miR-Intess™

other hairpins

novel_shortStem_loopOverlap_randfoldOK (39 loci)

block2399126 [novel_shortStem_loopOverlap_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

no

0.010

no

no

0.46/0.46

24/24/1.00

0.0

0.0

1

0

1

0

2

-4

3arm_loop

1

nd

0.25

3

1

1

na

na

		reads	miRBase family seed
seed	--------------------------CAAUCCC------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------TCAATCCCCTAACACTCTCCATTG--	24	1
rat	gcagggggtccaggcttgggggaaaTCAATCCCCTAACACTCTCCATTGcg
	***************************************************
	-------------------------------------------------------------	ENSRNOT00000048347 ENSRNOG00000030910 Grik4
rat	((((((((...((..((((((((......))))))))..)))))).)))).	1.000 -21.80

rat

chromosome:8:45610677:45610727:1

Opposite_strand|Intronic_coding|ENSRNOT00000048347|ENSRNOG00000030910 ## ENSRNOG00000030910|protein_coding|Grik4|Glutamate receptor, ionotropic kainate 4 precursor (Glutamate receptor KA-1) (KA1). [Source:UniProtKB/Swiss-Prot;Acc:Q01812]

block2423395 [novel_shortStem_loopOverlap_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

no

0.001

no

no

0.52/0.52

21/21/1.00

0.0

0.0

1

0

1

0

1

-2

3arm_loop

1

nd

0.29

3

1

1

na

na

		reads	miRBase family seed
seed	-----------------------CAGGAAC--------------	1	miR-873
		len	cloning frequencies
			T1S2
	----------------------GCAGGAACACAGAACAGCACA-	21	1
rat	ctgtcgggttctgtgggcctgaGCAGGAACACAGAACAGCACAg
	********************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000021757 ENSRNOG00000016042 Aldh1a2
rat	((((...((((((((..(((....)))..))))))))...))))	1.000 -21.70

rat

chromosome:8:75703858:75703901:1

Same_strand|Intronic_coding|ENSRNOT00000021757|ENSRNOG00000016042 ## ENSRNOG00000016042|protein_coding|Aldh1a2|Retinal dehydrogenase 2 (EC 1.2.1.36) (RalDH2) (RALDH 2) (RALDH(II)) (Retinaldehyde-specific dehydrogenase type 2) (Aldehyde dehydrogenase family 1 member A2). [Source:UniProtKB/Swiss-Prot;Acc:Q63639]

novel_lenNOK_loopOverlap_mirtron_nonpairedHIGH (38 loci)

block6403 [novel_lenNOK_loopOverlap_mirtron_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

0.297

no

no

0.61/0.61

18/18/0.00

0.0

0.0

1

0

1

0

14

-1

5arm_loop

1

0

0.50

3

1

1

na

na

		reads	miRBase family seed
seed	---------------GUCCCUG------------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	--------------GGTCCCTGACTGTCCTGT--------------------------------	18	1
rat	ctcagccctgtagtGGTCCCTGACTGTCCTGTggccagtaagttcttgaaggcacagagctggg
	****************************************************************
	...........>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000060779 ENSRNOG00000039635
rat	((((((.((((.((..((...((((...(((....)))..))))...))..)))))).))))))	0.910 -20.20

rat

chromosome:10:13664718:13664781:-1

Same_strand|Boundary_coding|ENSRNOT00000060779|ENSRNOG00000039635 ## ENSRNOG00000039635|protein_coding||

block20478 [novel_lenNOK_loopOverlap_mirtron_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

0.550

no

no

0.47/0.47

19/19/0.00

0.0

0.0

1

0

1

0

21

-4

3arm_loop

1

4

0.42

3

1

1

na

na

		reads	miRBase family seed
seed	-----------------------------------------GGUUCUU--------------------------------	1	novel
		len	cloning frequencies
			T2S2
	----------------------------------------TGGTTCTTTTCTCCCTGTC---------------------	19	1
rat	tgataagctgcttattctttactgtatgagataaggttatTGGTTCTTTTCTCCCTGTCgtaggtttgtgaagttttcca
	********************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000004438 ENSRNOG00000003315 Cops3
rat	((..(((((...((..((.(((..((.((((.((((........)))).))))..))..)))))..))...)))))..))	0.590 -11.20

rat

chromosome:10:46156780:46156859:-1

Same_strand|Intronic_coding|ENSRNOT00000004438|ENSRNOG00000003315 ## ENSRNOG00000003315|protein_coding|Cops3|COP9 signalosome complex subunit 3 (Signalosome subunit 3) (SGN3). [Source:UniProtKB/Swiss-Prot;Acc:Q68FW9]

block98859 [novel_lenNOK_loopOverlap_mirtron_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

0.569

no

no

0.53/0.53

19/19/0.00

0.0

0.0

1

0

1

0

14

-2

5arm_loop

1

2

0.47

3

1

1

na

na

		reads	miRBase family seed
seed	---------------GAGACAC-------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	--------------TGAGACACAGTTGGGCCAA--------------------------------------	19	1
rat	tatcgcaaggacggTGAGACACAGTTGGGCCAAgggttctacaggctatctttctcatctattatggggtg
	***********************************************************************
	>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000010816 ENSRNOG00000008078 Kcnh6
rat	((((.((.....(((((((...((...((((............))))..)).))))))).....)).))))	0.900 -16.30

rat

chromosome:10:95401939:95402009:1

Same_strand|Intronic_coding|ENSRNOT00000010816|ENSRNOG00000008078 ## ENSRNOG00000008078|protein_coding|Kcnh6|Potassium voltage-gated channel subfamily H member 6 (Voltage-gated potassium channel subunit Kv11.2) (Ether-a-go-go-related gene potassium channel 2) (Ether-a-go-go-related protein 2) (Eag-related protein 2). [Source:UniProtKB/Swiss-Prot;Acc:O54853]

block106130 [novel_lenNOK_loopOverlap_mirtron_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

0.442

no

no

0.53/0.61

19/23/0.50

0.0

1.5

4

0

4

0

31

-3

3arm_loop

1

2

0.38

3

4

4

na

na

		reads	miRBase family seed
seed	---------------------------------------CAACACU----------------------------------------------	4	novel
		len	cloning frequencies
			T1S1	T3S1	T5S1	T5S2
	--------------------------------------CCAACACTGTTCCCTCAAC-----------------------------------	19	-	1	1	-
	--------------------------------------CCAACACTGTTCCCTCAACCG---------------------------------	21	1	-	-	-
	--------------------------------------CCAACACTGTTCCCTCAACCGGC-------------------------------	23	-	-	-	1
rat	ctcttcccgggtgtggggtgttccggccgaggcgggtcCCAACACTGTTCCCTCAACCGGCagaatgcactataccagtcctgtcacgaaga
	********************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000054977 ENSRNOG00000036702 RGD1306500_predicted
rat	.(((((.((((..((((((((.((((..(((((((((....)).)))...))))..))))......)))))...)))..))))....)))))	0.440 -27.30

rat

chromosome:10:109734897:109734988:1

Same_strand|Intronic_coding|ENSRNOT00000054977|ENSRNOG00000036702 ## ENSRNOG00000036702|protein_coding|RGD1306500_predicted|

block135763 [novel_lenNOK_loopOverlap_mirtron_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

0.249

no

no

0.50/0.50

18/18/0.00

0.0

0.0

1

0

1

0

34

-2

5arm_loop

1

3

0.33

3

1

1

na

na

		reads	miRBase family seed
seed	-----------------------------------CCCUGUG------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	----------------------------------TCCCTGTGTTTGGTCCTT--------------------------------------------------------	18	1
rat	tttgtactcaagaggctatgtagtaatttcctttTCCCTGTGTTTGGTCCTTcaggattgatcactggaacaacgagaaagagaagatcctgctactcacggacaaga
	************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000002634 ENSRNOG00000001923 Tprg
rat	(((((.((...(((.....((((...(((((((((((..(((.(((((((....))))))).))).))))........))).))))...))))..)))..))))))).	0.520 -23.30

rat

chromosome:11:77538919:77539026:-1

Same_strand|Intronic_coding|ENSRNOT00000002634|ENSRNOG00000001923 ## ENSRNOG00000001923|protein_coding|Tprg|transformation related protein 63 regulated [Source:RefSeq_peptide;Acc:NP_001101790]

block141092 [novel_lenNOK_loopOverlap_mirtron_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

0.565

no

no

0.61/0.61

18/18/0.00

0.0

0.0

2

0

1

0

30

-4

3arm_loop

1

2

0.39

3

2

1

na

na

		reads	miRBase family seed
seed	----------------------------------------------CGUUGGU----------------------------------------	2	novel
		len	cloning frequencies
			T1S1
	---------------------------------------------GCGTTGGTACAGAGCTCC------------------------------	18	2
rat	tccagaccatgatcatacagggttcttgacagagtatgtagccacGCGTTGGTACAGAGCTCCnagaaattatgttgaattccaaggtaagaa
	*********************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++>>>>>>>>>>>>>>>>>>>>>++++++++++++	ENSRNOT00000002533 ENSRNOG00000001849 Mapk1
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++>>>>>>>>>>>>>>>>>>>>>++++++++++++	ENSRNOT00000027901 ENSRNOG00000001849 Mapk1
rat	((...(((.((.(((.(((...((((.....((((.(((.((((.....)))))))..))))..))))....))))))....)).)))..)).	0.680 -17.50

rat

chromosome:11:85988814:85988906:-1

Same_strand|Boundary_coding|ENSRNOT00000027901|ENSRNOG00000001849 ## ENSRNOG00000001849|protein_coding|Mapk1|Mitogen-activated protein kinase 1 (EC 2.7.11.24) (Extracellular signal-regulated kinase 2) (ERK-2) (Mitogen-activated protein kinase 2) (MAP kinase 2) (MAPK 2) (p42-MAPK) (ERT1). [Source:UniProtKB/Swiss-Prot;Acc:P63086]

block171765 [novel_lenNOK_loopOverlap_mirtron_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

0.248

no

no

0.47/0.48

19/25/0.00

0.0 0.0

0.0 0.0

1 2

0 0

1 1

0 0

18 8

-2 2

3arm_loop 3arm

1 1

11 1

0.32 0.36

3 3

3

2

na

na

		reads	miRBase family seed
seed	---------------------------------------CGUGGUA-------------------------	2	novel
seed	-----------------------------------CUACCGU-----------------------------	1	novel
		len	cloning frequencies
			T3S2	T5S2
	--------------------------------------CCGTGGTAACTCTGTTTGTCTTGCA--------	25	2	-
	----------------------------------ACTACCGTGGTAACTCTGT------------------	19	-	1
rat	cggggaagacaaggcacagagatgctttgtgaccACTACCGTGGTAACTCTGTTTGTCTTGCAgtggcctg
	***********************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>	ENSRNOT00000002522 ENSRNOG00000001843 NP_001100554.1
rat	((((.....((((((((((((.((((..(((.....)))...)))).))))))..))))))......))))	0.630 -20.70

rat

chromosome:11:79019051:79019121:1

Same_strand|Intronic_coding|ENSRNOT00000002522|ENSRNOG00000001843 ## ENSRNOG00000001843|protein_coding|NP_001100554.1|B-cell leukemia/lymphoma 6 [Source:RefSeq_peptide;Acc:NP_001100554]

block318856 [novel_lenNOK_loopOverlap_mirtron_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

0.134

no

no

0.17/0.17

18/18/0.00

0.0

0.0

1

0

1

0

20

-2

3arm_loop

1

3

0.33

2

1

1

na

na

		reads	miRBase family seed
seed	--------------------------------------------------UUUAAUU------------------------------	1	novel
		len	cloning frequencies
			T1S1
	-------------------------------------------------TTTTAATTTTTGTAGGAA--------------------	18	1
rat	gatgtagaaacctggtgaaagttatggatgtcctgtgagatttaatcttTTTTAATTTTTGTAGGAAagttaaaggggggaatattg
	***************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000003448 ENSRNOG00000002544 NP_001099434.1
rat	(((((.....(((..(((............(((((..(((.((((......)))).)))..)))))...)))..)))....))))).	0.620 -15.36

rat

chromosome:13:79547231:79547317:1

Same_strand|Boundary_coding|ENSRNOT00000003448|ENSRNOG00000002544 ## ENSRNOG00000002544|protein_coding|NP_001099434.1|kinesin-associated protein 3 [Source:RefSeq_peptide;Acc:NP_001099434]

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other hairpins:

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