Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_shortStem_mirtron_nonpairedHIGH_bulgeHIGH (40 loci)

block2185949 [novel_lenNOK_shortStem_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	0.116	no	no	0.61/0.61	18/18/0.00	0.0	0.0	1	0	1	0	2	0	5arm	1	4	0.44	4	1	1	na	na

		reads	miRBase family seed
seed	---AAAGGUG-----------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	--TAAAGGTGCCCACGGGAC-------------------------------	18	1
rat	ccTAAAGGTGCCCACGGGACagggaaggaaggtcctaggcacagagcaagg
	***************************************************
	>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000041034 ENSRNOG00000032895 Cyp4f4
	>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000034309 ENSRNOG00000032895 Cyp4f4
rat	(((....(((((...(((((...........))))).)))))......)))	1.000 -14.70

rat

chromosome:7:13308088:13308138:1

Same_strand|Boundary_coding|ENSRNOT00000034309|ENSRNOG00000032895 ## ENSRNOG00000032895|protein_coding|Cyp4f4|Cytochrome P450 4F4 (EC 1.14.14.1) (CYPIVF4). [Source:UniProtKB/Swiss-Prot;Acc:P51869]

block2254151 [novel_lenNOK_shortStem_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	0.319	no	no	0.58/0.58	19/19/0.00	0.0	0.0	1	0	1	0	1	32	5arm	1	4	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	--UGGCGUU---------------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	-GTGGCGTTGGTGTCTGTTG----------------------------------------------------------------------------------------------------	19	1
rat	tGTGGCGTTGGTGTCTGTTGgcagagctgtctctgatcacgctgcactggttcctcacggccttcgccagcgtggtgcacatcagactgctgctgcgcatctgggacctgttcttctacg
	************************************************************************************************************************
	+++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000025382 ENSRNOG00000018745 Rutbc3
rat	.((((....(((.((...(((((((((.((((.((((((((((((...((((......))))...)).)))))))).))....)))).))).)))).))...)).))).......)))).	0.700 -41.80

rat

chromosome:7:119301961:119302080:1

Same_strand|Intronic_coding|ENSRNOT00000025382|ENSRNOG00000018745 ## Same_strand|Boundary_non-coding|ENSRNOT00000056108|ENSRNOG00000018745 ## ENSRNOG00000018745|protein_coding|Rutbc3|Small G protein signaling modulator 3 (RUN and TBC1 domain-containing protein 3) (BDIF-1). [Source:UniProtKB/Swiss-Prot;Acc:Q6P6R7]

block2697983 [novel_lenNOK_shortStem_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	0.259	no	no	0.42/0.42	19/19/0.00	0.0	0.0	1	0	1	0	3	19	3arm	1	3	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------GAGGUAU--------------	1	novel
		len	cloning frequencies
			T3S2
	-------------------------------------------------------------------------AGAGGTATGCTACCATGAA---	19	1
rat	ccctccaccgcctcctacagttcctctccattgttgccaggcatgctgaagataatgtcagcaaagatggacaAGAGGTATGCTACCATGAAggg
	***********************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++	ENSRNOT00000040311 ENSRNOG00000003956 Arhgap6
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++	ENSRNOT00000051655 ENSRNOG00000003956 Arhgap6
rat	((((.((...........(((.((((((((((.((((..(((((..........))))).)))).))))))...))))...)))....)).))))	0.590 -23.96

rat

chromosome:X:45678520:45678614:-1

Same_strand|Boundary_coding|ENSRNOT00000051655|ENSRNOG00000003956 ## Same_strand|Boundary_non-coding|ENSRNOT00000036502|ENSRNOG00000003956 ## ENSRNOG00000003956|protein_coding|Arhgap6|Rho GTPase activating protein 6 Gene [Source:MGI (curated);Acc:Arhgap6-001]

block2013427 [novel_lenNOK_shortStem_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	0.784	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	2	26	3arm	1	0	0.39	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------UGGAUCU------------	1	novel
		len	cloning frequencies
			T4S2
	----------------------------------------------------------------------------------GTGGATCTCTCTGAACAG--	18	1
rat	ttcttacagttgtcttacagttacagtggatgtggcaggggtggggcgtcttataaagttgctttgtcttggccctaacgcaGTGGATCTCTCTGAACAGaa
	******************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>	ENSRNOT00000060408 ENSRNOG00000006056 NP_001102174.1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>	ENSRNOT00000008173 ENSRNOG00000006056 NP_001102174.1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>	ENSRNOT00000031371 ENSRNOG00000006056 NP_001102174.1
rat	.(((..(((..((((.......((.(((.....(((..(((..(((((.((.....)).)))))..)))..)))....))).))))))....)))...))).	0.420 -22.61

rat

chromosome:6:41825001:41825102:1

Same_strand|Intronic_coding|ENSRNOT00000031371|ENSRNOG00000006056 ## ENSRNOG00000006056|protein_coding|NP_001102174.1|development and differentiation enhancing factor 2 [Source:RefSeq_peptide;Acc:NP_001102174]

block22059 [novel_lenNOK_shortStem_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	0.737	no	no	0.26/0.26	19/19/0.00	0.0	0.0	1	0	1	0	0	34	5arm	2	2	0.37	4	1	1	na	na

		reads	miRBase family seed
seed	-GAGUUUG--------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	TGAGTTTGACTTTTCTTTT---------------------------------------------------------------------------------	19	1
rat	TGAGTTTGACTTTTCTTTTgtggttttaaagttgcttcttagtgtatgaagacattttgtccagggcctataactgctaagcccgaaaaagccccattca
	****************************************************************************************************
	>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000004291 ENSRNOG00000003215 NP_001100478.1
rat	.((((....(((...(((((.(((((...(((((.....(((.((.....(((.....)))....))))))))))...)))))))))))))....)))).	0.420 -16.50

rat

chromosome:10:48912619:48912718:-1

Same_strand|Intronic_coding|ENSRNOT00000004291|ENSRNOG00000003215 ## ENSRNOG00000003215|protein_coding|NP_001100478.1|zinc finger protein 287 [Source:RefSeq_peptide;Acc:NP_001100478]

block79138 [novel_lenNOK_shortStem_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	0.187	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	2	26	3arm	1	3	0.56	4	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------------------UCCAAGG------------	1	novel
		len	cloning frequencies
			T2S2
	-----------------------------------------------------------------------------GTCCAAGGATTCCTGTTG--	18	1
rat	gctggaaaaggtgaaagtggtctgggcacagcctccatgctcctggtcaggggagagcctggatgtgcctctgacctGTCCAAGGATTCCTGTTGca
	*************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>	ENSRNOT00000040488 ENSRNOG00000033508 LOC687705
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>	ENSRNOT00000043732 ENSRNOG00000033508 LOC687705
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>	ENSRNOT00000044539 ENSRNOG00000033508 LOC687705
rat	((.((((....((.....((((.(((((((...((((.((((((.......)).)))).)))))))))))..))))....))....))))....)).	0.680 -34.50

rat

chromosome:10:57494072:57494168:1

Same_strand|Intronic_coding|ENSRNOT00000040488|ENSRNOG00000033508 ## ENSRNOG00000033508|protein_coding|LOC687705|LOC303259 protein (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q5EB61]

novel_lenNOK_Multihit_shortStem_loopOverlap_nonpairedHIGH_bulgeHIGH (39 loci)

block479831 [novel_lenNOK_Multihit_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	0.025	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	4	-4	5arm_loop	13	nd	0.33	5	1	1	na	na

		reads	miRBase family seed
seed	-----UCUGUGU------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	----TTCTGTGTGCACAAAGAC--------------------------	18	1
rat	tttaTTCTGTGTGCACAAAGACtagcatgattggtatcacagggtaga
	************************************************
rat	((((((((((((((.(((............)))))).)))))))))))	1.000 -12.60

rat

chromosome:15:21473483:21473530:1

intergenic ## {Repeats: dust 21473450 21473452 0 class=dust}

block704444 [novel_lenNOK_Multihit_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	0.024	no	no	0.37/0.37	19/19/0.00	0.0	0.0	1	0	1	0	2	-4	5arm_loop	18	nd	0.53	5	1	1	na	na

		reads	miRBase family seed
seed	---CAUAAAG-------------------------------	1	novel
		len	cloning frequencies
			T5S1
	--CCATAAAGCTATCAGAAGA--------------------	19	1
rat	gtCCATAAAGCTATCAGAAGAaatcctgacactcagtggat
	*****************************************
rat	((((((..((...((((........))))..))..))))))	1.000 -9.40

rat

chromosome:18:44778511:44778551:-1

intergenic

block732755 [novel_lenNOK_Multihit_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	0.422	no	no	0.32/0.32	19/19/0.00	0.0	0.0	1	0	1	0	4	-3	5arm_loop	21	nd	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	-----AGACUUC--------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	----AAGACTTCTTCAATGGAAA---------------------------------------------------	19	1
rat	ctgcAAGACTTCTTCAATGGAAAagaacagaataagagcattaaccccagtgaagctgttgcctatggtgcagc
	**************************************************************************
rat	(((((.(((..(((((.(((..........................))).)))))..)))........))))).	0.520 -13.87

rat

chromosome:18:23138558:23138631:1

intergenic

block842881 [novel_lenNOK_Multihit_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	0.303	no	no	0.58/0.58	19/19/0.00	0.0	0.0	4	0	3	0	4	-4	5arm_loop	17	nd	0.37	5	4	3	na	na

		reads	miRBase family seed
seed	-----CCCAGAA--------------------------------------------------	4	novel
		len	cloning frequencies
			T2S1	T4S2	T5S1
	----TCCCAGAACCTGCACTACC---------------------------------------	19	1	1	2
rat	actgTCCCAGAACCTGCACTACCctaagacctcccttgtcgcaggacatccactgtggtagt
	**************************************************************
rat	((((.(((((..(((((((..................)).))))).......))).))))))	0.660 -11.87

rat

chromosome:1:49002786:49002847:-1

intergenic

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