Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_multiarm_DicerNOK_shortStem_nonpairedHIGH_bulgeHIGH (2 loci)

sblock2398 [novel_multiarm_DicerNOK_shortStem_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	0.131	no	no	0.50/0.60	19/22/0.83	0.8 0.0 0.0	1.5 0.0 0.0	4 1 1	0 0 0	4 1 1	0 0 0	2 31 10	18 -10 6	5arm 5arm_loop_3arm 3arm	1 52 52	nd nd nd	0.35 0.50 0.36	5 5 4	6	6	-9	-7

		reads	miRBase family seed
seed	----AGGGGCA-------------------------------------------------------------------------	3	novel
seed	-----------------------------------------------------UUGGUGG------------------------	1	novel
seed	---CAGGGGC--------------------------------------------------------------------------	1	novel
seed	--------------------------------CAUCCUA---------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T2S2	T3S1	T4S2	T5S1	T5S2
	---CAGGGGCAGAGCAGATGTAG-------------------------------------------------------------	20	1	-	1	-	1	-
	-------------------------------TCATCCTAGCTTGATGCCTG---------------------------------	20	-	1	-	-	-	-
	--TCAGGGGCAGAGCAGATGT---------------------------------------------------------------	19	-	-	-	1	-	-
	----------------------------------------------------CTTGGTGGCCAAAGCTGTTTCA----------	22	-	-	-	-	-	1
rat	agTCAGGGGCAGAGCAGATGTAGgcctttgtTCATCCTAGCTTGATGCCTGgCTTGGTGGCCAAAGCTGTTTCAtgcctagggc
	************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000049048 ENSRNOG00000030628 Eif4a1
rat	.(((..(((((((((((.....((((.....(((.((..((.....))..))..))).))))....))))))..)))))..)))	0.920 -29.10

rat

chromosome:10:56487077:56487160:-1

Same_strand|Intronic_coding|ENSRNOT00000049048|ENSRNOG00000030628 ## ENSRNOG00000030628|protein_coding|Eif4a1|eukaryotic translation initiation factor 4A1 [Source:RefSeq_peptide;Acc:NP_955404]

novel_multiarm_DicerNOK_shortStem_randfoldOK (2 loci)

sblock1124 [novel_multiarm_DicerNOK_shortStem_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	0.35/0.38	21/23/1.00	0.0 0.0	0.0 0.7	1 3	0 0	1 3	0 0	2 3	4 4	5arm 3arm	1 1	nd nd	0.22 0.18	3 2	4	3	2	0

		reads	miRBase family seed
seed	----------------------------------------UGCUAGA-----------------	3	novel
seed	---CUUACUG------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S2	T3S1	T4S1
	---------------------------------------ATGCTAGAACTTACAGTGTAGA---	22	1	1	-
	--ACTTACTGTATTTCTTAGCATCC---------------------------------------	23	-	1	-
	---------------------------------------ATGCTAGAACTTACAGTGTAG----	21	-	-	1
rat	gtACTTACTGTATTTCTTAGCATCCgactttgttcagtaATGCTAGAACTTACAGTGTAGAtac
	****************************************************************
rat	((((((((((((.(((.((((((...(((......))).)))))))))..))))))).)).)))	1.000 -17.20

rat

chromosome:1:265826037:265826100:-1

intergenic

sblock7321 [novel_multiarm_DicerNOK_shortStem_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	0.003	no	no	0.38/0.50	20/23/1.00	0.0 0.0	0.0 0.0	4 2	0 0	1 1	0 0	4 0	2 12	5arm 3arm	1 1	nd nd	0.14 0.37	2 4	7	1	9	4

		reads	miRBase family seed
seed	-----GCUAGUU---------------------------------------------------	5	novel
seed	--------------------------------------------GCAGAAA------------	2	novel
		len	cloning frequencies
			T5S1
	----TGCTAGTTCTTGTCATAACTG--------------------------------------	21	4
	-------------------------------------------TGCAGAAAAGGCAAGAGGAC	20	2
	----TGCTAGTTCTTGTCATAACTGCC------------------------------------	23	1
rat	gtctTGCTAGTTCTTGTCATAACTGccagagggcagcttctgaTGCAGAAAAGGCAAGAGGAC
	***************************************************************
	-------------------------------------------------------------------------	ENSRNOT00000035355 ENSRNOG00000023712 Stox1_predicted
rat	.(((((((..(((((((((.(((((((....))))).)).))))).))))..)))))))....	1.000 -24.80

rat

chromosome:20:29934250:29934312:1

Opposite_strand|Intronic_non-coding|ENSRNOT00000035355|ENSRNOG00000023712 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000057578|ENSRNOG00000023712 ## ENSRNOG00000023712|protein_coding|Stox1_predicted|

novel_multiarm_DicerOK_5varHIGH_loopOverlap (2 loci)

sblock10936 [novel_multiarm_DicerOK_5varHIGH_loopOverlap]

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	0.270	no	no	0.50/0.70	18/21/0.75	0.0 1.5 0.0	0.0 1.0 0.0	1 2 1	0 0 0	1 2 1	0 0 0	4 38 2	27 -10 34	5arm 5arm_loop_3arm 3arm	1 1 1	nd nd nd	0.25 0.40 0.33	2 4 3	4	3	3	1

		reads	miRBase family seed
seed	---------------------------------------UCACCAG---------------------------------------------------------------	1	novel
seed	------------------------------------------CCAGAUU------------------------------------------------------------	1	novel
seed	------------------------------------------------------------------------------------------GGAGCUG------------	1	novel
seed	-----GGCUCGC-------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1
	-----------------------------------------ACCAGATTTCCACAGACGTC------------------------------------------------	20	-	1	-
	-----------------------------------------------------------------------------------------TGGAGCTGAGCGGATCTC--	18	1	-	-
	--------------------------------------CTCACCAGATTTCCACAGACG--------------------------------------------------	21	1	-	-
	----AGGCTCGCCCAGCAGACTGC-------------------------------------------------------------------------------------	20	-	-	1
rat	gagcAGGCTCGCCCAGCAGACTGCgtcacagctgcctgCTCACCAGATTTCCACAGACGTCtctaaagactgcagactgcggcacggctTGGAGCTGAGCGGATCTCtt
	*************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000012261 ENSRNOG00000027569 Trappc9
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000038172 ENSRNOG00000027569 Trappc9
rat	(((.(((..(((.((((((.(((.(((.(((((((...((....((((.((....)).))))....))...)))).))).))).)))))....)))).)))..))))))	0.540 -35.90

rat

chromosome:7:110541206:110541314:-1

Same_strand|Intronic_coding|ENSRNOT00000038172|ENSRNOG00000027569 ## ENSRNOG00000027569|protein_coding|Trappc9|trafficking protein particle complex 9 Gene [Source:MGI Symbol;Acc:MGI:1923760]

sblock6768 [novel_multiarm_DicerOK_5varHIGH_loopOverlap]

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	0.047	no	no	0.41/0.65	18/25/0.78	0.0 5.6	0.2 6.4	4 5	0 0	3 2	0 0	8 8	-1 -18	5arm_loop 3arm	1 1	nd nd	0.29 0.33	3 4	9	3	1	1

		reads	miRBase family seed
seed	---------UCGAACC----------------------------------------------------	4	novel
seed	--------------------------------------GACAGGA-----------------------	2	novel
seed	------------------------------GCAAGUU-------------------------------	2	novel
seed	---------------------------CAUGCAA----------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T5S1
	--------TTCGAACCAGAGTTACTGTCA---------------------------------------	21	-	1	2
	--------------------------TCATGCAAGTTTGACAGGAAC---------------------	21	-	-	1
	-----------------------------TGCAAGTTTGACAGGAACACTG-----------------	22	-	-	1
	--------TTCGAACCAGAGTTACTGTCAT--------------------------------------	22	1	-	-
	-------------------------------------TGACAGGAACACTGGGGG-------------	18	-	-	1
	-------------------------------------TGACAGGAACACTGGGGGAGGGG--------	23	-	-	1
	-----------------------------TGCAAGTTTGACAGGAACACTGGGG--------------	25	1	-	-
rat	gtggtttaTTCGAACCAGAGTTACTGTCATGCAAGTTTGACAGGAACACTGGGGGAGGGGgggagcgc
	********************************************************************
rat	(((.(((.(((...((((.(((.((((((........)))))).))).))))....)))..))).)))	1.000 -21.80

rat

chromosome:20:5525976:5526043:-1

intergenic ## {Repeats: dust 5525984 5525993 0 class=dust}

novel_multiarm_DicerOK_nonpairedHIGH (2 loci)

sblock10146 [novel_multiarm_DicerOK_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	0.268	no	no	0.44/0.55	18/23/0.80	0.0 0.0 0.0	0.0 1.0 0.0	1 3 1	0 0 0	1 1 1	0 0 0	8 6 0	0 1 12	5arm 3arm 3arm	1 1 1	nd nd nd	0.41 0.45 0.53	3 4 5	5	1	1	1

		reads	miRBase family seed
seed	--------------------------------------------UCAGGAU---------------------	3	novel
seed	-------------------------------------------------------GAAGCUG----------	1	novel
seed	---------AGCAGAA--------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------------------------TTCAGGATCAGTGAAGCTGGAGA------	23	2
	------------------------------------------------------TGAAGCTGGAGATCTTGT	18	1
	--------AAGCAGAAGACTGGTAGGGAGC------------------------------------------	22	1
	-------------------------------------------TTCAGGATCAGTGAAGCTGG---------	20	1
rat	ggcaggcgAAGCAGAAGACTGGTAGGGAGCgagggctggggagTTCAGGATCAGTGAAGCTGGAGATCTTGT
	************************************************************************
rat	.(((((.....(((...((((((...((((............))))...))))))....))).....)))))	0.980 -16.40

rat

chromosome:6:122578980:122579051:-1

intergenic

sblock8151 [novel_multiarm_DicerOK_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	0.149	no	no	0.40/0.60	20/20/1.00	0.0 0.0 0.0	0.0 0.0 0.0	1 2 1	0 0 0	1 1 1	0 0 0	17 21 0	12 15 36	5arm 3arm 3arm	1 1 1	nd nd nd	0.35 0.40 0.58	3 4 8	4	2	2	1

		reads	miRBase family seed
seed	-----------------------------------------------------------------------GCUCCAG---------------------------------	2	novel
seed	--------------------------------------------------------------------------------------------GACUAAG------------	1	novel
seed	------------------AUGAGAC--------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S2	T5S1
	----------------------------------------------------------------------TGCTCCAGCTAGGATCAGCT---------------------	20	-	2
	-----------------GATGAGACAGCAGAGGCACC--------------------------------------------------------------------------	20	1	-
	-------------------------------------------------------------------------------------------TGACTAAGGAAGACTCTTGT	20	-	1
rat	gggaggtgggtagagcaGATGAGACAGCAGAGGCACCaggggaggaagtaaagggactgggtattgatggTGCTCCAGCTAGGATCAGCTaTGACTAAGGAAGACTCTTGT
	***************************************************************************************************************
rat	(((((...(((..(((...(((...(((...(((((((........(((......))).........)))))))...)))....))))))...)))........)))))..	0.960 -24.53

rat

chromosome:3:115229471:115229581:1

intergenic

novel_multiarm_Multihit_loopOverlap_randfoldOK_nonpairedHIGH_bulgeHIGH (2 loci)

sblock1344 [novel_multiarm_Multihit_loopOverlap_randfoldOK_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	0.001	no	no	0.42/0.52	19/21/0.75	0.0 0.7	0.0 0.0	1 3	0 0	1 1	0 0	31 10	-3 20	5arm_loop 3arm	7 25	nd nd	0.38 0.53	4 8	4	2	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------CUCCAAA-----------------------	2	novel
seed	---------------------------------------------------------------------------------CCAAAGU---------------------	1	novel
seed	--------------------------------ACUGUCC----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	------------------------------------------------------------------------------CCTCCAAAGTTGGAAGAACTG----------	21	-	2
	-------------------------------TACTGTCCCAGAACCTCCACT---------------------------------------------------------	21	1	-
	--------------------------------------------------------------------------------TCCAAAGTTGGAAGAACTG----------	19	-	1
rat	tgatgcagcacctcctttttcccatcaccttTACTGTCCCAGAACCTCCACTttcccaggaactgttctgttgcagggCCTCCAAAGTTGGAAGAACTGtactgtatca
	*************************************************************************************************************
rat	.(((((((.((....(((((((...........((((..((((((.(((.........)))...))))))..)))).............)))))))..)).))))))).	0.610 -29.55

rat

chromosome:1:47970593:47970701:1

intergenic

sblock4654 [novel_multiarm_Multihit_loopOverlap_randfoldOK_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	0.001	no	no	0.42/0.52	19/21/0.75	0.0 0.7	0.0 0.0	1 3	0 0	1 1	0 0	31 10	-3 20	5arm_loop 3arm	7 25	nd nd	0.38 0.53	4 8	4	2	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------CUCCAAA-----------------------	2	novel
seed	---------------------------------------------------------------------------------CCAAAGU---------------------	1	novel
seed	--------------------------------ACUGUCC----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	------------------------------------------------------------------------------CCTCCAAAGTTGGAAGAACTG----------	21	-	2
	-------------------------------TACTGTCCCAGAACCTCCACT---------------------------------------------------------	21	1	-
	--------------------------------------------------------------------------------TCCAAAGTTGGAAGAACTG----------	19	-	1
rat	tgatgcagcacctcctttttcccatcaccttTACTGTCCCAGAACCTCCACTttcccaggaactgttctgttgcagggCCTCCAAAGTTGGAAGAACTGtactgtatca
	*************************************************************************************************************
rat	.(((((((.((....(((((((...........((((..((((((.(((.........)))...))))))..)))).............)))))))..)).))))))).	0.610 -29.55

rat

chromosome:15:80381069:80381177:1

intergenic

novel_multiarm_loopOverlap_mirtron (2 loci)

block1376091 [novel_multiarm_loopOverlap_mirtron]

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	0.099	no	no	0.33/0.33	21/24/1.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	2 9	-1 -11	5arm_loop 5arm_loop_3arm	1 1	9 1	0.29 0.42	3 8	2	1	na	na

		reads	miRBase family seed
seed	----------AUAAUAA---------------------------------------	1	novel
seed	---UGACGUC----------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	---------CATAATAATTTCTCTCCACACAGA-----------------------	24	1
	--GTGACGTCATAATAATTTCTC---------------------------------	21	1
rat	tgGTGACGTCATAATAATTTCTCTCCACACAGAaattgctagcattctgtctgcca
	********************************************************
	+++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000032008 ENSRNOG00000022637 Q7TN00_RAT
rat	.(((((((...((.((((((((........)))))))).))......)))).))).	0.970 -10.30

rat

chromosome:3:59601502:59601557:-1

Same_strand|Boundary_non-coding|ENSRNOT00000047867|ENSRNOG00000022637 ## Same_strand|Boundary_coding|ENSRNOT00000032008|ENSRNOG00000022637 ## ENSRNOG00000022637|protein_coding|Q7TN00_RAT|Cardiac titin N2BA isoform (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q7TN00]

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