miR-Intess™

other hairpins

miRNAunknown_Multihit_randfoldOK (14 loci)

block192482 (miRNA) [miRNAunknown_Multihit_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

Ensembl miRNA

0.001

no

no

0.22/0.22

23/23/1.00

0.0

0.0

1

0

1

0

32

1

5arm

130

nd

0.00

0

1

1

na

na

		reads	miRBase family seed
seed	---------------------------------GUGUGUA----------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	--------------------------------TGTGTGTATATATATATATGTGT-------------------------------------------------------------	23	1
rat	tatatatatatatgtgtgtgtgtgtatatatgTGTGTGTATATATATATATGTGTgtgtgtatatatatgtatatatatatatatatatatatacacacacacatatatatatatg
	********************************************************************************************************************
	...........<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<....	ENSRNOT00000063358 ENSRNOG00000041605
rat	((((((((((((((((((((((((((((((((((((((((((((((((((((((((....))))))))))))))))))))))))))))))))))))))))))))))))))))))))	1.000 -69.30

rat

chromosome:12:25099627:25099742:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000063358|ENSRNOG00000041605 ## ENSRNOG00000041605|miRNA|| ## {Repeats: dust 25099726 25099749 0 class=dust,trf 99 122 0 class=trf,(TA)n 1 180 -1 class=Simple_repeat,(TA)n 94 117 -1 class=Simple_repeat,trf 71 94 0 class=trf}

block675540 (miRNA) [miRNAunknown_Multihit_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

Ensembl miRNA

0.001

no

no

0.40/0.40

20/20/1.00

0.0

0.0

1

0

1

0

19

18

5arm

196

nd

0.10

1

1

1

na

na

		reads	miRBase family seed
seed	--------------------CAUAUGU---------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	-------------------GCATATGTGTGTATGTGTGT---------------------------------------------------------------------------------	20	1
rat	tgtgtctgtgtgtgtgtttGCATATGTGTGTATGTGTGTgtgtgtgtgtgtgtatatcttcatatacacacatgtacatactcacagacatatacacacatgcacatatataggggtacc
	************************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000042430 ENSRNOG00000029235 Sfmbt2
	...........<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<.......................	ENSRNOT00000063076 ENSRNOG00000041323
rat	.((..((.(((((((((..((((.(((((((((((.((((((((..(((((((((((....)))))))))))..))))....)))).))))))))))).))))))))))))).))..)).	1.000 -60.80

rat

chromosome:17:79285754:79285873:1

Opposite_strand|Intronic_coding|ENSRNOT00000042430|ENSRNOG00000029235 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000051529|ENSRNOG00000029235 ## Opposite_strand|Exonic_non-coding|ENSRNOT00000063076|ENSRNOG00000041323 ## ENSRNOG00000041323|miRNA|| ## ENSRNOG00000029235|protein_coding|Sfmbt2|Scm-like with four mbt domains 2 Gene [Source:MGI (curated);Acc:Sfmbt2-001] ## {Repeats: trf 203 223 0 class=trf,trf 15 35 0 class=trf,(TG)n 20 40 1 class=Simple_repeat,dust 79285768 79285788 0 class=dust,(TG)n 2 54 1 class=Simple_repeat}

block1117823 (miRNA) [miRNAunknown_Multihit_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

Ensembl miRNA

0.001

no

no

0.35/0.35

20/20/1.00

0.0

0.0

1

0

1

0

24

5

3arm

127

nd

0.00

0

1

1

na

na

		reads	miRBase family seed
seed	----------------------------------------------------------CAUACAU------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	---------------------------------------------------------GCATACATACATACATACAC------------------------	20	1
rat	gatgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtacatGCATACATACATACATACACacacacaaatacacacacacatca
	*****************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000000330 ENSRNOG00000000302 Sesn1
	......<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<..........	ENSRNOT00000063044 ENSRNOG00000041291
rat	(((((((((((((((.((((((((((((((((((((((((((((((((....)))))))))))))))))))))))))))))))).))))))))))))))).	1.000 -77.20

rat

chromosome:20:45836938:45837038:1

Same_strand|Intronic_coding|ENSRNOT00000000330|ENSRNOG00000000302 ## Opposite_strand|Exonic_non-coding|ENSRNOT00000063044|ENSRNOG00000041291 ## Same_strand|Boundary_non-coding|ENSRNOT00000057129|ENSRNOG00000000302 ## ENSRNOG00000041291|miRNA|| ## ENSRNOG00000000302|protein_coding|Sesn1|sestrin 1 Gene [Source:MGI (curated);Acc:Sesn1-001] ## {Repeats: trf 23 43 0 class=trf,dust 45836961 45836981 0 class=dust,(CATA)n 7 27 1 class=Simple_repeat,(CATA)n 4 47 1 class=Simple_repeat}

novel_Multihit_shortStem_loopOverlap (14 loci)

block253588 [novel_Multihit_shortStem_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

0.060

no

no

0.59/0.59

22/22/1.00

0.0

0.0

1

0

1

0

4

-2

3arm_loop

15

nd

0.27

2

1

1

na

na

		reads	miRBase family seed
seed	---------------------------------AGUAGCC------------------	1	novel
		len	cloning frequencies
			T1S1
	--------------------------------CAGTAGCCAGGGATCCTAGCCA----	22	1
rat	gtagccagggatcctagccatacaacctacagCAGTAGCCAGGGATCCTAGCCAtaca
	**********************************************************
rat	(((((..((((((((.((..(((...........)))))..)))))))).))..))).	0.990 -14.70

rat

chromosome:13:36436631:36436688:-1

intergenic ## {Repeats: trf 30 52 0 class=trf}

block253602 [novel_Multihit_shortStem_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

0.060

no

no

0.59/0.59

22/22/1.00

0.0

0.0

1

0

1

0

4

-2

3arm_loop

15

nd

0.27

2

1

1

na

na

		reads	miRBase family seed
seed	---------------------------------AGUAGCC------------------	1	novel
		len	cloning frequencies
			T1S1
	--------------------------------CAGTAGCCAGGGATCCTAGCCA----	22	1
rat	gtagccagggatcctagccatacaacctacagCAGTAGCCAGGGATCCTAGCCAtaca
	**********************************************************
rat	(((((..((((((((.((..(((...........)))))..)))))))).))..))).	0.990 -14.70

rat

chromosome:13:36437243:36437300:-1

intergenic ## {Repeats: trf 676 698 0 class=trf}

block695392 [novel_Multihit_shortStem_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

0.065

no

no

0.55/0.55

20/20/1.00

0.0

0.0

1

0

1

0

2

-2

5arm_loop

13

nd

0.20

3

1

1

na

na

		reads	miRBase family seed
seed	---CAGACCC------------------------------------------	1	novel
		len	cloning frequencies
			T4S1
	--TCAGACCCACTCCCAAGAAC------------------------------	20	1
rat	ttTCAGACCCACTCCCAAGAACtcacttttaggagtggtggcaggtttgggg
	****************************************************
	--------------------------------------------------------------	ENSRNOT00000026112 ENSRNOG00000019177 NP_001100865.1
rat	.((((((((((((((.((((......)))).)))))))......))))))).	1.000 -16.50

rat

chromosome:18:28578001:28578052:-1

Opposite_strand|Intronic_non-coding|ENSRNOT00000026112|ENSRNOG00000019177 ## ENSRNOG00000019177|protein_coding|NP_001100865.1|pleckstrin and Sec7 domain containing 2 [Source:RefSeq_peptide;Acc:NP_001100865]

block698794 [novel_Multihit_shortStem_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

0.034

no

no

0.67/0.67

21/21/1.00

0.0

0.0

1

0

1

0

3

-1

3arm

11

nd

0.19

2

1

1

na

na

		reads	miRBase family seed
seed	-------------------------CUUUCCG----------------	1	novel
		len	cloning frequencies
			T3S1
	------------------------CCTTTCCGCTCGGCCGTTCTC---	21	1
rat	aggaaggaaggaagagggaaggggCCTTTCCGCTCGGCCGTTCTCctg
	************************************************
	----------------------------------------------------------	ENSRNOT00000036613 ENSRNOG00000027250 NP_001101899.1
rat	(((.((((.((..(((((((((...)))))).)))..)).))))))).	1.000 -19.40

rat

chromosome:18:35658822:35658869:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000060199|ENSRNOG00000027250 ## Opposite_strand|Intronic_coding|ENSRNOT00000036613|ENSRNOG00000027250 ## ENSRNOG00000027250|protein_coding|NP_001101899.1|RNA binding motif protein 27 [Source:RefSeq_peptide;Acc:NP_001101899]

block843773 [novel_Multihit_shortStem_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

0.429

no

no

0.30/0.30

20/20/1.00

0.0

0.0

1

0

1

0

4

-2

3arm_loop

22

nd

0.20

2

1

1

na

na

		reads	miRBase family seed
seed	---------------------------------------------UACAAGA----------------	1	novel
		len	cloning frequencies
			T5S1
	--------------------------------------------TTACAAGAACTGCAATTTTG----	20	1
rat	atgtccactgttgctagatttccactgtcacaacaccgcaaccaTTACAAGAACTGCAATTTTGgcat
	********************************************************************
rat	(((.(((..(((((.((..(((...(((..................))).))))))))))..))))))	0.670 -8.07

rat

chromosome:1:49951045:49951112:-1

intergenic

block844336 [novel_Multihit_shortStem_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

0.429

no

no

0.30/0.30

20/20/1.00

0.0

0.0

1

0

1

0

4

-2

3arm_loop

22

nd

0.20

2

1

1

na

na

		reads	miRBase family seed
seed	---------------------------------------------UACAAGA----------------	1	novel
		len	cloning frequencies
			T5S1
	--------------------------------------------TTACAAGAACTGCAATTTTG----	20	1
rat	atgtccactgttgctagatttccactgtcacaacaccgcaaccaTTACAAGAACTGCAATTTTGgcat
	********************************************************************
	------------------------------------------------------------------------------	ENSRNOT00000041575 ENSRNOG00000031160 LOC685793
rat	(((.(((..(((((.((..(((...(((..................))).))))))))))..))))))	0.670 -8.07

rat

chromosome:1:50179107:50179174:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000049496|ENSRNOG00000031160 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000041575|ENSRNOG00000031160 ## ENSRNOG00000031160|protein_coding|LOC685793|

block962789 [novel_Multihit_shortStem_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

0.429

no

no

0.30/0.30

20/20/1.00

0.0

0.0

1

0

1

0

4

-2

3arm_loop

22

nd

0.20

2

1

1

na

na

		reads	miRBase family seed
seed	---------------------------------------------UACAAGA----------------	1	novel
		len	cloning frequencies
			T5S1
	--------------------------------------------TTACAAGAACTGCAATTTTG----	20	1
rat	atgtccactgttgctagatttccactgtcacaacaccgcaaccaTTACAAGAACTGCAATTTTGgcat
	********************************************************************
	------------------------------------------------------------------------------	ENSRNOT00000059938 ENSRNOG00000039174 RGD1563865_predicted
rat	(((.(((..(((((.((..(((...(((..................))).))))))))))..))))))	0.670 -8.07

rat

chromosome:1:51540018:51540085:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000059936|ENSRNOG00000039174 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000059938|ENSRNOG00000039174 ## ENSRNOG00000039174|protein_coding|RGD1563865_predicted|

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other hairpins:

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