miR-Intess™

other hairpins

novel_shortStem_mirtron (51 loci)

block2256380 [novel_shortStem_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

0.184

no

no

0.52/0.55

22/23/1.00

0.0

0.2

4

0

2

0

4

29

5arm

1

1

0.22

3

4

2

na

na

		reads	miRBase family seed
seed	-----CAUGCUC----------------------------------------------------------------------------------------------------------	4	novel
		len	cloning frequencies
			T1S1	T1S2
	----TCATGCTCTGCTCTGTCTCCAC--------------------------------------------------------------------------------------------	22	1	2
	----TCATGCTCTGCTCTGTCTCCACA-------------------------------------------------------------------------------------------	23	1	-
rat	ggccTCATGCTCTGCTCTGTCTCCACAggtcatcgagaactgtgttgctgccgctggattcagcgtgggggagtttgcagcccttgtgtttgctggagccatggagtttgcggaaggt
	**********************************************************************************************************************
	+++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++	ENSRNOT00000013994 ENSRNOG00000010539 RGD1306698_predicted
rat	.((((..(((...((((((((((((((((.((.((((..((((...(((.((((((....))))....)).)))..))))..)))))))))).)))))..)))))))..)))..))))	1.000 -43.60

rat

chromosome:7:121367130:121367247:1

Same_strand|Intronic_coding|ENSRNOT00000013994|ENSRNOG00000010539 ## ENSRNOG00000010539|protein_coding|RGD1306698_predicted|

block2267203 [novel_shortStem_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

0.055

no

no

0.33/0.33

21/21/1.00

0.0

0.0

1

0

1

0

3

2

3arm

1

0

0.19

3

1

1

na

na

		reads	miRBase family seed
seed	-------------------------------------------CAUUACU----------------	1	novel
		len	cloning frequencies
			T4S1
	------------------------------------------CCATTACTTCATTCTCTATAG---	21	1
rat	gcctctggcaggacttcactggagtacaacaatgtcacctcaCCATTACTTCATTCTCTATAGgca
	******************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>	ENSRNOT00000013374 ENSRNOG00000009628 Pfkm
rat	((((.(((.((((......(((((((......((......))....)))))))))))))).)))).	0.980 -13.80

rat

chromosome:7:136845453:136845518:1

Same_strand|Intronic_coding|ENSRNOT00000013374|ENSRNOG00000009628 ## ENSRNOG00000009628|protein_coding|Pfkm|6-phosphofructokinase, muscle type (EC 2.7.1.11) (Phosphofructokinase 1) (Phosphohexokinase) (Phosphofructo-1-kinase isozyme A) (PFK-A) (Phosphofructokinase-M). [Source:UniProtKB/Swiss-Prot;Acc:P47858]

block2280665 [novel_shortStem_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

0.131

no

no

0.50/0.50

22/22/1.00

0.0

0.0

1

0

1

0

4

18

3arm

1

0

0.23

3

1

1

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------------ACUAUCU------------------	1	novel
		len	cloning frequencies
			T1S1
	----------------------------------------------------------------AACTATCTGCTTCACCTCCCAG----	22	1
rat	gtgtcagggtcggtggggatatgttggggggaaaggaaggcaagcctgcgcttccttcatttggAACTATCTGCTTCACCTCCCAGgtac
	******************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>	ENSRNOT00000013577 ENSRNOG00000010060 Panx1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>	ENSRNOT00000045203 ENSRNOG00000010060 Panx1
rat	(((((.(((..((((((((((.(((..(((..((((((((((....))).)))))))..)))..))))))))...))))).))).)))))	0.990 -30.40

rat

chromosome:8:11827864:11827953:-1

Same_strand|Intronic_coding|ENSRNOT00000013577|ENSRNOG00000010060 ## ENSRNOG00000010060|protein_coding|Panx1|Pannexin-1. [Source:UniProtKB/Swiss-Prot;Acc:P60570]

block2603739 [novel_shortStem_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

0.197

no

no

0.27/0.30

22/23/1.00

0.0

0.5

2

0

1

0

1

19

3arm

1

0

0.14

2

2

1

na

na

		reads	miRBase family seed
seed	------------------------------------------------------------------CUGUCAU----------------	2	novel
		len	cloning frequencies
			T2S2
	-----------------------------------------------------------------TCTGTCATTTTCTCTTTTCAAA--	22	1
	-----------------------------------------------------------------TCTGTCATTTTCTCTTTTCAAAG-	23	1
rat	ttttggatgcccacagaggctgtgacagggatctctcctgagaataagggggtactgtgagaactTCTGTCATTTTCTCTTTTCAAAGa
	*****************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>	ENSRNOT00000021389 ENSRNOG00000015354 Aox1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>	ENSRNOT00000058780 ENSRNOG00000015354 Aox1
rat	(((((((.......(((((..(((((((((.((((((((.......))))........)))).)).)))))))..))))).))))))).	0.420 -23.20

rat

chromosome:9:56724317:56724405:1

Same_strand|Intronic_coding|ENSRNOT00000058780|ENSRNOG00000015354 ## ENSRNOG00000015354|protein_coding|Aox1|Aldehyde oxidase (EC 1.2.3.1). [Source:UniProtKB/Swiss-Prot;Acc:Q9Z0U5]

block2618757 [novel_shortStem_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

0.774

no

no

0.52/0.52

21/21/1.00

0.0

0.0

1

0

1

0

4

8

5arm

1

3

0.19

3

1

1

na

na

		reads	miRBase family seed
seed	-----UUGGUAU-------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	----TTTGGTATGGTTCCCCACTCC------------------------------------------------	21	1
rat	tcatTTTGGTATGGTTCCCCACTCCgaataggctgagcaaacatcgtgggtgtgacagggcgtgcccagagga
	*************************************************************************
	>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000026941 ENSRNOG00000019850 SPEG_RAT
rat	((.(((.((((((...(((((((((((....((...)).....))).))))).....))))))))).))).))	0.550 -18.00

rat

chromosome:9:74683881:74683953:1

Same_strand|Boundary_coding|ENSRNOT00000026941|ENSRNOG00000019850 ## ENSRNOG00000019850|protein_coding|SPEG_RAT|Striated muscle-specific serine/threonine protein kinase (EC 2.7.11.1) (Aortic preferentially expressed protein 1) (APEG-1). [Source:UniProtKB/Swiss-Prot;Acc:Q63638]

block3077541 [novel_shortStem_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

0.049

no

no

0.41/0.41

22/22/1.00

0.0

0.0

1

0

1

0

4

16

5arm

1

0

0.27

3

1

1

na

na

		reads	miRBase family seed
seed	-----CACUGAA----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	----CCACTGAAATCATTTCTTGCAG--------------------------------------------------------------------	22	1
rat	gtatCCACTGAAATCATTTCTTGCAGaaatatggtagtattcgctatgaagatatacatagcatgcgctgtcgaaataggttgtatgtgataca
	**********************************************************************************************
	+++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000051757 ENSRNOG00000012105 RGD1563084_predicted
	+++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000044338 ENSRNOG00000012105 RGD1563084_predicted
	+++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000029861 ENSRNOG00000012105 RGD1563084_predicted
	+++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000016171 ENSRNOG00000012105 RGD1563084_predicted
	+++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000056961 ENSRNOG00000012105 RGD1563084_predicted
	+++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000056960 ENSRNOG00000012105 RGD1563084_predicted
	+++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000029846 ENSRNOG00000012105 RGD1563084_predicted
	+++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000056959 ENSRNOG00000012105 RGD1563084_predicted
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000016213 ENSRNOG00000012105 RGD1563084_predicted
rat	((((.(((...(((((((((..((((...((((.((((((((........)).)))).)).))))..)))).))))).))))....))))))).	0.580 -22.30

rat

chromosome:X:127463338:127463431:1

Same_strand|Intronic_coding|ENSRNOT00000056961|ENSRNOG00000012105 ## ENSRNOG00000012105|protein_coding|RGD1563084_predicted|Putative uncharacterized protein (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q2TBJ6]

novel_cloningOK_nonpairedHIGH_bulgeHIGH (50 loci)

block204120 [novel_cloningOK_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

0.128

no

no

0.33/0.48

20/25/0.95

0.7

0.2

13

0

4

0

20

6

5arm

4

nd

0.33

4

22

4

na

na

		reads	miRBase family seed
seed	---------------------CCUAGAU---------------------------------------------------------------------------------	16	novel
seed	------------------------AGAUACU------------------------------------------------------------------------------	4	novel
seed	--------------------UCCUAGA----------------------------------------------------------------------------------	1	novel
seed	----------------------------ACUCUUU--------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T4S1	T4S2	T5S1
	--------------------TCCTAGATACTCTTTTCTCCTGTT-----------------------------------------------------------------	24	2	1	1	10
	-----------------------TAGATACTCTTTTCTCCTGT------------------------------------------------------------------	20	-	-	-	3
	--------------------TCCTAGATACTCTTTTCTCCTG-------------------------------------------------------------------	22	1	-	-	-
	-----------------------TAGATACTCTTTTCTCCTGTT-----------------------------------------------------------------	21	-	-	-	1
	-------------------TTCCTAGATACTCTTTTCTCCTGTT-----------------------------------------------------------------	25	-	-	-	1
	---------------------------TACTCTTTTCTCCTGTTGTCCCC-----------------------------------------------------------	23	-	-	-	1
	--------------------TCCTAGATACTCTTTTCTCCTGT------------------------------------------------------------------	23	-	-	-	1
rat	cgtggatgtcgggggaagctTCCTAGATACTCTTTTCTCCTGTTgtccccgctgtctcaggggacagctgaaccagagctgcactgggaagagggtcttacagtgtacg
	*************************************************************************************************************
rat	((((.((.....((((..((((((((...((((.(((....(((((((((.........))))))))).)))..)))).....))))))))....))))...)).))))	0.830 -38.80

rat

chromosome:12:44299523:44299631:-1

intergenic

block209359 [novel_cloningOK_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

0.262

no

no

0.30/0.32

20/23/1.00

0.0

0.8

11

0

3

0

5

17

3arm

1

nd

0.45

4

15

3

na

na

		reads	miRBase family seed
seed	------------------------------------------------------------ACGAUAU--------------------	14	novel
seed	-------------------------------------------------------------CGAUAUU-------------------	1	novel
		len	cloning frequencies
			T1S2	T4S1	T5S1
	-----------------------------------------------------------TACGATATTCTTTAAGCTCATCT-----	23	2	1	8
	-----------------------------------------------------------TACGATATTCTTTAAGCTCA--------	20	-	-	3
	------------------------------------------------------------ACGATATTCTTTAAGCTCATCT-----	22	-	-	1
rat	gtctggagctgagtaggggaaagtgtaagatcaacctagaatggtggccagacgagagaTACGATATTCTTTAAGCTCATCTaagac
	***************************************************************************************
rat	((((.(((((....((((....((((....((.(((......)))........))...))))....))))...))))).....))))	0.560 -17.40

rat

chromosome:12:5630140:5630226:1

intergenic

block210121 [novel_cloningOK_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

0.092

no

no

0.28/0.37

19/25/0.75

0.0

1.6

20

0

5

0

5

24

3arm

1

nd

0.53

4

20

5

na

na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------GGGGGUU----------------------	20	novel
		len	cloning frequencies
			T1S1	T2S1	T3S1	T3S2	T4S2
	--------------------------------------------------------------------------TGGGGGTTTGGTTTTTTTTTTTT-------	23	3	1	1	1	-
	--------------------------------------------------------------------------TGGGGGTTTGGTTTTTTTT-----------	19	2	2	-	-	-
	--------------------------------------------------------------------------TGGGGGTTTGGTTTTTTTTTT---------	21	1	1	-	-	1
	--------------------------------------------------------------------------TGGGGGTTTGGTTTTTTTTTTTTT------	24	2	1	-	-	-
	--------------------------------------------------------------------------TGGGGGTTTGGTTTTTTTTTTT--------	22	2	-	-	-	-
	--------------------------------------------------------------------------TGGGGGTTTGGTTTTTTTTT----------	20	1	-	-	-	-
	--------------------------------------------------------------------------TGGGGGTTTGGTTTTTTTTTTTTTT-----	25	1	-	-	-	-
rat	gagaatatactgaaaggagcttagtgtgcctgagaagctgaggtcagagtgacttagcaattttggctgttcctTGGGGGTTTGGTTTTTTTTTTTTTTttctt
	********************************************************************************************************
rat	((((((..(((..(((((((.......(((.(((..(((((.(((.....))))))))..))).))).)))))))...)))...))))))..............	0.630 -25.20

rat

chromosome:12:6845306:6845409:1

intergenic ## {Repeats: dust 6845393 6845406 0 class=dust}

block233451 [novel_cloningOK_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

0.030

no

no

0.33/0.48

20/25/0.95

0.7

0.2

13

0

4

0

9

6

5arm

4

nd

0.33

4

22

4

na

na

		reads	miRBase family seed
seed	----------CCUAGAU-----------------------------------------------------------------------	16	novel
seed	-------------AGAUACU--------------------------------------------------------------------	4	novel
seed	-----------------ACUCUUU----------------------------------------------------------------	1	novel
seed	---------UCCUAGA------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T4S1	T4S2	T5S1
	---------TCCTAGATACTCTTTTCTCCTGTT-------------------------------------------------------	24	2	1	1	10
	------------TAGATACTCTTTTCTCCTGT--------------------------------------------------------	20	-	-	-	3
	--------TTCCTAGATACTCTTTTCTCCTGTT-------------------------------------------------------	25	-	-	-	1
	------------TAGATACTCTTTTCTCCTGTT-------------------------------------------------------	21	-	-	-	1
	---------TCCTAGATACTCTTTTCTCCTG---------------------------------------------------------	22	1	-	-	-
	----------------TACTCTTTTCTCCTGTTGTCCCC-------------------------------------------------	23	-	-	-	1
	---------TCCTAGATACTCTTTTCTCCTGT--------------------------------------------------------	23	-	-	-	1
rat	ggggaagctTCCTAGATACTCTTTTCTCCTGTTgtccccgctgtctcaggggacagctgaaccagagctgcactgggaagagggtctt
	****************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000056932 ENSRNOG00000037566 RGD1560398_predicted
rat	.((((..((((((((...((((.(((....(((((((((.........))))))))).)))..)))).....))))))))....))))	0.860 -33.80

rat

chromosome:12:43042352:43042439:1

Same_strand|Intronic_non-coding|ENSRNOT00000056932|ENSRNOG00000037566 ## ENSRNOG00000037566|protein_coding|RGD1560398_predicted|

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