome:11:31819095:31819208:1

Same_strand|Boundary_non-coding|ENSRNOT00000050209|ENSRNOG00000002001 ## Same_strand|Intronic_coding|ENSRNOT00000047843|ENSRNOG00000002001 ## ENSRNOG00000002001|protein_coding|Itsn1|Intersectin-1 (EH domain and SH3 domain regulator of endocytosis 1). [Source:UniProtKB/Swiss-Prot;Acc:Q9WVE9]

sblock4525 [novel_multiarm_DicerNOK_loopOverlap_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	0.36/0.45	20/22/1.00	0.0 0.0 0.0	0.0 0.0 0.0	1 1 1	0 0 0	1 1 1	0 0 0	15 20 0	1 -6 13	5arm 5arm_loop_3arm 3arm	1 1 1	nd nd nd	0.30 0.45 0.38	4 6 3	3	2	12	13

		reads	miRBase family seed
seed	----------------UAGGAUG------------------------------------------------------	1	novel
seed	--------------------------------------------------------AGAACUA--------------	1	novel
seed	---------------------UGAACAG-------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T3S2
	---------------CTAGGATGAACAGATGCAAC------------------------------------------	20	1	-
	-------------------------------------------------------CAGAACTAAGAACTCCTTAGAG	22	-	1
	--------------------ATGAACAGATGCAACCAGATTT-----------------------------------	22	1	-
rat	ttctgagtaaccttcCTAGGATGAACAGATGCAACCAGATTTggtctgcagccttCAGAACTAAGAACTCCTTAGAG
	*****************************************************************************
	---------------------------------------------------------------------------------------	ENSRNOT00000013381 ENSRNOG00000010080
rat	.((((((.....(((.(((..((((....(((((((......))).))))...))))...))).)))...)))))).	0.530 -19.20

rat

chromosome:15:87080822:87080898:-1

Opposite_strand|Intronic_coding|ENSRNOT00000013381|ENSRNOG00000010080 ## ENSRNOG00000010080|protein_coding||

sblock5797 [novel_multiarm_DicerNOK_loopOverlap_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	0.042	no	no	0.50/0.55	20/20/1.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	31 0	-4 28	5arm_loop 3arm	2 2	nd nd	0.30 0.58	5 11	2	2	0	-14

		reads	miRBase family seed
seed	--------------------------------GGCUGUG----------------------------------------------------------------	1	novel
seed	------------------------------------------------------------------------------------GAGGCCC------------	1	novel
		len	cloning frequencies
			T1S2	T5S2
	-----------------------------------------------------------------------------------AGAGGCCCAGAGATCTGTGT	20	-	1
	-------------------------------TGGCTGTGAGGAGCTGAAAA----------------------------------------------------	20	1	-
rat	tggagtttcctgtcctctaggttgacttagaTGGCTGTGAGGAGCTGAAAAgcagtggcatttcataggacctacctagaggcAGAGGCCCAGAGATCTGTGT
	*******************************************************************************************************
rat	(((.((((.(((.(((((((((..........((((((((((.((((........)))).))))))))..)).)))))))))))))))))))...........	0.870 -34.50

rat

chromosome:19:45492709:45492811:-1

intergenic

sblock7152 [novel_multiarm_DicerNOK_loopOverlap_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	0.634	no	no	0.48/0.60	19/23/0.75	0.0 0.0	0.5 0.5	2 2	0 0	2 2	0 0	10 12	-3 -2	5arm_loop 3arm_loop	1 1	nd nd	0.41 0.26	6 4	4	3	1	4

		reads	miRBase family seed
seed	-----------------------------------GGUUUCU------------------------	2	novel
seed	-----------GUUCAGG------------------------------------------------	2	novel
		len	cloning frequencies
			T3S2	T5S1	T5S2
	----------------------------------TGGTTTCTTCTGGACCCCCC------------	20	-	1	-
	----------GGTTCAGGTTGCTTGGAAATGC----------------------------------	22	-	-	1
	----------------------------------TGGTTTCTTCTGGACCCCC-------------	19	-	-	1
	----------GGTTCAGGTTGCTTGGAAATGCT---------------------------------	23	1	-	-
rat	cagcccgtcaGGTTCAGGTTGCTTGGAAATGCTcTGGTTTCTTCTGGACCCCCCtcctttgacctg
	******************************************************************
rat	......((((((((((((......((((((......)))))))))))))).........))))...	0.580 -13.70

rat

chromosome:20:5544968:5545033:1

intergenic

sblock8716 [novel_multiarm_DicerNOK_loopOverlap_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	0.040	no	no	0.45/0.62	20/22/1.00	0.0 0.0 0.0	0.0 0.0 0.0	1 1 1	0 0 0	1 1 1	0 0 0	25 37 19	7 -6 22	5arm 5arm_loop_3arm 3arm	1 1 1	nd nd nd	0.24 0.36 0.35	4 6 4	3	2	11	11

		reads	miRBase family seed
seed	----------------------------------------------------------------------------------UACAGGU-------------------------------	1	novel
seed	--------------------------------------UCCACCC---------------------------------------------------------------------------	1	novel
seed	--------------------------ACUUCCA---------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T5S1
	---------------------------------------------------------------------------------GTACAGGTCATGCTATGTTG-------------------	20	-	1
	-------------------------------------CTCCACCCCCAAGCATAACCAC-------------------------------------------------------------	22	1	-
	-------------------------GACTTCCATCTCCTCCACCCC--------------------------------------------------------------------------	21	1	-
rat	tggccagctgataatgctagctcatGACTTCCATCTCCTCCACCCCCAAGCATAACCACatcctctgtggggaggaggccaGTACAGGTCATGCTATGTTGgtacttcttacgtgtccca
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000022874 ENSRNOG00000016778 Cops7a_predicted
rat	.((...(((((.(((((((((.((((((((....(((((((.((((((((.((......)).)).)).)))).)))))..))...))))))))....))))))).)).))).))...)).	0.950 -35.10

rat

chromosome:4:161086325:161086444:-1

Same_strand|Boundary_non-coding|ENSRNOT00000038281|ENSRNOG00000016778 ## Same_strand|Intronic_coding|ENSRNOT00000022874|ENSRNOG00000016778 ## ENSRNOG00000016778|protein_coding|Cops7a_predicted|COP9 (constitutive photomorphogenic) homolog, subunit 7a [Source:RefSeq_peptide;Acc:NP_001040563]

sblock8764 [novel_multiarm_DicerNOK_loopOverlap_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	0.039	no	no	0.35/0.65	19/23/0.83	0.0 0.0 0.0	1.5 2.7 0.0	2 3 1	0 0 0	2 2 1	0 0 0	18 38 23	11 -4 14	5arm 3arm_loop 3arm	2 5 5	nd nd nd	0.45 0.35 0.30	5 4 4	6	4	0	0

		reads	miRBase family seed
seed	--------------------------------------------------------CUCAGCC-----------------------------------------------------	3	novel
seed	-------------------UCUGUUU------------------------------------------------------------------------------------------	2	novel
seed	--------------------------------------------------------------------------AGGGCGC-----------------------------------	1	novel
		len	cloning frequencies
			T3S2	T4S1	T4S2	T5S1
	-------------------------------------------------------TCTCAGCCCTCGGCTCTTTAGGG--------------------------------------	23	1	-	-	1
	-------------------------------------------------------TCTCAGCCCTCGGCTCTTT------------------------------------------	19	-	-	-	1
	------------------TTCTGTTTTCGACCTTTTCCTTT---------------------------------------------------------------------------	23	-	-	1	-
	------------------TTCTGTTTTCGACCTTTTCC------------------------------------------------------------------------------	20	-	-	-	1
	-------------------------------------------------------------------------TAGGGCGCCACATGGAGACC-----------------------	20	-	1	-	-
rat	ccactttcgtccaggtgtTTCTGTTTTCGACCTTTTCCTTTagcttggggtttcaTCTCAGCCCTCGGCTCTTTAGGGCGCCACATGGAGACCggcttggactgatttttagagga
	********************************************************************************************************************
rat	((.((.((((((((((((((((((...((.((((.......((((.((((((.......)))))).))))....))))))....))))))))..)))))))).)).....)).)).	0.990 -36.40

rat

chromosome:4:164896377:164896492:-1

intergenic

sblock9098 [novel_multiarm_DicerNOK_loopOverlap_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	0.35/0.48	19/23/0.83	0.0 0.7 0.0	0.0 2.3 0.0	1 3 2	0 0 0	1 3 1	0 0 0	2 7 7	6 -4 -1	5arm 5arm_loop 3arm	1 1 1	nd nd nd	0.25 0.25 0.26	4 4 5	6	3	3	5

		reads	miRBase family seed
seed	--------AGUUGCA-----------------------------------------------------	2	novel
seed	---------------------------------------CAGACUA----------------------	2	novel
seed	---CAAAUAG----------------------------------------------------------	1	novel
seed	----------UUGCAGG---------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T5S1	T5S2
	--------------------------------------GCAGACTACTGCATATTATGTCA-------	23	-	2	-
	-------TAGTTGCAGGTTATGGATC------------------------------------------	19	-	1	-
	--TCAAATAGTTGCAGGTTATG----------------------------------------------	20	-	1	-
	-------TAGTTGCAGGTTATGGATCT-----------------------------------------	20	-	-	1
	---------GTTGCAGGTTATGGATCTGGAGA------------------------------------	23	1	-	-
rat	gtTCAAATAGTTGCAGGTTATGGATCTGGAGAggagaaGCAGACTACTGCATATTATGTCAtgtggac
	********************************************************************
rat	(((((.((((((((((....(((.((((...........)))))))))))).)))))......)))))	0.620 -13.20

rat

chromosome:4:164260980:164261047:1

intergenic

novel_multiarm_DicerNOK_loopOverlap_randfoldOK (9 loci)

sblock1004 [novel_multiarm_DicerNOK_loopOverlap_randfoldOK]

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	0.004	no	no	0.50/0.85	18/22/0.75	0.0 1.0 0.0	0.0 0.0 0.0	1 2 1	0 0 0	1 2 1	0 0 0	17 37 28	22 -21 5	5arm 3arm_loop 3arm	1 1 1	nd nd nd	0.50 0.25 0.24	7 2 2	4	4	0	18

		reads	miRBase family seed
seed	-----------------------------------------------------------CCGCCGG-------------------------------------------------	1	novel
seed	---------------------------------------------------------UCCCGCC---------------------------------------------------	1	novel
seed	------------------CCUAAAA------------------------------------------------------------------------------------------	1	novel
seed	-------------------------------------------------------------------AGCCCCA-----------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T5S1
	----------------------------------------------------------CCCGCCGGGAGCCCCAACCC-------------------------------------	20	-	1	-	-
	------------------------------------------------------------------GAGCCCCAACCCGGCCCGTGT----------------------------	21	-	-	1	-
	-----------------GCCTAAAACGTAGACCAG--------------------------------------------------------------------------------	18	1	-	-	-
	--------------------------------------------------------TTCCCGCCGGGAGCCCCAACCC-------------------------------------	22	-	-	-	1
rat	ggcagaccctgcccagcGCCTAAAACGTAGACCAGggccgggtttcggccacccggTTCCCGCCGGGAGCCCCAACCCGGCCCGTGTggtgggctctggtgttcctcgctggcca
	*******************************************************************************************************************
rat	(((((.....((((((.(((((..(((.......((((((((((..(((..((((((....)))))).)))..)))))))))).)))..))))).)))).))......))).)).	0.970 -61.40

rat

chromosome:1:210177801:210177915:-1

intergenic ## {SimpF: oe = 0.88 -1 CpG}

sblock11650 [novel_multiarm_DicerNOK_loopOverlap_randfoldOK]

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	0.41/0.45	20/22/1.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	25 31	-1 -3	5arm_loop 3arm_loop	1 1	nd nd	0.23 0.20	2 2	2	1	-2	-4

		reads	miRBase family seed
seed	-----------------------------------------------------CCCUGUG-------------------------------------------	1	novel
seed	--------------------------CAGCCUG----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------TCAGCCTGTTAAATCACACAGT--------------------------------------------------------	22	1
	----------------------------------------------------TCCCTGTGTGAATTAGCAAG-------------------------------	20	1
rat	ggcagtggtgtccccaaagagctctTCAGCCTGTTAAATCACACAGTtttccTCCCTGTGTGAATTAGCAAGcagaagaggaggtggagtgctccctactgct
	*******************************************************************************************************
rat	((((((((.((..(((.....((((((.((.((((((.((((((((.........)))))))).)))))).)).))))))....)))...))...))))))))	0.920 -41.50

rat

chromosome:8:57725223:57725325:-1

intergenic

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