miR-Intess: classification

other hairpins

miRNAunknown_rep_lenNOK_multiarm_DicerNOK (1 loci)

miRNAunknown_rep_lenNOK_multiarm_DicerNOK_Multihit (1 loci)

sblock11852 (miRNA) [miRNAunknown_rep_lenNOK_multiarm_DicerNOK_Multihit]

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
Ensembl miRNA	0.014	no	SINE,SINE/Alu	0.45/0.68	19/20/0.22	0.1 0.0	0.2 0.0	8 1	0 0	6 1	0 0	20 3	1 21	5arm 3arm	265 265	nd nd	0.25 0.30	3 4	9	7	18	16

		reads	miRBase family seed
seed	---------------------AGUUCGA----------------------------------------------------------------	7	novel
seed	----------------------GUUCGAG---------------------------------------------------------------	1	novel
seed	----------------------------------------------------------------------UACAUAG---------------	1	novel
		len	cloning frequencies
			T1S2	T2S1	T2S2	T3S1	T3S2	T5S1	T5S2
	--------------------GAGTTCGAGGCCAGCCTGG-----------------------------------------------------	19	1	2	1	2	-	1	-
	---------------------------------------------------------------------CTACATAGAGAAACCCTGTC---	20	-	-	-	-	-	-	1
	---------------------AGTTCGAGGCCAGCCTGGTC---------------------------------------------------	20	-	-	-	-	1	-	-
rat	gaaggcagacagatccctgtGAGTTCGAGGCCAGCCTGGTCtacagagggaattccaggacagccaggaCTACATAGAGAAACCCTGTCtca
	********************************************************************************************
	------------------------------------------------------------------------------------------------------	ENSRNOT00000037650 ENSRNOG00000025332 Cd109
	------------------------------------------------------------------------------------------------------	ENSRNOT00000037665 ENSRNOG00000025332 Cd109
	------------------------------------------------------------------------------------------------------	ENSRNOT00000037657 ENSRNOG00000025332 Cd109
	------------------------------------------------------------------------------------------------------	ENSRNOT00000057088 ENSRNOG00000025332 Cd109
	------------------------------------------------------------------------------------------------------	ENSRNOT00000057087 ENSRNOG00000025332 Cd109
	...>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063257 ENSRNOG00000041504
rat	((.(((((.....((.((((((((((..(((...((((((((......)))...)))))...))).))))).))))).))....))))))).	1.000 -33.00

rat

chromosome:8:83612177:83612268:-1

Opposite_strand|Intronic_coding|ENSRNOT00000037657|ENSRNOG00000025332 ## Same_strand|Exonic_non-coding|ENSRNOT00000063257|ENSRNOG00000041504 ## ENSRNOG00000041504|miRNA|| ## ENSRNOG00000025332|protein_coding|Cd109|CD109 antigen Gene [Source:MGI Symbol;Acc:MGI:2445221] ## {Repeats: B1_Mur4 61 82 1 class=SINE/Alu,B1_Mur4 -7 143 1 class=SINE,B1_Mur4 110 130 1 class=SINE/Alu}

miRNAunknown_rep_lenNOK_multiarm_DicerNOK_Multihit_randfoldOK (1 loci)

sblock11890 (miRNA) [miRNAunknown_rep_lenNOK_multiarm_DicerNOK_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
Ensembl miRNA	0.001	no	LTR/ERVK	0.32/0.39	18/19/0.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	6 10	4 3	5arm 3arm	152 306	nd nd	0.05 0.06	1 1	2	2	-1	-2

		reads	miRBase family seed
seed	-------------------------------------UACACAU--------------------	1	novel
seed	-------UGUGUGU--------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T4S2
	------ATGTGTGTGTGTATATGTA---------------------------------------	19	-	1
	------------------------------------ATACACATGCACACATAC----------	18	1	-
rat	atgattATGTGTGTGTGTATATGTAtatatatatatATACACATGCACACATACatacactcat
	****************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000014519 ENSRNOG00000010911 RGD1311530_predicted
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<....	ENSRNOT00000063206 ENSRNOG00000041453
rat	((((.(((((((((((((((.((((((((....)))))))).)))))))))))))))...))))	1.000 -28.80

rat

chromosome:8:108565675:108565738:-1

Same_strand|Intronic_coding|ENSRNOT00000014519|ENSRNOG00000010911 ## Opposite_strand|Exonic_non-coding|ENSRNOT00000063206|ENSRNOG00000041453 ## ENSRNOG00000010911|protein_coding|RGD1311530_predicted| ## ENSRNOG00000041453|miRNA|| ## {Repeats: RMER12 805 823 1 class=LTR/ERVK,RMER12 775 794 1 class=LTR/ERVK,dust 108565700 108565703 0 class=dust,(TATATG)n 2 51 -1 class=Simple_repeat,dust 108565714 108565721 0 class=dust}

miRNAunknown_rep_lenNOK_multiarm_Multihit_5varHIGH_loopOverlap_randfoldOK_nonpairedHIGH (1 loci)

sblock12020 (miRNA) [miRNAunknown_rep_lenNOK_multiarm_Multihit_5varHIGH_loopOverlap_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
Ensembl miRNA	0.001	no	SINE,SINE/MIR	0.33/0.47	19/24/0.60	0.0 0.0 1.7	0.0 0.0 0.7	1 1 3	0 0 0	1 1 2	0 0 0	36 48 0	-6 -21 27	5arm_loop_3arm 5arm_loop_3arm 3arm	127 196 291	nd nd nd	0.38 0.38 0.33	6 6 2	5	3	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------------------------------GUGUAUG-----------	2	novel
seed	-------------------------------------------------------------------------------------UAUGUGU----------------	1	novel
seed	-------------------------------------UGUAUGU----------------------------------------------------------------	1	miR-297
seed	-------------------------------------------------UGUGUGU----------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1	T5S2
	-----------------------------------------------------------------------------------------TGTGTATGTGTGTGTGTGC	19	2	-	-
	------------------------------------TTGTATGTGTGTATGTGTGTG---------------------------------------------------	21	-	1	-
	------------------------------------------------------------------------------------GTATGTGTGTATGTGTGTGTGT--	22	-	1	-
	------------------------------------------------ATGTGTGTGTATGTGTATGTATGT------------------------------------	24	-	-	1
rat	gtgtgtgtgcatgtgtgtgtgtgcatgtgtgtatatTTGTATGTGTGTATGTGTGTGTATGTGTATGTATGTgtgtgtgcatgtGTATGTGTGTATGTGTGTGTGTGC
	************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------	ENSRNOT00000010964 ENSRNOG00000008219 LOC315712
	----------------------------------------------------------------------------------------------------------------------	ENSRNOT00000058490 ENSRNOG00000008219 LOC315712
	----------------------------------------------------------------------------------------------------------------------	ENSRNOT00000058489 ENSRNOG00000008219 LOC315712
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.......	ENSRNOT00000063362 ENSRNOG00000041609
rat	(((..((..((((((..((..((((((((..(((((.((((((((..((((......))))..)))))))).)))))..))))))))..))..))))))..))..)))	1.000 -39.90

rat

chromosome:8:61849376:61849483:1

Opposite_strand|Intronic_coding|ENSRNOT00000010964|ENSRNOG00000008219 ## Same_strand|Exonic_non-coding|ENSRNOT00000063362|ENSRNOG00000041609 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000058488|ENSRNOG00000008219 ## Same_strand|Boundary_non-coding|ENSRNOT00000063362|ENSRNOG00000041609 ## ENSRNOG00000041609|miRNA|| ## ENSRNOG00000008219|protein_coding|LOC315712|Coiled-coil domain-containing protein 33. [Source:UniProtKB/Swiss-Prot;Acc:Q5XIR4] ## {Repeats: trf 18 42 0 class=trf,dust 61849382 61849403 0 class=dust,(TG)n 1 178 1 class=Simple_repeat,dust 61849367 61849391 0 class=dust,(TG)n 155 178 1 class=Simple_repeat,trf 54 78 0 class=trf,trf 69 90 0 class=trf,dust 61849331 61849355 0 class=dust,MIRm -100 162 -1 class=SINE,(TG)n 107 128 1 class=Simple_repeat,MIRm 161 161 -1 class=SINE/MIR,(TG)n 119 143 1 class=Simple_repeat}

miRNAunknown_rep_lenNOK_nonpairedHIGH_bulgeHIGH (1 loci)

block3196885 (miRNA) [miRNAunknown_rep_lenNOK_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
Ensembl miRNA	0.461	no	SINE,SINE/Alu	0.44/0.45	18/20/0.25	0.0	0.5	4	0	3	0	11	10	5arm	1	nd	0.35	4	4	3	na	na

		reads	miRBase family seed
seed	------------GGUCUGA----------------------------------------------------------------	4	novel
		len	cloning frequencies
			T1S1	T4S1	T4S2
	-----------TGGTCTGAAAGTCAGAGA------------------------------------------------------	18	-	1	2
	-----------TGGTCTGAAAGTCAGAGATC----------------------------------------------------	20	1	-	-
rat	gtagattatgcTGGTCTGAAAGTCAGAGATCctcctgcctctgcctcccgagtgctgggattaaaggcttgcaccaccactgc
	***********************************************************************************
	..................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063396 ENSRNOG00000041643
rat	((((....((.((((....(((((...((((((...(((((........))).)).))))))...)))))..)))).))))))	0.850 -21.80

rat

chromosome:X:160347494:160347576:1

Same_strand|Boundary_non-coding|ENSRNOT00000063396|ENSRNOG00000041643 ## ENSRNOG00000041643|miRNA|| ## {Repeats: B1_Rn 60 80 -1 class=SINE/Alu,B1_Rn -5 143 -1 class=SINE}

miRNAunknown_rep_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH (1 loci)

block2937844 (miRNA) [miRNAunknown_rep_lenNOK_shortStem_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
Ensembl miRNA	0.096	no	SINE,SINE/B2	0.42/0.42	19/19/0.00	0.0	0.0	1	0	1	0	1	33	5arm	2	nd	0.47	4	1	1	na	na

		reads	miRBase family seed
seed	--CAGAAAA-------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	-CCAGAAAAGGTGTTGGATT--------------------------------------------------------------------------------	19	1
rat	gCCAGAAAAGGTGTTGGATTctccagagctggaattacaggcagttttaagccaaatggttgctgtgagtagaactttggtcctcccaacactgttaagc
	****************************************************************************************************
	>>>>>>>>>>....................................................................................................	ENSRNOT00000062968 ENSRNOG00000041215
rat	((..((...((((((((.....((((((......((((..(((((....((((....)))))))))..))))..)))))).....)))))))).))..))	0.800 -28.30

rat

chromosome:X:13226990:13227089:1

Same_strand|Boundary_non-coding|ENSRNOT00000062968|ENSRNOG00000041215 ## ENSRNOG00000041215|miRNA|| ## {Repeats: B3A -48 150 -1 class=SINE,B3A 123 142 -1 class=SINE/B2}

miRNAunknown_rep_randfoldOK (1 loci)

block1140691 (miRNA) [miRNAunknown_rep_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
Ensembl miRNA	0.001	no	LINE,LINE/CR1	0.36/0.36	22/22/1.00	0.0	0.0	2	0	2	0	28	4	3arm	1	nd	0.09	1	2	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------GUAACUG------------------------------------------	2	novel
		len	cloning frequencies
			T2S2	T5S2
	----------------------------------------------------------AGTAACTGGTTGAACAACTGTA----------------------------	22	1	1
rat	gtttccaactttgcaccctttgggttcagttgttcaacaggttacaattagttagattAGTAACTGGTTGAACAACTGTAtccaaagagtacagattactagggagat
	************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------	ENSRNOT00000015138 ENSRNOG00000011099 NM_001113328.1
	..............<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<.......................	ENSRNOT00000062187 ENSRNOG00000040434
rat	((((((...((((.((.((((((((.((((((((((((.((((((((((.....)))).)))))).)))))))))))).)))))))).)).)))).......))))))	0.970 -44.50

rat

chromosome:2:40714098:40714205:-1

Opposite_strand|Intronic_coding|ENSRNOT00000015138|ENSRNOG00000011099 ## Opposite_strand|Exonic_non-coding|ENSRNOT00000062187|ENSRNOG00000040434 ## ENSRNOG00000040434|miRNA|| ## ENSRNOG00000011099|protein_coding|NM_001113328.1|phosphodiesterase 4D, cAMP specific (Pde4d), transcript variant 1, mRNA [Source:RefSeq_dna;Acc:NM_001113328] ## {Repeats: L3 3452 3474 1 class=LINE/CR1,L3 -901 3588 1 class=LINE}

miRNAunknown_shortStem (1 loci)

block1786309 (miRNA) [miRNAunknown_shortStem]

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
Ensembl miRNA	0.070	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	2	25	5arm	3	nd	0.30	3	1	1	na	na

		reads	miRBase family seed
seed	---CAUCUGG----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	--GCATCTGGCATTGTGGTTCC----------------------------------------------------------------------	20	1
rat	tgGCATCTGGCATTGTGGTTCCtgcatgaaaacagtggccggcggggcctggacctacaataccacttctgcagtcacagtgaagtctgcca
	********************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000050705 ENSRNOG00000030438 LOC689401
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>......	ENSRNOT00000054580 ENSRNOG00000036472
rat	.((((.((..((((((((...(((((.((....(((((......(((......)))......)))))))))))))))))))).))..)))).	0.700 -31.50

rat

chromosome:5:146450651:146450742:-1

Same_strand|Exonic_non-coding|ENSRNOT00000054580|ENSRNOG00000036472 ## Same_strand|Exonic_coding|ENSRNOT00000050705|ENSRNOG00000030438 ## ENSRNOG00000036472|miRNA|| ## ENSRNOG00000030438|protein_coding|LOC689401|60S ribosomal protein L37a. [Source:UniProtKB/Swiss-Prot;Acc:P61515]

novel_5varHIGH_loopOverlap_randfoldOK_bulgeHIGH (1 loci)

block1848593 [novel_5varHIGH_loopOverlap_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	0.003	no	no	0.48/0.67	19/22/0.86	9.1	8.7	7	0	1	0	10	-5	3arm	1	nd	0.27	4	7	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------CAGGAUC--------------------------	1	novel
seed	--------------------------------------------------------UCAGGAU---------------------------	1	novel
seed	------------------------------------------------------CUUCAGG-----------------------------	1	novel
seed	----------------------------------------------------------AGGAUCU-------------------------	1	novel
seed	------------------------------------------------------------GAUCUGU-----------------------	1	novel
seed	-------------------------------------------------GCCGUCU----------------------------------	1	novel
seed	---------------------------------------------AGUUGCC--------------------------------------	1	miR-543
		len	cloning frequencies
			T5S1
	-----------------------------------------------------------GGATCTGTGAGGGACCGGGTG----------	21	1
	--------------------------------------------------------TCAGGATCTGTGAGGGACC---------------	19	1
	------------------------------------------------TGCCGTCTTCAGGATCTGTGAG--------------------	22	1
	--------------------------------------------TAGTTGCCGTCTTCAGGATCT-------------------------	21	1
	-----------------------------------------------------TCTTCAGGATCTGTGAGGGAC----------------	21	1
	---------------------------------------------------------CAGGATCTGTGAGGGACCGG-------------	20	1
	-------------------------------------------------------TTCAGGATCTGTGAGGGACC---------------	20	1
rat	aaccctgctttaagggacaatgcagagtgactgaggaggatggcTAGTTGCCGTCTTCAGGATCTGTGAGGGACCGGGTGagcccagggt
	******************************************************************************************
rat	.(((((((((...((......(((((....((...(((((((((.....))))))))).)).)))))......))....))))..)))))	0.580 -34.10

rat

chromosome:5:79249484:79249573:1

intergenic

novel_5varHIGH_mirtron_bulgeHIGH (1 loci)

block1099057 [novel_5varHIGH_mirtron_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	0.042	no	no	0.42/0.45	22/24/1.00	1.5	2.5	2	0	1	0	28	1	5arm	1	0	0.29	4	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------CCUUGAC----------------------------------------------------------------------	1	novel
seed	--------------------------------UGACUCA-------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	-------------------------------TTGACTCATCACTTTTCTCCGTAG---------------------------------------------------	24	1
	----------------------------CCCTTGACTCATCACTTTTCTC--------------------------------------------------------	22	1
rat	tccctcctcactaggaggctccacccatCCCTTGACTCATCACTTTTCTCCGTAGggtccttatggacggcctgggtacaagggtgaaattggcttccctggacgg
	**********************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++	ENSRNOT00000045315 ENSRNOG00000001229 Col18a1
rat	.((.(((......(((((((.....((.(((((((((((...((....((((((((...)))))))).))..))))).)))))))).....)))))))..))).))	0.690 -35.00

rat

chromosome:20:11968337:11968442:1

novel_5varHIGH_randfoldOK_nonpairedHIGH (1 loci)

block2140737 [novel_5varHIGH_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	0.008	no	no	0.55/0.57	20/21/1.00	3.0	2.7	3	0	1	0	7	2	3arm	1	nd	0.35	3	3	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------AGGACAU--------------------------	1	novel
seed	----------------------------------------------------GCUAGCA-------------------	1	novel
seed	-----------------------------------------------GACAUGC------------------------	1	novel
		len	cloning frequencies
			T5S1
	---------------------------------------------------TGCTAGCAGCAGAGGAACTG-------	20	1
	----------------------------------------------GGACATGCTAGCAGCAGAGGA-----------	21	1
	--------------------------------------------CAGGACATGCTAGCAGCAGAG-------------	21	1
rat	gctcactctcctgacatactgccagccctgggctccctcacaccCAGGACATGCTAGCAGCAGAGGAACTGgggagca
	******************************************************************************
rat	((((.(((((((......((((.(((((((((..........))))))....))).))))...))))...))))))).	1.000 -29.30