Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_Multihit (678 loci)

block911058 [novel_Multihit]

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	0.526	no	no	0.46/0.46	24/24/1.00	0.0	0.0	1	0	1	0	20	9	5arm	11	nd	0.25	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------AAGGUAC----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	--------------------AAAGGTACCGGATACATTCTCCTG------------------------------------------------------------------	24	1
rat	agtgagactctgacagaagaAAAGGTACCGGATACATTCTCCTGacaacatgacacctcaatggtaatttagagaatgtactagtcctctgaaaatacctgggaaaagct
	**************************************************************************************************************
rat	(((....(((............(((.((.((.(((((((((..((..((.(((....)))...))..))..))))))))))).)))))............)))....)))	0.440 -19.15

rat

chromosome:1:203005670:203005779:-1

intergenic

block1711821 [novel_Multihit]

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	0.021	no	no	0.74/0.74	23/23/1.00	0.0	0.0	1	0	1	0	9	1	3arm	88	nd	0.30	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------AGGCUGG------------------------	1	novel
		len	cloning frequencies
			T2S2
	----------------------------------------CAGGCTGGGGCGCCTGGTCCACA---------	23	1
rat	gtgtcgaaagatgggggtgccctactgctgagggaaaggcCAGGCTGGGGCGCCTGGTCCACAggaagacat
	************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000041054 ENSRNOG00000028991 Kcnb2
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000045460 ENSRNOG00000028991 Kcnb2
rat	(((((......(((((((((((((..(((...((.....)).)))))))))))))...)))......)))))	0.780 -29.40

rat

chromosome:5:2702737:2702808:-1

Same_strand|Intronic_coding|ENSRNOT00000045460|ENSRNOG00000028991 ## ENSRNOG00000028991|protein_coding|Kcnb2|Potassium voltage-gated channel subfamily B member 2 (Voltage-gated potassium channel subunit Kv2.2) (CDRK). [Source:UniProtKB/Swiss-Prot;Acc:Q63099]

block911290 [novel_Multihit]

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	0.526	no	no	0.46/0.46	24/24/1.00	0.0	0.0	1	0	1	0	20	9	5arm	11	nd	0.25	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------AAGGUAC----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	--------------------AAAGGTACCGGATACATTCTCCTG------------------------------------------------------------------	24	1
rat	agtgagactctgacagaagaAAAGGTACCGGATACATTCTCCTGacaacatgacacctcaatggtaatttagagaatgtactagtcctctgaaaatacctgggaaaagct
	**************************************************************************************************************
rat	(((....(((............(((.((.((.(((((((((..((..((.(((....)))...))..))..))))))))))).)))))............)))....)))	0.440 -19.15

rat

chromosome:1:203032666:203032775:-1

intergenic

block1401129 [novel_Multihit]

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	0.50/0.50	22/22/1.00	0.0	0.0	1	0	1	0	5	2	3arm	12	nd	0.27	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------UUGGUGG-------------------	1	novel
		len	cloning frequencies
			T5S2
	--------------------------------------CTTGGTGGCCAAAGCTGTTTCA-----	22	1
rat	gggcagatggcctttgctcatcctagcttggtgcctggCTTGGTGGCCAAAGCTGTTTCAtgcct
	*****************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000045443 ENSRNOG00000010659 RGD1560391_predicted
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000014227 ENSRNOG00000010659 RGD1560391_predicted
rat	((((((((((.(((((..((((..((((........)))).))))..))))))))))...)))))	0.670 -22.50

rat

chromosome:3:114180102:114180166:-1

Same_strand|Intronic_coding|ENSRNOT00000014227|ENSRNOG00000010659 ## ENSRNOG00000010659|protein_coding|RGD1560391_predicted|GA repeat binding protein, beta 1 [Source:RefSeq_peptide;Acc:NP_001034125]

block1618877 [novel_Multihit]

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	0.131	no	no	0.50/0.50	22/22/1.00	0.0	0.0	1	0	1	0	10	2	3arm	12	nd	0.27	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------UUGGUGG------------------------	1	novel
		len	cloning frequencies
			T5S2
	--------------------------------------------CTTGGTGGCCAAAGCTGTTTCA----------	22	1
rat	agcacatggcaggaggcctttgctcatcctagcttgatgcctggCTTGGTGGCCAAAGCTGTTTCAtgcctagggc
	****************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000016909 ENSRNOG00000012392 Dnajc2
rat	.((....((((.((((((((((..((((..((((........)))).))))..)))))..))))).))))....))	0.860 -26.20

rat

chromosome:4:8729368:8729443:1

Same_strand|Intronic_coding|ENSRNOT00000016909|ENSRNOG00000012392 ## ENSRNOG00000012392|protein_coding|Dnajc2|DnaJ homolog subfamily C member 2 (Zuotin-related factor 1) (Gliosarcoma-related antigen MIDA1). [Source:UniProtKB/Swiss-Prot;Acc:Q7TQ20]

block2106503 [novel_Multihit]

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	0.109	no	no	0.38/0.38	21/21/1.00	0.0	0.0	2	0	1	0	27	4	3arm	110	nd	0.24	3	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------CAAGUAU----------------------------------------	2	novel
		len	cloning frequencies
			T2S1
	----------------------------------------------------------------CCAAGTATGATGACATCAAGA---------------------------	21	2
rat	ggcactgtctttgccattcctatttccaatgtcatggatctaacatgctgcatggagaaacctgCCAAGTATGATGACATCAAGAaggtagtgaagtaggcatctgagggcc
	****************************************************************************************************************
rat	(((.((.....((((.((((((((((..(((((((........(((((((((.((.....)))))..)))))))))))))...)))).))).)))...)))).....)))))	0.950 -31.30

rat

chromosome:7:41676180:41676291:-1

intergenic

block2748389 [novel_Multihit]

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	0.50/0.50	22/22/1.00	0.0	0.0	1	0	1	0	10	2	3arm	12	nd	0.18	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------UUGGUGG------------------------	1	novel
		len	cloning frequencies
			T5S2
	----------------------------------------------------CTTGGTGGCCAAAGCTGTTTCA----------	22	1
rat	gtcaggggcagagcagatggcagtcctttgttcatcctagcttgatgcctggCTTGGTGGCCAAAGCTGTTTCAtgcctagggc
	************************************************************************************
rat	(((..(((((.....((.(((((..(((((..((((..((((........)))).))))..)))))))))))).)))))..)))	0.550 -28.10

rat

chromosome:X:91215851:91215934:-1

intergenic

block3034906 [novel_Multihit]

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	0.883	no	no	0.40/0.40	20/20/1.00	0.0	0.0	1	0	1	0	28	2	3arm	18	nd	0.30	2	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------GUCACAG----------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	------------------------------------------------------------TGTCACAGAATTTTGAGACC----------------------------	20	1
rat	gtgtgtatgtgtgtgagctttatgttattagtttttaaaatcagtgcttgaccccaaatcTGTCACAGAATTTTGAGACCaattaaagtaagtttaatgagataacac
	************************************************************************************************************
rat	((((.........(((((((......(((.(((((.(((.((.(((...((.......))...))).)).))).))))).)))......)))))))........))))	0.930 -15.03

rat

chromosome:X:101050791:101050898:1

intergenic

block1714387 [novel_Multihit]

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	0.196	no	no	0.38/0.38	21/21/1.00	0.0	0.0	2	0	1	0	9	17	3arm	110	nd	0.29	2	2	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------CAAGUAU----------------------	2	novel
		len	cloning frequencies
			T2S1
	--------------------------------------------------------------------CCAAGTATGATGACATCAAGA---------	21	2
rat	catggccttctgtgttcctacttccaatgtatctgttgtggatctgacacgccacctggagaaacctgCCAAGTATGATGACATCAAGAaggtggtga
	**************************************************************************************************
rat	(((.(((((((((((((.(((((.....((.(((...((((..........))))....))).)).....))))).))..))))..))))))).))).	0.530 -25.00

rat

chromosome:5:8009048:8009145:-1

intergenic

novel_lenNOK_shortStem_loopOverlap_nonpairedHIGH_bulgeHIGH (676 loci)

block128 [novel_lenNOK_shortStem_loopOverlap_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	0.071	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	3	-4	5arm_loop	2	nd	0.44	5	1	1	na	na

		reads	miRBase family seed
seed	----GGCAAGA----------------------------	1	miR-31
		len	cloning frequencies
			T2S2
	---AGGCAAGAGTTCTTACTC------------------	18	1
rat	gtcAGGCAAGAGTTCTTACTCcaagatctcagggcccac
	***************************************
rat	....(((..(((.((((.....)))).)))...)))...	1.000 -10.10

rat

chromosome:10:274934:274972:-1

intergenic

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