Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_bulgeHIGH (1520 loci)

block1848544 [novel_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	0.064	no	no	0.50/0.50	22/22/1.00	0.0	0.0	1	0	1	0	21	7	3arm	1	nd	0.27	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------GUUGUAU-----------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------------------------------------------------------TGTTGTATCCTCAGAGTGGGTG---------------------	22	1
rat	agcatgcaagcccttgcatggccgattgtccccttgactctctgtcccctacgataggtaaggactcctgcccTGTTGTATCCTCAGAGTGGGTGctgcctggtgagattgtgtgt
	********************************************************************************************************************
rat	.((((((((...(((((..(((.....((.(((......(((((.....(((((((((..(((...)))..)))))))))....))))).))).)).)))..))))).))))))))	0.970 -39.70

rat

chromosome:5:79247876:79247991:1

intergenic

block1865490 [novel_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	0.176	no	no	0.41/0.41	22/22/1.00	0.0	0.0	1	0	1	0	22	10	5arm	5	nd	0.27	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------GUGUCAA------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S1
	----------------------GGTGTCAATGTTGAACCTTTCT----------------------------------------------------------------------------	22	1
rat	cgatgccctcattaaagcagctGGTGTCAATGTTGAACCTTTCTggcctggcttgtttgcaaaggtcctggccaatgaatgtcaacatcgggagctcatgtgcaatgtaggggctggtgg
	************************************************************************************************************************
rat	((..(((((((((...(((...(((.((.(((((((....((((((((.(((((........)))))..)))))..)))..))))))).))..)))..)))..))))..)))))...)).	1.000 -38.00

rat

chromosome:5:117925088:117925207:1

intergenic

block1865751 [novel_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	0.616	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	31	9	5arm	1	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------GGGAAGC-------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	-------------------------------AGGGAAGCTGCCATTGATGG-------------------------------------------------------------------	20	1
rat	ggcaactgtgcacgctagagttctgacagtcAGGGAAGCTGCCATTGATGGtgaagtactcctgggtagctgtggcagagtcctcatggagaagcaataggagtagctggtgatggcc
	**********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000057987 ENSRNOG00000006966 Nfia
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000009651 ENSRNOG00000006966 Nfia
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000004017 ENSRNOG00000006966 Nfia
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000009505 ENSRNOG00000006966 Nfia
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000057984 ENSRNOG00000006966 Nfia
rat	(((.((((.((((.(((..(((((..((....((((..(((((((....(((....((((....))))))))))))))..))))..)).))).))..)))..)).))))))....)))	0.500 -33.70

rat

chromosome:5:118395959:118396076:1

Same_strand|Intronic_coding|ENSRNOT00000009505|ENSRNOG00000006966 ## ENSRNOG00000006966|protein_coding|Nfia|Nuclear factor 1 A-type (Nuclear factor 1/A) (NF1-A) (NFI-A) (NF-I/A) (CCAAT-box-binding transcription factor) (CTF) (TGGCA-binding protein). [Source:UniProtKB/Swiss-Prot;Acc:P09414]

block841557 [novel_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	0.130	no	no	0.39/0.39	23/23/1.00	0.0	0.0	1	0	1	0	21	6	3arm	3	nd	0.22	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------AUCCAGG------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	------------------------------------------------------------------------GATCCAGGCTGTTAATATTTGCA---------------------	23	1
rat	gattttggcttttggtttcttatccaacatattatttgtttgtcctgtgattattctgtgcccctgagagtaGATCCAGGCTGTTAATATTTGCAtaaactttgccaggccttgtc
	********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000043239 ENSRNOG00000033820
rat	(((...((((..((((...((((.(((.((((((.........((((.(((((((((.........))))).))))))))....))))))))).)))).....))))))))..)))	0.860 -23.62

rat

chromosome:1:47789556:47789671:-1

Same_strand|Intronic_coding|ENSRNOT00000043239|ENSRNOG00000033820 ## ENSRNOG00000033820|protein_coding||

block1886248 [novel_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	0.213	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	32	3	5arm	1	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------GGGAGUU----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	--------------------------------GGGGAGTTAGGAAAGTGACC----------------------------------------------------------	20	1
rat	taaggcattaggatgggatgggggttgttctaGGGGAGTTAGGAAAGTGACCttgacagcgtagagttacctgaatcacctgtttagctaattcattctgtgtgaccttg
	**************************************************************************************************************
rat	((((((((((((((.((((...(((((...((((.((.(((((....((((((((....)).)).))))))))).)).))))..))))).)))))))))).))).)))))	0.610 -28.10

rat

chromosome:5:150935046:150935155:1

intergenic

block1900117 [novel_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	0.450	no	no	0.50/0.50	20/20/1.00	0.0	0.0	1	0	1	0	12	28	3arm	2	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------------GUUUGUC------------------------	1	novel
		len	cloning frequencies
			T4S2
	--------------------------------------------------------------------------------------CGTTTGTCCTTAAGACTCCC------------	20	1
rat	ggggagaagtgggtggggcctaacgagcaggctaggaagtcggagtgggaggcgcttagtgctgctccggtaccgagtcgcgctcaCGTTTGTCCTTAAGACTCCCttcggtgtctcc
	**********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000024106 ENSRNOG00000017895 Eno1
rat	(((((((((.(((((((((..(((((((.((((.((...(((((((....(((((...))))))))))))..)).))))..))))..))).)))))....)))).))))....)))))	0.760 -44.80

rat

chromosome:5:167394579:167394696:1

Same_strand|Intronic_non-coding|ENSRNOT00000024106|ENSRNOG00000017895 ## ENSRNOG00000017895|protein_coding|Eno1|Alpha-enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Non- neural enolase) (NNE) (Enolase 1). [Source:UniProtKB/Swiss-Prot;Acc:P04764]

block1066367 [novel_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	0.251	no	no	0.70/0.70	20/20/1.00	0.0	0.0	1	0	1	0	12	9	3arm	4	nd	0.25	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------CCUGGCU------------------------	1	novel
		len	cloning frequencies
			T3S2
	--------------------------------------------------GCCTGGCTCGGTGGCCAAAG------------	20	1
rat	tggtgttgttcttctaccagtcaggggcgaggagagggcagttctttgatGCCTGGCTCGGTGGCCAAAGctgtcttatacc
	**********************************************************************************
	--------------------------------------------------------------------------------------------	ENSRNOT00000001728 ENSRNOG00000001276 LOC690211
	--------------------------------------------------------------------------------------------	ENSRNOT00000048218 ENSRNOG00000001276 LOC690211
rat	.(((((.(((...((((((((((((..(((((((.......)))))))...))))))).)))))....)))......)))))	0.620 -25.70

rat

chromosome:20:12623123:12623204:-1

Opposite_strand|Intronic_non-coding|ENSRNOT00000001728|ENSRNOG00000001276 ## Opposite_strand|Intronic_coding|ENSRNOT00000048218|ENSRNOG00000001276 ## ENSRNOG00000001276|protein_coding|LOC690211|

block2666377 [novel_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	0.074	no	no	0.57/0.57	23/23/1.00	0.0	0.0	1	0	1	0	8	0	5arm	4	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	---------GGUUACA------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	--------TGGTTACAGGAAGTCCCTCACCC---------------------------------------	23	1
rat	gacatagaTGGTTACAGGAAGTCCCTCACCCacccaaaaggggaggatgaccatgtccatgccctgagtc
	**********************************************************************
	--------------------------------------------------------------------------------	ENSRNOT00000005623 ENSRNOG00000004150 NP_001101712.1
rat	(((.(((..(((....(((.(((((((.(((........)))))))..)))....)))..)))))).)))	0.990 -21.00

rat

chromosome:X:13699905:13699974:-1

Opposite_strand|Intronic_coding|ENSRNOT00000005623|ENSRNOG00000004150 ## ENSRNOG00000004150|protein_coding|NP_001101712.1|solute carrier family 9 (sodium/hydrogen exchanger), member 7 [Source:RefSeq_peptide;Acc:NP_001101712]

block2938672 [novel_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	0.074	no	no	0.57/0.57	23/23/1.00	0.0	0.0	1	0	1	0	8	0	5arm	4	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	---------GGUUACA------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	--------TGGTTACAGGAAGTCCCTCACCC---------------------------------------	23	1
rat	gacatagaTGGTTACAGGAAGTCCCTCACCCacccaaaaggggaggatgaccatgtccatgccctgagtc
	**********************************************************************
rat	(((.(((..(((....(((.(((((((.(((........)))))))..)))....)))..)))))).)))	0.990 -21.00

rat

chromosome:X:13905337:13905406:1

intergenic

novel_lenNOK_loopOverlap_randfoldOK (1244 loci)

block5887 [novel_lenNOK_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	0.67/0.67	18/18/0.00	0.0	0.0	1	0	1	0	38	-1	5arm_loop	1	nd	0.28	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------GGCGCUU------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	--------------------------------------GGGCGCTTTCTCCCAGCA--------------------------------------------------------------	18	1
rat	accttctctggaggcgcggcgagcagggcggaggggtgGGGCGCTTTCTCCCAGCAgctgagcatagagggtagtgtcctgcctgcctgtggttgcggtggcttgtcgggaggaggtg
	**********************************************************************************************************************
rat	(((((((((.(((((((.((((.((((((....(((..((((((((((((...((......))...))))).)))))))..))))))).)).)))).))).))..)).))))))))).	1.000 -59.10

rat

chromosome:10:12865925:12866042:-1

intergenic

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