miR-Intess: classification

other hairpins

block912 [novel_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
no	0.028	no	no	0.43/0.43	23/23/1.00	0.0	0.0	1	0	1	0	14	0	5arm	1	nd	0.35	4	1	1	na	na

		reads	miRBase family seed
seed	---------------AUGAAUG----------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	--------------GATGAATGACAGAAGATCGACAG-------------------------------------------	23	1
celegans	acgaattggatatcGATGAATGACAGAAGATCGACAGaaaactgggagtgatttagattttatcgattgatatgcaatcg
	********************************************************************************
celegans	.((.((((.((((((((..((((....((((((.(((....)))....)))))).....))))..)))))))).))))))	0.960 -18.40

celegans

chromosome:I:6145326:6145405:1

intergenic ## {SimpF: F56F4.7 1 Expression_profile,WRM0611dF11 1 fosmid,WRM0613cG12 1 fosmid,WRM0628dG06 1 fosmid,WRM0621bH03 1 fosmid,WRM065bH05 1 fosmid,WRM068cH02 1 fosmid,WRM0624dG10 1 fosmid}

block1378 [novel_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
no	0.134	no	no	0.41/0.41	22/22/1.00	0.0	0.0	1	0	1	0	14	4	3arm	1	nd	0.41	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------UCUUAUG----------------------------	1	novel
		len	cloning frequencies
			CE1
	--------------------------------------------GTCTTATGATGTGAAGCTACTG--------------	22	1
celegans	gtccgacttgactcggctgatcatcaagacgtgtttaactgcgtGTCTTATGATGTGAAGCTACTGcatctatgtcagaa
	********************************************************************************
celegans	.((.(((.((....((((...(((((((((((((......))))))))..)))))...))))....)).....))).)).	0.530 -20.70

celegans

chromosome:I:15064629:15064708:1

intergenic ## {SimpF: WRM066aE11 1 fosmid,WRM068cA11 1 fosmid,WRM067aB07 1 fosmid,WRM0628aC12 1 fosmid,WRM0625cG10 1 fosmid,WRM0629dE08 1 fosmid,WRM0637dE09 1 fosmid,WRM0623dH11 1 fosmid,WRM0631aD12 1 fosmid,WRM0640bG08 1 fosmid,WRM0626cH01 1 fosmid,WRM0615cH09 1 fosmid}

block2740 [novel_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
no	0.323	no	no	0.52/0.52	21/21/1.00	0.0	0.0	2	0	1	0	11	16	3arm	1	nd	0.43	4	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------AAAUUGU------------------------	2	novel
		len	cloning frequencies
			CE1
	----------------------------------------------------------GAAATTGTGTGACGGTGGTGG-----------	21	2
celegans	gggggatttatggcaggaatataagcctctcggctccccgatgagtggcgatgaggcgGAAATTGTGTGACGGTGGTGGtgctgctcccg
	******************************************************************************************
celegans	(((((..((((.((....((((((((((((((((((......))))..))).))))).....))))))....)).)))).....))))).	0.610 -28.90

celegans

chromosome:II:14746997:14747086:1

intergenic ## {SimpF: WRM062bA05 1 fosmid}

block2817 [novel_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
no	0.012	no	no	0.32/0.32	22/22/1.00	0.0	0.0	1	0	1	0	10	20	5arm	1	nd	0.36	4	1	1	na	na

		reads	miRBase family seed
seed	-----------UGAAAAU---------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	----------GTGAAAATGAGTGAAAATATCG-------------------------------------------------------------------------------	22	1
celegans	aatttttaagGTGAAAATGAGTGAAAATATCGatttttcaggcaaatttcagggaaaaattgaacattttgagtgaaaaaaagggctttttgcggaattttaagtgaaaat
	***************************************************************************************************************
celegans	.(((((((...(((((....(((((((..((..(((((((..((((.(((((.......)))))...))))..)))))))..))..)))))))....)))))..)))))))	0.990 -20.70

celegans

chromosome:III:2347134:2347244:-1

intergenic ## {SimpF: CEOP3075 -1 Operon}

block2858 [novel_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
no	0.481	no	no	0.40/0.40	20/20/1.00	0.0	0.0	1	0	1	0	8	14	3arm	1	nd	0.35	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------AACUUUA--------------------	1	novel
		len	cloning frequencies
			CE1
	-------------------------------------------------------------CAACTTTATGTCGCAATGTC--------	20	1
celegans	tcagctaaactaatgacatattgagatgctcggcaatgtatggaggacgaacacaaccggaCAACTTTATGTCGCAATGTCaccgtgaa
	*****************************************************************************************
celegans	(((.....((...(((((((..(((.((..(((...(((.((.....)).)))...)))..)).))))))))))....)).....))).	0.780 -16.80

celegans

chromosome:III:3831087:3831175:-1

intergenic ## {SimpF: WRM0634bH05 -1 fosmid,WRM0626aB12 -1 fosmid,WRM0640dH02 -1 fosmid,WRM065cE05 -1 fosmid,WRM062aH09 -1 fosmid,WRM0613aC06 -1 fosmid,C36A4.10 -1 Expression_profile,WRM063dB07 -1 fosmid,WRM0624bD07 -1 fosmid}

block3198 [novel_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
no	0.133	no	no	0.38/0.38	21/21/1.00	0.0	0.0	1	0	1	0	9	12	5arm	1	nd	0.48	5	1	1	na	na

		reads	miRBase family seed
seed	----------UAGAUGG------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	---------GTAGATGGTCCAGAAACAATT-----------------------------------------------------------------	21	1
celegans	attttgggtGTAGATGGTCCAGAAACAATTggttggaagggcaggaagccatctacaatgatcggtttgaggagtacacgtacacatttgaggta
	***********************************************************************************************
	---------------------------------------------------------------------------------------------------------	R10E11.1c R10E11.1 cbp-1
	---------------------------------------------------------------------------------------------------------	R10E11.1a R10E11.1 cbp-1
	---------------------------------------------------------------------------------------------------------	R10E11.1b R10E11.1 cbp-1
celegans	((((..(((((..(((.(((..((((.....((((....(((.....))).....)))).....))))..))).....)))..)))))..)))).	0.910 -21.80

celegans

chromosome:III:9774092:9774186:-1

Opposite_strand|Intronic_coding|R10E11.1a|R10E11.1 ## R10E11.1|protein_coding|cbp-1|cbp-1 encodes a homolog of the mammalian transcriptional cofactors CBP (OMIM:600140) and p300 (E1A-BINDING PROTEIN, 300-KD. OMIM:602700) that have been shown to possess histone acetyltransferase activity, and which, when mutated, lead to Rubinstein-Taybi syndrome (OMIM:180849) and colorectal cancer (OMIM:114500). at least one splicing form of CBP-1 exhibits histone acetyltransferase (HAT) activity in vitro and has a glutamine/asparagine-rich domain. CBP-1 is required during embryogenesis for differentiation of all non-neuronal somatic cell types. CBP-1 is expressed very early in embryogenesis, suggesting that it may interact with maternally provided transcription factors, such as SKN-1, to specific developmental fates. [Source: WormBase] ## {SimpF: WRM0625bD02 -1 fosmid,WRM0637cA07 -1 fosmid,WRM0626aE07 -1 fosmid,WRM069bA04 -1 fosmid,WRM0610bH10 -1 fosmid,WRM0611cD01 -1 fosmid,WRM0628dE06 -1 fosmid}

block3286 [novel_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
no	0.896	no	no	0.33/0.33	24/24/1.00	0.0	0.0	1	0	1	0	12	10	5arm	1	nd	0.38	4	1	1	na	na

		reads	miRBase family seed
seed	-------------CCAAUUU------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	------------GCCAATTTGAGGAATGAATTTTGT--------------------------------------------------------------------	24	1
celegans	gttatgaataacGCCAATTTGAGGAATGAATTTTGTgaaatgttgagaataaattaaaattgaaaaaaaaaacgatctttctagactttggaatttttaaaaca
	********************************************************************************************************
	<<<...............................................................................................................	Y66D12A.11 Y66D12A.11 Y66D12A.11
celegans	(((.((((.....((((....(((((.((...((((..(((.((((.......)))).)))..........))))))))))).....))))....)))).))).	0.680 -9.30

celegans

chromosome:III:11563305:11563408:-1

intergenic

block3549 [novel_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
no	0.017	no	no	0.26/0.26	23/23/1.00	0.0	0.0	1	0	1	0	7	25	5arm	1	nd	0.39	4	1	1	na	na

		reads	miRBase family seed
seed	--------AAUUGAA-----------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	-------GAATTGAAATCAGTCATCTTTTT--------------------------------------------------------------------------------	23	1
celegans	ttcattcGAATTGAAATCAGTCATCTTTTTatgattttccgtcctcgtttcaatggaatcacacaaatgacgggcggactgaagaagatcaccaaatttgatgatatgaa
	**************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	M88.7 M88.7 M88.7
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<...........................................................................................	M88.3 M88.3 M88.3
celegans	.((((....((..((....((.((((((((.......(((((((((((((...((......)).)))))).)))))))...)))))))).))....))..))...)))).	0.400 -26.40

celegans

chromosome:III:4544918:4545027:1

Opposite_strand|Boundary_non-coding|M88.3|M88.3 ## Same_strand|Intronic_coding|M88.7|M88.7 ## M88.7|protein_coding|M88.7|M88.7 [Source:RefSeq_peptide;Acc:NP_497920] ## M88.3|protein_coding|M88.3|M88.3 [Source:RefSeq_peptide;Acc:NP_497921] ## {SimpF: WRM0611dC02 1 fosmid,WRM0618aF05 1 fosmid,WRM061bH07 1 fosmid,WRM0622dB10 1 fosmid,WRM0640cE01 1 fosmid,M88.3 1 Expression_profile,WRM0631cD12 1 fosmid,WRM0625cB01 1 fosmid,WRM0624dG04 1 fosmid,WRM0626cG09 1 fosmid,WRM0627cC04 1 fosmid}

block4243 [novel_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
no	0.914	no	no	0.57/0.57	21/21/1.00	0.0	0.0	1	0	1	0	12	10	3arm	1	nd	0.52	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------UCCCUGU-------------------------	1	novel
		len	cloning frequencies
			CE1
	------------------------------------------------GTCCCTGTATGCGCCTTTGCT------------	21	1
celegans	atacgtttgttgcctggcgacctcactgactggaccgctccagattttGTCCCTGTATGCGCCTTTGCTgaaaagaaagta
	*********************************************************************************
	---------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<-------------------	ZK616.5 ZK616.5 ZK616.5
celegans	.(((.(((...((..((((....((..(((((((....))))......)))..))....))))...))....)))...)))	0.610 -14.80

celegans

chromosome:IV:5392266:5392346:-1

Opposite_strand|Boundary_coding|ZK616.5|ZK616.5 ## ZK616.5|protein_coding|ZK616.5|ZK616.5 [Source:RefSeq_peptide;Acc:NP_500800] ## {SimpF: WRM0621dF11 -1 fosmid,WRM0612dE10 -1 fosmid,WRM066cH08 -1 fosmid,WRM0636bF04 -1 fosmid,WRM0635cB02 -1 fosmid,WRM0614bB03 -1 fosmid,WRM0621cG07 -1 fosmid}

block4270 [novel_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
no	0.047	no	no	0.25/0.25	20/20/1.00	0.0	0.0	1	0	1	0	6	12	5arm	1	nd	0.50	4	1	1	na	na

		reads	miRBase family seed
seed	-------AAUUGUG------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	------TAATTGTGTTTTCTAGCAAA------------------------------------------------------	20	1
celegans	ggctagTAATTGTGTTTTCTAGCAAAaagtagtaaacttaaaagttttgcaacggtaggaattcagaaaaggcaaagcct
	********************************************************************************
	------------------------------------------------------------------------------------------	F26D12.1a F26D12.1 fkh-7
celegans	((((.((..((.((..((((.((.....((.(((((((....))))).)).)).)).))))..)).))...))..)))).	0.450 -16.10

celegans

chromosome:IV:5594344:5594423:-1

Opposite_strand|Boundary_non-coding|F26D12.1b|F26D12.1 ## Opposite_strand|Intronic_coding|F26D12.1a|F26D12.1 ## F26D12.1|protein_coding|fkh-7|fkh-7 encodes one of 15 forkhead transcriptional regulators encoded by the C. elegans genome. by homology, FKH-7 is predicted to function as a transcription factor that regulates gene expression during development. however, as loss of fkh-7 activity via RNA-mediated interference (RNAi) does not result in any obvious abnormalities, the precise role of FKH-7 in C. elegans development and/or behavior is not yet known. however, reporter gene studies indicate that fkh-7 expression is detected only in neurons of the head and tail ganglia, the nerve cord, and the male tail, suggesting that FKH-7 likely functions in nervous system differentiation. [Source: WormBase] ## {SimpF: WRM0627bB10 -1 fosmid,WRM0618dB04 -1 fosmid,WRM063bD03 -1 fosmid,WRM0615dA02 -1 fosmid}

Page 13

Jump 10 pages forward

Page 45

miR-Intess™

block912 [novel_nonpairedHIGH_bulgeHIGH]

block1378 [novel_nonpairedHIGH_bulgeHIGH]

block2740 [novel_nonpairedHIGH_bulgeHIGH]

block2817 [novel_nonpairedHIGH_bulgeHIGH]

block2858 [novel_nonpairedHIGH_bulgeHIGH]

block3198 [novel_nonpairedHIGH_bulgeHIGH]

block3286 [novel_nonpairedHIGH_bulgeHIGH]

block3549 [novel_nonpairedHIGH_bulgeHIGH]

block4243 [novel_nonpairedHIGH_bulgeHIGH]

block4270 [novel_nonpairedHIGH_bulgeHIGH]