Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_shortStem_loopOverlap_bulgeHIGH (78 loci)

block2543814 [novel_lenNOK_shortStem_loopOverlap_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	0.229	no	no	0.33/0.33	18/18/0.00	0.0	0.0	1	0	1	0	2	-4	5arm_loop	1	nd	0.28	5	1	1	na	na

		reads	miRBase family seed
seed	---ACAAUGU--------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	--TACAATGTAGCCAAAAAG----------------------------	18	1
rat	ggTACAATGTAGCCAAAAAGcattgcagttacattttgtgtgggtacc
	************************************************
rat	((((((((((((((((......)))..))))))))........)))))	0.610 -9.60

rat

chromosome:9:97277968:97278015:-1

intergenic

block2548601 [novel_lenNOK_shortStem_loopOverlap_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	0.025	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	3	-1	3arm	2	nd	0.21	4	1	1	na	na

		reads	miRBase family seed
seed	------------------------------GGGAACA--------------	1	novel
		len	cloning frequencies
			T1S1
	-----------------------------TGGGAACAGGACTCAGAAG---	19	1
rat	gtctttgttcttctagtttcccttcccgcTGGGAACAGGACTCAGAAGacg
	***************************************************
rat	((((((....((((.((.((((........))))))))))....)))))).	1.000 -15.90

rat

chromosome:9:103630621:103630671:-1

intergenic

block2552678 [novel_lenNOK_shortStem_loopOverlap_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	0.123	no	no	0.61/0.61	18/18/0.00	0.0	0.0	1	0	1	0	4	-3	5arm_loop	1	nd	0.28	4	1	1	na	na

		reads	miRBase family seed
seed	-----GACCUUC----------------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	----GGACCTTCAAGGGCGTTG------------------------------------	18	1
rat	atgaGGACCTTCAAGGGCGTTGggctgcctgcaatagaagtgaaggtggtacctggta
	**********************************************************
rat	((.((((((((((.(((((......)))))..........)))))))....))).)).	0.950 -16.60

rat

chromosome:9:106580785:106580842:-1

intergenic

block2627938 [novel_lenNOK_shortStem_loopOverlap_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	0.684	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	2	-1	3arm	2	nd	0.28	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------CCAAGGU------------	1	novel
		len	cloning frequencies
			T2S2
	----------------------------CCCAAGGTTGACATGTCT--	18	1
rat	tgagctgcagctgaaggccctggaactcCCCAAGGTTGACATGTCTta
	************************************************
rat	((((..(((......((((.(((......))).))))....)))))))	0.650 -9.20

rat

chromosome:9:85384597:85384644:1

intergenic

block2642568 [novel_lenNOK_shortStem_loopOverlap_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	0.106	no	no	0.67/0.67	18/18/0.00	0.0	0.0	1	0	1	0	0	-3	5arm_loop	1	nd	0.28	4	1	1	na	na

		reads	miRBase family seed
seed	-CUCUGUG----------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	GCTCTGTGTCAGCCACGC------------------------------	18	1
rat	GCTCTGTGTCAGCCACGCgatggctgtgttacattaaattgccagggc
	************************************************
rat	((((((.((((((((.....))))))..............))))))))	0.670 -14.93

rat

chromosome:9:103914499:103914546:1

intergenic

block2677952 [novel_lenNOK_shortStem_loopOverlap_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	0.023	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	4	-1	3arm	1	nd	0.28	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------GGAGUGU--------------	1	miR-122
		len	cloning frequencies
			T2S2
	----------------------------TGGAGTGTGCAGTATTAC----	18	1
rat	gatgttctctgcgcgccttaaaagaaagTGGAGTGTGCAGTATTACgttt
	**************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000051135 ENSRNOG00000003749 Xk
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000004983 ENSRNOG00000003749 Xk
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000040359 ENSRNOG00000003749 Xk
rat	(((((...((((((((((...........)).))))))))....))))).	1.000 -15.10

rat

chromosome:X:25622892:25622941:-1

Same_strand|Intronic_coding|ENSRNOT00000040359|ENSRNOG00000003749 ## ENSRNOG00000003749|protein_coding|Xk|Membrane transport protein XK (XK-related protein 1) (XK homolog). [Source:UniProtKB/Swiss-Prot;Acc:Q5GH61]

block2904609 [novel_lenNOK_shortStem_loopOverlap_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	0.043	no	no	0.33/0.33	18/18/0.00	0.0	0.0	1	0	1	0	2	-4	5arm_loop	1	nd	0.28	5	1	1	na	na

		reads	miRBase family seed
seed	---AGUGUUU-----------------------------------	1	novel
		len	cloning frequencies
			T1S1
	--TAGTGTTTTTTGAGGCTA-------------------------	18	1
rat	tgTAGTGTTTTTTGAGGCTAcagactctttaaaaaaggacattat
	*********************************************
rat	.(((((((((((((((........)))......))))))))))))	0.820 -9.30

rat

chromosome:X:154602243:154602287:-1

intergenic

block182551 [novel_lenNOK_shortStem_loopOverlap_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	0.319	no	no	0.52/0.52	25/25/0.00	0.0	0.0	1	0	1	0	3	-1	3arm	1	nd	0.28	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------UGCCAUG--------------------	1	novel
		len	cloning frequencies
			T5S2
	------------------------------------CTGCCATGGCCAGTTACCAAAAGAC---	25	1
rat	ggctgctgttgctgtgaccctggccctttcatactgCTGCCATGGCCAGTTACCAAAAGACgcc
	****************************************************************
rat	(((..((.(((..(((((..(((((....((......))....))))))))))))).))..)))	0.950 -17.00

rat

chromosome:12:11038800:11038863:-1

intergenic

novel_lenNOK_shortStem_mirtron (78 loci)

block22927 [novel_lenNOK_shortStem_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	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	4	22	5arm	1	4	0.17	1	1	1	na	na

		reads	miRBase family seed
seed	-----AGUAUCC----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	----CAGTATCCTCTGGTAGCT------------------------------------------------------------------------	18	1
rat	ggtaCAGTATCCTCTGGTAGCTacgaggccactttcagtctcttaaagcaagcaagctgtgtggtagtgagctcggcaagagggtgaatgcgcc
	**********************************************************************************************
	>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000057583 ENSRNOG00000003603 Q5EB79_RAT
	>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000004829 ENSRNOG00000003603 Q5EB79_RAT
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000057581 ENSRNOG00000003603 Q5EB79_RAT
rat	((..((.((((((((.((((((.((..(((((...((((..(((.....)))...)))).)))))..))))))..)).))))))))..))..))	1.000 -32.80

rat

chromosome:10:51324545:51324638:-1

Same_strand|Intronic_coding|ENSRNOT00000004829|ENSRNOG00000003603 ## Same_strand|Intronic_non-coding|ENSRNOT00000057583|ENSRNOG00000003603 ## ENSRNOG00000003603|protein_coding|Q5EB79_RAT|RGD1305664 protein (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q5EB79]

block41883 [novel_lenNOK_shortStem_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	0.190	no	no	0.32/0.32	19/19/0.00	0.0	0.0	2	0	1	0	0	12	5arm	1	4	0.26	3	2	1	na	na

		reads	miRBase family seed
seed	-UGUUCUA--------------------------------------------------------	2	novel
		len	cloning frequencies
			T1S1
	ATGTTCTATTATCTGTCCT---------------------------------------------	19	2
rat	ATGTTCTATTATCTGTCCTatagatatgtgtcctaaaaatgccagctattacggtaatcgagca
	****************************************************************
	++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000024321 ENSRNOG00000017781 Dnajc7
rat	.(((((.((((.((((...((((...((.((.........)))).)))).)))))))).)))))	0.900 -11.30

rat

chromosome:10:89543081:89543144:-1

Same_strand|Intronic_coding|ENSRNOT00000024321|ENSRNOG00000017781 ## ENSRNOG00000017781|protein_coding|Dnajc7|cytoplasmic CAR retention protein [Source:RefSeq_peptide;Acc:NP_998790]

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