miR-Intess™

other hairpins

novel_lenNOK_gcHIGH_shortStem_nonpairedHIGH (22 loci)

block1443141 [novel_lenNOK_gcHIGH_shortStem_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

0.049

no

no

0.95/0.95

19/19/0.00

0.0

0.0

1

0

1

0

1

14

5arm

1

nd

0.32

3

1

1

na

na

		reads	miRBase family seed
seed	--CCCCCGC------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	-CCCCCCGCCGGGGCAGGGG-------------------------------------------------------	19	1
rat	gCCCCCCGCCGGGGCAGGGGttgtcttcctggccaggaaggggtagatggatagggctgtctgggaggaggagca
	***************************************************************************
rat	((.((((.((.((((((...((((((..(((.((......)).)))..))))))..)))))).)).)).)).)).	0.990 -32.50

rat

chromosome:3:18495315:18495389:1

intergenic ## {Repeats: GC_rich 12 26 1 class=Low_complexity,GC_rich 1 26 1 class=Low_complexity,dust 18495306 18495312 0 class=dust}

novel_lenNOK_mirtron_bulgeHIGH (22 loci)

block38512 [novel_lenNOK_mirtron_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

0.143

no

no

0.47/0.47

19/19/0.00

0.0

0.0

1

0

1

0

11

7

3arm

1

1

0.26

4

1

1

na

na

		reads	miRBase family seed
seed	-----------------------------------------------UGAGAUU----------------------	1	novel
		len	cloning frequencies
			T3S2
	----------------------------------------------GTGAGATTTTCCTCAGCTG-----------	19	1
rat	gatgctcaagtattggaaagggaagcacctagttttaaagagacagGTGAGATTTTCCTCAGCTGcctgtggtgtc
	****************************************************************************
	--------------------------------------------------------------------------------------	ENSRNOT00000006875 ENSRNOG00000004686 Spop
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++	ENSRNOT00000031274 ENSRNOG00000022664 Myst2
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++	ENSRNOT00000031252 ENSRNOG00000022664 Myst2
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++	ENSRNOT00000031266 ENSRNOG00000022664 Myst2
rat	((((((((.((((((...((((((.(((((.(((((...))))))))))....))))))))).))).)).))))))	0.980 -20.30

rat

chromosome:10:83962391:83962466:-1

Same_strand|Boundary_coding|ENSRNOT00000031252|ENSRNOG00000022664 ## Opposite_strand|Intronic_coding|ENSRNOT00000006875|ENSRNOG00000004686 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000006230|ENSRNOG00000004686 ## ENSRNOG00000004686|protein_coding|Spop|Spop protein (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q5BJL3] ## ENSRNOG00000022664|protein_coding|Myst2|Histone acetyltransferase MYST2 (EC 2.3.1.48) (MYST protein 2) (MOZ, YBF2/SAS3, SAS2 and TIP60 protein 2) (Histone acetyltransferase binding to ORC1). [Source:UniProtKB/Swiss-Prot;Acc:Q810T5]

block56845 [novel_lenNOK_mirtron_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

0.340

no

no

0.44/0.44

18/18/0.00

0.0

0.0

2

0

1

0

28

7

5arm

1

1

0.28

4

2

1

na

na

		reads	miRBase family seed
seed	-----------------------------CUCUUUC------------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T3S1
	----------------------------CCTCTTTCTCTTGATAGC--------------------------------------------------------------------------	18	2
rat	ttttcttaggagtgtgtttaaacaagtgCCTCTTTCTCTTGATAGCttaagatgaaaatcacggactttgagaacaggagaagttttaagtgtatatggttaaacagccaatttagggaa
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++	ENSRNOT00000050277 ENSRNOG00000025496 Usp7
	++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++	ENSRNOT00000046232 ENSRNOG00000025496 Usp7
rat	.(((((((((.((.(((((((.((.((((((.(((((((((....((((((((....))).......)))))..))))))))).....)).)))).)).)))))))))...)))))))))	0.850 -25.41

rat

chromosome:10:6960463:6960582:1

Same_strand|Boundary_non-coding|ENSRNOT00000050277|ENSRNOG00000025496 ## Same_strand|Boundary_coding|ENSRNOT00000046232|ENSRNOG00000025496 ## ENSRNOG00000025496|protein_coding|Usp7|Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.1.2.15) (Ubiquitin thioesterase 7) (Ubiquitin-specific-processing protease 7) (Deubiquitinating enzyme 7) (Herpesvirus-associated ubiquitin-specific protease) (rHAUSP). [Source:UniProtKB/Swiss-Prot;Acc:Q4VSI4]

block79140 [novel_lenNOK_mirtron_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

0.042

no

no

0.50/0.50

18/18/0.00

0.0

0.0

3

0

1

0

14

3

3arm

1

3

0.22

4

3

1

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------GUCUACC------------------------	3	novel
		len	cloning frequencies
			T2S2
	----------------------------------------------------------AGTCTACCTTCTTCTCCC--------------	18	3
rat	ggactgtgggacgagggagaccaacccattctagacatcagacgtgaggaccccacccAGTCTACCTTCTTCTCCCtagatccagagcca
	******************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>	ENSRNOT00000040488 ENSRNOG00000033508 LOC687705
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>	ENSRNOT00000043732 ENSRNOG00000033508 LOC687705
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>	ENSRNOT00000044539 ENSRNOG00000033508 LOC687705
rat	((.((.((((...(((((((............(((....((((.((.((......))))))))....))))))))))...)))).)))).	0.840 -27.60

rat

chromosome:10:57495162:57495251:1

Same_strand|Intronic_coding|ENSRNOT00000043732|ENSRNOG00000033508 ## ENSRNOG00000033508|protein_coding|LOC687705|LOC303259 protein (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q5EB61]

block149710 [novel_lenNOK_mirtron_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

0.124

no

no

0.42/0.42

19/19/0.00

0.0

0.0

1

0

1

0

31

4

3arm

6

3

0.21

4

1

1

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------------CUCCAGU------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	----------------------------------------------------------------TCTCCAGTATTACCTCAAC-------------------------------	19	1
rat	ctttgggcgaacgcagctggcggtaaacgtactggtgtattttctgttgaggggcagtcatgttTCTCCAGTATTACCTCAACtagcagggcgatcgcgtctatactctaaaga
	******************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000002631 ENSRNOG00000001920
rat	((((((((((.(((.(((((.((((...(((((((..............((..(((....)))..)))))))))))))....)))))...))).)))).........)))))).	0.490 -34.83

rat

chromosome:11:22965565:22965678:1

Same_strand|Intronic_coding|ENSRNOT00000002631|ENSRNOG00000001920 ## ENSRNOG00000001920|protein_coding||

block213699 [novel_lenNOK_mirtron_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

0.50/0.57

18/21/0.50

0.5

2.0

4

0

2

0

31

5

3arm

2

0

0.24

4

4

2

na

na

		reads	miRBase family seed
seed	---------------------------------------------------------------------AUCCUUU--------------------------------------------	2	miR-501
seed	--------------------------------------------------------------------CAUCCUU---------------------------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2
	--------------------------------------------------------------------CATCCTTTCCTCCCTCTCCAG-------------------------------	21	2	-
	-------------------------------------------------------------------TCATCCTTTCCTCCCTCT-----------------------------------	18	-	2
rat	ttggaaattgagagggtgctgaggtgacttggagagggagatggtgctttgggaaccttggtgggtcTCATCCTTTCCTCCCTCTCCAGggccctccctgagctgcttccactggcccag
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000033998 ENSRNOG00000024456 RGD1306155_predicted
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000040448 ENSRNOG00000024456 RGD1306155_predicted
rat	.(((....((.((((..(((.(((.(((((((((((((((..((.....((((.((((....)))))))).))....)))))))))))))....))))).)))..)))))).....))).	0.960 -49.90

rat

chromosome:12:12475637:12475756:1

Same_strand|Intronic_coding|ENSRNOT00000033998|ENSRNOG00000024456 ## ENSRNOG00000024456|protein_coding|RGD1306155_predicted|Rap GTPase interactor [Source:RefSeq_peptide;Acc:NP_001032295]

block304541 [novel_lenNOK_mirtron_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

0.309

no

no

0.61/0.63

18/19/0.00

0.0

0.5

2

0

1

0

7

22

3arm

1

3

0.28

4

2

1

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------CUUCCCG------------------	2	novel
		len	cloning frequencies
			T3S1
	----------------------------------------------------------------------TCTTCCCGGTGACCTCCT--------	18	1
	----------------------------------------------------------------------TCTTCCCGGTGACCTCCTG-------	19	1
rat	gaggtgtgtagccctcagtctgggaaagaagaggcaggaggccactggtgtctgatgccatgcccttctcTCTTCCCGGTGACCTCCTGaagcctt
	************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>	ENSRNOT00000038822 ENSRNOG00000004441 Faim3
rat	(((((...(((...(((..((((((((((((.((((((.((.((....)).))....)).)))))))))...))))))))))....)))..)))))	0.810 -32.60

rat

chromosome:13:43827207:43827302:1

Same_strand|Intronic_coding|ENSRNOT00000038822|ENSRNOG00000004441 ## ENSRNOG00000004441|protein_coding|Faim3|Fas apoptotic inhibitory molecule 3 precursor (Regulator of Fas- induced apoptosis Toso). [Source:UniProtKB/Swiss-Prot;Acc:Q5M871]

block340926 [novel_lenNOK_mirtron_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

0.017

no

no

0.53/0.53

19/19/0.00

0.0

0.0

1

0

1

0

13

13

3arm

1

1

0.26

4

1

1

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------GGUGUGU------------------------	1	novel
		len	cloning frequencies
			T2S1
	----------------------------------------------------------------------AGGTGTGTGTGTCAGCTGT-------------	19	1
rat	tttagtgggagataacccagcaagccacacctacgtcaggaataagatcagagccgcttctgctgtaggtAGGTGTGTGTGTCAGCTGTaattgtcactaaa
	******************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++	ENSRNOT00000047708 ENSRNOG00000021347 AC109311.12
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++	ENSRNOT00000039849 ENSRNOG00000021347 AC109311.12
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++	ENSRNOT00000048395 ENSRNOG00000021347 AC109311.12
rat	.(((((((.((.((...((((..(((((((((((..(((.........(((((....))))))))...))))))))).))....)))))).)).))))))).	0.780 -31.60

rat

chromosome:14:18648086:18648187:-1

Same_strand|Boundary_coding|ENSRNOT00000047708|ENSRNOG00000021347 ## Same_strand|Boundary_non-coding|ENSRNOT00000042526|ENSRNOG00000021347 ## ENSRNOG00000021347|protein_coding|AC109311.12|methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like [Source:RefSeq peptide;Acc:NP_081064]

block372347 [novel_lenNOK_mirtron_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

0.732

no

no

0.53/0.53

19/19/0.00

0.0

0.0

1

0

1

0

17

15

3arm

1

2

0.26

4

1

1

na

na

		reads	miRBase family seed
seed	---------------------------------------------------------------CCUCUGA----------------------------	1	novel
		len	cloning frequencies
			T3S1
	--------------------------------------------------------------CCCTCTGATGCTGTCTTCT-----------------	19	1
rat	cattggagccagtgcgtggttggtcgttggtggcttgtggcttggaaaagagacttaactttCCCTCTGATGCTGTCTTCTaggtagtggtgtcattg
	**************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000007044 ENSRNOG00000005214 Plek
rat	((.((..((((.(((.(((.(((.((((((.((...((..(((....)))..)).........)).)))))))))....))).))).))))..)).))	0.640 -24.50

rat

chromosome:14:97856174:97856271:-1

Same_strand|Boundary_non-coding|ENSRNOT00000057002|ENSRNOG00000005214 ## Same_strand|Intronic_coding|ENSRNOT00000007044|ENSRNOG00000005214 ## ENSRNOG00000005214|protein_coding|Plek|Pleckstrin. [Source:UniProtKB/Swiss-Prot;Acc:Q4KM33]

block387624 [novel_lenNOK_mirtron_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

0.677

no

no

0.44/0.44

18/18/0.00

0.0

0.0

1

0

1

0

30

1

5arm

1

3

0.22

4

1

1

na

na

		reads	miRBase family seed
seed	-------------------------------GUCUGUU--------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	------------------------------TGTCTGTTGACCAACATG----------------------------------------------------	18	1
rat	gaaggctaattttgggggggcatttgttttTGTCTGTTGACCAACATGcaggggtggcactgaatcaacaagacaagcaactcagttgatcaatgctttg
	****************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000035592 ENSRNOG00000002940 Q99MD2_RAT
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000004068 ENSRNOG00000002940 Q99MD2_RAT
rat	.(((((..(((...(((..((........(((((((((((....(((((.......))).))..)))))).)))))))..)))....)))....))))).	0.770 -21.10

rat

chromosome:14:19369462:19369561:1

Same_strand|Intronic_coding|ENSRNOT00000035592|ENSRNOG00000002940 ## ENSRNOG00000002940|protein_coding|Q99MD2_RAT|Serologically defined breast cancer antigen NY-BR-16-like protein (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q99MD2]

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other hairpins:

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