Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_Multihit_loopOverlap (282 loci)

block1258920 [novel_lenNOK_Multihit_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	0.399	no	no	0.37/0.39	18/19/0.00	0.7	1.0	3	0	2	0	11	-1	3arm	15	nd	0.11	2	3	2	na	na

		reads	miRBase family seed
seed	------------------------------------------------------UGGAAAC------------------------	2	novel
seed	--------------------------------------------------------GAAACAA----------------------	1	novel
		len	cloning frequencies
			T2S1	T5S2
	-----------------------------------------------------ATGGAAACAACTTGACCA--------------	18	2	-
	-------------------------------------------------------GGAAACAACTTGACCAAAA-----------	19	-	1
rat	tgtgggggggggggcagttttaagttataagttttcaaaatcagtactttttaATGGAAACAACTTGACCAAAAatctgtcacag
	*************************************************************************************
rat	(((((.(((...((.....(((((((....(((((((.................)))))))))))))))).....))).))))).	0.880 -15.63

rat

chromosome:2:53365417:53365501:1

intergenic

block1817864 [novel_lenNOK_Multihit_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	0.119	no	no	0.58/0.58	19/19/0.00	0.0	0.0	2	0	2	0	38	-1	3arm	137	nd	0.16	3	2	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------AGGCUGU-------------------------------------------------	2	novel
		len	cloning frequencies
			T1S2	T5S2
	----------------------------------------------------AAGGCTGTGGGCAAGGTCA--------------------------------------	19	1	1
rat	gatggcccctctgaaaagctgtggcgtgatggccacatccactggtactgctAAGGCTGTGGGCAAGGTCAtcccagagctaaatggaaagttcactggcatggccttc
	*************************************************************************************************************
rat	((.((((((..((((.((((.(((...(((((((...(((((.(((.((....))))))))))...)))))))))).))))..........))))..))...)))).))	0.580 -37.30

rat

chromosome:5:19373020:19373128:1

intergenic

block2652624 [novel_lenNOK_Multihit_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	0.163	no	no	0.53/0.53	19/19/0.00	0.0	0.0	2	0	2	0	25	-2	3arm_loop	14	nd	0.21	2	2	2	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------GGCAAGC------------------------------------	2	novel
		len	cloning frequencies
			T3S2	T5S1
	-----------------------------------------------------------------AGGCAAGCTCCAAAGTTGC-------------------------	19	1	1
rat	gcagttttaaatggtcctggctgttttgctctttgtcctgcctttggattctgtgaggcatgctcAGGCAAGCTCCAAAGTTGCgacatggtgagcacagggtcactgc
	*************************************************************************************************************
rat	((((.......((..((((.......(((((..((((..(((((((((.........((.(((....))).)))))))))..))))))....)))))))))..))))))	0.870 -33.72

rat

chromosome:9:113281910:113282018:1

intergenic

novel_lenNOK_cloningOK_loopOverlap_nonpairedHIGH_bulgeHIGH (282 loci)

block16774 [novel_lenNOK_cloningOK_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	0.158	no	no	0.50/0.55	18/20/0.04	0.0	0.0	22	0	7	0	23	-4	5arm_loop_3arm	1	nd	0.42	4	47	7	na	na

		reads	miRBase family seed
seed	------------------------GGAGAGA--------------------------------------------------	47	miR-185
		len	cloning frequencies
			T1S1	T1S2	T3S1	T3S2	T4S1	T4S2	T5S1
	-----------------------TGGAGAGAAAGGCAGATCC---------------------------------------	19	22	2	3	2	5	3	5
	-----------------------TGGAGAGAAAGGCAGATC----------------------------------------	18	3	-	-	-	-	-	-
	-----------------------TGGAGAGAAAGGCAGATCCC--------------------------------------	20	1	1	-	-	-	-	-
rat	ccacaaagctctccaagttgaggTGGAGAGAAAGGCAGATCCctcttttctaagcaccaagtcgctgaggcagcccagtgg
	*********************************************************************************
rat	((((...(((.((..((.(((((((...(((((((.((....)))))))))...))))...)))))..)).)))...))))	0.420 -22.50

rat

chromosome:10:38189075:38189155:-1

intergenic

block19729 [novel_lenNOK_cloningOK_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	0.156	no	no	0.21/0.22	18/19/0.00	0.0	0.1	10	0	4	0	37	-4	5arm_loop_3arm	1	nd	0.42	4	10	4	na	na

		reads	miRBase family seed
seed	--------------------------------------AGGAAUU---------------------------------------------------------------	10	novel
		len	cloning frequencies
			T1S2	T2S1	T2S2	T3S2
	-------------------------------------TAGGAATTTGAAAGTTTT-----------------------------------------------------	18	1	3	2	3
	-------------------------------------TAGGAATTTGAAAGTTTTT----------------------------------------------------	19	-	-	-	1
rat	tctaatctcaaccatattttaggaactatgtctatgtTAGGAATTTGAAAGTTTTTattttcaccttatataaacagaccttcagccagcactaaaatcttgagtgga
	************************************************************************************************************
rat	((((..(((((....((((((((((...(((.(((((.(((....(((((((....)))))))))).))))).)))....)))........))))))).)))))))))	0.560 -17.70

rat

chromosome:10:44791434:44791541:-1

intergenic

block23099 [novel_lenNOK_cloningOK_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	0.057	no	no	0.47/0.50	18/19/0.00	0.0	0.1	16	0	9	0	21	-3	3arm_loop	1	nd	0.32	4	16	9	na	na

		reads	miRBase family seed
seed	--------------------------------------AAAGACG--------------------------------	16	miR-743a
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S2
	-------------------------------------TAAAGACGCCTGACAGGAA---------------------	19	2	2	1	1	1	2	2	2	1
	-------------------------------------TAAAGACGCCTGACAGGA----------------------	18	-	-	-	-	-	1	-	1	-
rat	gggaaagctggcatcgtcttcctgttatcatttggatTAAAGACGCCTGACAGGAAgcgatttggagagtgctcccc
	*****************************************************************************
rat	((((..(((...((((.((((((((((...(((.......)))....))))))))))))))......)))..)))).	0.990 -23.70

rat

chromosome:10:51847316:51847392:-1

intergenic

block27555 [novel_lenNOK_cloningOK_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	0.314	no	no	0.15/0.17	18/20/0.06	0.0	0.2	31	0	2	0	29	-4	5arm_loop	2	nd	0.33	4	36	2	na	na

		reads	miRBase family seed
seed	------------------------------GGAAUUU----------------------------------------------------------	36	novel
		len	cloning frequencies
			T4S1	T4S2
	-----------------------------TGGAATTTAAAGTTTTAA------------------------------------------------	18	10	14
	-----------------------------TGGAATTTAAAGTTTTAAA-----------------------------------------------	19	3	7
	-----------------------------TGGAATTTAAAGTTTTAAAA----------------------------------------------	20	2	-
rat	tttacagaggaatttaatattgagtggtgTGGAATTTAAAGTTTTAAAatgtttagattataaatctttatctttcaaaaatttagaaatgtgag
	***********************************************************************************************
rat	.(((((...((((((....(((((.((((.((.(((((.(((((..........))))).))))))).)))).))))))))))).....))))).	0.980 -13.60

rat

chromosome:10:61445525:61445619:-1

intergenic

block29073 [novel_lenNOK_cloningOK_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	0.572	no	no	0.32/0.33	18/19/0.00	0.0	0.3	21	0	10	0	9	-4	5arm_loop	2	nd	0.39	4	32	10	na	na

		reads	miRBase family seed
seed	----------AGCAGCA-------------------------------------------	32	miR-15b/16/195/322/497
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	---------TAGCAGCACAGATTTTAA---------------------------------	18	9	1	1	1	5	1	2	-	1	2
	---------TAGCAGCACAGATTTTAAA--------------------------------	19	1	1	-	-	3	-	-	4	-	-
rat	ggattactcTAGCAGCACAGATTTTAAAggagatacagatcttggccctgcaaaagagcc
	************************************************************
	----------------------------------------------------------------------	ENSRNOT00000056246 ENSRNOG00000009673 Dhrs13
	----------------------------------------------------------------------	ENSRNOT00000056234 ENSRNOG00000009566 Q5BJL0_RAT
	----------------------------------------------------------------------	ENSRNOT00000035130 ENSRNOG00000009566 Q5BJL0_RAT
rat	......((((.((((..(((((((............))))).))...))))...))))..	0.980 -9.70

rat

chromosome:10:64062761:64062820:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000056245|ENSRNOG00000009673 ## Opposite_strand|Intronic_coding|ENSRNOT00000056246|ENSRNOG00000009673 ## ENSRNOG00000009673|protein_coding|Dhrs13|dehydrogenase/reductase (SDR family) member 13 Gene [Source:MGI (curated);Acc:Dhrs13-003] ## ENSRNOG00000009566|protein_coding|Q5BJL0_RAT|Phf12 protein. [Source:UniProtKB/TrEMBL;Acc:Q5BJL0]

block30389 [novel_lenNOK_cloningOK_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	0.242	no	no	0.53/0.56	18/19/0.00	0.0	0.0	15	0	6	0	31	-4	3arm_loop	1	nd	0.56	4	16	6	na	na

		reads	miRBase family seed
seed	---------------------------------------AGAGGCG-----------------------------------------	16	novel
		len	cloning frequencies
			T2S1	T3S1	T3S2	T4S1	T4S2	T5S2
	--------------------------------------TAGAGGCGCAGACCAATG-------------------------------	18	4	2	2	4	3	-
	--------------------------------------TAGAGGCGCAGACCAATGA------------------------------	19	-	-	-	-	-	1
rat	tggtctctgcgagggccccgccctttcggttccagaagTAGAGGCGCAGACCAATGaaggggcctccgaaacccctcgcacgcgcca
	***************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000056128 ENSRNOG00000022536 RGD1309650_predicted
	-------------------------------------------------------------------------------------------------	ENSRNOT00000010691 ENSRNOG00000022615 NP_001099288.1
rat	.(((...((((((((....((((((((((((((.........))....))))...)))))))).........))))))))...))).	0.710 -31.72

rat

chromosome:10:66605204:66605290:-1

Same_strand|Boundary_non-coding|ENSRNOT00000031618|ENSRNOG00000022536 ## Opposite_strand|Intronic_coding|ENSRNOT00000010691|ENSRNOG00000022615 ## Same_strand|Intronic_coding|ENSRNOT00000056128|ENSRNOG00000022536 ## ENSRNOG00000022615|protein_coding|NP_001099288.1|tumor protein p53 inducible protein 13 [Source:RefSeq_peptide;Acc:NP_001099288] ## ENSRNOG00000022536|protein_coding|RGD1309650_predicted|

block37356 [novel_lenNOK_cloningOK_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	0.028	no	no	0.39/0.39	18/18/0.00	0.0	0.0	9	0	3	0	40	-4	5arm_loop_3arm	1	nd	0.44	4	11	3	na	na

		reads	miRBase family seed
seed	-----------------------------------------GUAAGGU---------------------------------------------------------	11	novel
		len	cloning frequencies
			T3S2	T4S2	T5S2
	----------------------------------------AGTAAGGTCAGCATTGAT-----------------------------------------------	18	1	1	9
rat	attaaaaattagtccaataatcccagaacagtgaaagaacAGTAAGGTCAGCATTGATatgttccttccttcaagttaccagctgtgaggtggactaatccttga
	*********************************************************************************************************
rat	.((((..(((((((((....((.(((....((((..((..((.((((...((((....)))).)))).))))...))))...))).))..)))))))))..))))	0.960 -25.20

rat

chromosome:10:81399116:81399220:-1

intergenic

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