miR-Intess™

other hairpins

novel_shortStem_mirtron_nonpairedHIGH (29 loci)

novel_lenNOK_cloningOK_loopOverlap_randfoldOK (28 loci)

block1822 [novel_lenNOK_cloningOK_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

0.006

no

no

0.32/0.33

18/19/0.00

0.0

0.1

25

0

8

0

11

-1

3arm_loop

1

nd

0.05

1

28

8

na

na

		reads	miRBase family seed
seed	------------------------------------GCAGCAU----------------------	28	miR-103/107
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T4S1	T4S2	T5S1	T5S2
	-----------------------------------AGCAGCATTGTAGTTTTA------------	18	5	1	3	1	6	2	3	4
	-----------------------------------AGCAGCATTGTAGTTTTAT-----------	19	1	-	-	-	2	-	-	-
rat	ggaggctgtgagactagaaacaaggcttgccgggcAGCAGCATTGTAGTTTTATagcaagtgcca
	*****************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000003150 ENSRNOG00000002294 LOC687335
rat	((..(((((((((((....((((.((.(((......))))).))))))))))))))).....)).	0.960 -22.20

rat

chromosome:10:4080721:4080785:-1

Same_strand|Intronic_coding|ENSRNOT00000003150|ENSRNOG00000002294 ## ENSRNOG00000002294|protein_coding|LOC687335|similar to kinesin-like motor protein C20orf23 (LOC689142), mRNA [Source:RefSeq_dna;Acc:NM_001109526]

block105424 [novel_lenNOK_cloningOK_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

0.005

no

no

0.50/0.53

18/20/0.11

0.0

0.0

14

0

8

0

39

-2

3arm_loop

2

nd

0.28

2

19

8

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------UGGCUUU-------------------------------------------------	19	novel
		len	cloning frequencies
			T1S1	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S2
	----------------------------------------------------------TTGGCTTTGGCTTTGGGT---------------------------------------	18	2	2	4	3	3	-	1	1
	----------------------------------------------------------TTGGCTTTGGCTTTGGGTCT-------------------------------------	20	-	1	-	-	-	1	-	-
	----------------------------------------------------------TTGGCTTTGGCTTTGGGTC--------------------------------------	19	-	-	1	-	-	-	-	-
rat	aaagccagtatgtcctcaccctgatcaccctgggacctagtacctggccctttgggtcTTGGCTTTGGCTTTGGGTctcacttcctgggtagaaggggtggggttttgtttgttt
	*******************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000048472 ENSRNOG00000003148 Timp2
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000004290 ENSRNOG00000003148 Timp2
rat	.((((.((((...(((((((((..((((((((((((((((..((.((((...........))))..))..))))))))))......)))).)).)))))))))...)))).))))	0.700 -44.50

rat

chromosome:10:108355584:108355698:1

Opposite_strand|Intronic_coding|ENSRNOT00000004290|ENSRNOG00000003148 ## ENSRNOG00000003148|protein_coding|Timp2|Metalloproteinase inhibitor 2 precursor (TIMP-2) (Tissue inhibitor of metalloproteinases 2). [Source:UniProtKB/Swiss-Prot;Acc:P30121]

block170047 [novel_lenNOK_cloningOK_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

0.64/0.72

18/22/0.60

0.2

1.1

10

0

3

0

6

-4

3arm_loop

1

nd

0.17

2

10

3

na

na

		reads	miRBase family seed
seed	------------------------CACCGGA--------------------	9	novel
seed	--------------------------CCGGAGC------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T4S1
	-----------------------ACACCGGAGCCGGCAGCTTGT-------	21	3	-	-
	-----------------------ACACCGGAGCCGGCAGCTTGTT------	22	-	2	-
	-----------------------ACACCGGAGCCGGCAGCTT---------	19	1	-	1
	-------------------------ACCGGAGCCGGCAGCTTG--------	18	-	1	-
	-----------------------ACACCGGAGCCGGCAGCTTG--------	20	1	-	-
	-----------------------ACACCGGAGCCGGCAGCT----------	18	1	-	-
rat	ggaatgctgctgctggctccgtaACACCGGAGCCGGCAGCTTGTTgatttc
	***************************************************
rat	(((((((.(((((((((((((......)))))))))))))..))..)))))	1.000 -29.30

rat

chromosome:11:73732868:73732918:1

intergenic ## {SimpF: oe = 0.83 1 CpG}

block507538 [novel_lenNOK_cloningOK_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

0.002

no

no

0.68/0.72

18/19/0.00

0.0

0.3

17

0

7

0

26

-1

5arm_loop

1

nd

0.22

3

24

7

na

na

		reads	miRBase family seed
seed	---------------------------CUCUGGG------------------------------------------------------	23	miR-326/330
seed	----------------------------UCUGGGC-----------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S2	T3S1	T3S2	T4S2	T5S2
	--------------------------CCTCTGGGCCCTTCCTGCA-------------------------------------------	19	5	4	1	1	-	1	3
	--------------------------CCTCTGGGCCCTTCCTGC--------------------------------------------	18	3	1	1	-	1	-	2
	---------------------------CTCTGGGCCCTTCCTGCAC------------------------------------------	19	-	1	-	-	-	-	-
rat	cctgcaggttggtggcttcctgtttgCCTCTGGGCCCTTCCTGCAcagggctgaggaggggctctcctggctgtcaccagcttttgga
	****************************************************************************************
rat	((...(((((((((((.........(((...(((((((((((((.....))..)))))))))))....))).)))))))))))..)).	1.000 -42.90

rat

chromosome:15:88725358:88725445:1

intergenic

block583593 [novel_lenNOK_cloningOK_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

0.008

no

no

0.47/0.50

18/19/0.00

0.0

0.1

13

0

7

0

9

-1

3arm

1

nd

0.21

2

13

7

na

na

		reads	miRBase family seed
seed	-------------------------------------------GGUCUGA--------------------	13	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S2	T4S2	T5S1	T5S2
	------------------------------------------TGGTCTGAAAGTCACCTC----------	18	1	2	1	1	3	1	3
	------------------------------------------TGGTCTGAAAGTCACCTCT---------	19	-	-	-	-	-	-	1
rat	ctaacaaggaaatctggggactcttggacctaaccacacattTGGTCTGAAAGTCACCTCTagatgttag
	**********************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000015879 ENSRNOG00000011858 Unc5d
rat	((((((......((((((((((.(((((((.............))))))).)))).)))..)))))))))	0.950 -20.02

rat

chromosome:16:67410079:67410148:1

Same_strand|Intronic_coding|ENSRNOT00000015879|ENSRNOG00000011858 ## ENSRNOG00000011858|protein_coding|Unc5d|unc-5 homolog D (C. elegans) Gene [Source:MGI Symbol;Acc:MGI:2389364]

block681186 [novel_lenNOK_cloningOK_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

0.007

no

no

0.53/0.61

18/19/0.00

0.6

0.8

23

0

8

0

8

-3

3arm_loop

1

nd

0.16

1

23

8

na

na

		reads	miRBase family seed
seed	-------------------------------------AGCUGGG-------------------	13	novel
seed	------------------------------------AAGCUGG--------------------	10	novel
		len	cloning frequencies
			T1S1	T1S2	T2S2	T3S2	T4S1	T4S2	T5S1	T5S2
	-----------------------------------GAAGCTGGGTTGAGAGGG----------	18	2	1	-	-	-	3	1	3
	------------------------------------AAGCTGGGTTGAGAGGGA---------	18	2	-	-	1	1	1	2	1
	------------------------------------AAGCTGGGTTGAGAGGGAA--------	19	1	1	1	-	1	-	-	1
rat	ccttgctgagacccagtctcaaacaaaaccagcagGAAGCTGGGTTGAGAGGGAAgttaaggc
	***************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000034157 ENSRNOG00000022249 Mllt10
rat	(((((((....(((..((((((......(((((.....))))).))))))))).))).)))).	0.990 -22.40

rat

chromosome:17:92387706:92387768:1

Same_strand|Intronic_coding|ENSRNOT00000034157|ENSRNOG00000022249 ## ENSRNOG00000022249|protein_coding|Mllt10|myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 Gene [Source:MGI (curated);Acc:Mllt10-001]

block790286 [novel_lenNOK_cloningOK_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

0.008

no

no

0.42/0.45

18/22/0.14

0.0

0.2

15

0

7

0

24

-1

5arm_loop

1

nd

0.22

3

22

7

na

na

		reads	miRBase family seed
seed	-------------------------GAUUUGG------------------------------------------------------	22	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S2	T4S2	T5S1	T5S2
	------------------------TGATTTGGCTTCCACAGA--------------------------------------------	18	1	1	1	1	5	3	4
	------------------------TGATTTGGCTTCCACAGAA-------------------------------------------	19	-	-	-	-	-	-	3
	------------------------TGATTTGGCTTCCACAGAAGTC----------------------------------------	22	1	-	-	-	-	1	-
	------------------------TGATTTGGCTTCCACAGAAG------------------------------------------	20	-	-	-	-	1	-	-
rat	gcctgaggtacctgggtcactggaTGATTTGGCTTCCACAGAAgtcctctggcttgagccaaatctgatgactttagggcctatgc
	**************************************************************************************
rat	((...((((.(((((((((......((((((((((...((((.....))))....))))))))))...)))))).)))))))..))	0.960 -31.80

rat

chromosome:19:54295803:54295888:-1

intergenic

block867214 [novel_lenNOK_cloningOK_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

0.003

no

no

0.72/0.75

18/20/0.25

0.0

0.8

12

0

5

0

30

-4

5arm_loop

1

nd

0.17

3

12

5

na

na

		reads	miRBase family seed
seed	-------------------------------AGGUGGG------------------------------------------------------------	12	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T4S1	T5S1
	------------------------------TAGGTGGGGGGTGGGCTG--------------------------------------------------	18	1	3	1	1	-
	------------------------------TAGGTGGGGGGTGGGCTGG-------------------------------------------------	19	1	1	-	-	1
	------------------------------TAGGTGGGGGGTGGGCTGGG------------------------------------------------	20	-	2	-	1	-
rat	cacccccacgcagggacacacagatggacaTAGGTGGGGGGTGGGCTGGGagcccacagcctccccatttctgtctgtctctcacacccgcaggcggt
	**************************************************************************************************
	------------------------------------------------------------------------------------------------------------	ENSRNOT00000026100 ENSRNOG00000019207 Shank1
	------------------------------------------------------------------------------------------------------------	ENSRNOT00000048805 ENSRNOG00000019207 Shank1
	------------------------------------------------------------------------------------------------------------	ENSRNOT00000044257 ENSRNOG00000019207 Shank1
	------------------------------------------------------------------------------------------------------------	ENSRNOT00000049346 ENSRNOG00000019207 Shank1
	------------------------------------------------------------------------------------------------------------	ENSRNOT00000046418 ENSRNOG00000019207 Shank1
rat	.(((.((..((.(((......(((((((((.(((((((((((((((.....))))))....))))))))).)))))))))......))))).)).)))	1.000 -46.10

rat

chromosome:1:94818109:94818206:-1

Opposite_strand|Intronic_coding|ENSRNOT00000044257|ENSRNOG00000019207 ## ENSRNOG00000019207|protein_coding|Shank1|SH3 and multiple ankyrin repeat domains protein 1 (Shank1) (GKAP/SAPAP-interacting protein) (SPANK-1) (Synamon) (Somatostatin receptor-interacting protein) (SSTR-interacting protein) (SSTRIP). [Source:UniProtKB/Swiss-Prot;Acc:Q9WV48]

block1115254 [novel_lenNOK_cloningOK_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

0.005

no

no

0.67/0.72

18/18/0.00

0.1

0.1

13

0

8

0

33

-5

3arm_loop

1

nd

0.22

3

13

8

na

na

		reads	miRBase family seed
seed	-----------------------------------------------UGGACGG--------------------------------------------	12	novel
seed	------------------------------------------------GGACGGU-------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T5S1	T5S2
	----------------------------------------------GTGGACGGTGTGAGGCCG----------------------------------	18	3	3	2	1	-	1	1	1
	-----------------------------------------------TGGACGGTGTGAGGCCGA---------------------------------	18	-	-	-	-	1	-	-	-
rat	ggggcctgagcagtccgcctgaaggattcaacccggcctcgcgctgGTGGACGGTGTGAGGCCGAggtagctcctctttggctcttagtaacaggtct
	**************************************************************************************************
rat	.(((((((.((.....(((.((((((....((((((((((((((((.....))))))))))))).)))...)))).)).))).....))..)))))))	0.940 -48.00

rat

chromosome:20:41258404:41258501:1

intergenic

block1197915 [novel_lenNOK_cloningOK_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

0.005

no

no

0.60/0.72

18/20/0.38

0.4

0.4

13

0

3

0

22

-2

3arm

1

nd

0.06

1

13

3

na

na

		reads	miRBase family seed
seed	-------------------------------------------------UGCAGGC-----------------------------------	8	novel
seed	--------------------------------------------------GCAGGCC----------------------------------	3	novel
seed	------------------------------------------------GUGCAGG------------------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1
	------------------------------------------------GTGCAGGCCCTGCTTCCCT------------------------	19	2	3	-
	-------------------------------------------------TGCAGGCCCTGCTTCCCT------------------------	18	-	2	-
	------------------------------------------------GTGCAGGCCCTGCTTCCCTA-----------------------	20	-	1	1
	-----------------------------------------------AGTGCAGGCCCTGCTTCCCT------------------------	20	-	2	-
	------------------------------------------------GTGCAGGCCCTGCTTCCC-------------------------	18	-	1	-
	-------------------------------------------------TGCAGGCCCTGCTTCCCTAA----------------------	20	1	-	-
rat	tgggcctggaagacgggcagcagcagagaggaagtagggcctccgagAGTGCAGGCCCTGCTTCCCTAAgagcccccacagctggctccag
	*******************************************************************************************
rat	((((((.((.....((((........((.(((((((((((((.((....)).)))))))))))))))....))))......))))).))).	0.500 -41.60

rat

chromosome:2:180475197:180475287:-1

intergenic

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other hairpins:

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