Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_5varHIGH_loopOverlap_bulgeHIGH (6 loci)

block1725934 [novel_5varHIGH_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	0.239	no	no	0.45/0.45	20/22/1.00	1.5	2.5	2	0	2	0	7	-3	3arm	3	nd	0.18	4	2	2	na	na

		reads	miRBase family seed
seed	------------------------------AAGAUCU------------------------	1	novel
seed	---------------------------------AUCUUUU---------------------	1	novel
		len	cloning frequencies
			T2S1	T2S2
	--------------------------------GATCTTTTGAGCAGGACCCTTA-------	22	-	1
	-----------------------------CAAGATCTTTTGAGCAGGAC------------	20	1	-
rat	tttatctaagttgcttcccaagtggattcCAAGATCTTTTGAGCAGGACCCTTAgacagaa
	*************************************************************
rat	(((.(((((((((((...((((.(((((....))))))))))))))....)))))).))).	0.970 -11.50

rat

chromosome:5:31436478:31436538:-1

intergenic

block1973528 [novel_5varHIGH_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	0.721	no	no	0.33/0.36	22/24/1.00	3.0	3.8	4	0	2	0	18	-19	5arm_loop_3arm	1	nd	0.25	4	4	2	na	na

		reads	miRBase family seed
seed	----------------------------------GCUAACA----------------------------------	2	novel
seed	----------------------------GGCAAUG----------------------------------------	2	novel
		len	cloning frequencies
			T1S2	T5S1
	---------------------------------TGCTAACATTTCAAAGATGGTACT------------------	24	2	-
	---------------------------TGGCAATGCTAACATTTCAAAG--------------------------	22	-	1
	---------------------------TGGCAATGCTAACATTTCAAAGA-------------------------	23	-	1
rat	agatcagactgtggccacatgaggtctTGGCAATGCTAACATTTCAAAGATGGTACTgttttaggggaggggtct
	***************************************************************************
rat	(((((((((.((.((((..((((((.(((((...))))).))))))....)))))).)))).........)))))	0.610 -15.20

rat

chromosome:6:122578889:122578963:-1

intergenic

block1027791 [novel_5varHIGH_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	0.447	no	no	0.55/0.60	18/23/0.75	5.5	5.8	4	0	4	0	40	-11	5arm_loop_3arm	1	nd	0.30	4	4	4	na	na

		reads	miRBase family seed
seed	--------------------------------------------------CCACUGG------------------------------------------------------------	2	novel
seed	-----------------------------------------GAUUGGU---------------------------------------------------------------------	1	novel
seed	---------------------------------------------GGUGGCC-----------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T3S1	T3S2	T5S2
	-------------------------------------------------GCCACTGGTACAGACTTGTG------------------------------------------------	20	-	1	-	-
	----------------------------------------CGATTGGTGGCCACTGGTAC---------------------------------------------------------	20	-	-	1	-
	--------------------------------------------TGGTGGCCACTGGTACAGACTTG--------------------------------------------------	23	-	-	-	1
	-------------------------------------------------GCCACTGGTACAGACTTG--------------------------------------------------	18	1	-	-	-
rat	gggggccggatacactacgggtccctgagttatggttgctCGATTGGTGGCCACTGGTACAGACTTGTGgccctagggcacatctcttttgagcgcagcgggccggcacaggttcct
	*********************************************************************************************************************
rat	(((..((.......((...((((((((.(((..((((((((...(((.((((((.(((....))).)))))))))))))).))).......))).))).)))))))....))..)))	0.430 -42.30

rat

chromosome:1:201601946:201602062:1

intergenic

block234823 [novel_5varHIGH_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	0.641	no	no	0.50/0.55	19/24/0.80	1.2	0.6	5	0	1	0	8	-6	5arm_loop	1	nd	0.29	4	5	1	na	na

		reads	miRBase family seed
seed	-------------AGAAGGC-----------------------------------------------	3	novel
seed	-----------UCAGAAG-------------------------------------------------	1	novel
seed	---------GUUCAGA---------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	------------CAGAAGGCGTCGTTCACAGA-----------------------------------	20	3
	--------TGTTCAGAAGGCGTCGTTCACAGA-----------------------------------	24	1
	----------TTCAGAAGGCGTCGTTCAC--------------------------------------	19	1
rat	gagacccgTGTTCAGAAGGCGTCGTTCACAGAtggatagcaagttttgtacggatttgcacggtttt
	*******************************************************************
rat	((((.((((((.(((((.((.(((((....)))))...))...))))).........))))))))))	0.540 -13.80

rat

chromosome:12:44302792:44302858:1

intergenic

novel_5varHIGH_loopOverlap_randfoldOK (6 loci)

block50406 [novel_5varHIGH_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	0.007	no	no	0.58/0.64	22/24/1.00	2.5	1.5	2	0	2	0	5	-3	5arm_loop	1	nd	0.08	1	2	2	na	na

		reads	miRBase family seed
seed	------GCUAGGC----------------------------------------------------	1	novel
seed	-----------GCUGCUC-----------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2
	-----AGCTAGGCTGCTCTGCTGCTTCTG------------------------------------	24	-	1
	----------GGCTGCTCTGCTGCTTCTGCGA---------------------------------	22	1	-
rat	gcggaAGCTAGGCTGCTCTGCTGCTTCTGCGAtcgggcggcggcggggcgagccaagctgcggcg
	*****************************************************************
	---------------------------------------------------------------------------	ENSRNOT00000005035 ENSRNOG00000003673 Pcnt1
rat	((...((((.(((((((((((((((((((....)))).))))))))))).)))).))))...)).	0.980 -36.60

rat

chromosome:10:105818705:105818769:-1

Opposite_strand|Intronic_non-coding|ENSRNOT00000005035|ENSRNOG00000003673 ## ENSRNOG00000003673|protein_coding|Pcnt1|pericentrin 1 [Source:RefSeq_peptide;Acc:NP_001020572]

block97131 [novel_5varHIGH_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	0.59/0.62	21/23/1.00	1.7	2.1	7	0	3	0	6	-2	3arm	1	nd	0.10	1	7	3	na	na

		reads	miRBase family seed
seed	------------------------------------------------------ACCCCAG---------------------	5	novel
seed	-------------------------------------------------UUGGUAC--------------------------	1	novel
seed	-----------------------------------------------UCUUGGU----------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T4S1
	-----------------------------------------------------TACCCCAGAGCCACACTCCATC-------	22	3	1	-
	------------------------------------------------CTTGGTACCCCAGAGCCACAC-------------	21	-	1	-
	-----------------------------------------------------TACCCCAGAGCCACACTCCATCC------	23	1	-	-
	----------------------------------------------CTCTTGGTACCCCAGAGCCAC---------------	21	-	-	1
rat	agactaagtttagagttccagaagctggttctggggttccgagaacCTCTTGGTACCCCAGAGCCACACTCCATCCttggtc
	**********************************************************************************
	--------------------------------------------------------------------------------------------	ENSRNOT00000047383 ENSRNOG00000003033 NP_001099315.2
rat	.(((((((....((((.........((((((((((((.(((((.....))))).)))))))))))).))))....)))))))	0.850 -39.10

rat

chromosome:10:92276005:92276086:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000004140|ENSRNOG00000003033 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000047383|ENSRNOG00000003033 ## ENSRNOG00000003033|protein_coding|NP_001099315.2|phospholipase C, delta 3 [Source:RefSeq_peptide;Acc:NP_001099315]

block188298 [novel_5varHIGH_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	0.003	no	no	0.70/0.71	21/23/1.00	3.0	2.0	2	0	2	0	24	-1	3arm	1	nd	0.17	1	2	2	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------CACCCUU-------------------------------------	1	miR-336
seed	--------------------------------------------------------------CAACGCC-------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2
	-------------------------------------------------------------ACAACGCCACCCTTCGCGCTGGG----------------------------	23	1	-
	-------------------------------------------------------------------CCACCCTTCGCGCTGGGGACT------------------------	21	-	1
rat	gcaaagctgcagcgataatgctgtaaaatccacaacgcgaaaggtggcattgacgataacaACAACGCCACCCTTCGCGCTGGGGACTgatgcgcaggcgccgcactgtagc
	****************************************************************************************************************
rat	((..((.(((.(((....(((.(((...(((.((.((((((.((((((.(((..........))).)))))).)))))).)).)))....))))))..))).)))))...))	0.680 -42.40

rat

chromosome:12:19854257:19854368:-1

intergenic ## {SimpF: oe = 0.83 -1 CpG}

block913040 [novel_5varHIGH_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	0.005	no	no	0.59/0.64	22/22/1.00	3.0	3.0	2	0	2	0	23	-1	3arm	1	nd	0.09	2	2	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------CCAGCUG-------------------------------------	1	novel
seed	-----------------------------------------------------------------GCAGGAC-------------------------------------------	1	novel
		len	cloning frequencies
			T2S2	T5S1
	----------------------------------------------------------------------ACCAGCTGAAGCACAGGAGCAC-----------------------	22	1	-
	----------------------------------------------------------------CGCAGGACCAGCTGAAGCACAG-----------------------------	22	-	1
rat	tgtcctgaatgctcctgtgttgggatgacttctgtgtcttcagaaggtcttgctgctgccatccCGCAGGACCAGCTGAAGCACAGGAGCACatgccacttgctgggcctctgca
	*******************************************************************************************************************
rat	.((...((..((.((.(((.(((.(((.((((((((.((((((..((((((((............))))))))..))))))))))))))..))).)))..))).)))).)).)).	0.890 -46.60

rat

chromosome:1:206839700:206839814:-1

intergenic

block998955 [novel_5varHIGH_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	0.003	no	no	0.29/0.35	20/24/1.00	2.3	0.7	3	0	1	0	6	-7	3arm_loop	1	nd	0.10	1	3	1	na	na

		reads	miRBase family seed
seed	------------------------------------------UAUAAGA------------------	1	novel
seed	-------------------------------------AGAAUUA-----------------------	1	novel
seed	---------------------------------------AAUUAUA---------------------	1	novel
		len	cloning frequencies
			T5S1
	--------------------------------------GAATTATAAGACTTTCCAGACAG------	23	1
	------------------------------------TAGAATTATAAGACTTTCCAGACA-------	24	1
	-----------------------------------------TTATAAGACTTTCCAGACAG------	20	1
rat	tagttgggatgtaagaacactggaaacagttttgttTAGAATTATAAGACTTTCCAGACAGccagct
	*******************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000016427 ENSRNOG00000012031 St8sia2
rat	.((((((..(((.......((((((..((((((((........))))))))))))))))).))))))	0.560 -19.61

rat

chromosome:1:129037901:129037967:1

Same_strand|Intronic_coding|ENSRNOT00000016427|ENSRNOG00000012031 ## ENSRNOG00000012031|protein_coding|St8sia2|Alpha-2,8-sialyltransferase 8B (EC 2.4.99.-) (ST8Sia II) (Sialyltransferase X) (STX). [Source:UniProtKB/Swiss-Prot;Acc:Q07977]

block1093435 [novel_5varHIGH_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	0.003	no	no	0.45/0.62	20/26/0.89	7.0	7.1	9	0	1	0	32	-24	5arm_loop_3arm	1	nd	0.18	3	9	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------CAGAGUC----------------------------------------------	3	novel
seed	-----------------------------------------------------AGAGACC-------------------------------------------------------	2	novel
seed	------------------------------------------------GACAUAG------------------------------------------------------------	2	novel
seed	----------------------------------------------------UAGAGAC--------------------------------------------------------	1	novel
seed	-------------------------------------------------------AGACCAU-----------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------------------------------------------TCAGAGTCGTCGCTGTCCCTCA--------------------------------	22	3
	-----------------------------------------------TGACATAGAGACCATCAGAGTC----------------------------------------------	22	2
	----------------------------------------------------TAGAGACCATCAGAGTCGTC-------------------------------------------	20	2
	---------------------------------------------------ATAGAGACCATCAGAGTCGTC-------------------------------------------	21	1
	------------------------------------------------------GAGACCATCAGAGTCGTCGCTGTCCC-----------------------------------	26	1
rat	ccagaattagagcctctgtaggccagcagggaccttggacaatgtgaTGACATAGAGACCATCAGAGTCGTCGCTGTCCCTCAtgcgaggttgcgaggctctaatgtagactggt
	*******************************************************************************************************************
rat	((((.(((((((((((.(((.(((.((((((.....(((((..((((((((...((.....))...)))))))))))))))).)))..))))))))))))))))).....)))).	0.990 -49.00

rat

chromosome:20:5535218:5535332:1

intergenic

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