Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_rep_randfoldOK (90 loci)

block2458728 [novel_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
no	0.006	no	SINE/MIR	0.57/0.57	21/21/1.00	0.0	0.0	1	0	1	0	20	5	3arm	1	nd	0.24	3	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------------UCUCCCU---------------------------------	1	novel
		len	cloning frequencies
			T3S1
	-----------------------------------------------------------------------TTCTCCCTGGCTCCTTCCTGT--------------------	21	1
rat	CCCCGTAGCTACGCCACAGGTCACCACAGGAGCCGGGCATGAAGAAATGTTTTCA------ATGTCTTTCTTTCTCCCTGGCTCCTTCCTGTAAAACTCCCTGCAGAGGGGG
mouse	CCCAGGAG-------------------AAGAGGCGGCAATGGA-----ACGTTCAGGGGTCACATTCTCCGTTCTCCCTGGCTCCTTCCT-------------------GAG
	*** * ** * * * *** * **** * * * * ******************* * *
	------------------------------------------------------------ --------------------------------------------------------	ENSRNOT00000039904 ENSRNOG00000025881 LOC680726
	------------------------------------------------------------ --------------------------------------------------------	ENSRNOT00000036642 ENSRNOG00000025881 LOC680726
	------------------------------------------------------------ --------------------------------------------------------	ENSRNOT00000041548 ENSRNOG00000025881 LOC680726
rat	((((((((.......(((((.......((((((((((...(((((((........ .....)))))))...)))))))))).)))))........))))...)))).	0.530 -36.58
mouse	..(((((( ..(((.(((....((( (((....((((......))))))))))..))).))).))))) )..	0.990 -22.40

rat	chromosome:8:121433672:121433777:1	Opposite_strand\|Boundary_non-coding\|ENSRNOT00000055981\|ENSRNOG00000025881 ## Opposite_strand\|Intronic_coding\|ENSRNOT00000041548\|ENSRNOG00000025881 ## ENSRNOG00000025881\|protein_coding\|LOC680726\|
mouse	chromosome:11:52718799:52718944:1	Same_strand\|Intronic_coding\|ENSMUST00000036796\|ENSMUSG00000036264\|protein_coding\|follistatin-like 4 Gene [Source:MGI (curated);Acc:Fstl4-001] ## {Repeats: MIRb 1 class=SINE/MIR}

block2516038 [novel_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
no	0.010	no	LINE/L2	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	21	4	5arm	1	nd	0.29	3	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------UGGCCAG----------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	-----------------------------------------CTGGCCAGATGAACAAGACAC---------------------------------------------------------------------------------	21	1
rat	CTGG--TGAA------------------GCCGCTTGTTTCCCTGGCCAGATGAACAAGACACCTG--------CAGCAGCTTTTCCACAGTTGGGTC---TCTCTGGCTGGCCATGG-AGACTGCACACCAGC----------
human	GTGGAATGAACAGATGGATGGATGGATGGATGGGTGGGTGGGTGGCCAGATGAACAAAATGCCAGTCAGTTGTCAGTGGGATTT----AATGGGGCCCTATCTCCACGTCATCTTGATATGATGCATGTCTGTAGGCTTTGAC
	* ** * * ** * *************** * ** * *** * *** * * *** * **** * * ** * **** * *
rat	(((( ((.. ...((..((((((.(((((((..((...((((.((.( (...............)).))))) ).))...))))))).)) )))).)).)))))).	0.900 -38.66
human	((.(((...(((((((.....(((...(((((((((((..((.((((..((.....((((.(((............))).)))) .))..))))))...))))).))))))...)))......)))))))....))).))	0.877 -32.50

rat	chromosome:9:63437476:63437576:-1	intergenic
human	chromosome:8:125159594:125159732:1	Same_strand\|Intronic_coding\|ENST00000399018\|ENSG00000214814\|protein_coding\|Fer-1-like protein 6 [Source:UniProtKB/Swiss-Prot;Acc:Q2WGJ9] ## {Repeats: L2 1 class=LINE/L2,trf 0 class=trf}

block2620427 [novel_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
no	0.002	no	LINE/L1	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	28	0	5arm	1	nd	0.10	1	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------CUGAUGG---------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	----------------------------GCTGATGGGTACAGTCTCTCA--------------------------------------------------------------------	21	1
rat	TGGCTCTGAGCTCCTACGTCTCCCCGGTGCTGATGGGTACAGTCTCTCAGGAGACCAAGATGAGAGGCTGTACCCGCAGAAACTTGTACCACAACCCCGCGTTGTTCTGGATGCCAA
mouse	----------------------------GCTGATGGGTAGAGTCTCTCATAGGACAAATATGCTAGGC------------------------------------TCCTGTCTGC---
	********* ***** * * **** * * *
rat	(((((((((((....((((......(((((((.((((((((((((((((...........)))))))))))))))))).......)))))........)))).)))).))).)))).	0.650 -47.15
mouse	((.((((((...(((((..((((.......))))..)))) ))))))).))	0.999 -14.50

rat	chromosome:9:76821673:76821789:1	intergenic
mouse	chromosome:12:31194756:31194912:1	intergenic ## {Repeats: Lx5 -1 class=LINE/L1}

block2633099 [novel_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
no	0.001	no	SINE/Alu	0.60/0.60	20/20/1.00	0.0	0.0	1	0	1	0	31	1	5arm	1	nd	0.15	2	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------GGGGUUG-----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	-------------------------------TGGGGTTGGGGGTTTGT----GTG-------------------------------------------------------------------	20	1
rat	AGATTGTGCTAAGCAAATCTTCAAGCCAGCATGGGGTTGGGGGTTTGT----GTGGCATACCTTACC----ACTCTCAGGCTCAAGACCCCATACAGCTTGGATGTTTGCCTCTGTGGAATT
human	-------------------------------TGGGGTTGGGGGTTTGCCATGTTGCCCTGCCTGGTCTCAAACTCCTGGGCTCA--------------------------------------
mouse	-------------------------------TGGGGTTGGGGGTTTGT------GGACTACCATGG-----ACACACAGACTCA--------------------------------------
	**************** * * * * ****
rat	.((((.(((...((((((.(((((((....((((((((..(((((((. ((((.........)) ))...)))))))..))))))))...))))))).))))))....))).))))	1.000 -45.50
human	.(((.((((((((((((((.((......)).)))...))))))))))).))).	1.000 -20.60
mouse	..(((((....(((..( ((....)))..) )).....))))).	1.000 -14.30

rat	chromosome:9:91512065:91512178:1	intergenic
human	chromosome:16:61995098:61995251:1	intergenic ## {Repeats: AluJb -1 class=SINE/Alu,dust 0 class=dust}
mouse	chromosome:15:72968827:72968980:-1	Same_strand\|Intronic_coding\|ENSMUST00000044113\|ENSMUSG00000036698\|protein_coding\|eukaryotic translation initiation factor 2C, 2 Gene [Source:MGI Symbol;Acc:MGI:2446632]

block2655143 [novel_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
no	0.001	no	LINE/L1	0.38/0.38	21/21/1.00	0.0	0.0	1	0	1	0	26	9	3arm	1	nd	0.05	1	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------GUGGCCC---------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	----------------------------------------------------------------------AGTGGCCCTAAAAATTTCTCA--------------------------	21	1
rat	CAAGACAGGGACTTCCTGGCTTAAATGAGAAATTTTCAGGGCTACTGAACACTGCAAATACGTGGTGTTCAGTGGCCCTAAAAATTTCTCATTTCTTATCTGTGTTGGTCCAATCTT
mouse	--------GGA-----------AGAAGTCAAAATATCACTATTTGCATATAATAAAATCATCTATATGTAAGTGGCCCTAAAAATTTC--------------------ACCA-----
	*** * * * *** * *** * * * * ** * * * **************** *
rat	.((((...(((((....((...((((((((((((((.((((((((((((((((((......)))))))))))))))))).))))))))))))))....))......)))))..))))	0.860 -55.50
mouse	((. .(((((..........(((((((((((((...........)))))))))))))........))))) .)).	0.956 -13.47

rat	chromosome:X:1943787:1943903:-1	intergenic
mouse	chromosome:6:60187796:60187952:-1	intergenic ## {Repeats: L1_Mus3 1 class=LINE/L1}

block2805595 [novel_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
no	0.001	no	LTR/ERV1	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	26	2	5arm	1	nd	0.19	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------------GGAAUGA---------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S1
	--------------------------TGGAATGAGGGAGGGTGATAG--------------------------------------------------------------	21	1
rat	TAGAGGAGTGGTTCATTGCTGAGGACTGGAATGAGGGAGGGTGATAGTCTAAAAATGACAATTAAAAATTACTCTCGGGGATCTAGCTCAGTGGTAGAGCACTTGCCTA
human	--------------------------TGGAATGAGGGAGGGT-----CTTATGACCTACAGCCAAACAACG---TAAGACATATACTTTCTTA----------TGGCTA
	************** * * * * * * * * *
rat	(((..(((((.((.((..(((((..(((((.((((((((..((((.(((.......))).))))....)).))))))....))))))))))..)).)).)))))..)))	1.000 -34.70
human	(((.(((((..((.(( ((((((................)) )))))).....))..)))) )..)))	0.983 -16.49

rat	chromosome:X:127525279:127525387:-1	intergenic
human	chromosome:6:26339404:26339552:-1	intergenic ## {Repeats: MER39B -1 class=LTR/ERV1}

block2895933 [novel_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
no	0.001	no	DNA/AcHobo,LTR/ERV1	0.45/0.45	20/20/1.00	0.0	0.0	1	0	1	0	16	2	3arm	1	nd	0.20	2	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------GAAAUUC--------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------------------------------------------------TGAAATTCACCATGGTGGGT--------------------------------	20	1
rat	TATGGGCAGTA-----------CTGTC-TTCACCATGGTGTTTT----TGACATAAGTAG----CTATGAAATTCACCATGGTGGGTAAAGTAAGGCTCATAA----------------
human	GGTGTGTTGGAGCCAATCATGGTTGTCTCTTTCCAAGGCCATGTTCAGTGACACCAGGTTAGTAATTTGAAATTCACCATGGTGGGAGTAGTTACACCATGGAAATTGGCAAACACTTC
mouse	------CAGAA-----------------CACCCCAGGAAAATTTAAAATTACACG---------CTTTGAAATTCACCATGGGGGACTG------------------------------
	* * *** * * * * *** * *************
rat	(((((((..(( ((... ((((((((((((..(( (..((((..... .)))))))..))))))))))))...))))..))))))).	1.000 -35.90
human	...(((((...(((((((((((.(((..((((((...((((((....((((...(((((.....)))))....)))))))))).)))).))..))))))))...)))))).)))))...	0.958 -37.60
mouse	(((.. ..(((((((..(((((.(((....... .))).)))))..)).)))))..)))	0.999 -12.80

rat	chromosome:X:152841100:152841182:-1	intergenic
human	chromosome:17:32190095:32190213:-1	intergenic ## {Repeats: MER63A 1 class=DNA/AcHobo}
mouse	supercontig:NT_161906:270486:270608:-1	intergenic ## {Repeats: MuRRS-int 1 class=LTR/ERV1}

block2948233 [novel_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
no	0.001	no	LINE/RTE	0.50/0.50	22/22/1.00	0.0	0.0	1	0	1	0	28	1	5arm	1	nd	0.14	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------GUCUUUG--------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	----------------------------TGTCTTTGTCTC--------CAGCTAGAGC----------------------------------------------------------------------------	22	1
rat	TGAAAATGAAATCAAAACACCCACAGGTTGTCTTTGTCTC--------CAGCTAGAGCTGACATTGGG------CACTAAGCTTGCAGGGCTGGGAACAAAGATAACCTGTGGATGTGCAGCCTTTCATAGTCC
mouse	-------GAAACCAAAACATCCACAGGTAGTCTTTGTCTCGAGCCCTGCAGCTAGAGCCAACATTGGGCTGTATCGGTAAGCTTGCAGGGCTGGGAACAAAGATAACCTGTGGATGTGCAGCCTTC--------
	** *** **** ******* ****** ****** * ************************************************
rat	.((..((((((.....(((.(((((((((((((((((..( (((((.(((((......... .....)))))....))))))..))))))))))))))))).)))......))))))..)).	1.000 -55.14
mouse	.........((((((((((((.((((((((.((.(((((((((((((.((((.......)))).)).......))).)))))))).)).)))))))).)))))))))))).........	0.929 -61.11

rat	chromosome:X:23148702:23148821:1	intergenic
mouse	chromosome:X:11325804:11325922:-1	intergenic ## {Repeats: L4 -1 class=LINE/RTE}

block1644919 [novel_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
no	0.001	no	SINE/MIR	0.62/0.62	21/21/1.00	0.0	0.0	1	0	1	0	19	3	5arm	1	nd	0.14	2	1	1	na	na

		reads	miRBase family seed
seed	--------------------AAGGCCC---------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	-------------------CAAGGCCCAGGGCTGGAATGT--------------------------------------------------------------	21	1
rat	TCACTCCAGGTTAGTGTGCCAAGGCCCAGGGCTGGAATGTGAACCCATATCATTCATGTCCAGACCTTGGGCTCTGCACACTGCTTTGGCAATACTGGTGAA
human	-------------------CAAGGCCCAGGGCTGGCATGCTCAGCACCAGGGCTCA-GGCCAGGCAGAGGGCACTTA-------------------------
mouse	-------------------CAAGGCCCAGGGTTGAAATGTGAGCCAATATCATTCATGTCCAGACCTTGGTCTCT---------------------------
	********** *** * * *** * **** * ** * **
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000017675 ENSRNOG00000013004 Akr1d1
rat	((((((((((.(((((((.((..((((((((((((.(((((((.........))))))))))).))))))))..))))))))).))))).......))))).	0.960 -48.41
human	.(((((((...((((((..((((.......))))... .)))).))...)))).))).	0.823 -24.00
mouse	..(((.((((((((...(((((((.........)))))))...)))))))))))..	1.000 -16.10

rat	chromosome:4:64974817:64974918:1	Same_strand\|Intronic_coding\|ENSRNOT00000017675\|ENSRNOG00000013004 ## ENSRNOG00000013004\|protein_coding\|Akr1d1\|3-oxo-5-beta-steroid 4-dehydrogenase (EC 1.3.1.3) (Delta(4)-3- ketosteroid 5-beta-reductase) (Aldo-keto reductase family 1 member D1). [Source:UniProtKB/Swiss-Prot;Acc:P31210]
human	chromosome:15:38381666:38381807:1	Opposite_strand\|Boundary_non-coding\|ENST00000389812\|ENSG00000137841\|protein_coding\|1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta-2 (EC 3.1.4.11)(Phosphoinositide phospholipase C)(Phospholipase C-beta-2)(PLC-beta-2) [Source:UniProtKB/Swiss-Prot;Acc:Q00722] ## Opposite_strand\|Boundary_coding\|ENST00000260402\|ENSG00000137841\|protein_coding\|1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta-2 (EC 3.1.4.11)(Phosphoinositide phospholipase C)(Phospholipase C-beta-2)(PLC-beta-2) [Source:UniProtKB/Swiss-Prot;Acc:Q00722]
mouse	chromosome:6:37482144:37482285:1	Same_strand\|Intronic_coding\|ENSMUST00000040987\|ENSMUSG00000038641\|protein_coding\|aldo-keto reductase family 1, member D1 Gene [Source:MGI (curated);Acc:Akr1d1-001] ## {Repeats: MIRb -1 class=SINE/MIR}

novel_lenNOK_shortStem_loopOverlap_randfoldOK_nonpairedHIGH (89 loci)

block4079 [novel_lenNOK_shortStem_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
no	0.008	no	no	0.33/0.33	18/18/0.00	0.0	0.0	1	0	1	0	0	-4	3arm_loop	1	nd	0.35	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------UAUCUCU----------	1	novel
		len	cloning frequencies
			T3S1
	--------------------TTATCTCTTCAATTCTGC	18	1
rat	agcagaggagagtttaaattTTATCTCTTCAATTCTGC
	**************************************
rat	.(((((((((((............))))))...)))))	1.000 -10.70

rat

chromosome:10:8931532:8931569:-1

intergenic

Back to summary page

other hairpins:

Jump 10 pages back

Page 30260

Jump 10 pages forward

©2008 InteRNA Genomics B.V.