miR-Intess: classification

noncloned miRBase miRNAs

miRBaseNonMapped_rep_Multihit_randfoldOK (5 loci)

rno-mir-297

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-297 3arm	0	0	0	0	0.013	0	0	0	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-297 3arm	0	0	0	0	0.000	0	0	0	0	0

block17610 (miRBaseNonMapped rno-mir-297) [miRBaseNonMapped_rep_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
miRBaseNonMapped rno-mir-297	0.001	no	LTR/ERVK	0.39/0.39	23/23/1.00	nd	nd	0	0	0	0	8	20	5arm	13	nd	0.17	2	0	0	na	na

		reads	miRBase family seed
seed	---------UGUAUGU---------------------------------------------------------------------------------------------	0	miR-297
		len	cloning frequencies

rno-miR-297	--------ATGTATGTGTGCATGTATGCATG------------------------------------------------------------------------------	23
rat	gtgtgtgcATGTATGTGTGCATGTATGCATGtatgtacacacgagtgtgcatgtgtgcacacacgtgagtatgtgcatgtgtgtacatgtgtacaacttataacaacac
	*************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------	ENSRNOT00000036822 ENSRNOG00000026596 RGD1566120_predicted
rat	((((((....((.((((..(((((((((((((((((((.((((.(((((((....))))))).)))).))))))))))))..)))))))..)))))).....))).)))	0.510 -52.00

rat

chromosome:10:39801526:39801634:-1

Opposite_strand|Intronic_coding|ENSRNOT00000036822|ENSRNOG00000026596 ## ENSRNOG00000026596|protein_coding|RGD1566120_predicted| ## {Repeats: trf 57 62 0 class=trf,trf 1 20 0 class=trf,trf 6 29 0 class=trf,RMER12 817 840 1 class=LTR/ERVK,trf 24 47 0 class=trf,dust 39801604 39801627 0 class=dust,(CATA)n 3 58 -1 class=Simple_repeat}

block681390 (miRBaseNonMapped rno-mir-297) [miRBaseNonMapped_rep_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
miRBaseNonMapped rno-mir-297	0.001	no	LTR/ERVK	0.39/0.39	23/23/1.00	nd	nd	0	0	0	0	21	13	3arm	13	nd	0.17	2	0	0	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------UGUAUGU------------------------------------	0	miR-297
		len	cloning frequencies

rno-miR-297	----------------------------------------------------------------------------ATGTATGTGTGCATGTATGCATG---------------------	23
rat	tgcacgtgtatgtatgtgtgcactgtgtatgtgtgcacgtgtgtatgtgcacatgtatgtgtgcatgtgtgtgcacATGTATGTGTGCATGTATGCATGtgcatatgtatgtttgtgcac
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000002513 ENSRNOG00000022021 NP_001099595.1
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000038823 ENSRNOG00000022021 NP_001099595.1
rat	((((((...((((((((((((((.(((((((..((((((..((((((((((((..((((....))))..))))))))))))..))))))..))))))))))))))))))))).)))))).	0.620 -70.00

rat

chromosome:17:92840435:92840554:1

Same_strand|Intronic_coding|ENSRNOT00000002513|ENSRNOG00000022021 ## ENSRNOG00000022021|protein_coding|NP_001099595.1|sperm associated antigen 6 [Source:RefSeq_peptide;Acc:NP_001099595] ## {Repeats: dust 92840477 92840500 0 class=dust,(TATG)n 4 114 1 class=Simple_repeat,trf 32 55 0 class=trf,trf 1 20 0 class=trf,RLTR21 823 846 1 class=LTR/ERVK,trf 1 17 0 class=trf}

block1071645 (miRBaseNonMapped rno-mir-297) [miRBaseNonMapped_rep_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
miRBaseNonMapped rno-mir-297	0.001	no	LTR/ERVK	0.39/0.39	23/23/1.00	nd	nd	0	0	0	0	8	25	5arm	13	nd	0.09	2	0	0	na	na

		reads	miRBase family seed
seed	---------UGUAUGU------------------------------------------------------------------------------------------------------	0	miR-297
		len	cloning frequencies

rno-miR-297	--------ATGTATGTGTGCATGTATGCATG---------------------------------------------------------------------------------------	23
rat	atatgtatATGTATGTGTGCATGTATGCATGcacatgtgtgtacatatttgtgtatgtgtgtatatgtgtatatgtatatgtatgtgtgtatgtatgcgtgcacatgtgtgtacatat
	**********************************************************************************************************************
rat	((((((((((..((((((((((((((((((((((((((((((((((((.(((((((....)))))))...))))))))))..))))))))))))))))))))))))))))))))))))	0.980 -57.20

rat

chromosome:20:21055199:21055316:-1

intergenic ## {Repeats: RMER12 914 937 1 class=LTR/ERVK,dust 21055286 21055309 0 class=dust,trf 312 335 0 class=trf,trf 264 287 0 class=trf,(CATATA)n 1 300 -1 class=Simple_repeat}

block1421463 (miRBaseNonMapped rno-mir-297) [miRBaseNonMapped_rep_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
miRBaseNonMapped rno-mir-297	0.001	no	LTR/ERVK	0.39/0.39	23/23/1.00	nd	nd	0	0	0	0	30	4	3arm	13	nd	0.17	2	0	0	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------UGUAUGU---------------------------------------------	0	miR-297
		len	cloning frequencies

rno-miR-297	-----------------------------------------------------------------ATGTATGTGTGCATGTATGCATG------------------------------	23
rat	tgtgcttgtgtgtgcacatatgtgcatgtgtgtacatgtttgtgcacgtgtgtacacctgtgtgtATGTATGTGTGCATGTATGCATGtgagtgcatgtgtgtgtgtatgtgtgttca
	**********************************************************************************************************************
rat	((.((.((..((..(((((((((((((((((((((((((....(((((((..(((((....)))))..)))))))))))))))))))....)))))))))))))..))..)).)).))	0.930 -53.40

rat

chromosome:3:154036000:154036117:-1

intergenic ## {Repeats: (CA)n 2 117 -1 class=Simple_repeat,trf 28 51 0 class=trf,RLTR21 817 840 1 class=LTR/ERVK,dust 154036030 154036053 0 class=dust,trf 17 40 0 class=trf}

block2620432 (miRBaseNonMapped rno-mir-297) [miRBaseNonMapped_rep_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
miRBaseNonMapped rno-mir-297	0.001	no	LTR/ERVK	0.39/0.39	23/23/1.00	nd	nd	0	0	0	0	9	22	3arm	13	nd	0.09	2	0	0	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------------------UGUAUGU------------------------	0	miR-297
		len	cloning frequencies

rno-miR-297	-----------------------------------------------------------------------------ATGTATGTGTGCATGTATGCATG---------	23
rat	tatgtatgtgtgtatatatgcacatatatgtacatctgtgtatctatgcatatatatgcatatgtgtatataaacgtATGTATGTGTGCATGTATGCATGtatgcatgt
	*************************************************************************************************************
rat	((((((((..(((((((((((((((((((((((...(((((((.(((((((....)))))))...)))))))...)))))))))))))))))))))))..)))))))).	0.730 -52.90

rat

chromosome:9:76837097:76837205:1

intergenic ## {Repeats: (TATG)n 4 171 1 class=Simple_repeat,dust 76837062 76837078 0 class=dust,trf 1 8 0 class=trf,trf 10 33 0 class=trf,RMER12 845 868 1 class=LTR/ERVK}

miRBaseNonMapped_Multihit_randfoldOK (2 loci)

block200189 (miRBaseNonMapped rno-mir-297) [miRBaseNonMapped_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
miRBaseNonMapped rno-mir-297	0.001	no	no	0.39/0.39	23/23/1.00	nd	nd	0	0	0	0	5	27	5arm	13	nd	0.17	2	0	0	na	na

		reads	miRBase family seed
seed	------UGUAUGU---------------------------------------------------------------------------------------------------------	0	miR-297
seed	--------------------------------------------------------------------------------------------UGUAUGU-------------------	0	miR-297
		len	cloning frequencies

rno-miR-297	-----ATGTATGTGTGCATGTATGCATG------------------------------------------------------------------------------------------	23
rno-miR-297	-------------------------------------------------------------------------------------------ATGTATGTGTGCATGTATGCATG----	23
rat	tatgtATGTATGTGTGCATGTATGCATGcatctatgtatgtatgtgcatgcatgtgtgtacatgtatgtgtgcatgcatgtatgtggaagtATGTATGTGTGCATGTATGCATGcata
	**********************************************************************************************************************
rat	((((((((((((..((((..(((((((((.(((((((((((((((((((((((((....))))))))))..)))))))..)))))))).)))))))))..))))..))))))))))))	0.970 -63.60

rat

chromosome:12:38433455:38433572:-1

intergenic ## {Repeats: dust 38433459 38433482 0 class=dust,(CATA)n 52 75 -1 class=Simple_repeat,trf 1 24 0 class=trf,trf 56 79 0 class=trf,(CATA)n 4 171 -1 class=Simple_repeat}

block200190 (miRBaseNonMapped rno-mir-297) [miRBaseNonMapped_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
miRBaseNonMapped rno-mir-297	0.001	no	no	0.39/0.39	23/23/1.00	nd	nd	0	0	0	0	5	27	5arm	13	nd	0.17	2	0	0	na	na

		reads	miRBase family seed
seed	------UGUAUGU---------------------------------------------------------------------------------------------------------	0	miR-297
seed	--------------------------------------------------------------------------------------------UGUAUGU-------------------	0	miR-297
		len	cloning frequencies

rno-miR-297	-----ATGTATGTGTGCATGTATGCATG------------------------------------------------------------------------------------------	23
rno-miR-297	-------------------------------------------------------------------------------------------ATGTATGTGTGCATGTATGCATG----	23
rat	tatgtATGTATGTGTGCATGTATGCATGcatctatgtatgtatgtgcatgcatgtgtgtacatgtatgtgtgcatgcatgtatgtggaagtATGTATGTGTGCATGTATGCATGcata
	**********************************************************************************************************************
rat	((((((((((((..((((..(((((((((.(((((((((((((((((((((((((....))))))))))..)))))))..)))))))).)))))))))..))))..))))))))))))	0.970 -63.60

rat

chromosome:12:38433455:38433572:-1

intergenic ## {Repeats: trf 142 165 0 class=trf,dust 38433545 38433568 0 class=dust,trf 87 110 0 class=trf,(CATA)n 138 161 -1 class=Simple_repeat,(CATA)n 4 171 -1 class=Simple_repeat}

miRBaseNonMapped_rep_Multihit_loopOverlap_randfoldOK (1 loci)

block1214608 (miRBaseNonMapped rno-mir-297) [miRBaseNonMapped_rep_Multihit_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
miRBaseNonMapped rno-mir-297	0.001	no	LTR/ERVK	0.39/0.39	23/23/1.00	nd	nd	0	0	0	0	33	-3	3arm_loop	13	nd	0.22	2	0	0	na	na

		reads	miRBase family seed
seed	------------------------------------------------------UGUAUGU------------------------------------------------	0	miR-297
		len	cloning frequencies

rno-miR-297	-----------------------------------------------------ATGTATGTGTGCATGTATGCATG---------------------------------	23
rat	gggtatcaagcatgtatgtgtgtgcgcgcatgtatgcatgtgtgtatgggtgtATGTATGTGTGCATGTATGCATGatgaatgtacatgcacatgcatgcatctaccta
	*************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------	ENSRNOT00000020267 ENSRNOG00000015029 Dbt
rat	(((((....(((((((((((((((..((((((((((((((((..((((........))))..)))))))))))))).....))..)))))))))))))))...))))).	0.810 -50.70

rat

chromosome:2:212769353:212769461:-1

Opposite_strand|Intronic_coding|ENSRNOT00000020267|ENSRNOG00000015029 ## ENSRNOG00000015029|protein_coding|Dbt|dihydrolipoamide branched chain transacylase E2 [Source:RefSeq_peptide;Acc:NP_445764] ## {Repeats: RMER12 811 834 1 class=LTR/ERVK,(CATA)n 3 75 -1 class=Simple_repeat,dust 212769386 212769409 0 class=dust}

miRBaseNonMapped_rep_Multihit_loopOverlap_randfoldOK_bulgeHIGH (1 loci)

block2536762 (miRBaseNonMapped rno-mir-297) [miRBaseNonMapped_rep_Multihit_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
miRBaseNonMapped rno-mir-297	0.001	no	LTR/ERVK	0.39/0.39	23/23/1.00	nd	nd	0	0	0	0	40	-4	5arm_loop_3arm	13	nd	0.26	4	0	0	na	na

		reads	miRBase family seed
seed	-----------------------------------------UGUAUGU------------------------------------------------------------------------	0	miR-297
		len	cloning frequencies

rno-miR-297	----------------------------------------ATGTATGTGTGCATGTATGCATG---------------------------------------------------------	23
rat	gtatatatgtatgtgtatacgcgtatatctgtgtgtgaatATGTATGTGTGCATGTATGCATGtgtatgtgtgtatatgcgtttgtatgtgcgtgtatgtgtattgtgtatatatgtatg
	************************************************************************************************************************
rat	(((((((((((..((.((((((((((((..(((..((...(((((((((..((((((((....))))))))..)))))))))...))..)))))))))))))))))..))))))))))).	0.990 -45.80

rat

chromosome:9:88522108:88522227:-1

intergenic ## {Repeats: (CATA)n 1 180 -1 class=Simple_repeat,dust 88522165 88522188 0 class=dust,RLTR21 1215 1238 1 class=LTR/ERVK,(CA)n 1 92 -1 class=Simple_repeat}

miRBaseNonMapped_rep_Multihit_shortStem_randfoldOK (1 loci)

block1802172 (miRBaseNonMapped rno-mir-297) [miRBaseNonMapped_rep_Multihit_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
miRBaseNonMapped rno-mir-297	0.001	no	SINE,SINE/B2	0.39/0.39	23/23/1.00	nd	nd	0	0	0	0	0	34	3arm	13	nd	0.00	0	0	0	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------------------------------------UGUAUGU---------------	0	miR-297
		len	cloning frequencies

rno-miR-297	-----------------------------------------------------------------------------------------------ATGTATGTGTGCATGTATGCATG	23
rat	catgtatatatgtacacatgtatgtgcgtgtgtacttgtgtatgtgcatgtgcattcgtatatgtgcatgtatgtgtgtgtgcgtgtatgtatgtATGTATGTGTGCATGTATGCATG
	**********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000055617 ENSRNOG00000013498 Pex14
rat	((((((((((((((((((..((((((((((..(((.((..((((((((((..(((......)))..)))))))....)))..)).)))..))))))))))))))))))))))))))))	0.850 -57.10

rat

chromosome:5:166097074:166097191:-1

Same_strand|Intronic_coding|ENSRNOT00000055617|ENSRNOG00000013498 ## Same_strand|Boundary_non-coding|ENSRNOT00000018167|ENSRNOG00000013498 ## ENSRNOG00000013498|protein_coding|Pex14|peroxisomal biogenesis factor 14 [Source:RefSeq_peptide;Acc:NP_742060] ## {Repeats: B3 178 201 -1 class=SINE/B2,B3 5 203 -1 class=SINE,trf 14 37 0 class=trf,trf 8 31 0 class=trf,dust 166097074 166097097 0 class=dust,trf 1 17 0 class=trf}

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noncloned miRBase miRNAs:

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miR-Intess™