miR-Intess™

other hairpins

miRNAunknown_rep_lenNOK_cloningOK_multiarm_DicerNOK_Multihit_randfoldOK (2 loci)

sblock5210 (miRNA) [miRNAunknown_rep_lenNOK_cloningOK_multiarm_DicerNOK_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

LTR

0.30/0.45

18/23/0.67

0.0 0.1

0.8 1.2

6 24

0 0

3 8

0 0

23 11

0 12

5arm 3arm

17 287

nd nd

0.10 0.10

1 1

39

8

8

11

		reads	miRBase family seed
seed	--------------------------------------------------------------ACAUACA--------------------------	30	novel
seed	------------------------GUCUGUG----------------------------------------------------------------	6	novel
seed	-------------------------------------------------------------UACAUAC---------------------------	2	novel
seed	-----------------------------------------------------------------UACACAC-----------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T5S1	T5S2
	-------------------------------------------------------------TACATACACACATATACACAC-------------	21	-	1	6	4	1	-	-	-
	-------------------------------------------------------------TACATACACACATATACAC---------------	19	-	-	3	2	2	1	-	1
	-------------------------------------------------------------TACATACACACATATACACACAC-----------	23	-	-	2	1	-	-	3	-
	-------------------------------------------------------------TACATACACACATATACACA--------------	20	1	-	1	1	-	-	-	-
	------------------------------------------------------------ATACATACACACATATACAC---------------	20	-	-	-	2	-	-	-	-
	-----------------------TGTCTGTGTGTATGTCCA------------------------------------------------------	18	-	-	-	1	1	-	-	-
	-----------------------TGTCTGTGTGTATGTCCAT-----------------------------------------------------	19	-	-	2	-	-	-	-	-
	-----------------------TGTCTGTGTGTATGTCCATGT---------------------------------------------------	21	-	-	1	-	-	-	-	-
	-----------------------TGTCTGTGTGTATGTCCATG----------------------------------------------------	20	-	-	1	-	-	-	-	-
	----------------------------------------------------------------ATACACACATATACACACACC----------	21	-	-	-	-	-	1	-	-
rat	ctatgtatgcgcatgtatgtataTGTCTGTGTGTATGTCCATgtttgtatatgaatacacATACATACACACATATACACACACcgaagaataga
	***********************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042430 ENSRNOG00000029235 Sfmbt2
	................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>...	ENSRNOT00000062931 ENSRNOG00000041178
rat	((((.....((..(((.(((((((((.(((((((((((.(((((....))))).....))))))))))).))))))))).))).))....)))).	0.990 -31.70

rat

chromosome:17:79293019:79293113:-1

Same_strand|Boundary_non-coding|ENSRNOT00000051529|ENSRNOG00000029235 ## Same_strand|Intronic_coding|ENSRNOT00000042430|ENSRNOG00000029235 ## Same_strand|Exonic_non-coding|ENSRNOT00000062931|ENSRNOG00000041178 ## ENSRNOG00000041178|miRNA|| ## ENSRNOG00000029235|protein_coding|Sfmbt2|Scm-like with four mbt domains 2 Gene [Source:MGI (curated);Acc:Sfmbt2-001] ## {Repeats: trf 1067 1088 0 class=trf,(CATATA)n 2 66 -1 class=Simple_repeat,RMER12 725 819 -1 class=LTR,RMER12 820 848 -1 class=LTR,(CATATA)n 34 55 -1 class=Simple_repeat,dust 79293070 79293091 0 class=dust,(CATATA)n 2 18 -1 class=Simple_repeat,dust 79293030 79293054 0 class=dust,trf 1026 1051 0 class=trf,(TG)n 2 31 -1 class=Simple_repeat,(TG)n 2 26 -1 class=Simple_repeat}

miRNAunknown_rep_lenNOK_randfoldOK (2 loci)

block775335 (miRNA) [miRNAunknown_rep_lenNOK_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

0.007

no

SINE,SINE/Alu

0.33/0.33

18/18/0.00

0.0

0.0

1

0

1

0

8

25

5arm

1

nd

0.22

2

1

1

na

na

		reads	miRBase family seed
seed	---------GGCAAGA------------------------------------------------------------------------------------------------------	1	miR-31
		len	cloning frequencies
			T2S2
	--------AGGCAAGAGGATTTTTTT--------------------------------------------------------------------------------------------	18	1
rat	ggaggcagAGGCAAGAGGATTTTTTTctatgtgtatggggtgggtgtgtgtctgtgtgcacgcatgcaccacagtattcatatggagatcagagtacaacttgaaggcgtcagttttc
	**********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000008104 ENSRNOG00000006049 NP_001099414.1
	>>>>>>>>>>>>>>>>>>>>>>>>>.......................................................................................................	ENSRNOT00000054528 ENSRNOG00000036416
rat	((((((.((.((..(((.(((((((((((((((..((.((((.((((((((......)))))))).)))).)).....))))))))))..)))))....)))....)).)).))))))	0.950 -41.80

rat

chromosome:19:25756784:25756901:-1

Same_strand|Boundary_non-coding|ENSRNOT00000054528|ENSRNOG00000036416 ## Same_strand|Intronic_coding|ENSRNOT00000008104|ENSRNOG00000006049 ## ENSRNOG00000036416|miRNA|| ## ENSRNOG00000006049|protein_coding|NP_001099414.1|regulatory factor X, 1 (influences HLA class II expression) [Source:RefSeq_peptide;Acc:NP_001099414] ## {Repeats: B1F2 -87 62 1 class=SINE,B1F2 48 62 1 class=SINE/Alu}

block1306327 (miRNA) [miRNAunknown_rep_lenNOK_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

LINE,LTR/ERVK

0.37/0.39

18/19/0.00

0.0

0.5

2

0

1

0

11

19

3arm

9

nd

0.05

1

2

1

na

na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------AUACACA----------------------	2	novel
		len	cloning frequencies
			T3S1
	-------------------------------------------------------------------------TATACACACACACATACG------------	18	1
	-------------------------------------------------------------------------TATACACACACACATACGT-----------	19	1
rat	atatgtatatatatgtgtgtgtgtatgtatatatgtatgaatgtatgtatatgtgtatgtatatgtatatgtaTATACACACACACATACGTatttctaagta
	*******************************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<..........	ENSRNOT00000063369 ENSRNOG00000041616
rat	.(((......((((((((((((((.((((((((((((((.((((((((((....)))))))))).)))))))))))))).))))))))))))))......)))	1.000 -40.70

rat

chromosome:2:171282456:171282558:1

Opposite_strand|Exonic_non-coding|ENSRNOT00000063369|ENSRNOG00000041616 ## ENSRNOG00000041616|miRNA|| ## {Repeats: RMER12 844 851 1 class=LTR/ERVK,trf 1 5 0 class=trf,Lx9 -130 7514 -1 class=LINE,dust 171282428 171282431 0 class=dust}

novel_5varHIGH_loopOverlap_mirtron_nonpairedHIGH_bulgeHIGH (2 loci)

block1031659 [novel_5varHIGH_loopOverlap_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

0.044

no

no

0.71/0.77

21/22/1.00

1.5

1.0

2

0

2

0

16

-6

3arm_loop

1

1

0.33

4

2

2

na

na

		reads	miRBase family seed
seed	-------------------------------CCACCGU--------------------------------	1	novel
seed	----------------------------------CCGUCCC-----------------------------	1	novel
		len	cloning frequencies
			T5S1	T5S2
	---------------------------------ACCGTCCCCTGTGGCCGCAGT----------------	21	1	-
	------------------------------CCCACCGTCCCCTGTGGCCGCA------------------	22	-	1
rat	tccaggctgcgagggccactggggaccgagCCCACCGTCCCCTGTGGCCGCAGTtggcagaggagctgga
	**********************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000038016 ENSRNOG00000027456 Cdc42bpg_predicted
rat	(((((.((((.((((((((.((((((..........)))))).))))))....)).)))).....)))))	0.600 -34.40

rat

chromosome:1:209092577:209092646:1

Same_strand|Boundary_coding|ENSRNOT00000038016|ENSRNOG00000027456 ## ENSRNOG00000027456|protein_coding|Cdc42bpg_predicted|

block1141625 [novel_5varHIGH_loopOverlap_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

0.080

no

no

0.57/0.59

21/22/1.00

1.5

1.0

2

0

1

0

28

-19

3arm_loop

1

1

0.32

4

2

1

na

na

		reads	miRBase family seed
seed	----------------------------------------CUGGUUU-----------------------------------------	1	novel
seed	-------------------------------------GCUCUGG--------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	---------------------------------------TCTGGTTTGGTCTCCCGCAGA----------------------------	21	1
	------------------------------------TGCTCTGGTTTGGTCTCCCGCA------------------------------	22	1
rat	atgtgggtgccatgcaaagctgctgtggaagctcaaTGCTCTGGTTTGGTCTCCCGCAGAttgcgagtgcaactactgcaccatccat
	****************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000017968 ENSRNOG00000013177 Map3k1
rat	.....(((((..((((..((..((((((.((..(((.((....)))))..)).))))))...))...))))......)))))......	0.420 -28.80

rat

chromosome:2:43062556:43062643:-1

Same_strand|Boundary_coding|ENSRNOT00000017968|ENSRNOG00000013177 ## ENSRNOG00000013177|protein_coding|Map3k1|Mitogen-activated protein kinase kinase kinase 1 (EC 2.7.11.25) (MAPK/ERK kinase kinase 1) (MEK kinase 1) (MEKK 1). [Source:UniProtKB/Swiss-Prot;Acc:Q62925]

novel_5varHIGH_mirtron_nonpairedHIGH_bulgeHIGH (2 loci)

block1099058 [novel_5varHIGH_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

0.070

no

no

0.50/0.57

20/23/1.00

1.5

0.0

2

0

2

0

34

2

5arm

1

0

0.39

4

2

2

na

na

		reads	miRBase family seed
seed	-----------------------------------CCUGCUA---------------------------------------------------------------------------	1	novel
seed	--------------------------------------GCUACUC------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T2S2
	-------------------------------------TGCTACTCTATCCTGTCCAG------------------------------------------------------------	20	-	1
	----------------------------------CCCTGCTACTCTATCCTGTCCAG------------------------------------------------------------	23	1	-
rat	ggggctgtgcacaggctgtccagtgtccaagaagCCCTGCTACTCTATCCTGTCCAGggtcgtcccggaacaaatggcttaaagggagagaaaggggagcctggagaggccagcctt
	*********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000045315 ENSRNOG00000001229 Col18a1
rat	.((((((.((.((((((.(((....((.......((((..((..((((....(((.(((....))))))....))))..)).))))...))..))).)))))).....)))))))).	0.450 -43.40

rat

chromosome:20:11968764:11968880:1

Same_strand|Intronic_coding|ENSRNOT00000045315|ENSRNOG00000001229 ## ENSRNOG00000001229|protein_coding|Col18a1|Collagen XVIII (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q9QZD2]

block2084095 [novel_5varHIGH_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

0.738

no

no

0.58/0.65

20/24/1.00

3.0

1.0

2

0

2

0

10

12

5arm

1

3

0.40

4

2

2

na

na

		reads	miRBase family seed
seed	-----------UCUGACU------------------------------------------------------------------------------	1	novel
seed	-----------------UACCCCA------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T5S2
	----------ATCTGACTACCCCAACTCCACCCC--------------------------------------------------------------	24	-	1
	----------------CTACCCCAACTCCACCCCTG------------------------------------------------------------	20	1	-
rat	cctgcccacgATCTGACTACCCCAACTCCACCCCTGcaggaaggaccgcaagatggcactgatccagatgggctctgtggaggaggcagtgcaggc
	************************************************************************************************
	----------------------------------------------------------------------------------------------------------	ENSRNOT00000060576 ENSRNOG00000027940 Prg-2
	++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000030357 ENSRNOG00000010448 Ptbp1
	++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000044865 ENSRNOG00000010448 Ptbp1
	++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000041277 ENSRNOG00000010448 Ptbp1
	++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000030365 ENSRNOG00000010448 Ptbp1
	++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000041219 ENSRNOG00000010448 Ptbp1
rat	(((((..........(((.((....(((((((((....(((((..(((.....)))..))..)))....)))....))))))..)).)))))))).	0.830 -28.00

rat

chromosome:7:11356697:11356792:-1

Same_strand|Intronic_coding|ENSRNOT00000030357|ENSRNOG00000010448 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000031315|ENSRNOG00000027940 ## Opposite_strand|Intronic_coding|ENSRNOT00000060576|ENSRNOG00000027940 ## ENSRNOG00000010448|protein_coding|Ptbp1|Polypyrimidine tract-binding protein 1 (PTB) (Heterogeneous nuclear ribonucleoprotein I) (hnRNP I) (Pyrimidine-binding protein) (PYBP). [Source:UniProtKB/Swiss-Prot;Acc:Q00438] ## ENSRNOG00000027940|protein_coding|Prg-2|plasticity-related protein PRG-2 [Source:RefSeq_peptide;Acc:NP_853665]

novel_Multihit_5varHIGH_nonpairedHIGH_bulgeHIGH (2 loci)

block1283043 [novel_Multihit_5varHIGH_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

0.155

no

no

0.55/0.59

20/22/1.00

2.5

1.5

2

0

2

0

9

0

3arm

12

nd

0.45

5

2

2

na

na

		reads	miRBase family seed
seed	------------------------------------------AUCCAGG--------------------------	1	novel
seed	-----------------------------------------------GGAGCUG---------------------	1	novel
		len	cloning frequencies
			T4S1	T5S2
	-----------------------------------------CATCCAGGAGCTGTGGAGGAAG------------	22	-	1
	----------------------------------------------AGGAGCTGTGGAGGAAGAAG---------	20	1	-
rat	tctggcagcaaccatcaagtgagccaagatgcacacaaacaCATCCAGGAGCTGTGGAGGAAGAAGcagtcagac
	***************************************************************************
rat	((((((.((..((..(((((...((..((((..........))))..)).))).))..)).....)).)))))).	0.660 -17.90

rat

chromosome:2:115483639:115483713:1

intergenic

block2089713 [novel_Multihit_5varHIGH_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

0.796

no

no

0.41/0.61

22/25/0.80

2.2

1.4

5

0

1

0

10

4

5arm

16

nd

0.43

5

5

1

na

na

		reads	miRBase family seed
seed	-------------------GGAGCAC----------------------------------------------------------	3	novel
seed	----------------GCUGGAG-------------------------------------------------------------	1	novel
seed	-----------CCCCUGC------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	------------------TGGAGCACACTCAGTATTTACA--------------------------------------------	22	3
	---------------TGCTGGAGCACACTCAGTATTTACA--------------------------------------------	25	1
	----------TCCCCTGCTGGAGCACACTCAGT---------------------------------------------------	23	1
rat	ggtcaggaagTCCCCTGCTGGAGCACACTCAGTATTTACAcgaaccttttcatgttagtaggccctagaagaggctaatggctg
	************************************************************************************
rat	(((((...((.((.((.((((.((..(((........(((.(((....))).))).)))..)).)))).)).))))..))))).	0.640 -18.10

rat

chromosome:7:17806486:17806569:-1

intergenic

novel_Multihit_shortStem_5varHIGH_nonpairedHIGH (2 loci)

block2469525 [novel_Multihit_shortStem_5varHIGH_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

0.282

no

no

0.52/0.55

20/23/1.00

2.0

0.5

2

0

2

0

2

29

3arm

29

nd

0.35

3

2

2

na

na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------CUUGAGG------------------	1	miR-327
seed	------------------------------------------------------------------------------AGGAUGU--------------	1	novel
		len	cloning frequencies
			T3S1	T4S1
	-------------------------------------------------------------------------CCTTGAGGATGTTCCCCAACTCT---	23	1	-
	-----------------------------------------------------------------------------GAGGATGTTCCCCAACTCTG--	20	-	1
rat	ggtttgtttttgaaaaatcccaaggctcctgcttgtaaggcctagtcttagaaggcacatctcaaacctacctCCTTGAGGATGTTCCCCAACTCTGcc
	***************************************************************************************************
	-------------------------------------------------------------------------------------------------------------	ENSRNOT00000046551 ENSRNOG00000040154 LOC685769
	-------------------------------------------------------------------------------------------------------------	ENSRNOT00000041178 ENSRNOG00000031939 LOC680475
	-------------------------------------------------------------------------------------------------------------	ENSRNOT00000041659 ENSRNOG00000031939 LOC680475
	-------------------------------------------------------------------------------------------------------------	ENSRNOT00000043269 ENSRNOG00000031939 LOC680475
rat	(((..(((...(((..(((((((((....(((((.((((((...))))))..)))))................))))).)))).)))...)))...)))	0.660 -20.95

rat

chromosome:9:5826378:5826476:-1

Opposite_strand|Intronic_coding|ENSRNOT00000041659|ENSRNOG00000031939 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000041178|ENSRNOG00000031939 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000050026|ENSRNOG00000031939 ## ENSRNOG00000031939|protein_coding|LOC680475|LOC363306 protein (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q5BK04] ## ENSRNOG00000040154|protein_coding|LOC685769|

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other hairpins:

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