Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_randfoldOK_bulgeHIGH (220 loci)

block1348965 [novel_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	0.008	no	no	0.57/0.60	20/21/1.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	16 23	13 5	5arm 5arm	1 1	nd nd	0.25 0.48	4 4	2	1	na	na

		reads	miRBase family seed
seed	------------------------AGCUCAA------------------------------------------------------------------------------------	1	novel
seed	-----------------GCUACAG-------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	----------------GGCTACAGAGCTCAACCCCT-------------------------------------------------------------------------------	20	1
	-----------------------GAGCTCAACCCCTTCCAGTCT-----------------------------------------------------------------------	21	1
rat	acagtccatccctcatGGCTACAGAGCTCAACCCCTTCCAGTCTaggtccccacacaaactcagcaaaagaccaacaaagggttaaaggcttcatcctctagcctgaggtggctg
	*******************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000018560 ENSRNOG00000013102 Entpd2
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000017829 ENSRNOG00000013102 Entpd2
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000047049 ENSRNOG00000013102 Entpd2
rat	.(((.(((..(((((.(((((.((((((....(((((...((...((((....................)))).)).))))).....)))).....)).))))))))))))))))	0.930 -31.25

rat

chromosome:3:3565022:3565136:-1

Opposite_strand|Intronic_coding|ENSRNOT00000017829|ENSRNOG00000013102 ## ENSRNOG00000013102|protein_coding|Entpd2|Ectonucleoside triphosphate diphosphohydrolase 2 (EC 3.6.1.-) (NTPDase 2) (Ecto-ATPase) (CD39 antigen-like 1). [Source:UniProtKB/Swiss-Prot;Acc:O35795]

block1402151 [novel_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	0.001	no	no	0.43/0.43	21/21/1.00	0.0	0.0	1	0	1	0	8	17	3arm	1	nd	0.24	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------GCUUCCA---------------------	1	novel
		len	cloning frequencies
			T4S1
	--------------------------------------------------------------------AGCTTCCAAAAACTTCCCTAC--------	21	1
rat	ggtggcggtggggaggatgtgggtgctgtttcccctgactatgtaggtgtcacacagacaggttcttcAGCTTCCAAAAACTTCCCTACtgccactg
	*************************************************************************************************
rat	((((((((((((((((...((((.((((.....((((.((.(((.......))).)).)))).....)))).))))....)))))))))))))))).	0.980 -48.90

rat

chromosome:3:115977896:115977992:-1

intergenic

block1577780 [novel_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	0.46/0.46	24/24/1.00	0.0	0.0	1	0	1	0	8	16	3arm	1	nd	0.29	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------CCUGAUG------------------------	1	novel
		len	cloning frequencies
			T5S1
	--------------------------------------------------------------------TCCTGATGCATCACAAAATGGGGT--------	24	1
rat	ctcagggatttaccttacacttgtccatcctggagcccctatctaattcttaggagaccagggacagcTCCTGATGCATCACAAAATGGGGTacttgaga
	****************************************************************************************************
rat	((((((....(((((((...((((.((((..(((((((((.(((........)))....))))...))))).))))....))))..))))))))))))).	1.000 -31.00

rat

chromosome:4:122181645:122181744:-1

intergenic

block1858319 [novel_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	0.001	no	no	0.67/0.67	21/21/1.00	0.0	0.0	1	0	1	0	23	13	3arm	1	nd	0.24	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------GCGCCAC------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	----------------------------------------------------------------------------AGCGCCACTGGCTGTGGTTCC-----------------------	21	1
rat	gccacgggagggcaggggcctgtaccgcggtgggcgtggcgccagtgggtagtggagcctggacagtacccgacctAGCGCCACTGGCTGTGGTTCCttgcggttccctgccacgtggcc
	************************************************************************************************************************
rat	((((((....(((((((..((((((((((((.((..((((((.((((((((.((.........)).))))))..)).)))))))).)))))))).....))))..))))))).)))))).	1.000 -70.00

rat

chromosome:5:101421589:101421708:1

intergenic

novel_lenNOK_multiarm_DicerNOK_nonpairedHIGH_bulgeHIGH (216 loci)

sblock1000 [novel_lenNOK_multiarm_DicerNOK_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	0.421	no	no	0.64/0.83	18/22/0.50	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	16 23	28 6	5arm 3arm	1 1	nd nd	0.39 0.32	5 4	2	2	-18	-15

		reads	miRBase family seed
seed	-----------------CGCCGCG---------------------------------------------------------------------------------------------	1	novel
seed	-------------------------------------------------------------------------CCGUUCC-------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T3S2
	------------------------------------------------------------------------TCCGTTCCCGTCGGGGTTCCAT-----------------------	22	1	-
	----------------ACGCCGCGGGGCCAGAGC-----------------------------------------------------------------------------------	18	-	1
rat	tggcgggcgggcgctgACGCCGCGGGGCCAGAGCgggccgcgcgggagcgtgtggagaaagcagtggcaccgTCCGTTCCCGTCGGGGTTCCATaggtccccgagccgcccctggct
	*********************************************************************************************************************
rat	.(((.((.(((((.....((((.((((((.....(((((.((((((((((..(((.....((....)).)))..)))))))).)).)))))....)))))))).))))))))).)))	0.720 -60.80

rat

chromosome:1:209643688:209643804:-1

intergenic ## {SimpF: 1 Eponine}

sblock10075 [novel_lenNOK_multiarm_DicerNOK_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	0.032	no	no	0.40/0.47	19/25/0.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	14 11	11 19	5arm 3arm	1 1	nd nd	0.36 0.42	4 3	2	2	11	6

		reads	miRBase family seed
seed	--------------------------------------------------------------------------GAAACUA----------------------	1	novel
seed	---------------AGUAUGU---------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T5S1
	--------------CAGTATGTTGGAAAGAGTTGAGGAA----------------------------------------------------------------	25	-	1
	-------------------------------------------------------------------------TGAAACTAGACTGGACTGG-----------	19	1	-
rat	cctgagaaactagaCAGTATGTTGGAAAGAGTTGAGGAAcaatggctccttcccaggggcagattcccaagtcTGAAACTAGACTGGACTGGgtggagaaagg
	*******************************************************************************************************
rat	(((......((((.((((..(((....(((.(((.((((.....((((((....))))))...))))))).)))..)))...))))..))))........)))	0.990 -31.34

rat

chromosome:6:122555428:122555530:-1

intergenic

sblock1012 [novel_lenNOK_multiarm_DicerNOK_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	0.784	no	no	0.58/0.67	18/19/0.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	6 5	7 5	5arm 3arm	1 1	nd nd	0.58 0.50	7 4	2	2	0	-5

		reads	miRBase family seed
seed	--------------------------------------------CCGAGUC---------------	1	novel
seed	-------UACAACC----------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T5S1
	------GTACAACCCCAGATGTGGC-----------------------------------------	19	-	1
	-------------------------------------------ACCGAGTCTCCCTGGTCC-----	18	1	-
rat	cggcccGTACAACCCCAGATGTGGCtcccccgcgcttacggacACCGAGTCTCCCTGGTCCcggcc
	******************************************************************
	----------------------------------------------------------------------------	ENSRNOT00000027141 ENSRNOG00000019913 Mta2
rat	.((((.........((((....(((((..(((......))).....)))))...))))....))))	0.440 -16.72

rat

chromosome:1:211618864:211618929:-1

Opposite_strand|Intronic_coding|ENSRNOT00000027141|ENSRNOG00000019913 ## ENSRNOG00000019913|protein_coding|Mta2|Mta2 protein (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q4FZS6]

sblock10217 [novel_lenNOK_multiarm_DicerNOK_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	0.409	no	no	0.39/0.50	18/18/0.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	0 14	22 14	5arm 3arm	1 9	nd nd	0.39 0.50	4 4	2	1	-14	-14

		reads	miRBase family seed
seed	-----------------------------------------------------------AAGACAC------------------------	1	novel
seed	-CAGCUUA----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	ACAGCTTACGTGGAACTC------------------------------------------------------------------------	18	1
	----------------------------------------------------------CAAGACACAGTGTTGTAA--------------	18	1
rat	ACAGCTTACGTGGAACTCagcatcctggtatgtgaggactctgtggtctattactatgCAAGACACAGTGTTGTAAccacatcctgagtg
	******************************************************************************************
rat	...(((((.((((....((((((..(((((((((((((((....))))).)))).))))....))..))))))...))))....))))).	0.480 -21.60

rat

chromosome:6:142527239:142527328:-1

intergenic

sblock10363 [novel_lenNOK_multiarm_DicerNOK_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	0.944	no	no	0.63/0.79	19/19/0.00	0.0 0.0	0.0 0.0	1 2	0 0	1 2	0 0	20 10	0 8	5arm 3arm	1 1	nd nd	0.58 0.37	6 4	3	2	9	10

		reads	miRBase family seed
seed	----------------------------------------------------CCAGUCC---------------------	2	novel
seed	---------------------UCCCUGC----------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2	T5S2
	---------------------------------------------------GCCAGTCCGCGCTCACCCC----------	19	1	1
	--------------------TTCCCTGCGTTCCTCCGCA-----------------------------------------	19	-	1
rat	gggagggggcggccccggcgTTCCCTGCGTTCCTCCGCAtttctgcctcccGCCAGTCCGCGCTCACCCCgccgccgctg
	********************************************************************************
	------------------------------------------------------------------------<<<<<<<<<<<<<<<<<<	ENSRNOT00000005015 ENSRNOG00000003759 Galc
rat	.((.((.(((((....(((((...(((.((......(((....))).....)))))...)))))....))))).)).)).	0.490 -27.50

rat

chromosome:6:122416730:122416809:1

Opposite_strand|Intronic_coding|ENSRNOT00000005015|ENSRNOG00000003759 ## Opposite_strand|Boundary_coding|ENSRNOT00000005015|ENSRNOG00000003759 ## ENSRNOG00000003759|protein_coding|Galc|galactosylceramidase [Source:RefSeq_peptide;Acc:NP_001005888]

sblock10400 [novel_lenNOK_multiarm_DicerNOK_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	0.757	no	no	0.33/0.50	18/18/0.00	0.0 0.0	0.0 0.0	1 3	0 0	1 1	0 0	9 0	10 19	5arm 3arm	1 1	nd nd	0.33 0.41	4 3	4	2	10	8

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------UGUAAGU----------	3	novel
seed	----------UCAACAA-----------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T5S2
	----------------------------------------------------------------------------TTGTAAGTTTGGCACTTT	18	3	-
	---------CTCAACAAAGCCTTGGAG-------------------------------------------------------------------	18	-	1
rat	gtgtatataCTCAACAAAGCCTTGGAGctcttatgatcaaatatattgcctacaaaagtctaagaaggttttttttTTGTAAGTTTGGCACTTT
	**********************************************************************************************
rat	((((....(((..((((((....((((((((((.(((....................))))))))..)))))..)))))).)))...))))...	0.680 -12.75

rat

chromosome:6:123190536:123190629:1

intergenic ## {Repeats: dust 123190604 123190606 0 class=dust}

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