miR-Intess™

other hairpins

novel_lenNOK_cloningOK_randfoldOK_nonpairedHIGH_bulgeHIGH (39 loci)

block2616140 [novel_lenNOK_cloningOK_randfoldOK_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

0.010

no

no

0.61/0.63

18/19/0.00

0.0

0.6

12

0

3

0

8

18

5arm

1

nd

0.37

4

13

3

na

na

		reads	miRBase family seed
seed	---------CACAGUG----------------------------------------------------------------------------------	13	miR-128
		len	cloning frequencies
			T1S1	T1S2	T2S1
	--------TCACAGTGAACCCCAGGG------------------------------------------------------------------------	18	3	4	1
	--------TCACAGTGAACCCCAGGGG-----------------------------------------------------------------------	19	5	-	-
rat	acattcaaTCACAGTGAACCCCAGGGGacgtcatctatttttccttaactataggcctcgcagatactggatttcccctccccttcactaatcgatgt
	**************************************************************************************************
rat	(((((.......((((((....((((((.(((((((......(((.......)))......))))....))).))))))....))))))....)))))	0.920 -21.60

rat

chromosome:9:71884410:71884507:1

intergenic

block2723555 [novel_lenNOK_cloningOK_randfoldOK_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

0.009

no

no

0.15/0.17

18/20/0.07

0.0

0.0

9

0

7

0

24

5

5arm

3

nd

0.39

4

15

7

na

na

		reads	miRBase family seed
seed	-------------------------UGGAAUA---------------------------------------------------------------------	12	novel
seed	--------------------------GGAAUAC--------------------------------------------------------------------	3	novel
		len	cloning frequencies
			T1S1	T2S1	T2S2	T3S1	T3S2	T4S2	T5S2
	------------------------TTGGAATACAAATATTTT-----------------------------------------------------------	18	2	3	1	4	-	-	1
	-------------------------TGGAATACAAATATTTTTT---------------------------------------------------------	19	-	-	-	-	1	-	1
	------------------------TTGGAATACAAATATTTTTT---------------------------------------------------------	20	-	-	-	-	-	1	-
	-------------------------TGGAATACAAATATTTTT----------------------------------------------------------	18	-	-	-	1	-	-	-
rat	atttgtacaatgtttatgcattcaTTGGAATACAAATATTTTttcattagcacacatgaaatttcatttgtacaccttgtgctcaaactttgcaataaatg
	*****************************************************************************************************
	---------------------------------------------------------------------------------------------------------------	ENSRNOT00000035692 ENSRNOG00000003667 Dmd
rat	((((((.(((.((((..((((.....((..(((((((....((((((........))))))....)))))))..))..))))..)))).)))..)))))).	1.000 -20.00

rat

chromosome:X:70993090:70993190:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000058357|ENSRNOG00000003667 ## Opposite_strand|Intronic_coding|ENSRNOT00000035692|ENSRNOG00000003667 ## ENSRNOG00000003667|protein_coding|Dmd|Dystrophin (Fragment). [Source:UniProtKB/Swiss-Prot;Acc:P11530]

block1060322 [novel_lenNOK_cloningOK_randfoldOK_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

0.005

no

no

0.48/0.60

18/26/0.62

0.7

1.3

12

0

6

0

7

12

5arm

1

nd

0.40

4

29

6

na

na

		reads	miRBase family seed
seed	--------GUCACAA-----------------------------------------------------------------	14	novel
seed	----------CACAACG---------------------------------------------------------------	11	novel
seed	-------UGUCACA------------------------------------------------------------------	3	novel
seed	-----------ACAACGG--------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S2	T5S1	T5S2
	-------TGTCACAACGGCAGACAGCT-----------------------------------------------------	20	-	-	1	1	8	-
	---------TCACAACGGCAGACAGCTAACA-------------------------------------------------	22	-	-	-	-	4	-
	---------TCACAACGGCAGACAGCTAACACCCC---------------------------------------------	26	-	-	1	-	2	-
	-------TGTCACAACGGCAGACAGCTAACACC-----------------------------------------------	26	1	-	-	-	1	-
	------TTGTCACAACGGCAGACAGCTAACAC------------------------------------------------	26	-	-	-	-	-	1
	---------TCACAACGGCAGACAGCTA----------------------------------------------------	19	-	-	-	-	1	-
	------TTGTCACAACGGCAGACAGCTAAC--------------------------------------------------	24	-	-	-	-	1	-
	-------TGTCACAACGGCAGACAGCTAACA-------------------------------------------------	24	-	-	-	-	1	-
	------TTGTCACAACGGCAGACAGCTAACA-------------------------------------------------	25	-	-	-	1	-	-
	---------TCACAACGGCAGACAGCTAACACCC----------------------------------------------	25	-	-	-	-	1	-
	----------CACAACGGCAGACAGCTAACACCCC---------------------------------------------	25	-	-	-	-	1	-
	---------TCACAACGGCAGACAGCT-----------------------------------------------------	18	-	-	-	-	1	-
	-------TGTCACAACGGCAGACAGCTA----------------------------------------------------	21	-	-	-	-	1	-
	---------TCACAACGGCAGACAGCTAA---------------------------------------------------	20	-	1	-	-	-	-
rat	ggcatttTGTCACAACGGCAGACAGCTAACAccccatggggtctctgggcccctgggggctccctgccactgacctggtc
	********************************************************************************
rat	(((.....((((....(((((..(((.....(((((.((((((....))))))))))))))..)))))..))))...)))	0.740 -35.80

rat

chromosome:20:5500692:5500771:-1

intergenic

block1093731 [novel_lenNOK_cloningOK_randfoldOK_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

0.002

no

no

0.54/0.58

18/25/0.46

0.0

2.8

21

0

3

0

8

1

5arm

1

nd

0.32

4

24

3

na

na

		reads	miRBase family seed
seed	---------AGCAUGU----------------------------------------------------	24	novel
		len	cloning frequencies
			T1S1	T1S2	T5S1
	--------TAGCATGTGGCAGTGGAG------------------------------------------	18	2	-	4
	--------TAGCATGTGGCAGTGGAGCACAG-------------------------------------	23	-	-	5
	--------TAGCATGTGGCAGTGGAGC-----------------------------------------	19	-	-	4
	--------TAGCATGTGGCAGTGGAGCAC---------------------------------------	21	-	-	3
	--------TAGCATGTGGCAGTGGAGCACAGTG-----------------------------------	25	-	-	3
	--------TAGCATGTGGCAGTGGAGCA----------------------------------------	20	-	-	1
	--------TAGCATGTGGCAGTGGAGCACA--------------------------------------	22	-	1	-
	--------TAGCATGTGGCAGTGGAGCACAGT------------------------------------	24	-	1	-
rat	ggcatggcTAGCATGTGGCAGTGGAGCACAGTGgtccagccgtgtgtcacactgcccagggcaaggcc
	********************************************************************
rat	(((...(((....((.(((((((..(((((.(((.....))))))))..))))))))).)))...)))	1.000 -34.80

rat

chromosome:20:5546429:5546496:1

intergenic

novel_lenNOK_loopOverlap_mirtron (39 loci)

block7451 [novel_lenNOK_loopOverlap_mirtron]

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

0.047

no

no

0.61/0.61

18/18/0.00

0.0

0.0

1

0

1

0

10

-3

3arm_loop

1

3

0.22

2

1

1

na

na

		reads	miRBase family seed
seed	-----------------------------------GACACUG--------------------	1	novel
		len	cloning frequencies
			T5S2
	----------------------------------TGACACTGCCATGTCCCC----------	18	1
rat	ggacaccttgtcccagcaagggcatagcccagtgTGACACTGCCATGTCCCCtaggacaacc
	**************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>	ENSRNOT00000027467 ENSRNOG00000032152 RGD1308952
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>	ENSRNOT00000027439 ENSRNOG00000032152 RGD1308952
rat	.......((((((.((...((((((.((..((((...)))))).)))))).)).))))))..	0.640 -19.50

rat

chromosome:10:15250464:15250525:-1

Same_strand|Boundary_non-coding|ENSRNOT00000027593|ENSRNOG00000032152 ## Same_strand|Intronic_coding|ENSRNOT00000027467|ENSRNOG00000032152 ## ENSRNOG00000032152|protein_coding|RGD1308952|Peroxisomal 2,4-dienoyl-CoA reductase (EC 1.3.1.34) (2,4-dienoyl-CoA reductase 2) (DCR-AKL) (pVI-AKL). [Source:UniProtKB/Swiss-Prot;Acc:Q9Z2M4]

block13720 [novel_lenNOK_loopOverlap_mirtron]

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

0.242

no

no

0.67/0.67

18/18/0.00

0.0

0.0

1

0

1

0

29

-2

3arm_loop

1

4

0.06

1

1

1

na

na

		reads	miRBase family seed
seed	----------------------------------------------------------CCCUGUG---------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	---------------------------------------------------------GCCCTGTGAGTGCTGTGG-----------------------------	18	1
rat	gcgacgccagggcccggggcgcagcaagaaggcaccccgcaacgtgctcacgcggatGCCCTGTGAGTGCTGTGGgggcagccggaggtctagggagggcttgc
	********************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000007267 ENSRNOG00000005450 RGD1565523_predicted
rat	((((.(((....(((.((((..........(((.(((((((..(((((((((.((....))))))))))))))))))...)))....)))).)))..)))))))	0.600 -47.24

rat

chromosome:10:31083817:31083920:-1

Same_strand|Boundary_coding|ENSRNOT00000007267|ENSRNOG00000005450 ## ENSRNOG00000005450|protein_coding|RGD1565523_predicted|

block81062 [novel_lenNOK_loopOverlap_mirtron]

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

0.045

no

no

0.50/0.50

18/18/0.00

0.0

0.0

1

0

1

0

24

-3

3arm_loop

1

2

0.28

2

1

1

na

na

		reads	miRBase family seed
seed	-------------------------------------------AGGUGGU----------------------------------	1	novel
		len	cloning frequencies
			T1S2
	------------------------------------------TAGGTGGTTCTTCCTTCC------------------------	18	1
rat	ggattctgacaaaactactctccgaagaggaattgacataggTAGGTGGTTCTTCCTTCCataggtttacattgtcagactcta
	************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000056416 ENSRNOG00000002764 LOC360568
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000003750 ENSRNOG00000002764 LOC360568
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000056415 ENSRNOG00000002764 LOC360568
rat	(((.((((((((....(((....(((((((((((.((........)))))))))).)))....))).....)))))))).))).	0.410 -22.00

rat

chromosome:10:62101414:62101497:1

Same_strand|Intronic_coding|ENSRNOT00000003750|ENSRNOG00000002764 ## ENSRNOG00000002764|protein_coding|LOC360568|

block211861 [novel_lenNOK_loopOverlap_mirtron]

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

0.181

no

no

0.32/0.32

25/25/0.00

0.0

0.0

1

0

1

0

22

-2

5arm_loop

1

3

0.28

3

1

1

na

na

		reads	miRBase family seed
seed	-----------------------CGUUUUC------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	----------------------TCGTTTTCTTTGTGGTTTTGATACA-------------------------------------------------------------	25	1
rat	ccatcctctgcattttcaaacaTCGTTTTCTTTGTGGTTTTGATACAtaggagtcatatcgccagatcatgaagatgcgaccaaaagacctgaagaagcgcctgatgg
	************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000038143 ENSRNOG00000000999 RGD1309707_predicted
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000031901 ENSRNOG00000000999 RGD1309707_predicted
rat	(((((...(((.((((((....((((..((((..(((((((((((...........)))))..))))))..)))).))))..........)))))).)))...)))))	0.970 -25.24

rat

chromosome:12:10029520:10029627:1

Same_strand|Intronic_non-coding|ENSRNOT00000038143|ENSRNOG00000000999 ## Same_strand|Intronic_coding|ENSRNOT00000031901|ENSRNOG00000000999 ## Same_strand|Boundary_non-coding|ENSRNOT00000038175|ENSRNOG00000000999 ## ENSRNOG00000000999|protein_coding|RGD1309707_predicted|similar to Smad ubiquitination regulatory factor 1 isoform 2 (LOC690516), mRNA [Source:RefSeq_dna;Acc:NM_001109598]

block221594 [novel_lenNOK_loopOverlap_mirtron]

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

0.087

no

no

0.47/0.47

19/19/0.00

0.0

0.0

2

0

1

0

34

-2

3arm_loop

1

2

0.21

2

2

1

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------CUGUGUU---------------------------------------------	2	novel
		len	cloning frequencies
			T2S1
	----------------------------------------------------------CCTGTGTTTTCTGTCTTCC----------------------------------	19	2
rat	gaggccagcctggactaaatgaagccgtcatggaaggcatggagcccattttctataaCCTGTGTTTTCTGTCTTCCagaggaacgagcacagagaccgcggctgcagctt
	***************************************************************************************************************
	-------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000059227 ENSRNOG00000001457 Rfc2
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000050059 ENSRNOG00000001454 Wbscr1
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000001978 ENSRNOG00000001454 Wbscr1
rat	.((((((((((((.((...((..((((((.(((((((((..((((.((............)).))))..)))))))))...)).)).)).)).)).))).)))))..))))	1.000 -37.00

rat

chromosome:12:23163127:23163237:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000001989|ENSRNOG00000001457 ## Same_strand|Intronic_coding|ENSRNOT00000050059|ENSRNOG00000001454 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000059227|ENSRNOG00000001457 ## ENSRNOG00000001454|protein_coding|Wbscr1|Eukaryotic translation initiation factor 4H (eIF-4H) (Williams-Beuren syndrome chromosomal region 1 protein homolog). [Source:UniProtKB/Swiss-Prot;Acc:Q5XI72] ## ENSRNOG00000001457|protein_coding|Rfc2|replication factor C 2 [Source:RefSeq_peptide;Acc:NP_446238]

block229857 [novel_lenNOK_loopOverlap_mirtron]

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

0.299

no

no

0.05/0.05

19/19/0.00

0.0

0.0

1

0

1

0

19

-3

3arm_loop

2

4

0.26

2

1

1

na

na

		reads	miRBase family seed
seed	-------------------------------AAAAAUA------------------------------	1	novel
		len	cloning frequencies
			T3S2
	------------------------------GAAAAATAATTTATTTTTA-------------------	19	1
rat	ggctcaggggggcaaaaatcaattgttttaGAAAAATAATTTATTTTTAtgttattggcgctttgcct
	********************************************************************
	++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++	ENSRNOT00000037995 ENSRNOG00000027887
rat	(((...((((.((((((((.((((((((.....)))))))).)))))).........)).))))))).	0.620 -11.90

rat

chromosome:12:36480415:36480482:1

Same_strand|Boundary_coding|ENSRNOT00000037995|ENSRNOG00000027887 ## ENSRNOG00000027887|protein_coding||

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other hairpins:

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