Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_multiarm_DicerNOK_nonpairedHIGH_bulgeHIGH (216 loci)

novel_lenNOK_shortStem_loopOverlap_randfoldOK (211 loci)

block4102 [novel_lenNOK_shortStem_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	0.008	no	no	0.28/0.28	18/18/0.00	0.0	0.0	1	0	1	0	4	-3	3arm_loop	1	nd	0.28	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------------UGAAUAG--------------	1	novel
		len	cloning frequencies
			T1S2
	--------------------------ATGAATAGAGCTATCATT----	18	1
rat	cctctctatggtagttaaagattattATGAATAGAGCTATCATTgagg
	************************************************
rat	((((...(((((((((....(((......)))..))))))))).))))	1.000 -13.40

rat

chromosome:10:9010042:9010089:-1

intergenic

block14234 [novel_lenNOK_shortStem_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	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	1	-4	3arm_loop	1	nd	0.28	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------AGUACUC-----------	1	novel
		len	cloning frequencies
			T4S2
	--------------------GAGTACTCTGGGAAATGT-	18	1
rat	tgcagggtcccagagtccctGAGTACTCTGGGAAATGTa
	***************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000003224 ENSRNOG00000002372 Sgcd
	+++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042561 ENSRNOG00000002372 Sgcd
rat	((((...(((((((((........)))))))))..))))	1.000 -17.90

rat

chromosome:10:32375503:32375541:-1

Same_strand|Intronic_coding|ENSRNOT00000042561|ENSRNOG00000002372 ## ENSRNOG00000002372|protein_coding|Sgcd|sarcoglycan, delta (dystrophin-associated glycoprotein) Gene [Source:MGI (curated);Acc:Sgcd-003]

block37889 [novel_lenNOK_shortStem_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	0.009	no	no	0.50/0.53	18/19/0.00	0.0	0.5	2	0	2	0	0	-1	3arm	3	nd	0.17	2	2	2	na	na

		reads	miRBase family seed
seed	-------------------------GGGCUGA-----------	2	novel
		len	cloning frequencies
			T1S1	T5S1
	------------------------AGGGCTGACACAGAAGAA-	18	1	-
	------------------------AGGGCTGACACAGAAGAAG	19	-	1
rat	cttctgcccatgtggcagcctggcAGGGCTGACACAGAAGAAG
	*******************************************
rat	(((((.....((((.((((((....)))))).))))..)))))	1.000 -18.80

rat

chromosome:10:82781809:82781851:-1

intergenic

block47442 [novel_lenNOK_shortStem_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	0.006	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	0	-3	3arm_loop	3	nd	0.24	2	1	1	na	na

		reads	miRBase family seed
seed	--------------------UUGCUGU----------	1	novel
		len	cloning frequencies
			T5S1
	-------------------GTTGCTGTGGGCTTTTTT	18	1
rat	aaaatagtctattgctattGTTGCTGTGGGCTTTTTT
	*************************************
	+++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000005489 ENSRNOG00000004040 Abca8b
rat	((((.(((((((.((.......)).))))))).))))	1.000 -9.70

rat

chromosome:10:99408860:99408896:-1

Same_strand|Intronic_coding|ENSRNOT00000005489|ENSRNOG00000004040 ## ENSRNOG00000004040|protein_coding|Abca8b|ATP-binding cassette, sub-family A (ABC1), member 8b Gene [Source:MGI (curated);Acc:Abca8b-002]

block47768 [novel_lenNOK_shortStem_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	0.002	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	0	-3	5arm_loop_3arm	1	nd	0.26	3	1	1	na	na

		reads	miRBase family seed
seed	-GUUGAAG----------------------------	1	novel
		len	cloning frequencies
			T4S1
	GGTTGAAGGTCTGGTTCCT-----------------	19	1
rat	GGTTGAAGGTCTGGTTCCTgactagatctttttccc
	************************************
rat	((..((((((((((((...))))))))))))..)).	1.000 -15.90

rat

chromosome:10:100072238:100072273:-1

intergenic

block84795 [novel_lenNOK_shortStem_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	0.009	no	no	0.56/0.56	18/18/0.00	0.0	0.0	1	0	1	0	4	-3	3arm_loop	1	nd	0.28	2	1	1	na	na

		reads	miRBase family seed
seed	-------------------------ACUGACC--------------	1	novel
		len	cloning frequencies
			T1S1
	------------------------CACTGACCATCCAGCACA----	18	1
rat	gtactgtgctgattcaataaaatgCACTGACCATCCAGCACAtact
	**********************************************
rat	(((.((((((((((((...........)))..))).))))))))).	1.000 -10.30

rat

chromosome:10:68719619:68719664:1

intergenic

block91345 [novel_lenNOK_shortStem_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	0.002	no	no	0.56/0.56	18/18/0.00	0.0	0.0	1	0	1	0	2	-3	3arm_loop	1	nd	0.28	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------CUGCUGG------------	1	novel
		len	cloning frequencies
			T3S2
	----------------------------------------CCTGCTGGGTTTGGAAAC--	18	1
rat	cagcctccagcccagctccctgcctttcttcccatctctcCCTGCTGGGTTTGGAAACtg
	************************************************************
	----------------------------------------------------------------------	ENSRNOT00000041615 ENSRNOG00000002981 Cacna1g
	----------------------------------------------------------------------	ENSRNOT00000004004 ENSRNOG00000002981 Cacna1g
	----------------------------------------------------------------------	ENSRNOT00000051536 ENSRNOG00000002981 Cacna1g
	----------------------------------------------------------------------	ENSRNOT00000055597 ENSRNOG00000002981 Cacna1g
	----------------------------------------------------------------------	ENSRNOT00000055596 ENSRNOG00000002981 Cacna1g
rat	(((..(((((((((((...........................)))))))).)))..)))	1.000 -18.23

rat

chromosome:10:83067654:83067713:1

Opposite_strand|Intronic_coding|ENSRNOT00000004004|ENSRNOG00000002981 ## ENSRNOG00000002981|protein_coding|Cacna1g|Voltage-dependent T-type calcium channel subunit alpha-1G (Voltage- gated calcium channel subunit alpha Cav3.1). [Source:UniProtKB/Swiss-Prot;Acc:O54898]

block125331 [novel_lenNOK_shortStem_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	0.33/0.33	18/18/0.00	0.0	0.0	1	0	1	0	3	-4	3arm_loop	2	nd	0.28	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------CAAGAUA-------------	1	novel
		len	cloning frequencies
			T4S1
	----------------------CCAAGATAAAGTAGCTAT---	18	1
rat	aaccaaattgctattttactcaCCAAGATAAAGTAGCTATggt
	*******************************************
rat	.((((....(((((((((.((.....)))))))))))..))))	1.000 -11.90

rat

chromosome:11:51970493:51970535:-1

intergenic

block130291 [novel_lenNOK_shortStem_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	0.010	no	no	0.56/0.56	18/18/0.00	0.0	0.0	1	0	1	0	2	-4	3arm_loop	1	nd	0.28	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------GGAGUGU------------	1	miR-122
		len	cloning frequencies
			T2S1
	--------------------------------------TGGAGTGTGGTGGGGTTT--	18	1
rat	ggaaccccagagaaggaagaaggaaagggggctgtgctTGGAGTGTGGTGGGGTTTca
	**********************************************************
rat	((((((((......................((..(((.....)))..)))))))))).	0.940 -15.14

rat

chromosome:11:65591449:65591506:-1

intergenic

block163427 [novel_lenNOK_shortStem_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	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	3	-2	3arm_loop	1	nd	0.11	1	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------AGCUCGU--------------	1	novel
		len	cloning frequencies
			T5S1
	--------------------------------CAGCTCGTGGACTAAGAGA---	19	1
rat	aggtctctgcttaagaatggtctagggtggagCAGCTCGTGGACTAAGAGAcct
	******************************************************
rat	((((((((.........(((((((((((......)))).)))))))))))))))	0.990 -20.90

rat

chromosome:11:58650697:58650750:1

intergenic

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