Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_shortStem_loopOverlap_randfoldOK_bulgeHIGH (7 loci)

block1601091 [novel_shortStem_loopOverlap_randfoldOK_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	0.002	no	no	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	0	-2	3arm_loop	7	nd	0.25	4	1	1	na	na

		reads	miRBase family seed
seed	----------------------GGGAACC-------------	1	novel
		len	cloning frequencies
			T5S1
	---------------------TGGGAACCTGTGGGGAATTCT	21	1
rat	ggagttcaccaggttccactcTGGGAACCTGTGGGGAATTCT
	******************************************
rat	(((((((..((((((((......))))))))....)))))))	1.000 -19.70

rat

chromosome:4:164816037:164816078:-1

intergenic

block2581385 [novel_shortStem_loopOverlap_randfoldOK_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	0.009	no	no	0.50/0.50	20/20/1.00	0.0	0.0	1	0	1	0	4	-2	3arm_loop	1	nd	0.25	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------AUGUAUC----------------	1	novel
		len	cloning frequencies
			T3S2
	-------------------------CATGTATCTTGGGTTGGCAG----	20	1
rat	aggactgtcaacctgattgtcaaacCATGTATCTTGGGTTGGCAGcttg
	*************************************************
rat	(((.((((((((((((....((.....))....))))))))))))))).	1.000 -16.80

rat

chromosome:9:29140829:29140877:1

intergenic

novel_5varHIGH_bulgeHIGH (6 loci)

block45470 [novel_5varHIGH_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	0.453	no	no	0.50/0.50	20/20/1.00	1.5	1.5	2	0	2	0	19	5	5arm	1	nd	0.30	4	2	2	na	na

		reads	miRBase family seed
seed	--------------------ACAUCCU--------------------------------------------------------------------------------	1	novel
seed	-----------------------UCCUGGA-----------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T5S2
	----------------------ATCCTGGATCTGGAGTATCC-----------------------------------------------------------------	20	1	-
	-------------------CACATCCTGGATCTGGAGTA--------------------------------------------------------------------	20	-	1
rat	gaggcctgcgggcttgcagCACATCCTGGATCTGGAGTATCCctggcaggagcggagtcagaggggctgcggatcctaaagctgggctgggaagaacttgcgaactt
	***********************************************************************************************************
rat	(((...((((((.((.((((.((....(((((((.(((.((((((((.........))))).)))))).)))))))......)).)))).))....))))))..)))	0.530 -36.50

rat

chromosome:10:95665884:95665990:-1

intergenic ## {SimpF: oe = 0.91 -1 CpG}

block1022036 [novel_5varHIGH_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	0.103	no	no	0.35/0.46	20/24/1.00	2.0	4.0	2	0	2	0	8	1	5arm	1	13	0.21	4	2	2	na	na

		reads	miRBase family seed
seed	---------UUACAGA----------------------------------------------------------------	1	novel
seed	-------------AGACUAU------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T3S2
	------------CAGACTATACCCAACAAGCAACTC--------------------------------------------	24	1	-
	--------TTTACAGACTATACCCAACA----------------------------------------------------	20	-	1
rat	tcccatctTTTACAGACTATACCCAACAAGCAACTCaaaggtgagtactgtttctggtctggtccttgtagacagcaagg
	********************************************************************************
	++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000031891 ENSRNOG00000023360 Fus
rat	.((...(((((((((((((.(((....((((((((((....)))))..)))))..))).)))))..)))))).))...))	0.440 -18.40

rat

chromosome:1:187252797:187252876:1

Same_strand|Boundary_coding|ENSRNOT00000031891|ENSRNOG00000023360 ## ENSRNOG00000023360|protein_coding|Fus|fusion (involved in t(12;16) in malignant liposarcoma) (predicted) [Source:RefSeq_peptide;Acc:NP_001012137]

block1145571 [novel_5varHIGH_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	0.137	no	no	0.50/0.62	21/22/1.00	2.0	1.7	3	0	2	0	24	4	3arm	1	nd	0.29	4	3	2	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------------------UAGGAGU-------------------------------------	2	novel
seed	----------------------------------------------------------------GUUUUCU-------------------------------------------	1	novel
		len	cloning frequencies
			T2S2	T3S1
	---------------------------------------------------------------------CTAGGAGTTCGCGGTCGGAAG------------------------	21	-	2
	---------------------------------------------------------------AGTTTTCTAGGAGTTCGCGGTC-----------------------------	22	1	-
rat	gctccaaaaagggggcggggctgggcggggccgcggaatataagcttctccggctgccgagccAGTTTTCTAGGAGTTCGCGGTCGGAAGtgcagctaaagcaccgggtggggc
	******************************************************************************************************************
rat	((((((....((..((..(((((.((..(((((((((..........((((((((....)))).........)))))))))))))....)).)))))...)).))...))))))	0.540 -47.80

rat

chromosome:2:51845421:51845534:-1

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

block1781264 [novel_5varHIGH_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	0.119	no	no	0.62/0.65	20/21/1.00	1.5	2.0	2	0	2	0	7	8	5arm	1	nd	0.30	4	2	2	na	na

		reads	miRBase family seed
seed	-----------CACCCUG---------------------------------------------------------------	1	novel
seed	--------GCUCACC------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2	T5S2
	----------TCACCCTGTGTCCCCACCAAC--------------------------------------------------	21	-	1
	-------TGCTCACCCTGTGTCCCCAC------------------------------------------------------	20	1	-
rat	gggtgagTGCTCACCCTGTGTCCCCACCAACaaatccacacacacagtgaagcctcgggtgggcagttgagctcctttcct
	*********************************************************************************
	-------------------------------------------------------------------------------------------	ENSRNOT00000047151 ENSRNOG00000007922 Cldn19
rat	(((.(((.(((((..(((....((((((........(((.......)))........))))))))).)))))..))).)))	0.890 -25.29

rat

chromosome:5:139841448:139841528:-1

Opposite_strand|Intronic_coding|ENSRNOT00000047151|ENSRNOG00000007922 ## ENSRNOG00000007922|protein_coding|Cldn19|Claudin-19. [Source:UniProtKB/Swiss-Prot;Acc:Q5QT56]

block914981 [novel_5varHIGH_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	0.382	no	no	0.55/0.55	20/20/1.00	1.5	1.5	2	0	2	0	21	6	3arm	1	nd	0.30	4	2	2	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------GGGCUAU---------------------------------	1	novel
seed	-----------------------------------------------------------------------------UCAGGGC------------------------------------	1	novel
		len	cloning frequencies
			T4S1	T5S2
	-------------------------------------------------------------------------------AGGGCTATTTGGGACTCTGC---------------------	20	1	-
	----------------------------------------------------------------------------CTCAGGGCTATTTGGGACTC------------------------	20	-	1
rat	gctcattgggaggaggatccgctcagagtaatagaggagggactggcgctgaaaggcaggggcagctggactgccaCTCAGGGCTATTTGGGACTCTGCactttgcattcctgctagaga
	************************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000028749 ENSRNOG00000021174 Lrp16
	----------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000040290 ENSRNOG00000021174 Lrp16
rat	.(((..(((.(((((........((((((..(((((....((.((((.((((..(((((...........)))))..)))).)))).))....))))).))))))..))))).)))))).	0.440 -39.30

rat

chromosome:1:209731725:209731844:-1

Opposite_strand|Intronic_coding|ENSRNOT00000028749|ENSRNOG00000021174 ## ENSRNOG00000021174|protein_coding|Lrp16|MACRO domain-containing protein 1 (Protein LRP16) (Fragment). [Source:UniProtKB/Swiss-Prot;Acc:Q8K4G6]

block881035 [novel_5varHIGH_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	0.29/0.29	21/21/1.00	1.5	1.5	2	0	2	0	8	9	3arm	1	nd	0.24	4	2	2	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------ACAUCCA------------------------	1	novel
seed	---------------------------------------------------------------UCCAUUC---------------------	1	novel
		len	cloning frequencies
			T1S2	T5S1
	--------------------------------------------------------------ATCCATTCGTTTAAAAGTTCA--------	21	-	1
	-----------------------------------------------------------TACATCCATTCGTTTAAAAGT-----------	21	1	-
rat	cttaagggtgaagttcaaggctttcagactccagggactgttggtcaccaggccaaagaTACATCCATTCGTTTAAAAGTTCAtcgttcag
	*******************************************************************************************
rat	((.((.(((((........(((((.((((.....(((.((((((((....))))).....))))))....)))).)))))))))).)).))	0.610 -18.60

rat

chromosome:1:129001158:129001248:-1

intergenic

novel_5varHIGH_loopOverlap_bulgeHIGH (6 loci)

block32035 [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	0.085	no	no	0.43/0.48	19/24/0.83	1.8	1.0	6	0	4	0	27	-5	5arm_loop_3arm	2	nd	0.29	4	6	4	na	na

		reads	miRBase family seed
seed	----------------------------GGUAACG----------------------------------------------------------------	3	novel
seed	-----------------------------GUAACGU---------------------------------------------------------------	1	novel
seed	----------------------------------GUAACUG----------------------------------------------------------	1	novel
seed	--------------------------------ACGUAAC------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T4S2	T5S1	T5S2
	---------------------------CGGTAACGTAACTGAATGTGGAG-------------------------------------------------	23	-	-	-	3
	---------------------------------CGTAACTGAATGTGGAGAC-----------------------------------------------	19	-	1	-	-
	-------------------------------AACGTAACTGAATGTGGAGAC-----------------------------------------------	21	1	-	-	-
	----------------------------GGTAACGTAACTGAATGTGGAGAC-----------------------------------------------	24	-	-	1	-
rat	ttccttaccctggatatggattcttcaCGGTAACGTAACTGAATGTGGAGACgtgttacgtgtgtgctaatgttgccgccttgatcagaatccaaggag
	***************************************************************************************************
rat	.((((...........((((((((((((((((((((.((((((..((....))..)).)).))......)))))))))...)))..)))))))))))).	0.400 -28.40

rat

chromosome:10:70223213:70223311:-1

intergenic

block770102 [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	0.150	no	no	0.55/0.65	20/26/0.80	1.2	1.6	5	0	1	0	8	-5	5arm_loop	1	nd	0.30	4	5	1	na	na

		reads	miRBase family seed
seed	---------GACUGCA--------------------------------------------------------	3	novel
seed	-----------CUGCAGC------------------------------------------------------	1	novel
seed	-------------GCAGCUC----------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	--------TGACTGCAGCTCCTCATGACCAG-----------------------------------------	23	3
	------------TGCAGCTCCTCATGACCAGCCCCTCC----------------------------------	26	1
	----------ACTGCAGCTCCTCATGACCA------------------------------------------	20	1
rat	ggctctccTGACTGCAGCTCCTCATGACCAGCCCCTCCacaggctgtgagaagttttgccttctctttgacc
	************************************************************************
rat	((.((....((..((((((.((((....(((((........))))))))).)))..)))..)).....))))	0.780 -17.20

rat

chromosome:19:15930331:15930402:-1

intergenic

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