Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_shortStem_bulgeHIGH (639 loci)

block1696503 [novel_shortStem_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	0.017	no	no	0.43/0.43	23/23/1.00	0.0	0.0	1	0	1	0	1	33	5arm	1	nd	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	--GUGACAC-------------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-TGTGACACTTTACTGGTTGGGAA----------------------------------------------------------------------------------------------	23	1
rat	gTGTGACACTTTACTGGTTGGGAAgcctttctgctagttgtcctgggtgacagtgacaaaatgtcctcttccctggaacaacaggcagctgtgttctcatgatacctgtttgatacac
	**********************************************************************************************************************
rat	(((((.((....((.(((((((((((....(((((.(((((((.(((....((.(((.....)))))...))).))).)))).)))))..)).))))))....))).)).)).)))))	0.970 -36.30

rat

chromosome:4:164277345:164277462:1

intergenic

block1696547 [novel_shortStem_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	0.088	no	no	0.36/0.36	22/22/1.00	0.0	0.0	1	0	1	0	0	14	5arm	1	nd	0.27	4	1	1	na	na

		reads	miRBase family seed
seed	-AAAUCUU-------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	TAAATCTTTTGGACTTGGCAGA-----------------------------------------------------	22	1
rat	TAAATCTTTTGGACTTGGCAGAttggttcttcctttactgaagcagaatgttcaatttgtttggtggtgaggttt
	***************************************************************************
rat	.(((((((....(((..(((((((((((((..((((...)))).)))))...))))))))..)))...)))))))	1.000 -16.90

rat

chromosome:4:164280129:164280203:1

intergenic

block1766506 [novel_shortStem_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	0.206	no	no	0.43/0.43	21/21/1.00	0.0	0.0	1	0	1	0	3	14	3arm	1	nd	0.29	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------GUCAAGA----------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------------------------------------------------------------TGTCAAGACTAGATGCTACTG---	21	1
rat	ggtagccatgagatctggcaagattgggttgcctgtgggatatatgaaaagaagaaagaggactgctggtgacacgTGTCAAGACTAGATGCTACTGcca
	****************************************************************************************************
rat	(((((.....((((((((...(((...((..((.((((........................)))).))..))....)))....)))))).)).))))).	0.630 -24.16

rat

chromosome:5:114518455:114518554:-1

intergenic

block1766651 [novel_shortStem_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	0.157	no	no	0.40/0.40	20/20/1.00	0.0	0.0	1	0	1	0	0	22	5arm	1	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	-GGCAUUG--------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	TGGCATTGAACGTATTCTGA--------------------------------------------------------------	20	1
rat	TGGCATTGAACGTATTCTGAtctaaatctttgatttactaagattccttagttgggaatttaggggcagaaatttaacagct
	**********************************************************************************
rat	.(((.(((((....(((((.((((((((((......((((((....)))))).)))).))))))..))))).)))))..)))	0.820 -16.80

rat

chromosome:5:114524326:114524407:-1

intergenic

novel_lenNOK_shortStem_loopOverlap_nonpairedHIGH (633 loci)

block2695 [novel_lenNOK_shortStem_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	0.142	no	no	0.67/0.67	18/18/0.00	0.0	0.0	1	0	1	0	4	-4	3arm_loop	1	nd	0.44	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------UCCGCUU--------------	1	novel
		len	cloning frequencies
			T1S1
	----------------CTCCGCTTGCCCCTTCAG----	18	1
rat	tagcttgagtggttgcCTCCGCTTGCCCCTTCAGagct
	**************************************
	------------------------------------------------	ENSRNOT00000044626 ENSRNOG00000033942 Grin2a
rat	.((((((((.(((.((....))..))).)))..)))))	1.000 -10.20

rat

chromosome:10:5614192:5614229:-1

Opposite_strand|Intronic_coding|ENSRNOT00000044626|ENSRNOG00000033942 ## ENSRNOG00000033942|protein_coding|Grin2a|Glutamate [NMDA] receptor subunit epsilon-1 precursor (N-methyl D- aspartate receptor subtype 2A) (NR2A) (NMDAR2A). [Source:UniProtKB/Swiss-Prot;Acc:Q00959]

block3776 [novel_lenNOK_shortStem_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	0.167	no	no	0.42/0.42	19/19/0.00	0.0	0.0	1	0	1	0	2	-1	3arm	1	nd	0.42	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------CCGAGUU-------------	1	novel
		len	cloning frequencies
			T1S1
	------------------------TCCGAGTTTTCAGCCTTTT--	19	1
rat	ctgatgcctgctgggaaaaggtcaTCCGAGTTTTCAGCCTTTTag
	*********************************************
rat	((((.....((((..((..((....))...))..))))...))))	1.000 -11.50

rat

chromosome:10:8022109:8022153:-1

intergenic

block5584 [novel_lenNOK_shortStem_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	0.326	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	4	-2	5arm_loop	1	nd	0.39	3	1	1	na	na

		reads	miRBase family seed
seed	-----GGUAAGG-----------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	----TGGTAAGGGTTTGGGGAA-------------------------------------	18	1
rat	ccccTGGTAAGGGTTTGGGGAAgtgtgatagggggaccctcaacctgtgtgtaatgggg
	***********************************************************
rat	((((...((.(((((.((((................)))).))))).....))..))))	0.940 -16.39

rat

chromosome:10:12342732:12342790:-1

intergenic

block10502 [novel_lenNOK_shortStem_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	0.340	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	4	-1	5arm_loop	1	nd	0.39	3	1	1	na	na

		reads	miRBase family seed
seed	-----GCACCCA-------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----TGCACCCATCTGTGAACA---------------------------	18	1
rat	tgaaTGCACCCATCTGTGAACAagactaaggtttatgtgtaagtgttca
	*************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000011922 ENSRNOG00000027341 Odz2
rat	.((((((...(((..((((((.........)))))))))...)))))).	0.890 -8.10

rat

chromosome:10:21698852:21698900:-1

Same_strand|Boundary_non-coding|ENSRNOT00000045307|ENSRNOG00000027341 ## Same_strand|Intronic_coding|ENSRNOT00000011922|ENSRNOG00000027341 ## ENSRNOG00000027341|protein_coding|Odz2|Teneurin-2 (Ten-2) (Tenascin-M2) (Ten-m2) (Protein Odd Oz/ten-m homolog 2) (Neurestin). [Source:UniProtKB/Swiss-Prot;Acc:Q9R1K2]

block10824 [novel_lenNOK_shortStem_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	0.093	no	no	0.61/0.61	18/18/0.00	0.0	0.0	1	0	1	0	0	-2	5arm_loop	1	nd	0.50	3	1	1	na	na

		reads	miRBase family seed
seed	-AUAGGCC--------------------------------	1	novel
		len	cloning frequencies
			T3S2
	CATAGGCCAGGGGCAAAG----------------------	18	1
rat	CATAGGCCAGGGGCAAAGacattcttgcttcttccttctg
	****************************************
rat	...(((..((..((((........))))..)).)))....	1.000 -9.70

rat

chromosome:10:22750395:22750434:-1

intergenic

block13650 [novel_lenNOK_shortStem_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	0.215	no	no	0.32/0.32	19/19/0.00	0.0	0.0	1	0	1	0	3	-2	3arm_loop	1	nd	0.37	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------UGACAAA--------------	1	novel
		len	cloning frequencies
			T2S1
	----------------------------ATGACAAAAGTGAGACTTA---	19	1
rat	gaggaagtagggccacttcaagtctaagATGACAAAAGTGAGACTTAgtc
	**************************************************
rat	.......((((..(((((...(((......)))..)))))...))))...	0.870 -8.80

rat

chromosome:10:30948389:30948438:-1

intergenic

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