Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_cloningOK_randfoldOK_nonpairedHIGH (37 loci)

block2181283 [novel_lenNOK_cloningOK_randfoldOK_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	0.001	no	no	0.47/0.50	18/20/0.06	0.0	0.0	20	0	9	0	6	12	5arm	1	nd	0.39	3	33	9	na	na

		reads	miRBase family seed
seed	-------AAAUUCC--------------------------------------------------------------	33	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1
	------CAAATTCCCTTTGGGGGT----------------------------------------------------	18	7	5	1	1	5	2	2	3	2
	------CAAATTCCCTTTGGGGGTT---------------------------------------------------	19	-	-	-	-	-	-	1	1	1
	------CAAATTCCCTTTGGGGGTTC--------------------------------------------------	20	-	1	-	-	1	-	-	-	-
rat	gggatcCAAATTCCCTTTGGGGGTtctctttttaaaaagaatttaaaaatagactcagaaggaagcctaagtccca
	****************************************************************************
rat	(((((.....((((.((((((...(((.((((((((.....)))))))).))))))))).))))......))))).	1.000 -22.30

rat

chromosome:7:8608275:8608350:1

intergenic

block2184068 [novel_lenNOK_cloningOK_randfoldOK_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	0.005	no	no	0.39/0.39	18/18/0.00	0.0	0.0	14	0	8	0	8	9	5arm	2	nd	0.33	2	17	8	na	na

		reads	miRBase family seed
seed	---------CUUUUGG------------------------------------------------------------	17	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S1	T3S2	T4S2	T5S1	T5S2
	--------TCTTTTGGTTTCCACCTT--------------------------------------------------	18	2	3	1	3	2	1	4	1
rat	acagccttTCTTTTGGTTTCCACCTTctgtgcgcctcagggcctttgcacaaggtgtggctcctgtaaggtgctgt
	****************************************************************************
	--------------------------------------------------------------------------------------	ENSRNOT00000013762 ENSRNOG00000009760 Palm
	--------------------------------------------------------------------------------------	ENSRNOT00000043152 ENSRNOG00000009760 Palm
rat	(((((...((((..((..(((((((..((((((((....)))....)))))))))).))..))...)))).)))))	1.000 -28.00

rat

chromosome:7:11403124:11403199:1

Opposite_strand|Intronic_coding|ENSRNOT00000043152|ENSRNOG00000009760 ## ENSRNOG00000009760|protein_coding|Palm|paralemmin [Source:RefSeq_peptide;Acc:NP_570842]

block2391412 [novel_lenNOK_cloningOK_randfoldOK_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	0.007	no	no	0.37/0.39	18/19/0.00	0.0	0.2	26	0	9	0	22	18	3arm	3	nd	0.32	3	30	9	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------GUAUCUG---------------------------------	30	novel
		len	cloning frequencies
			T1S1	T1S2	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--------------------------------------------------------------------------TGTATCTGCATGTGTGTTT----------------------	19	5	3	2	1	1	2	3	5	1
	--------------------------------------------------------------------------TGTATCTGCATGTGTGTT-----------------------	18	-	1	-	-	-	-	4	2	-
rat	gaagtgaaatataatgtttagtgggtgtgggtatgatagcaaaaatctgatagttggggattttgttgtttgtgTGTATCTGCATGTGTGTTTaaacaatggatagtttctttct
	*******************************************************************************************************************
rat	((((.(((((.((.(((((((((.(((..(((((((((((((((.(((........))).)))))))))).....)))))..))).))...))))))).))....))))))))).	0.960 -25.30

rat

chromosome:8:33931842:33931956:1

intergenic

block2410664 [novel_lenNOK_cloningOK_randfoldOK_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	0.002	no	no	0.44/0.44	18/18/0.00	0.0	0.0	20	0	4	0	12	11	5arm	1	nd	0.33	3	22	4	na	na

		reads	miRBase family seed
seed	-------------GGUGGAC------------------------------------------------------------------	22	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T3S2
	------------TGGTGGACTATGGAAACA--------------------------------------------------------	18	13	7	1	1
rat	aaggcacccagcTGGTGGACTATGGAAACAgctttgagtctatcaagagactcaactgaaccagcagccaagcagcctatggtcct
	**************************************************************************************
	------------------------------------------------------------------------------------------------	ENSRNOT00000058645 ENSRNOG00000018577 Neil1
	------------------------------------------------------------------------------------------------	ENSRNOT00000025181 ENSRNOG00000018577 Neil1
	------------------------------------------------------------------------------------------------	ENSRNOT00000025088 ENSRNOG00000018577 Neil1
rat	.(((.(((..((((.(((.((.(((...(((..((((((((......)))))))))))..)))..)))))..))))....))))))	0.880 -30.70

rat

chromosome:8:60902264:60902349:1

Opposite_strand|Intronic_coding|ENSRNOT00000025088|ENSRNOG00000018577 ## ENSRNOG00000018577|protein_coding|Neil1|nei endonuclease VIII-like 1 [Source:RefSeq_peptide;Acc:NP_001020925]

block2675553 [novel_lenNOK_cloningOK_randfoldOK_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	0.007	no	no	0.50/0.50	18/18/0.00	0.0	0.0	14	0	2	0	12	26	3arm	2	nd	0.39	3	14	2	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------CCUCACA----------------------	14	novel
		len	cloning frequencies
			T2S1	T2S2
	-------------------------------------------------------------------------------TCCTCACACTTCCACCAA------------	18	10	4
rat	ggactgctatttcctggtgcaaggctgtctgccaggaggttccctggtttagcaccaggagcctcgaatccggcgggaaTCCTCACACTTCCACCAAgagtcccagtct
	*************************************************************************************************************
rat	((((((....(((.(((((.(((..((((((((..((((((.((((((.....))))))))))))......))))))......))..))).))))).)))...))))))	0.820 -42.00

rat

chromosome:X:22725874:22725982:-1

intergenic

block1499880 [novel_lenNOK_cloningOK_randfoldOK_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	0.009	no	no	0.36/0.42	18/26/0.59	0.0	3.1	17	0	6	0	21	0	5arm	1	nd	0.39	2	17	6	na	na

		reads	miRBase family seed
seed	----------------------CCGUGAU---------------------------------------------------------------------	17	novel
		len	cloning frequencies
			T1S1	T2S1	T2S2	T4S1	T5S1	T5S2
	---------------------TCCGTGATTACTTTTCTGG----------------------------------------------------------	19	-	1	1	-	2	1
	---------------------TCCGTGATTACTTTTCTGGA---------------------------------------------------------	20	2	-	-	-	2	-
	---------------------TCCGTGATTACTTTTCTGGAAAGG-----------------------------------------------------	24	-	-	-	-	3	-
	---------------------TCCGTGATTACTTTTCTGGAAAG------------------------------------------------------	23	1	-	1	-	-	-
	---------------------TCCGTGATTACTTTTCTG-----------------------------------------------------------	18	-	-	-	1	-	-
	---------------------TCCGTGATTACTTTTCTGGAAA-------------------------------------------------------	22	-	-	-	-	1	-
	---------------------TCCGTGATTACTTTTCTGGAAAGGGA---------------------------------------------------	26	-	-	-	-	1	-
rat	caatgtcttctgctttagttcTCCGTGATTACTTTTCTGGAAAGGGAagcatcctgtggacataaagtaaagcagaactcgagagctccagacattga
	**************************************************************************************************
rat	((((((((...(((((((((((..((..(((((((..((....((((....)))).....)).))))))).))))))))..)))))...)))))))).	0.620 -30.30

rat

chromosome:3:141757841:141757938:1

intergenic

block1600463 [novel_lenNOK_cloningOK_randfoldOK_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	0.001	no	no	0.60/0.70	19/20/0.31	0.3 0.0	0.0 0.0	10 1	0 0	3 1	0 0	16 8	9 17	3arm 3arm	1 1	nd nd	0.32 0.35	2 3	13	3	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------GACCAGU---------------------------	9	novel
seed	-----------------------------------------------------------UGACCAG----------------------------	3	novel
seed	-------------------------------------------------------------------GCUCAGC--------------------	1	novel
		len	cloning frequencies
			T1S1	T2S1	T5S1
	-----------------------------------------------------------TGACCAGTGCTCAGCCCAG----------------	19	1	1	7
	----------------------------------------------------------TTGACCAGTGCTCAGCCCAG----------------	20	-	-	3
	------------------------------------------------------------------TGCTCAGCCCAGCTGGCCAC--------	20	-	-	1
rat	cctgtggtcttggtaaatactgtctctgaccactggaggcccacgttatatgggggccTTGACCAGTGCTCAGCCCAGctggccacgctcacag
	**********************************************************************************************
rat	.(((((((..((((.....(((...((((.((((((((((((.(((...))).))))))...)))))).))))..)))...)))).)).)))))	1.000 -39.20

rat

chromosome:4:164238888:164238981:-1

intergenic

novel_loopOverlap_mirtron_nonpairedHIGH_bulgeHIGH (37 loci)

block7637 [novel_loopOverlap_mirtron_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	0.022	no	no	0.65/0.65	20/20/1.00	0.0	0.0	1	0	1	0	32	-3	5arm_loop	1	1	0.35	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------GGUCAGC------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	--------------------------------AGGTCAGCCACCTGGGGAAG------------------------------------------------	20	1
rat	cttggttctttcatggcagtcaacttcttcacAGGTCAGCCACCTGGGGAAGgctctgggtggttgtcattggaggggtcagccctggctctctcccagg
	****************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000038962 ENSRNOG00000028241 ITFG3_RAT
rat	(((((.....(((.(((.....((..(((((..((.((((((((..(((....)))..))))))))))..)))))..))..))).))).......)))))	0.430 -39.30

rat

chromosome:10:15484671:15484770:-1

Same_strand|Boundary_coding|ENSRNOT00000038962|ENSRNOG00000028241 ## ENSRNOG00000028241|protein_coding|ITFG3_RAT|Protein ITFG3. [Source:UniProtKB/Swiss-Prot;Acc:Q5M7W6]

block182529 [novel_loopOverlap_mirtron_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	0.124	no	no	0.43/0.43	23/23/1.00	0.0	0.0	1	0	1	0	11	-3	3arm_loop	1	2	0.48	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------AUGUGAG--------------------------	1	novel
		len	cloning frequencies
			T1S1
	----------------------------------CATGTGAGTCATAATGATCGGAG-----------	23	1
rat	aggctttgcggtctttcaaggcggaaacacctacCATGTGAGTCATAATGATCGGAGccagcagggct
	********************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++	ENSRNOT00000034483 ENSRNOG00000001036
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++	ENSRNOT00000001369 ENSRNOG00000001036
rat	.(((((((((((((.(((.....((..(((.......)))..))....)))..))).)).))))))))	0.430 -18.30

rat

chromosome:12:10996663:10996730:-1

Same_strand|Boundary_coding|ENSRNOT00000034483|ENSRNOG00000001036 ## ENSRNOG00000001036|protein_coding||

block186149 [novel_loopOverlap_mirtron_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	0.309	no	no	0.43/0.46	23/24/1.00	0.0	0.5	2	0	1	0	22	-2	3arm_loop	1	0	0.39	4	2	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------UGAAAAC--------------------------------------	2	novel
		len	cloning frequencies
			T4S2
	-----------------------------------------------GTGAAAACACATGGTCATTGCAGG----------------------	24	1
	-----------------------------------------------GTGAAAACACATGGTCATTGCAG-----------------------	23	1
rat	cttgtcactcagggaagcagggctggagtatgattggggttatctttGTGAAAACACATGGTCATTGCAGGgactggaaaccgagtatcagga
	*********************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000001748 ENSRNOG00000001299 Unc84a
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000001757 ENSRNOG00000001299 Unc84a
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000043067 ENSRNOG00000001299 Unc84a
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000001760 ENSRNOG00000001299 Unc84a
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000047287 ENSRNOG00000001299 Unc84a
rat	((((..((((.((....(((..((.....(((((((..(((.((.....)).)))...)))))))....))..)))....))))))..)))).	0.910 -23.50

rat

chromosome:12:15899622:15899714:-1

Same_strand|Boundary_coding|ENSRNOT00000001748|ENSRNOG00000001299 ## ENSRNOG00000001299|protein_coding|Unc84a|unc-84 homolog A [Source:RefSeq_peptide;Acc:NP_001007148]

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