miR-Intess™

other hairpins

novel_multiarm_DicerNOK_randfoldOK (29 loci)

sblock9620 [novel_multiarm_DicerNOK_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

0.42/0.48

19/21/0.83

0.5 0.0

0.0 0.2

2 4

0 0

2 2

0 0

26 27

6 5

5arm 3arm

1 1

nd nd

0.05 0.05

1 1

6

2

-1

0

		reads	miRBase family seed
seed	---------------------------------------------------------------CUGCUUC----------------------------------------	4	novel
seed	----------------------------UUUCCAA---------------------------------------------------------------------------	1	novel
seed	---------------------------AUUUCCA----------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2
	--------------------------------------------------------------TCTGCTTCTGTCCTGGAAAT----------------------------	20	2	1
	--------------------------CATTTCCAAGACAGAAGCAG----------------------------------------------------------------	20	-	1
	---------------------------ATTTCCAAGACAGAAGCAG----------------------------------------------------------------	19	1	-
	--------------------------------------------------------------TCTGCTTCTGTCCTGGAAATG---------------------------	21	-	1
rat	ggctcagcagcagccaatcccagggcCATTTCCAAGACAGAAGCAGgacatgggtgacaggtTCTGCTTCTGTCCTGGAAATGgccctgggatcagctgctgctgagacc
	**************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000021197 ENSRNOG00000014986 Ube4b_predicted
rat	((((((((((((((..((((((((((((((((((.((((((((((((((.((.....)).)))))))))))))).))))))))))))))))))..)))))))))))).))	1.000 -92.60

rat

chromosome:5:166427171:166427280:-1

Same_strand|Intronic_coding|ENSRNOT00000021197|ENSRNOG00000014986 ## Same_strand|Boundary_non-coding|ENSRNOT00000055572|ENSRNOG00000014986 ## ENSRNOG00000014986|protein_coding|Ube4b_predicted|

novel_shortStem_mirtron_nonpairedHIGH (29 loci)

block125395 [novel_shortStem_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

0.057

no

no

0.65/0.65

23/23/1.00

0.0

0.0

1

0

1

0

0

2

3arm

1

2

0.32

2

1

1

na

na

		reads	miRBase family seed
seed	-------------------------------------------UGCUGUG---------------	1	novel
		len	cloning frequencies
			T3S1
	------------------------------------------CTGCTGTGCCCTTTTCCTCCCCC	23	1
rat	cggccacaggactgattgcaacatcagaatctcaacacatttCTGCTGTGCCCTTTTCCTCCCCC
	*****************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>	ENSRNOT00000002687 ENSRNOG00000001964 Cd47
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>	ENSRNOT00000050142 ENSRNOG00000001964 Cd47
rat	.((....((((..((..((.(((.(((((...........))))).)))))..)).))))..)).	0.910 -12.10

rat

chromosome:11:52114038:52114102:-1

Same_strand|Intronic_coding|ENSRNOT00000002687|ENSRNOG00000001964 ## ENSRNOG00000001964|protein_coding|Cd47|Leukocyte surface antigen CD47 precursor (Integrin-associated protein) (IAP). [Source:UniProtKB/Swiss-Prot;Acc:P97829]

block161396 [novel_shortStem_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

0.485

no

no

0.30/0.30

23/23/1.00

0.0

0.0

1

0

1

0

4

20

3arm

1

3

0.35

3

1

1

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------UCUCUUG-------------------	1	novel
		len	cloning frequencies
			T1S2
	----------------------------------------------------------------------------TTCTCTTGTCTTTCAAAAATCTG----	23	1
rat	cctggaagggattgaaaatcactttgagtgtacttgggatgactaaaaagagaatgctcacttggaatctcttcagTTCTCTTGTCTTTCAAAAATCTGtagg
	*******************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>	ENSRNOT00000002678 ENSRNOG00000001956 RGD1563278_predicted
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>	ENSRNOT00000059944 ENSRNOG00000001956 RGD1563278_predicted
rat	((((..(((..((((((..((....(((...(((.(((((..((((...(((....)))..)))).)))))...))).))).))..))))))...))).))))	0.400 -20.70

rat

chromosome:11:53122704:53122806:1

Same_strand|Intronic_coding|ENSRNOT00000002678|ENSRNOG00000001956 ## ENSRNOG00000001956|protein_coding|RGD1563278_predicted|

block190047 [novel_shortStem_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

0.303

no

no

0.55/0.55

20/20/1.00

0.0

0.0

1

0

1

0

4

5

5arm

1

4

0.35

3

1

1

na

na

		reads	miRBase family seed
seed	-----ACCUUCC------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	----TACCTTCCTTCCGTGTCTCC------------------------------------------	20	1
rat	gccaTACCTTCCTTCCGTGTCTCCtcaggagctgtacctgagctgggtggtggaagcccggaggca
	******************************************************************
	+++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000001961 ENSRNOG00000001442 Por
rat	(((...((...((((((...(((((((((.......))))))..)))...))))))...)).))).	0.940 -23.10

rat

chromosome:12:22080146:22080211:-1

Same_strand|Intronic_coding|ENSRNOT00000001961|ENSRNOG00000001442 ## ENSRNOG00000001442|protein_coding|Por|NADPH--cytochrome P450 reductase (EC 1.6.2.4) (CPR) (P450R). [Source:UniProtKB/Swiss-Prot;Acc:P00388]

block227229 [novel_shortStem_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

0.341

no

no

0.65/0.65

20/20/1.00

0.0

0.0

1

0

1

0

1

17

5arm

1

0

0.40

3

1

1

na

na

		reads	miRBase family seed
seed	--GACGCUU------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	-TGACGCTTGTCCCTCCCCAG------------------------------------------------------	20	1
rat	cTGACGCTTGTCCCTCCCCAGgctgctgtcaccaaggcccagcctcctcaccccagccggagatccccgggccag
	***************************************************************************
	++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000001334 ENSRNOG00000001004 NM_001108334.1
	++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000031011 ENSRNOG00000001004 NM_001108334.1
	++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000003126 ENSRNOG00000001004 NM_001108334.1
rat	(((..(((((...((((...(((((..((.....((((...))))....))..))))))))).....))))))))	0.540 -20.80

rat

chromosome:12:32698835:32698909:1

Same_strand|Intronic_coding|ENSRNOT00000003126|ENSRNOG00000001004 ## ENSRNOG00000001004|protein_coding|NM_001108334.1|nuclear receptor co-repressor 2 (predicted) (Ncor2_predicted), mRNA [Source:RefSeq_dna;Acc:NM_001108334]

block312918 [novel_shortStem_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

0.30/0.32

19/22/0.80

0.0

2.0

5

0

4

0

2

20

3arm

1

0

0.32

3

5

4

na

na

		reads	miRBase family seed
seed	---------------------------------------------------------------------CAUUACA----------------	5	novel
		len	cloning frequencies
			T1S2	T3S2	T4S2	T5S2
	--------------------------------------------------------------------TCATTACATCTCTTTTGTCTAG--	22	1	1	-	1
	--------------------------------------------------------------------TCATTACATCTCTTTTGTC-----	19	-	-	1	-
	--------------------------------------------------------------------TCATTACATCTCTTTTGTCT----	20	-	1	-	-
rat	atcattttaaaaatgtgtgatggggctagatgggtaaaaataaaaattttaagttaacgtatctgtgtTCATTACATCTCTTTTGTCTAGat
	********************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>	ENSRNOT00000003318 ENSRNOG00000002394 Tpr
rat	(((....(((((..((((((((((..((((((.((.((..(((.....)))..)).)).))))))..))))))))))...)))))....)))	0.940 -16.90

rat

chromosome:13:64693515:64693606:1

Same_strand|Intronic_coding|ENSRNOT00000003318|ENSRNOG00000002394 ## ENSRNOG00000002394|protein_coding|Tpr|translocated promoter region [Source:RefSeq_peptide;Acc:NP_001100655]

block379174 [novel_shortStem_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

0.432

no

no

0.62/0.62

21/21/1.00

0.0

0.0

1

0

1

0

4

29

5arm

1

1

0.38

3

1

1

na

na

		reads	miRBase family seed
seed	-----CUGACUG----------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----TCTGACTGCCCACCATCCCCA---------------------------------------------------------------------------------------------	21	1
rat	agctTCTGACTGCCCACCATCCCCAggacacgtatcaccaccactggagggaggggaatctgccttctggtgctcgatgtgaggtctgtaggaagacttgtggctcctcggatgtgct
	**********************************************************************************************************************
	+++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000032056 ENSRNOG00000024112 Dgkq
rat	(((.(((((..(((((...(((...((((.((((((..(((((..(((((.(((....))).))))))))))...))))))..))))...))).....)).)))...)))))...)))	0.800 -39.10

rat

chromosome:14:1605165:1605282:1

Same_strand|Intronic_coding|ENSRNOT00000032056|ENSRNOG00000024112 ## ENSRNOG00000024112|protein_coding|Dgkq|diacylglycerol kinase, theta Gene [Source:MGI (curated);Acc:Dgkq-001]

block645618 [novel_shortStem_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

0.304

no

no

0.50/0.52

21/22/1.00

0.0

0.5

2

0

2

0

4

13

3arm

2

1

0.48

3

2

2

na

na

		reads	miRBase family seed
seed	-------------------------------------------------------CUCCUGU------------------	2	novel
		len	cloning frequencies
			T1S2	T2S2
	------------------------------------------------------TCTCCTGTCTTACCCCTACCAA----	22	1	-
	------------------------------------------------------TCTCCTGTCTTACCCCTACCA-----	21	-	1
rat	gtaagagttgggttacaggccagcatcaacgggaagccactgttccttattgtgTCTCCTGTCTTACCCCTACCAAgacc
	********************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>	ENSRNOT00000022221 ENSRNOG00000016539 Rab24
rat	((....((.((((.(((((...(((.(((..((.(((....))).))..))))))..)))))...))))..))....)).	0.760 -18.90

rat

chromosome:17:15354106:15354185:1

Same_strand|Intronic_coding|ENSRNOT00000022221|ENSRNOG00000016539 ## ENSRNOG00000016539|protein_coding|Rab24|RAB24, member RAS oncogene family [Source:RefSeq_peptide;Acc:NP_001015023]

block733595 [novel_shortStem_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

0.901

no

no

0.57/0.57

23/23/1.00

0.0

0.0

1

0

1

0

1

27

5arm

1

0

0.52

3

1

1

na

na

		reads	miRBase family seed
seed	--CUGACUC----------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	-GCTGACTCATTCCCTATCCCCAG-------------------------------------------------------------------------------------------	23	1
rat	aGCTGACTCATTCCCTATCCCCAGagctctctcccggctgtggtggtggagaccttctcagcaactgtgaatggcgccgtggagggcagcactacgactggacgcttggatctgc
	*******************************************************************************************************************
	+++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000042287 ENSRNOG00000012852 Bin1
	+++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000017573 ENSRNOG00000012852 Bin1
	+++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000046655 ENSRNOG00000012852 Bin1
	+++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000051370 ENSRNOG00000012852 Bin1
	+++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000049898 ENSRNOG00000012852 Bin1
rat	.((.((..((...((..((...((.(((((((((((((.((.(((((.(((.....)))....)))....)).)))))).)))))).))).))..))..)).....))..)).))	0.780 -34.70

rat

chromosome:18:24868838:24868952:1

Same_strand|Intronic_coding|ENSRNOT00000042287|ENSRNOG00000012852 ## ENSRNOG00000012852|protein_coding|Bin1|Myc box-dependent-interacting protein 1 (Bridging integrator 1) (Amphiphysin-like protein) (Amphiphysin II). [Source:UniProtKB/Swiss-Prot;Acc:O08839]

block749563 [novel_shortStem_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

0.087

no

no

0.55/0.55

20/20/1.00

0.0

0.0

1

0

1

0

1

32

3arm

1

2

0.40

3

1

1

na

na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------------------AAGCAGG-------------	1	novel
		len	cloning frequencies
			T5S1
	--------------------------------------------------------------------------------------------TAAGCAGGGGCCACTATGTC-	20	1
rat	tgccatgggagcactggctactgctggtgtgtgttccccaacggcactgaggtccctcacaccaagagccgcgggcgccataactgcagtggTAAGCAGGGGCCACTATGTCa
	*****************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000025344 ENSRNOG00000018735 Cd74
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++	ENSRNOT00000025354 ENSRNOG00000018735 Cd74
rat	((.(((((..((.(((((((((((...((((.((.(((...((((.((..(((.......))).)).)))).))).))))))...))))))))...)))..))..))))).))	0.950 -44.20

rat

chromosome:18:56764482:56764594:1

Same_strand|Intronic_coding|ENSRNOT00000025344|ENSRNOG00000018735 ## ENSRNOG00000018735|protein_coding|Cd74|H-2 class II histocompatibility antigen gamma chain (MHC class II- associated invariant chain) (Ia antigen-associated invariant chain) (Ii) (CD74 antigen). [Source:UniProtKB/Swiss-Prot;Acc:P10247]

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other hairpins:

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