Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH (12710 loci)

block1890454 [novel_lenNOK_shortStem_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	0.267	no	no	0.33/0.33	18/18/0.00	0.0	0.0	1	0	1	0	4	24	3arm	1	nd	0.39	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------CCUAUAA--------------	1	novel
		len	cloning frequencies
			T5S2
	------------------------------------------------------------------------GCCTATAAATTTGTTCTC----	18	1
rat	tccggttgtcagattcccggcccagtgggtaaagtctattgtgataaccaggaggacttgagttagaatggaGCCTATAAATTTGTTCTCggat
	**********************************************************************************************
rat	(((((....((((((...((((((.......((((((.((.((.....)).)))))))).........))).)))....))))))...))))).	0.460 -24.19

rat

chromosome:5:155208564:155208657:1

intergenic

block1910259 [novel_lenNOK_shortStem_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	0.558	no	no	0.61/0.61	18/18/0.00	0.0	0.0	1	0	1	0	2	19	5arm	1	nd	0.39	4	1	1	na	na

		reads	miRBase family seed
seed	---ACACCUU------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	--GACACCTTCACGGGAGGA--------------------------------------------------------------------	18	1
rat	gcGACACCTTCACGGGAGGAgacgagctgtcgcctccgctgcaagccgcgggggctgcctcgccgcctcgctggttcttcgggtccgt
	****************************************************************************************
rat	..(((.((....(((((((...((((..((.((((((((........)))))))).))))))...)))).))).......)))))...	0.500 -36.10

rat

chromosome:6:9631082:9631169:-1

intergenic ## {SimpF: oe = 0.90 0 CpG}

block1930262 [novel_lenNOK_shortStem_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	0.015	no	no	0.33/0.33	18/18/0.00	0.0	0.0	1	0	1	0	2	4	5arm	1	nd	0.39	4	1	1	na	na

		reads	miRBase family seed
seed	---AAAGUGU--------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	--TAAAGTGTTTCCCTGTAA----------------------------	18	1
rat	ggTAAAGTGTTTCCCTGTAAgtttatatgaaaatggggtagctttgct
	************************************************
rat	((((((((....((((((...(((....))).))))))..))))))))	1.000 -13.50

rat

chromosome:6:45842423:45842470:-1

intergenic

block1937688 [novel_lenNOK_shortStem_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	0.833	no	no	0.28/0.28	18/18/0.00	0.0	0.0	1	0	1	0	0	28	3arm	1	nd	0.41	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------ACCCAAU----------	1	novel
		len	cloning frequencies
			T1S1
	----------------------------------------------------------------------------------TACCCAATAAACTTTAGA	18	1
rat	attaattgtattggtttctttatgaaatatagatctgttaaaaatgtataaactgtgccttttaaatgtgttgttttaattaTACCCAATAAACTTTAGA
	****************************************************************************************************
rat	.((((...((((((........(((((((........((((((..((((.....)))).))))))......))))))).......))))))....)))).	0.780 -10.40

rat

chromosome:6:61626294:61626393:-1

intergenic

block2090569 [novel_lenNOK_shortStem_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	0.061	no	no	0.37/0.39	18/19/0.00	0.0	0.5	2	0	1	0	0	32	5arm	6	nd	0.44	5	2	1	na	na

		reads	miRBase family seed
seed	-UGGGGAU----------------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T5S1
	CTGGGGATTTAGATTTCA------------------------------------------------------------------------------	18	1
	CTGGGGATTTAGATTTCAA-----------------------------------------------------------------------------	19	1
rat	CTGGGGATTTAGATTTCAAtttgccaagagaagtgagttgcaatgtcataggtcactgtgacaatatttgtctcttccatggtgtttactctcagt
	************************************************************************************************
rat	((((((...(((((........((((...((((.((.......((((((((....)))))))).......)).))))..))))))))).)))))).	0.530 -23.54

rat

chromosome:7:18782636:18782731:-1

intergenic

block2666378 [novel_lenNOK_shortStem_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	0.628	no	no	0.47/0.47	19/19/0.00	0.0	0.0	1	0	1	0	0	14	5arm	6	nd	0.32	4	1	1	na	na

		reads	miRBase family seed
seed	-GUGGCUG--------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	TGTGGCTGAGGACTTTGAT---------------------------------------------------------------	19	1
rat	TGTGGCTGAGGACTTTGATtgtacattgtttttgtttttgttcttcttttaaaaaataatcactccaagtatctatgacata
	**********************************************************************************
	--------------------------------------------------------------------------------------------	ENSRNOT00000005623 ENSRNOG00000004150 NP_001101712.1
rat	((((....(((((((.((.((...(((((((((..................))))))))))).)).)))).)))....))))	0.960 -9.77

rat

chromosome:X:13699969:13700050:-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]

novel_lenNOK_loopOverlap_nonpairedHIGH (12592 loci)

block808 [novel_lenNOK_loopOverlap_nonpairedHIGH]

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	0.518	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	14	-2	3arm_loop	1	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------AGCACCA------------------------	1	miR-29a/29b/29c
		len	cloning frequencies
			T3S2
	------------------------------CAGCACCATTTGAAGGTT--------------	18	1
rat	cagctcgtgtgtcttcttagtagtgcagccCAGCACCATTTGAAGGTTgattattaccgact
	**************************************************************
	------------------------------------------------------------------------	ENSRNOT00000047367 ENSRNOG00000003326 RGD1305001_predicted
	------------------------------------------------------------------------	ENSRNOT00000004459 ENSRNOG00000003326 RGD1305001_predicted
rat	.((.(((.((((((((..(((.((((......)))).))).)))))........))))))))	0.910 -11.70

rat

chromosome:10:1521504:1521565:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000004429|ENSRNOG00000003326 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000047367|ENSRNOG00000003326 ## Opposite_strand|Intronic_coding|ENSRNOT00000004459|ENSRNOG00000003326 ## ENSRNOG00000003326|protein_coding|RGD1305001_predicted|

block1034 [novel_lenNOK_loopOverlap_nonpairedHIGH]

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	0.104	no	no	0.56/0.56	18/18/0.00	0.0	0.0	1	0	1	0	10	-3	3arm_loop	1	nd	0.44	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------GGGGACU--------------------	1	novel
		len	cloning frequencies
			T3S2
	----------------------TGGGGACTTTCAGTGAGG----------	18	1
rat	accacgctccctgtttgtcctgTGGGGACTTTCAGTGAGGaacactgtgg
	**************************************************
rat	.((((((((.(((...((((.....))))...))).)))......)))))	0.990 -16.30

rat

chromosome:10:1942687:1942736:-1

intergenic

block1680 [novel_lenNOK_loopOverlap_nonpairedHIGH]

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	0.529	no	no	0.56/0.56	18/18/0.00	0.0	0.0	1	0	1	0	15	-1	5arm_loop	2	nd	0.39	3	1	1	na	na

		reads	miRBase family seed
seed	----------------CUGACAG-------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	---------------TCTGACAGTGAAGGGCTG---------------------------------	18	1
rat	ctggaatagttactgTCTGACAGTGAAGGGCTGctgtggtcctctctcgggactctgatttttggg
	******************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000003150 ENSRNOG00000002294 LOC687335
rat	((.(((.(((((..((((...((.((.(((((.....))))))).))..))))..)))))))).))	0.840 -15.80

rat

chromosome:10:3773823:3773888:-1

Same_strand|Intronic_coding|ENSRNOT00000003150|ENSRNOG00000002294 ## ENSRNOG00000002294|protein_coding|LOC687335|similar to kinesin-like motor protein C20orf23 (LOC689142), mRNA [Source:RefSeq_dna;Acc:NM_001109526]

block1689 [novel_lenNOK_loopOverlap_nonpairedHIGH]

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	0.394	no	no	0.47/0.47	19/19/0.00	0.0	0.0	1	0	1	0	16	-2	5arm_loop	1	nd	0.37	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------AGCUUCA----------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	----------------GAGCTTCATCCACATCTGT-----------------------------------	19	1
rat	ggagtcacagagctgaGAGCTTCATCCACATCTGTgtaaggtggtaaggtgagccagtcatgggtgagcc
	**********************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000003150 ENSRNOG00000002294 LOC687335
rat	((..((((...((((...((.(((((..(((((.....)))))....))))))))))).....)))).))	0.870 -19.10

rat

chromosome:10:3807838:3807907:-1

Same_strand|Intronic_coding|ENSRNOT00000003150|ENSRNOG00000002294 ## ENSRNOG00000002294|protein_coding|LOC687335|similar to kinesin-like motor protein C20orf23 (LOC689142), mRNA [Source:RefSeq_dna;Acc:NM_001109526]

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