Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_multiarm_Multihit_loopOverlap_randfoldOK (8 loci)

block964220 [novel_lenNOK_multiarm_Multihit_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	0.004	no	no	0.42/0.42	19/24/0.33	0.0 0.0	0.0 0.0	1 2	0 0	1 1	0 0	22 2	-21 1	5arm_loop_3arm 3arm	16 20	nd nd	0.38 0.11	8 1	3	2	na	na

		reads	miRBase family seed
seed	-----------------------------------AUCACAU-------------	2	novel
seed	-----------------------AGCACCU-------------------------	1	novel
		len	cloning frequencies
			T2S2	T5S1
	----------------------------------TATCACATGAAGCCCACTA--	19	-	2
	----------------------TAGCACCTCAACTATCACATGAAG---------	24	1	-
rat	tgatgttggactttcactgtggTAGCACCTCAACTATCACATGAAGCCCACTAtt
	*******************************************************
	-----------------------------------------------------------------	ENSRNOT00000048246 ENSRNOG00000039174 RGD1563865_predicted
rat	.((((.(((.((.(((.((((((((........))))))))))))).))).))))	1.000 -15.60

rat

chromosome:1:52052246:52052300:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000059936|ENSRNOG00000039174 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000048246|ENSRNOG00000039174 ## ENSRNOG00000039174|protein_coding|RGD1563865_predicted|

block961623 [novel_lenNOK_multiarm_Multihit_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	0.35/0.44	18/25/0.20	0.5 0.0 0.0	0.3 0.0 0.0	11 1 1	0 0 0	1 1 1	0 0 0	21 27 9	-12 -23 2	5arm_loop_3arm 5arm_loop_3arm 3arm	40 40 40	nd nd nd	0.47 0.40 0.17	6 6 2	15	1	na	na

		reads	miRBase family seed
seed	-----------------------UGACUAG----------------------------------	7	novel
seed	----------------------UUGACUA-----------------------------------	5	novel
seed	----------------------------AGCCUUA-----------------------------	1	novel
seed	---------------------UUUGACU------------------------------------	1	novel
seed	--------------------------------------UCAUAGG-------------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------TTGACTAGCCTTATGATCA-----------------------	19	6
	---------------------TTTGACTAGCCTTATGATC------------------------	19	3
	---------------------TTTGACTAGCCTTATGATCA-----------------------	20	2
	-------------------------------------ATCATAGGGAGACACTAG---------	18	1
	--------------------CTTTGACTAGCCTTATGATC------------------------	20	1
	---------------------------TAGCCTTATGATCATAGGGAGACAC------------	25	1
	----------------------TTGACTAGCCTTATGATC------------------------	18	1
rat	ccaatggctctttgtttcctcTTTGACTAGCCTTATGATCAtagggagacactaggccattgga
	****************************************************************
rat	((((((((.((.(((((((.((.(((.((......)).))).)))))))))..)))))))))).	1.000 -27.60

rat

chromosome:1:51023399:51023462:1

intergenic

block963715 [novel_lenNOK_multiarm_Multihit_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	0.44/0.44	18/25/0.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	28 8	-23 2	5arm_loop_3arm 3arm	26 26	nd nd	0.44 0.22	6 2	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------AGCCUUA----------------------------	1	novel
seed	---------------------------------------UCAUAGG------------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------------TAGCCTTATGATCATAGGGAGACAC-----------	25	1
	--------------------------------------ATCATAGGGAGACACTAG--------	18	1
rat	ccaatggtacttctgcttcttctgtgacTAGCCTTATGATCATAGGGAGACACTAGgccattgg
	****************************************************************
	--------------------------------------------------------------------------	ENSRNOT00000059938 ENSRNOG00000039174 RGD1563865_predicted
	--------------------------------------------------------------------------	ENSRNOT00000048246 ENSRNOG00000039174 RGD1563865_predicted
rat	((((((((.((..((..((.(((((((.((......)).)))))))))..))..))))))))))	1.000 -21.40

rat

chromosome:1:51892451:51892514:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000059936|ENSRNOG00000039174 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000048246|ENSRNOG00000039174 ## ENSRNOG00000039174|protein_coding|RGD1563865_predicted|

block965915 [novel_lenNOK_multiarm_Multihit_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	0.44/0.44	18/25/0.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	28 8	-23 2	5arm_loop_3arm 3arm	26 26	nd nd	0.44 0.22	6 2	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------AGCCUUA----------------------------	1	novel
seed	---------------------------------------UCAUAGG------------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------------TAGCCTTATGATCATAGGGAGACAC-----------	25	1
	--------------------------------------ATCATAGGGAGACACTAG--------	18	1
rat	ccaatggtacttctgcttcttctgtgacTAGCCTTATGATCATAGGGAGACACTAGgccattgg
	****************************************************************
rat	((((((((.((..((..((.(((((((.((......)).)))))))))..))..))))))))))	1.000 -21.40

rat

chromosome:1:52981968:52982031:1

intergenic

block844989 [novel_lenNOK_multiarm_Multihit_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	0.44/0.44	18/25/0.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	28 8	-23 2	5arm_loop_3arm 3arm	26 26	nd nd	0.44 0.22	6 2	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------AGCCUUA----------------------------	1	novel
seed	---------------------------------------UCAUAGG------------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------------TAGCCTTATGATCATAGGGAGACAC-----------	25	1
	--------------------------------------ATCATAGGGAGACACTAG--------	18	1
rat	ccaatggtacttctgcttcttctgtgacTAGCCTTATGATCATAGGGAGACACTAGgccattgg
	****************************************************************
rat	((((((((.((..((..((.(((((((.((......)).)))))))))..))..))))))))))	1.000 -21.40

rat

chromosome:1:50398231:50398294:-1

intergenic

block845673 [novel_lenNOK_multiarm_Multihit_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	0.35/0.44	18/25/0.20	0.5 0.0 0.0	0.3 0.0 0.0	11 1 1	0 0 0	1 1 1	0 0 0	21 27 9	-12 -23 2	5arm_loop_3arm 5arm_loop_3arm 3arm	40 40 40	nd nd nd	0.47 0.44 0.22	6 6 2	15	1	na	na

		reads	miRBase family seed
seed	-----------------------UGACUAG----------------------------------	7	novel
seed	----------------------UUGACUA-----------------------------------	5	novel
seed	----------------------------AGCCUUA-----------------------------	1	novel
seed	---------------------UUUGACU------------------------------------	1	novel
seed	--------------------------------------UCAUAGG-------------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------TTGACTAGCCTTATGATCA-----------------------	19	6
	---------------------TTTGACTAGCCTTATGATC------------------------	19	3
	---------------------TTTGACTAGCCTTATGATCA-----------------------	20	2
	-------------------------------------ATCATAGGGAGACACTAG---------	18	1
	--------------------CTTTGACTAGCCTTATGATC------------------------	20	1
	---------------------------TAGCCTTATGATCATAGGGAGACAC------------	25	1
	----------------------TTGACTAGCCTTATGATC------------------------	18	1
rat	ccaatggctctttgcttcctcTTTGACTAGCCTTATGATCAtagggagacactaggccattgga
	****************************************************************
rat	((((((((.((.((((((((...(((.((......)).))).)))))).))..)))))))))).	1.000 -24.20

rat

chromosome:1:50787170:50787233:-1

intergenic

novel_mirtron_randfoldOK_nonpairedHIGH (8 loci)

block202109 [novel_mirtron_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	0.003	no	no	0.62/0.62	21/21/1.00	0.0	0.0	1	0	1	0	14	25	3arm	1	0	0.38	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------CUGAUCC---------------------------	1	novel
		len	cloning frequencies
			T2S2
	----------------------------------------------------------------------------------TCTGATCCCTCGTCCTCGCAG--------------	21	1
rat	agctacatgcagctaatggtggtgcttgggatgaggacgtgaggaagcagggcgcatgctcctgagatgtcaaacctcacggTCTGATCCCTCGTCCTCGCAGgggctgatggagct
	*********************************************************************************************************************
	-------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000057025 ENSRNOG00000001145 RGD1310292_predicted
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>	ENSRNOT00000033594 ENSRNOG00000021871 Gcn1l1_predicted
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>	ENSRNOT00000001517 ENSRNOG00000021871 Gcn1l1_predicted
rat	((((.(((.(((((..((..((.((..(((((.((..(((((((...((((((....)).))))..........)))))))..)).)))))..))))...))..)))))))).))))	0.740 -50.32

rat

chromosome:12:42282801:42282917:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000001515|ENSRNOG00000001145 ## Opposite_strand|Intronic_coding|ENSRNOT00000057025|ENSRNOG00000001145 ## Same_strand|Intronic_coding|ENSRNOT00000033594|ENSRNOG00000021871 ## ENSRNOG00000021871|protein_coding|Gcn1l1_predicted| ## ENSRNOG00000001145|protein_coding|RGD1310292_predicted|

block206293 [novel_mirtron_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	0.010	no	no	0.65/0.65	20/20/1.00	0.0	0.0	1	0	1	0	16	7	3arm	1	1	0.35	2	1	1	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------AGGCCUG----------------------------	1	novel
		len	cloning frequencies
			T5S2
	---------------------------------------------------------TAGGCCTGCTCTCCCCTGCA----------------	20	1
rat	gcctggctcaggccaggcaggagtagggacccggccagtggtggctctcagcaaccaTAGGCCTGCTCTCCCCTGCAgggtgtagagtcggtg
	*********************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000001409 ENSRNOG00000001058 Timm44
rat	(((.(((((..(((..(((((...((((....((((.(((((.((.....)).))))).))))..))))..)))))..)))...)))))))).	0.890 -44.60

rat

chromosome:12:1522799:1522891:1

Same_strand|Intronic_coding|ENSRNOT00000001409|ENSRNOG00000001058 ## ENSRNOG00000001058|protein_coding|Timm44|Import inner membrane translocase subunit TIM44, mitochondrial precursor. [Source:UniProtKB/Swiss-Prot;Acc:O35094]

block916440 [novel_mirtron_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	0.67/0.68	21/22/1.00	0.0	0.5	2	0	2	0	10	5	3arm	1	0	0.33	3	2	2	na	na

		reads	miRBase family seed
seed	----------------------------------------------CUGCCCA------------------------	2	novel
		len	cloning frequencies
			T2S2	T4S2
	---------------------------------------------TCTGCCCACCTGCTCTCCCAG-----------	21	-	1
	---------------------------------------------TCTGCCCACCTGCTCTCCCAGC----------	22	1	-
rat	gggttgtagaagaagtggagagcttgggtcttgggttgcactcacTCTGCCCACCTGCTCTCCCAGCctcttcccca
	*****************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>	ENSRNOT00000027756 ENSRNOG00000020440 Fads2
rat	(((.....(((((.(((((((((.(((((..((((.....))))....)))))...)))))))..)).)))))))).	1.000 -32.00

rat

chromosome:1:212513333:212513409:-1

Same_strand|Boundary_coding|ENSRNOT00000027756|ENSRNOG00000020440 ## ENSRNOG00000020440|protein_coding|Fads2|Fatty acid desaturase 2 (EC 1.14.19.-) (Delta(6) fatty acid desaturase) (Delta(6) desaturase) (D6D). [Source:UniProtKB/Swiss-Prot;Acc:Q9Z122]

block1091875 [novel_mirtron_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	0.006	no	no	0.41/0.45	20/22/1.00	0.6	0.6	5	0	3	0	14	22	5arm	1	0	0.32	3	5	3	na	na

		reads	miRBase family seed
seed	----------------ACAACCU--------------------------------------------------------------------------------------------	3	novel
seed	---------------CACAACC---------------------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T2S2
	---------------CACAACCTCTACTTCTACTC--------------------------------------------------------------------------------	20	1	1	-
	--------------TCACAACCTCTACTTCTACTCA-------------------------------------------------------------------------------	22	-	-	2
	---------------CACAACCTCTACTTCTACTCAG------------------------------------------------------------------------------	22	1	-	-
rat	ggctggcagacttgTCACAACCTCTACTTCTACTCAGgcccatgagcaggctctggctgacctcaccaagaggctgggggctttggaggagcctgatgtgactggtcagttggct
	*******************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000000481 ENSRNOG00000000421 Skiv2l
rat	(((..((.((((.((((((...((..(((((.((.((((((.....(((.((((((.((....))))).))).))).)))))).)))))))...)))))))).)))).))..)))	0.950 -50.40

rat

chromosome:20:4091015:4091129:1

Same_strand|Intronic_coding|ENSRNOT00000000481|ENSRNOG00000000421 ## ENSRNOG00000000421|protein_coding|Skiv2l|superkiller viralicidic activity 2-like [Source:RefSeq_peptide;Acc:NP_998724]

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