Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_loopOverlap_nonpairedHIGH (1826 loci)

block30080 [novel_loopOverlap_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	0.622	no	no	0.38/0.38	21/21/1.00	0.0	0.0	3	0	1	0	23	-3	3arm_loop	7	nd	0.33	3	3	1	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------AAGUUCU------------------------------------	3	miR-148b
		len	cloning frequencies
			T4S1
	---------------------------------------------------------AAAGTTCTACAATGTGGCTGA-----------------------	21	3
rat	aaaactttccactggtacggtgaaactgacagcagttggttggagcaaacatcccccAAAGTTCTACAATGTGGCTGAggactgtgattggacattgtttt
	*****************************************************************************************************
	---------------------------------------------------------------------------------------------------------------	ENSRNOT00000044938 ENSRNOG00000013780 Nf1
	---------------------------------------------------------------------------------------------------------------	ENSRNOT00000046262 ENSRNOG00000013780 Nf1
rat	(((((..((((....((((((....((..((((.((((...(((((..............))))).))))...)))).))))))))..))))....)))))	0.720 -21.74

rat

chromosome:10:65710153:65710253:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000047858|ENSRNOG00000013780 ## Opposite_strand|Intronic_coding|ENSRNOT00000044938|ENSRNOG00000013780 ## ENSRNOG00000013780|protein_coding|Nf1|neurofibromatosis 1 Gene [Source:MGI (curated);Acc:Nf1-003]

block2122593 [novel_loopOverlap_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	0.853	no	no	0.38/0.38	24/24/1.00	0.0	0.0	1	0	1	0	19	-3	3arm_loop	3	nd	0.38	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------UGGACCA-----------------------------------	1	novel
		len	cloning frequencies
			T2S1
	--------------------------------------------GTGGACCATTTTTTTTTGTGTGTG-------------------	24	1
rat	tgataacaatgcatcgtaaaaccttcagaaggaaagaatgttttGTGGACCATTTTTTTTTGTGTGTGtggcagttttaagttatta
	***************************************************************************************
rat	(((((((.....((.((...((...((((((((((....(((.....)))..))))))))))...))...)).)).....)))))))	0.720 -11.60

rat

chromosome:7:67359943:67360029:-1

intergenic ## {Repeats: dust 67359969 67359977 0 class=dust}

novel_loopOverlap (1697 loci)

block1870 [novel_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	0.056	no	no	0.48/0.48	21/21/1.00	0.0	0.0	1	0	1	0	6	-1	3arm	1	nd	0.29	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------GUGCUCC-------------------	1	novel
		len	cloning frequencies
			T5S1
	------------------------------------AGTGCTCCAATGTCAGAAGTG------	21	1
rat	atgacatcacagggtggcgaattgtgggagaatgttAGTGCTCCAATGTCAGAAGTGgtgtta
	***************************************************************
rat	.(((((((((....(((((.......((((.((....)).))))..)))))...)))))))))	0.960 -16.50

rat

chromosome:10:4177436:4177498:-1

intergenic

block4801 [novel_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	0.445	no	no	0.65/0.67	20/21/1.00	0.0	0.5	2	0	1	0	13	-1	5arm_loop	1	nd	0.30	2	2	1	na	na

		reads	miRBase family seed
seed	--------------GGACAAC--------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T2S1
	-------------GGGACAACAGGCCTCTGGGAC-------------------------------------------------------	21	1
	-------------GGGACAACAGGCCTCTGGGA--------------------------------------------------------	20	1
rat	agcataatctgctGGGACAACAGGCCTCTGGGACacattccattttctctctctcaaaacagttttgttccctgaagtattctttgtgc
	*****************************************************************************************
	---------------------------------------------------------------------------------------------------	ENSRNOT00000004999 ENSRNOG00000003328 RGD1310686
rat	.((((((..((((((((..((((..((.(((((..................)))))....))..))))))))...))))....))))))	0.470 -15.37

rat

chromosome:10:10892939:10893027:-1

Opposite_strand|Intronic_non-coding|ENSRNOT00000004999|ENSRNOG00000003328 ## ENSRNOG00000003328|protein_coding|RGD1310686|LITAF-like protein. [Source:UniProtKB/Swiss-Prot;Acc:Q5U2U6]

block5848 [novel_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	0.081	no	no	0.50/0.50	24/24/1.00	0.0	0.0	1	0	1	0	19	-1	5arm_loop	1	nd	0.21	2	1	1	na	na

		reads	miRBase family seed
seed	--------------------CCAGUGG------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	-------------------ACCAGTGGGCTTCAGAAGAGTTTG--------------------------------------------------------------------	24	1
rat	ttcacattaccaggaacaaACCAGTGGGCTTCAGAAGAGTTTGaataaacatggaaaactccctctagcctctcattctttagctggcttttctgagtgagaagcgtggaa
	***************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000030704 ENSRNOG00000021872 LOC680728
rat	(((((.((((((((((....((((((((((..(((.((((((.............))))))..))))))))...........)))))..)))))).)))).....))))).	0.910 -28.22

rat

chromosome:10:12822864:12822974:-1

Same_strand|Intronic_non-coding|ENSRNOT00000030704|ENSRNOG00000021872 ## Same_strand|Boundary_non-coding|ENSRNOT00000030695|ENSRNOG00000021872 ## ENSRNOG00000021872|protein_coding|LOC680728|

block8406 [novel_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	0.083	no	no	0.45/0.45	20/20/1.00	0.0	0.0	1	0	1	0	8	-1	3arm	1	nd	0.30	2	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------GUCUGGA--------------------	1	novel
		len	cloning frequencies
			T1S1
	-------------------------------GGTCTGGAAAAGATGACATG--------	20	1
rat	gagggagttgtcttcttgaaactaaataatcGGTCTGGAAAAGATGACATGactttctt
	***********************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000028186 ENSRNOG00000020769 RGD1310862_predicted
rat	(((..(((((((.((((....(((.((.....)).)))..)))).))))..)))..)))	0.990 -13.10

rat

chromosome:10:16703490:16703548:-1

Same_strand|Intronic_non-coding|ENSRNOT00000028186|ENSRNOG00000020769 ## ENSRNOG00000020769|protein_coding|RGD1310862_predicted|

block8927 [novel_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	0.101	no	no	0.54/0.54	24/24/1.00	0.0	0.0	1	0	1	0	29	-2	3arm_loop	1	nd	0.29	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------UGGCCAU---------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	--------------------------------------------------------------CTGGCCATATCCAGCCTTCTCCTT-----------------------------	24	1
rat	cagggtcattctgttcttaaggagggcgccttggattcaatcgtcttagaaacacaaaaccaCTGGCCATATCCAGCCTTCTCCTTtgcatgagtctcagagtgtaaacacctgt
	*******************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000005874 ENSRNOG00000004395 Fbxw11
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000006078 ENSRNOG00000004395 Fbxw11
rat	(((((((((((((..(((((((((((.((..(((((......(((...................)))...))))))).))))))).....))))...)))))))...)).)))).	0.650 -30.01

rat

chromosome:10:17594290:17594404:-1

Opposite_strand|Intronic_coding|ENSRNOT00000006078|ENSRNOG00000004395 ## ENSRNOG00000004395|protein_coding|Fbxw11|F-box and WD-40 domain protein 11 Gene [Source:MGI (curated);Acc:Fbxw11-002]

block10335 [novel_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	0.077	no	no	0.74/0.74	23/23/1.00	0.0	0.0	1	0	1	0	34	-1	5arm_loop	1	nd	0.22	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------CGUUGGG------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	----------------------------------GCGTTGGGCGGTAGTGGGGGGAC---------------------------------------------------------------	23	1
rat	gggggtgggggagggagtggagagagagccagttGCGTTGGGCGGTAGTGGGGGGACgcatctcaaaccccacattgctttaacaatcagcaggaaaataaagagcacctcgtctaatcc
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000011922 ENSRNOG00000027341 Odz2
rat	.((..((((.((((..((..........((.((((.((((((((((.((((((.((......))...))))))))))))).)))...)))).))..........)).)))).))))..))	0.940 -40.25

rat

chromosome:10:21224843:21224962:-1

Same_strand|Boundary_non-coding|ENSRNOT00000045307|ENSRNOG00000027341 ## Same_strand|Intronic_coding|ENSRNOT00000011922|ENSRNOG00000027341 ## ENSRNOG00000027341|protein_coding|Odz2|Teneurin-2 (Ten-2) (Tenascin-M2) (Ten-m2) (Protein Odd Oz/ten-m homolog 2) (Neurestin). [Source:UniProtKB/Swiss-Prot;Acc:Q9R1K2]

block12449 [novel_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	0.716	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	13	-1	5arm_loop	1	nd	0.30	2	1	1	na	na

		reads	miRBase family seed
seed	--------------ACUGCUG----------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	-------------CACTGCTGAGTACAAGGTCC----------------------------------------	20	1
rat	gggataaaagcgtCACTGCTGAGTACAAGGTCCtgagacttccggtgtttgccctgctttgctgtagattcca
	*************************************************************************
	-----------------------------------------------------------------------------------	ENSRNOT00000004970 ENSRNOG00000003680 Gabrb2
rat	(((((...((((.((..((.((((((.(((((....)))))...))))))))..))...))))....))))).	0.530 -16.70

rat

chromosome:10:27754966:27755038:-1

Opposite_strand|Intronic_coding|ENSRNOT00000004970|ENSRNOG00000003680 ## ENSRNOG00000003680|protein_coding|Gabrb2|Gamma-aminobutyric acid receptor subunit beta-2 precursor (GABA(A) receptor subunit beta-2). [Source:UniProtKB/Swiss-Prot;Acc:P63138]

block13530 [novel_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	0.402	no	no	0.15/0.15	20/20/1.00	0.0	0.0	1	0	1	0	35	-4	3arm_loop	1	nd	0.30	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------CAAUUUG-----------------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	-------------------------------------------TCAATTTGTTTCTTTTTTTT-----------------------------------	20	1
rat	atccctggtggttctcccaatttcaagaaaacgagactgagcgTCAATTTGTTTCTTTTTTTTatttttcgaaaggggttgccagagaatgacagaga
	**************************************************************************************************
rat	.((.((.((.((((((.((((((((((((((.(((((.((.......)).))))).)))))))...........)))))))...)))))).)))).))	0.420 -19.10

rat

chromosome:10:30698910:30699007:-1

intergenic ## {Repeats: dust 30698945 30698952 0 class=dust}

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