miR-Intess™

candidate novel miRNAs

miRNAunknown_randfoldOK (1 loci)

novel_cloningHIGH_multiarm_DicerOK_mirtron_randfoldOK_bulgeHIGH (1 loci)

sblock11004_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock11004_cand 5arm	1	0	0	0	0	0	1	0	0	0
sblock11004_cand 3arm	16	17	1	3	2	10	3	7	7	4
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock11004_cand 5arm	0.000	0	0	0	0	0	0.000	0	0	0
sblock11004_cand 3arm	0.001	0.001	0.000	0.000	0.000	0.001	0.000	0.000	0.000	0.000

sblock11004 [novel_cloningHIGH_multiarm_DicerOK_mirtron_randfoldOK_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

0.004

no

no

0.52/0.61

18/24/0.79

1.0 0.0 0.0

0.5 0.0 0.5

2 1 49

0 0 0

2 1 10

0 0 0

7 16 5

18 9 21

5arm 3arm 3arm

1 1 1

64 10 0

0.24 0.43 0.27

4 4 4

72

10

2

1

		reads	miRBase family seed
seed	--------------------------------------------------------------------------CUGUCCU-------------------	64	novel
seed	---------------------------------------------------------------------------UGUCCUU------------------	2	novel
seed	-------------------------------------------------------------------------UCUGUCC--------------------	1	novel
seed	--------------------------------------------------------------CAGCCAC-------------------------------	1	novel
seed	-----------------------------------------------------------------------CUUCUGU----------------------	1	novel
seed	----------GUGGGUA-----------------------------------------------------------------------------------	1	novel
seed	------------------------------------------------------------------------UUCUGUC---------------------	1	novel
seed	--------CAGUGGG-------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-------------------------------------------------------------------------TCTGTCCTTGTGACCCACCAG------	21	10	6	-	1	-	1	3	4	6	2
	-------------------------------------------------------------------------TCTGTCCTTGTGACCCACC--------	19	-	5	-	-	2	1	-	2	1	1
	-------------------------------------------------------------------------TCTGTCCTTGTGACCCACCA-------	20	4	3	-	-	-	5	-	-	-	-
	-------------------------------------------------------------------------TCTGTCCTTGTGACCCACCAGC-----	22	1	3	-	2	-	-	-	-	-	1
	--------------------------------------------------------------------------CTGTCCTTGTGACCCACC--------	18	-	-	1	-	-	-	-	-	-	-
	-------TCAGTGGGTACCTAGGACAGTG-----------------------------------------------------------------------	22	1	-	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------TCTTCTGTCCTTGTGACCC-----------	19	-	-	-	-	-	1	-	-	-	-
	-------------------------------------------------------------ACAGCCACCTCTTCTGTCCTTGT----------------	23	-	-	-	-	-	1	-	-	-	-
	---------AGTGGGTACCTAGGACAGTGG----------------------------------------------------------------------	21	-	-	-	-	-	-	1	-	-	-
	-----------------------------------------------------------------------CTTCTGTCCTTGTGACCCACCAGC-----	24	1	-	-	-	-	-	-	-	-	-
	--------------------------------------------------------------------------CTGTCCTTGTGACCCACCA-------	19	-	-	-	-	-	-	-	1	-	-
	------------------------------------------------------------------------TTCTGTCCTTGTGACCCACC--------	20	-	-	-	-	-	1	-	-	-	-
rat	tgcagggtcagtgggtacctaggacagtggtggtgctgaggctgccaggagactcaccctcacagccacctctTCTGTCCTTGTGACCCACCAGCtgagt
	****************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>	ENSRNOT00000017944 ENSRNOG00000013076 Csnk1e
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>	ENSRNOT00000018126 ENSRNOG00000013076 Csnk1e
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>	ENSRNOT00000018008 ENSRNOG00000013076 Csnk1e
rat	.((..(((..((((((....(((((((.((((((..(((((.((..((....)))).)))))..))))))....)))))))....))))))..)))..))	1.000 -47.90

rat

chromosome:7:117407655:117407754:-1

Same_strand|Boundary_coding|ENSRNOT00000017944|ENSRNOG00000013076 ## Same_strand|Intronic_coding|ENSRNOT00000017944|ENSRNOG00000013076 ## ENSRNOG00000013076|protein_coding|Csnk1e|casein kinase 1 epsilon [Source:RefSeq_peptide;Acc:NP_113805]

novel_cloningHIGH_multiarm_DicerOK_randfoldOK_bulgeHIGH (1 loci)

sblock3662_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock3662_cand 5arm	4	2	2	1	1	0	4	2	33	1
sblock3662_cand 3arm	0	0	0	0	0	0	0	0	2	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock3662_cand 5arm	0.000	0.000	0.000	0.000	0.000	0	0.000	0.000	0.002	0.000
sblock3662_cand 3arm	0	0	0	0	0	0	0	0	0.000	0

sblock3662 [novel_cloningHIGH_multiarm_DicerOK_randfoldOK_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

0.48/0.59

18/24/0.94

2.0 0.0 0.0 0.0

1.5 0.0 0.0 0.0

2 20 2 2

0 0 0 0

2 9 2 1

0 0 0 0

10 24 36 23

9 0 -12 1

5arm 5arm 5arm_loop_3arm 3arm

1 1 1 1

nd nd nd nd

0.27 0.50 0.70 0.59

4 6 6 6

52

9

1

3

Families

Member of family miR-129* (seed AGCCCUU): block1001252_cand, sblock3662_cand

		reads	miRBase family seed
seed	-------------------------ACACAGC--------------------------------------------------------------	27	novel
seed	---------------------GACUACA------------------------------------------------------------------	18	novel
seed	--------------------------------------------------AGCCCUU-------------------------------------	2	miR-129*
seed	-------------------------------------CCCAUCU--------------------------------------------------	2	novel
seed	-----------CCCAGCU----------------------------------------------------------------------------	1	novel
seed	----------------------ACUACAC-----------------------------------------------------------------	1	novel
seed	---------------GCUAAUG------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T4S1	T4S2	T5S1	T5S2
	------------------------TACACAGCACCTTCCCATCT--------------------------------------------------	20	-	2	1	1	-	2	1	20	-
	--------------------TGACTACACAGCACCTTCCCATCT--------------------------------------------------	24	2	-	-	-	1	-	1	2	1
	--------------------TGACTACACAGCACCTTCCCA-----------------------------------------------------	21	2	-	-	-	-	-	-	3	-
	--------------------TGACTACACAGCACCTTCCCATC---------------------------------------------------	23	-	-	-	-	-	-	-	3	-
	------------------------------------TCCCATCTACTTGGAGCCCT--------------------------------------	20	-	-	-	-	-	1	-	1	-
	-------------------------------------------------GAGCCCTTGGTGGTGTCAGACT-----------------------	22	-	-	-	-	-	-	-	2	-
	--------------------TGACTACACAGCACCTTCC-------------------------------------------------------	19	-	-	-	-	-	-	-	2	-
	---------------------GACTACACAGCACCTTCCCA-----------------------------------------------------	20	-	-	-	-	-	-	-	1	-
	--------------------TGACTACACAGCACCTTC--------------------------------------------------------	18	-	-	-	-	-	1	-	-	-
	--------------AGCTAATGACTACACAGCACC-----------------------------------------------------------	21	-	-	1	-	-	-	-	-	-
	----------TCCCAGCTAATGACTACACAGC--------------------------------------------------------------	22	-	-	-	-	-	-	-	1	-
rat	ggtggggagttcccagctaatgacTACACAGCACCTTCCCATCTacttggagcccttggtggtgtcagacttccttggctgggggttgctccca
	**********************************************************************************************
rat	((.(((.((..(((((((((.((....(((.((((......(((....)))......)))).)))......)).)))))))))..)).))))).	0.970 -38.10

rat

chromosome:12:44310844:44310937:1

intergenic

novel_cloningHIGH_randfoldOK_bulgeHIGH (1 loci)

block1600401_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1600401_cand 5arm	14	7	7	2	2	7	4	6	68	3
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1600401_cand 5arm	0.000	0.000	0.000	0.000	0.000	0.001	0.000	0.000	0.004	0.000

block1600401 [novel_cloningHIGH_randfoldOK_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

0.001

no

no

0.39/0.48

18/25/0.96

0.0

0.0

59

0

10

0

15

14

5arm

1

nd

0.27

4

120

10

na

na

Clusters

Located in cluster 55: block1600371_cand, block1600401_cand

		reads	miRBase family seed
seed	----------------CCUCUCG-------------------------------------------------------------------------------	110	novel
seed	--------------AUCCUCU---------------------------------------------------------------------------------	3	novel
seed	---------------UCCUCUC--------------------------------------------------------------------------------	3	novel
seed	---------------------CGAAUGU--------------------------------------------------------------------------	2	novel
seed	-----------------CUCUCGA------------------------------------------------------------------------------	1	novel
seed	-------------------CUCGAAU----------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	---------------TCCTCTCGAATGTTCACTCTCT-----------------------------------------------------------------	22	13	6	5	2	2	7	4	6	59	1
	-------------TATCCTCTCGAATGTTCACTCTCT-----------------------------------------------------------------	24	1	-	-	-	-	-	-	-	1	1
	--------------ATCCTCTCGAATGTTCACTCTCT-----------------------------------------------------------------	23	-	-	-	-	-	-	-	-	3	-
	---------------TCCTCTCGAATGTTCACTCTCTTCC--------------------------------------------------------------	25	-	-	1	-	-	-	-	-	1	-
	--------------------TCGAATGTTCACTCTCTTCC--------------------------------------------------------------	20	-	-	1	-	-	-	-	-	-	-
	------------------TCTCGAATGTTCACTCTCT-----------------------------------------------------------------	19	-	-	-	-	-	-	-	-	-	1
	--------------------TCGAATGTTCACTCTCTTCCAAA-----------------------------------------------------------	23	-	1	-	-	-	-	-	-	-	-
	---------------TCCTCTCGAATGTTCACT---------------------------------------------------------------------	18	-	-	-	-	-	-	-	-	1	-
	---------------TCCTCTCGAATGTTCACTCT-------------------------------------------------------------------	20	-	-	-	-	-	-	-	-	1	-
	----------------CCTCTCGAATGTTCACTCTCT-----------------------------------------------------------------	21	-	-	-	-	-	-	-	-	1	-
	---------------TCCTCTCGAATGTTCACTC--------------------------------------------------------------------	19	-	-	-	-	-	-	-	-	1	-
rat	gttttcagcccagtaTCCTCTCGAATGTTCACTCTCTtccaaatcttactggcagcagagggatgtggggaagtgggatgtggggggaagaggggctgaaga
	******************************************************************************************************
rat	.((((((((((....((((((((....((((((.((.((((.((((..(((....)))..)))).))))))))))))...))))))))....))))))))))	1.000 -46.30

rat

chromosome:4:164236907:164237008:-1

intergenic

novel_cloningHIGH_shortStem_randfoldOK (1 loci)

block1125000_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1125000_cand 3arm	1	1.000	2	2	13	10.667	3.333	7.333	1	2
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1125000_cand 3arm	0.000	0.000	0.000	0.000	0.001	0.001	0.000	0.000	0.000	0.000

block1125000 [novel_cloningHIGH_shortStem_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

0.39/0.50

18/23/0.86

0.0

0.0

53

0

10

0

3

10

3arm

3

nd

0.13

2

130

10

na

na

Families

Member of family novel228 (seed AUACCAG): block735436_novel, block1125000_cand

		reads	miRBase family seed
seed	-----------------------------------------------------------AUACCAG---------------------	110	novel
seed	------------------------------------------------------------UACCAGG--------------------	8	novel
seed	--------------------------------------------------------------CCAGGAU------------------	3	novel
seed	-------------------------------------------------------------ACCAGGA-------------------	3	novel
seed	----------------------------------------------------------UAUACCA----------------------	3	novel
seed	---------------------------------------------------------CUAUACC-----------------------	2	novel
seed	---------------------------------------------------------------CAGGAUG-----------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	----------------------------------------------------------TATACCAGGATGTCAGCATAGTT------	23	-	-	1	3	23	18	1	12	2	4
	----------------------------------------------------------TATACCAGGATGTCAGCATAGT-------	22	2	1	3	1	2	-	3	4	1	-
	----------------------------------------------------------TATACCAGGATGTCAGCATAG--------	21	1	1	-	1	3	1	2	2	-	-
	----------------------------------------------------------TATACCAGGATGTCAGCA-----------	18	-	-	1	-	2	2	2	1	-	-
	----------------------------------------------------------TATACCAGGATGTCAGCATA---------	20	-	-	1	-	-	2	1	1	-	1
	-----------------------------------------------------------ATACCAGGATGTCAGCATAGTT------	22	-	-	-	1	-	3	-	-	-	1
	----------------------------------------------------------TATACCAGGATGTCAGCAT----------	19	-	-	-	-	2	1	-	1	-	-
	---------------------------------------------------------CTATACCAGGATGTCAGC------------	18	-	-	-	-	1	2	-	-	-	-
	-----------------------------------------------------------ATACCAGGATGTCAGCATAG--------	20	-	1	-	-	1	-	-	-	-	-
	------------------------------------------------------------TACCAGGATGTCAGCATAGTT------	21	-	-	-	-	1	-	1	-	-	-
	-------------------------------------------------------------ACCAGGATGTCAGCATAGTT------	20	-	-	-	-	1	1	-	-	-	-
	--------------------------------------------------------------CCAGGATGTCAGCATAGTT------	19	-	-	-	-	-	1	-	-	-	-
	-----------------------------------------------------------ATACCAGGATGTCAGCATAGT-------	21	-	-	-	-	1	-	-	-	-	-
	--------------------------------------------------------ACTATACCAGGATGTCAGC------------	19	-	-	-	-	-	1	-	-	-	-
	-------------------------------------------------------------ACCAGGATGTCAGCATAGT-------	19	-	-	-	-	-	-	-	1	-	-
	------------------------------------------------------------TACCAGGATGTCAGCATAGT-------	20	-	-	-	-	1	-	-	-	-	-
	--------------------------------------------------------ACTATACCAGGATGTCAGCA-----------	20	-	-	-	-	1	-	-	-	-	-
rat	CAGCAGCCAATAGCTGGTTGGCATTCTGGGCCTGGTTCATGCCAACTCTGTTGTTAACTATACCAGGATGTCAGCATAGTTGCT---
human	------CCAATATCTGTTTGGCATTCTGAGCCTCATTTATGCCAGCTCTG-CACTGACTATACCAGGATGCCAAAATAGTTGAAAGG
	****** *** *********** ****  ** ****** *****    * ************** **  *******
	-----------------------------------------------------------------------------------------   -----	ENSRNOT00000032974 ENSRNOG00000027089 Ell2
rat	.((((((...((....(((((((((((((...(((((.((..((....))..)).)))))..))))))))))))).))))))))	0.770 -29.60
human	.((((.....((((((((((((.......((..(((.......) ))..))......))))))))))))...)))).....	0.861 -19.02

rat	chromosome:2:2747480:2747563:-1	Opposite_strand|Intronic_coding|ENSRNOT00000032974|ENSRNOG00000027089 ## ENSRNOG00000027089|protein_coding|Ell2|Ell2 protein (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q2NL49]
human	chromosome:8:112293008:112293087:-1	intergenic

novel_cloningOK_5varHIGH_mirtron_randfoldOK (1 loci)

block6229_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block6229_cand 3arm	2	2	0	1	1	0	1	1	2	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block6229_cand 3arm	0.000	0.000	0	0.000	0.000	0	0.000	0.000	0.000	0

block6229 [novel_cloningOK_5varHIGH_mirtron_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

0.57/0.62

20/24/1.00

1.1

1.1

10

0

7

0

25

6

3arm

1

0

0.24

2

10

7

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------AACCACC------------------------------------------	7	novel
seed	------------------------------------------------------------------------ACCACCC-----------------------------------------	2	novel
seed	----------------------------------------------------------------------------CCCUUGU-------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S2	T3S1	T4S1	T4S2	T5S1
	----------------------------------------------------------------------GAACCACCCTTGTCCCTTCCCTCA--------------------------	24	-	1	-	-	1	-	-
	-----------------------------------------------------------------------AACCACCCTTGTCCCTTCCCTCA--------------------------	23	-	-	-	-	-	-	2
	----------------------------------------------------------------------GAACCACCCTTGTCCCTTCCC-----------------------------	21	1	1	-	-	-	-	-
	----------------------------------------------------------------------GAACCACCCTTGTCCCTTCCCTC---------------------------	23	1	-	-	-	-	1	-
	----------------------------------------------------------------------GAACCACCCTTGTCCCTTCCCT----------------------------	22	-	-	1	-	-	-	-
	---------------------------------------------------------------------------ACCCTTGTCCCTTCCCTCAG-------------------------	20	-	-	-	1	-	-	-
rat	gtggttaactcctttcaaaatgcccagttgggaagggaggggtggggctgctaggtgggaatgactgctaGAACCACCCTTGTCCCTTCCCTCAGgggtgcacttggaaggcccgttcat
	************************************************************************************************************************
	>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000008537 ENSRNOG00000006460 RGD1304601
rat	((((......((((((((..(((((....((((((((((((((((..((....(((((......)))))))..)))))))..)))))))))....)))))...)))))))).....))))	0.980 -54.40

rat

chromosome:10:13409755:13409874:-1

Same_strand|Intronic_coding|ENSRNOT00000008537|ENSRNOG00000006460 ## ENSRNOG00000006460|protein_coding|RGD1304601|Putative N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (GlcNAc 6-P deacetylase) (Amidohydrolase domain-containing protein 2). [Source:UniProtKB/Swiss-Prot;Acc:Q5BJY6]

novel_cloningOK_Multihit_randfoldOK (1 loci)

block1795608_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1795608_cand 5arm	0	0	0.143	0	0.071	0.429	0	0	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1795608_cand 5arm	0	0	0.000	0	0.000	0.000	0	0	0	0

block1795608 [novel_cloningOK_Multihit_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

0.56/0.59

18/22/0.89

0.0

0.0

12

0

3

0

23

4

5arm

14

nd

0.27

2

18

3

na

na

Clusters

Located in cluster 60: block1795608_cand, block1795620_cand

Families

Member of family novel31 (seed GGGUCCU): block1795608_cand, block1795608_cand, block1795620_cand

		reads	miRBase family seed
seed	------------------------GGGUCCU---------------------------------------------------------------------------	9	novel
seed	---------------------------------------------------------------------------------GGGUCCU------------------	9	novel
		len	cloning frequencies
			T2S1	T3S1	T3S2
	--------------------------------------------------------------------------------TGGGTCCTTCAGGAGTCATGCC----	22	2	1	4
	-----------------------TGGGTCCTTCAGGAGTCATGCC-------------------------------------------------------------	22	2	1	4
	-----------------------TGGGTCCTTCAGGAGTCATGC--------------------------------------------------------------	21	-	-	1
	-----------------------TGGGTCCTTCAGGAGTCA-----------------------------------------------------------------	18	-	-	1
	--------------------------------------------------------------------------------TGGGTCCTTCAGGAGTCATGC-----	21	-	-	1
	--------------------------------------------------------------------------------TGGGTCCTTCAGGAGTCA--------	18	-	-	1
rat	gcatggtaggtccctgtgggaccTGGGTCCTTCAGGAGTCATGCCaggtaatgagaagcatggtaggtccctgtgggaccTGGGTCCTTCAGGAGTCATGCCgggt
	**********************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000023143 ENSRNOG00000017037 RGD1560468_predicted
rat	((.(((((((..((((.((((((..(((((..((((..((.(((((.((........)).)))))))..))))..)))))..)))))).))))..)).))))).))	1.000 -58.70

rat

chromosome:5:157734782:157734887:-1

Same_strand|Intronic_coding|ENSRNOT00000023143|ENSRNOG00000017037 ## ENSRNOG00000017037|protein_coding|RGD1560468_predicted| ## {Repeats: trf 11 33 0 class=trf}

novel_cloningOK_loopOverlap_randfoldOK (1 loci)

block605272_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block605272_cand 3arm	0	1	6	12	2	0	0	0	1	5
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block605272_cand 3arm	0	0.000	0.000	0.001	0.000	0	0	0	0.000	0.000

block605272 [novel_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

0.004

no

no

0.38/0.43

18/22/0.89

0.2

0.2

18

0

6

0

34

-5

3arm_loop

1

nd

0.30

3

27

6

na

na

Families

Member of family novel97 (seed UUCCGUG): block605272_cand, block2390508_cand

		reads	miRBase family seed
seed	-----------------------------------------------------------------UUCCGUG------------------------------------------------	21	novel
seed	------------------------------------------------------------------UCCGUGA-----------------------------------------------	6	novel
		len	cloning frequencies
			T1S2	T2S1	T2S2	T3S1	T5S1	T5S2
	----------------------------------------------------------------CTTCCGTGATGTATAACTGAGA----------------------------------	22	-	5	9	2	-	1
	-----------------------------------------------------------------TTCCGTGATGTATAACTGAG-----------------------------------	20	-	-	-	-	-	4
	-----------------------------------------------------------------TTCCGTGATGTATAACTGAGA----------------------------------	21	-	-	1	-	-	-
	----------------------------------------------------------------CTTCCGTGATGTATAACTGA------------------------------------	20	-	-	1	-	-	-
	----------------------------------------------------------------CTTCCGTGATGTATAACTGAG-----------------------------------	21	-	-	1	-	-	-
	----------------------------------------------------------------CTTCCGTGATGTATAACT--------------------------------------	18	-	1	-	-	-	-
	-----------------------------------------------------------------TTCCGTGATGTATAACTG-------------------------------------	18	1	-	-	-	-	-
	----------------------------------------------------------------CTTCCGTGATGTATAACTG-------------------------------------	19	-	-	-	-	1	-
rat	gtaaaaaccaataattttctgctgacaccccgtgagtcctgctcctttagtgttatacatggctCTTCCGTGATGTATAACTGAGAagagtataggaaggaaggcagagtggttgttaca
	************************************************************************************************************************
rat	((((.(((((......(((((((......((.....((((((((.(((...(((((((((.((......)).)))))))))..))).))))..)))).))..)))))))))))).)))).	0.560 -38.80

rat

chromosome:17:23606625:23606744:-1

intergenic

novel_cloningOK_mirtron_randfoldOK_nonpairedHIGH (1 loci)

block275562_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block275562_cand 3arm	11.500	7.500	0	0	0	0	0	1	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block275562_cand 3arm	0.000	0.000	0	0	0	0	0	0.000	0	0

block275562 [novel_cloningOK_mirtron_randfoldOK_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

0.003

no

no

0.48/0.52

18/22/0.90

0.3

0.5

15

0

3

0

19

8

3arm

1

0

0.40

3

21

3

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------CUGCCUU---------------------------------	16	novel
seed	------------------------------------------------------------------------UGCCUUC--------------------------------	5	novel
		len	cloning frequencies
			T1S1	T1S2	T4S2
	----------------------------------------------------------------------TCTGCCTTCTCCTTCCTATCA--------------------	21	2	4	-
	----------------------------------------------------------------------TCTGCCTTCTCCTTCCTATC---------------------	20	3	1	1
	----------------------------------------------------------------------TCTGCCTTCTCCTTCCTATCAG-------------------	22	2	1	-
	-----------------------------------------------------------------------CTGCCTTCTCCTTCCTATCAG-------------------	21	2	1	-
	----------------------------------------------------------------------TCTGCCTTCTCCTTCCTA-----------------------	18	1	1	-
	-----------------------------------------------------------------------CTGCCTTCTCCTTCCTATCA--------------------	20	2	-	-
rat	ccctagtagtttatcttgacataatttggagagaggaatggggagggagaaaccaacatagctttctcttTCTGCCTTCTCCTTCCTATCAGgtgatcatggtgactgggg
	***************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000058143 ENSRNOG00000007290 Atp1a2
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000009964 ENSRNOG00000007290 Atp1a2
rat	(((((((....((((.((((((....(((..((..(((.(((((((((((((..........))))))))))).)))))..))..)))....))).))).)))))))))))	0.990 -37.20

rat

chromosome:13:88266897:88267007:-1

Same_strand|Intronic_coding|ENSRNOT00000009964|ENSRNOG00000007290 ## ENSRNOG00000007290|protein_coding|Atp1a2|Sodium/potassium-transporting ATPase subunit alpha-2 precursor (EC 3.6.3.9) (Sodium pump subunit alpha-2) (Na(+)/K(+) ATPase alpha-2 subunit) (Na(+)/K(+) ATPase alpha(+) subunit). [Source:UniProtKB/Swiss-Prot;Acc:P06686]

novel_cloningOK_multiarm_DicerOK_5varHIGH_mirtron (1 loci)

sblock11098_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock11098_cand 5arm	0	0	0	0	0	1	4	0	0	0
sblock11098_cand 3arm	0	0	1	1	0	0	4	3	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock11098_cand 5arm	0	0	0	0	0	0.000	0.000	0	0	0
sblock11098_cand 3arm	0	0	0.000	0.000	0	0	0.000	0.000	0	0

sblock11098 [novel_cloningOK_multiarm_DicerOK_5varHIGH_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

0.065

no

no

0.50/0.60

18/22/0.71

0.2 1.1

1.6 0.8

5 9

0 0

2 4

0 0

8 8

22 26

5arm 3arm

1 1

76 0

0.14 0.26

1 2

14

5

1

2

Families

Member of family novel70 (seed CUGGGAC): sblock11098_cand, sblock2235_cand

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------CUCUUAC----------------------	6	novel
seed	---------CUGGGAC---------------------------------------------------------------------------------------------------	4	novel
seed	---------------------------------------------------------------------------------------UCUUACC---------------------	2	novel
seed	-------------------------------------------------------------------------------------ACUCUUA-----------------------	1	novel
seed	----------UGGGACU--------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T2S2	T3S2	T4S1	T4S2
	--------ACTGGGACTGAGTTGTGA-----------------------------------------------------------------------------------------	18	-	-	1	1	-
	--------------------------------------------------------------------------------------CTCTTACCTCCGTCCCACAG---------	20	-	1	-	1	-
	-------------------------------------------------------------------------------------ACTCTTACCTCCGTCCCACA----------	20	-	-	-	1	1
	--------ACTGGGACTGAGTTGTGAGTGA-------------------------------------------------------------------------------------	22	-	-	-	2	-
	-------------------------------------------------------------------------------------ACTCTTACCTCCGTCCCAC-----------	19	-	-	-	1	1
	------------------------------------------------------------------------------------CACTCTTACCTCCGTCCCACA----------	21	-	-	-	1	-
	-------------------------------------------------------------------------------------ACTCTTACCTCCGTCCCACAG---------	21	1	-	-	-	-
	-------------------------------------------------------------------------------------ACTCTTACCTCCGTCCCACAGC--------	22	-	-	-	-	1
	---------CTGGGACTGAGTTGTGAGTGA-------------------------------------------------------------------------------------	21	-	-	-	1	-
rat	gggcctggACTGGGACTGAGTTGTGAGTGAaagaagggaaggcggggcaggcagcagagcctgggggttcccttcaaactgcttCACTCTTACCTCCGTCCCACAGCaagaacct
	*******************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>	ENSRNOT00000055277 ENSRNOG00000036832 NP_001101588.1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000055276 ENSRNOG00000036832 NP_001101588.1
rat	((..((....((((((.(((.((.(((((((...((.(((((.(((.(((((......)))))....))))))))...))..))))))).)).))).)))))).....))..)).	0.970 -44.70

rat

chromosome:7:142261058:142261172:-1

Same_strand|Boundary_coding|ENSRNOT00000055277|ENSRNOG00000036832 ## Same_strand|Intronic_coding|ENSRNOT00000055277|ENSRNOG00000036832 ## ENSRNOG00000036832|protein_coding|NP_001101588.1|integrin alpha 5 [Source:RefSeq_peptide;Acc:NP_001101588]

novel_cloningOK_multiarm_DicerOK_loopOverlap_mirtron (1 loci)

sblock2505_cand

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock2505_cand 5arm	0	0	0	0	0	0	1	0	0	1
sblock2505_cand 3arm	2	0	0	0	2	0	1	0	3	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
sblock2505_cand 5arm	0	0	0	0	0	0	0.000	0	0	0.000
sblock2505_cand 3arm	0.000	0	0	0	0.000	0	0.000	0	0.000	0

sblock2505 [novel_cloningOK_multiarm_DicerOK_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

0.055

no

no

0.50/0.57

18/23/0.70

0.0 1.0

0.5 1.5

2 8

0 0

2 4

0 0

14 12

3 -2

5arm 3arm

1 1

32 0

0.20 0.26

2 2

10

5

2

2

Families

Member of family novel33 (seed UGCCUGG): block767192_cand, block1043276_cand, sblock2505_cand

		reads	miRBase family seed
seed	------------------------------------------------UGCCUGG-------------------------	6	novel
seed	---------------GAAACCA----------------------------------------------------------	2	novel
seed	-----------------------------------------GAGUCUG--------------------------------	1	novel
seed	-------------------------------------------------GCCUGGU------------------------	1	novel
		len	cloning frequencies
			T1S1	T3S1	T4S1	T5S1	T5S2
	-----------------------------------------------GTGCCTGGTCTTGTGTTCAG-------------	20	-	1	-	2	-
	-----------------------------------------------GTGCCTGGTCTTGTGTTC---------------	18	2	-	-	-	-
	--------------GGAAACCAAGGCCAGAGACAG---------------------------------------------	21	-	-	-	-	1
	--------------GGAAACCAAGGCCAGAGACA----------------------------------------------	20	-	-	1	-	-
	------------------------------------------------TGCCTGGTCTTGTGTTCAGA------------	20	-	-	1	-	-
	----------------------------------------TGAGTCTGTGCCTGGTCTTGTGT-----------------	23	-	-	-	1	-
	-----------------------------------------------GTGCCTGGTCTTGTGTTCA--------------	19	-	1	-	-	-
rat	ccttttgtcccaaaGGAAACCAAGGCCAGAGACAGtttccTGAGTCTGTGCCTGGTCTTGTGTTCAGAacccatctaagg
	********************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>	ENSRNOT00000004532 ENSRNOG00000003278 NP_001101771.1
rat	((((...........(((..(((((((((..((((.((....)).))))..)))))))))..)))...........))))	0.660 -23.55

rat

chromosome:10:92410178:92410257:-1

Same_strand|Boundary_coding|ENSRNOT00000004532|ENSRNOG00000003278 ## Same_strand|Intronic_coding|ENSRNOT00000004532|ENSRNOG00000003278 ## ENSRNOG00000003278|protein_coding|NP_001101771.1|mitogen-activated protein kinase kinase kinase 14 [Source:RefSeq_peptide;Acc:NP_001101771]

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candidate novel miRNAs:

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