miR-Intess: classification

other hairpins

novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH (14 loci)

block6612 [novel_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
no	0.151	no	no	0.63/0.63	19/19/0.00	0.0	0.0	1	0	1	0	4	3	5arm	4	nd	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	-----GGAAGUG-------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	----GGGAAGTGGCAGAGTGACC--------------------------------	19	1
celegans	atggGGGAAGTGGCAGAGTGACCaagaaaaactatgcactttgtacattcggcat
	*******************************************************
celegans	......(((...((((((((....((.....))...))))))))...))).....	1.000 -12.00

celegans

chromosome:V:8895580:8895634:-1

intergenic ## {SimpF: WRM0627bB06 -1 fosmid,WRM0638aA04 -1 fosmid,WRM0625aH11 -1 fosmid,WRM0614bC01 -1 fosmid,WRM0620dF01 -1 fosmid,WRM0628bC09 -1 fosmid,WRM0630cG07 -1 fosmid,WRM0627cF05 -1 fosmid,WRM0626cG01 -1 fosmid,WRM064dE05 -1 fosmid,WRM063bH07 -1 fosmid,WRM0637cF09 -1 fosmid,WRM0614aB05 -1 fosmid}

block7217 [novel_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
no	0.151	no	no	0.63/0.63	19/19/0.00	0.0	0.0	1	0	1	0	4	3	5arm	4	nd	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	-----GGAAGUG-------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	----GGGAAGTGGCAGAGTGACC--------------------------------	19	1
celegans	atggGGGAAGTGGCAGAGTGACCaagaaaaactatgcactttgtacattcggcat
	*******************************************************
celegans	......(((...((((((((....((.....))...))))))))...))).....	1.000 -12.00

celegans

chromosome:V:8850254:8850308:1

intergenic ## {SimpF: WRM0612bC01 1 fosmid,WRM0620cD11 1 fosmid,WRM0615bD11 1 fosmid,WRM067aB04 1 fosmid,WRM0632cD08 1 fosmid,WRM0626cH02 1 fosmid,WRM0632aF08 1 fosmid,WRM0639cH11 1 fosmid,WRM0615bG03 1 fosmid,WRM0628dF12 1 fosmid}

block7221 [novel_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
no	0.151	no	no	0.63/0.63	19/19/0.00	0.0	0.0	1	0	1	0	4	3	5arm	4	nd	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	-----GGAAGUG-------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	----GGGAAGTGGCAGAGTGACC--------------------------------	19	1
celegans	atggGGGAAGTGGCAGAGTGACCaagaaaaactatgcactttgtacattcggcat
	*******************************************************
celegans	......(((...((((((((....((.....))...))))))))...))).....	1.000 -12.00

celegans

chromosome:V:8892349:8892403:1

intergenic ## {SimpF: WRM0620dF01 1 fosmid,WRM0630cG07 1 fosmid,WRM0614aB05 1 fosmid,WRM064dE05 1 fosmid,WRM0632cD08 1 fosmid,WRM0627bB06 1 fosmid,WRM0632aF08 1 fosmid,WRM0627cF05 1 fosmid,WRM0614bC01 1 fosmid,WRM063bH07 1 fosmid,WRM0638aA04 1 fosmid,WRM0625aH11 1 fosmid,WRM0626cG01 1 fosmid,WRM0628bC09 1 fosmid}

block7871 [novel_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
no	0.019	no	no	0.26/0.26	19/19/0.00	0.0	0.0	1	0	1	0	1	39	5arm	1	nd	0.37	4	1	1	na	na

		reads	miRBase family seed
seed	--UUAAAGC------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	-TTTAAAGCCAGAATCAAAA-------------------------------------------------------------------------------------	19	1
celegans	gTTTAAAGCCAGAATCAAAActagaatcaaagccagaaaaaaatacgtatgcagtttctagagaagaaacgggctattttagtttaaaaatttgttatttacaca
	*********************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	F13D2.1 F13D2.1 F13D2.1
celegans	((.((((..((((....((((((((((...((((...................((((((.....)))))).)))))))))))))).....))))...)))).)).	0.660 -18.35

celegans

chromosome:X:11170947:11171051:-1

Same_strand|Intronic_coding|F13D2.1|F13D2.1 ## F13D2.1|protein_coding|F13D2.1|F13D2.1 [Source:RefSeq_peptide;Acc:NP_509864] ## {SimpF: WRM0637cA02 -1 fosmid,WRM0641dG01 -1 fosmid,WRM0614aH03 -1 fosmid,WRM0610aC09 -1 fosmid,WRM0623dG11 -1 fosmid,WRM062bF07 -1 fosmid}

novel_shortStem_nonpairedHIGH_bulgeHIGH (13 loci)

block862 [novel_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
no	0.186	no	no	0.39/0.39	23/23/1.00	0.0	0.0	1	0	1	0	3	8	5arm	1	nd	0.43	4	1	1	na	na

		reads	miRBase family seed
seed	----ACUUUUC--------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	---GACTTTTCTTGGTCTTCTCTATC-----------------------------------------------	23	1
celegans	ttaGACTTTTCTTGGTCTTCTCTATCcgatttcggcgttgattttaaagatggtgccgacgaagatttctgaa
	*************************************************************************
celegans	(((((....((((.(((....(((((.((..(((....)))..))...)))))....))).))))..))))).	0.740 -14.90

celegans

chromosome:I:5487940:5488012:1

intergenic ## {SimpF: WRM0623cB08 1 fosmid,WRM0633dH04 1 fosmid,WRM0636cF03 1 fosmid,WRM066cC07 1 fosmid,WRM0633aG08 1 fosmid,WRM0613bH03 1 fosmid}

block2292 [novel_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
no	0.065	no	no	0.30/0.30	20/20/1.00	0.0	0.0	1	0	1	0	4	8	5arm	1	nd	0.35	4	1	1	na	na

		reads	miRBase family seed
seed	-----CUAAUAG------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	----TCTAATAGAAAAAGTGAGCT------------------------------------------------	20	1
celegans	ctttTCTAATAGAAAAAGTGAGCTtttaggtaaagtttacctgcaataaagagcattgagactgtagcaaag
	************************************************************************
	---------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	EGAP2.3.1 EGAP2.3 pho-1
	---------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	EGAP2.3.2 EGAP2.3 pho-1
celegans	((((.((.((((....((((..((((((((((.....))))))....))))..))))....)))))).))))	0.910 -14.30

celegans

chromosome:II:5233359:5233430:1

Opposite_strand|Intronic_coding|EGAP2.3.2|EGAP2.3 ## EGAP2.3|protein_coding|pho-1|pho-1 encodes the major C. elegans intestinal acid phosphatase. as loss of PHO-1 function via RNA-mediated interference (RNAi) does not result in any abnormalities, PHO-1 may function redundantly with other acid phosphatases. PHO-1 intestinal expression appears to be positively regulated by CKI-1, a cyclin-dependent kinase inhibitor, and negatively regulated by POP-1, a TCF/LEF transcription factor. PHO-1 is expressed along the intestinal brush border in all gut cells except the most anterior int-1 and int-2 cells, beginning at the three-fold stage of embryogenesis. [Source: WormBase] ## {SimpF: WRM0630bE03 1 fosmid,WRM0615aG03 1 fosmid,WRM0626bB12 1 fosmid,WRM0618bH03 1 fosmid}

block2377 [novel_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
no	0.752	no	no	0.43/0.43	21/21/1.00	0.0	0.0	1	0	1	0	4	38	5arm	1	nd	0.38	5	1	1	na	na

		reads	miRBase family seed
seed	-----CACAGAA------------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	----GCACAGAATGTTTCAGCCAAA-----------------------------------------------------------------------------------------------	21	1
celegans	gtttGCACAGAATGTTTCAGCCAAActagaatataatgaaatttcttattgtcaacagaacttgaaaaaggattttacgatttattagattctcagccaacaatattttgaatgataaca
	************************************************************************************************************************
celegans	(((..(((((((((((...((......(((((.(((((((...((.((..(((.......(((....))))))..)).))))))))).)))))..))....)))))))))..))..))).	0.480 -14.61

celegans

chromosome:II:7489381:7489500:1

intergenic ## {SimpF: WRM0636aC11 1 fosmid,WRM0613dH09 1 fosmid,WRM0621bG05 1 fosmid,WRM0629bF07 1 fosmid,WRM0621dE08 1 fosmid,WRM0611cE04 1 fosmid,WRM0633aE12 1 fosmid}

block2781 [novel_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
no	0.710	no	no	0.41/0.41	22/22/1.00	0.0	0.0	1	0	1	0	2	13	5arm	1	nd	0.36	4	1	1	na	na

		reads	miRBase family seed
seed	---UUUCCAA--------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	--CTTTCCAAAATGACTGCAACGT------------------------------------------------------	22	1
celegans	aaCTTTCCAAAATGACTGCAACGTcgaaaaaacgattattcaaatttacaactgacgaagaggagcattgtgtgagtt
	******************************************************************************
celegans	(((((..((.((((.((....(((((.......((((.....))))......)))))....))..)))).)).)))))	0.860 -8.52

celegans

chromosome:III:598718:598795:-1

intergenic ## {SimpF: WRM0614bA07 -1 fosmid}

block5102 [novel_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
no	0.584	no	no	0.38/0.38	21/21/1.00	0.0	0.0	1	0	1	0	0	27	5arm	1	nd	0.33	4	1	1	na	na

		reads	miRBase family seed
seed	-CAUGUUA---------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	TCATGTTACGATTTTTCTCGG--------------------------------------------------------------------------------------	21	1
celegans	TCATGTTACGATTTTTCTCGGaaaaatatttcaagtaaagtttataaatgcgtttttttgtctaaattttaattagtttttttttcaaaaaaagtcaaattatgtgg
	***********************************************************************************************************
celegans	.(((((...(((((((....((((((.........(((((((((((((........)))))..)))))))).........))))))...))))))).....))))).	0.990 -13.57

celegans

chromosome:IV:16451685:16451791:-1

intergenic ## {SimpF: WRM0621bE04 -1 fosmid}

block5158 [novel_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
no	0.038	no	no	0.43/0.43	21/21/1.00	0.0	0.0	1	0	1	0	1	31	5arm	1	nd	0.43	5	1	1	na	na

		reads	miRBase family seed
seed	--UAGAGCC------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	-GTAGAGCCATGTCGTTGATTT-----------------------------------------------------------------------------------------	21	1
celegans	tGTAGAGCCATGTCGTTGATTTatgaagactgatttaatttgaagagtctatgaattcagataagatctctaaactaaatgagttggcacgtgtgacgatgtgaaatgcaa
	***************************************************************************************************************
	-------------------------------------------------------------------------------------------------------------------------	Y116A8C.3 Y116A8C.3 Y116A8C.3
celegans	((((....((((((((((.....((..((((.(((((.(((..(((((((.((....))....))).))))))).))))).))))..))....))))))))))...)))).	1.000 -26.40

celegans

chromosome:IV:16918164:16918274:-1

Opposite_strand|Intronic_coding|Y116A8C.3|Y116A8C.3 ## Y116A8C.3|protein_coding|Y116A8C.3|Y116A8C.3 [Source:RefSeq_peptide;Acc:NP_503003] ## {SimpF: WRM0621dF01 -1 fosmid}

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miR-Intess™

block6612 [novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH]

block7217 [novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH]

block7221 [novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH]

block7871 [novel_lenNOK_shortStem_nonpairedHIGH_bulgeHIGH]

block862 [novel_shortStem_nonpairedHIGH_bulgeHIGH]

block2292 [novel_shortStem_nonpairedHIGH_bulgeHIGH]

block2377 [novel_shortStem_nonpairedHIGH_bulgeHIGH]

block2781 [novel_shortStem_nonpairedHIGH_bulgeHIGH]

block5102 [novel_shortStem_nonpairedHIGH_bulgeHIGH]

block5158 [novel_shortStem_nonpairedHIGH_bulgeHIGH]