miR-Intess: classification

other hairpins

novel_shortStem_nonpairedHIGH_bulgeHIGH (13 loci)

block6147 [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	0.029	no	no	0.29/0.29	21/21/1.00	0.0	0.0	1	0	1	0	4	24	5arm	1	nd	0.33	4	1	1	na	na

		reads	miRBase family seed
seed	-----AUCUAAG----------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	----TATCTAAGGAACTTGAAACTT---------------------------------------------------------------------------------	21	1
celegans	gtgaTATCTAAGGAACTTGAAACTTtagaacattttgttggctgaaaatttaattttcttcaaataaatatgttctatgcccaatttttaagttagtttttgatca
	**********************************************************************************************************
	--------------------------------------------------------------------------------------------------------------------	Y105C5B.21a Y105C5B.21 jac-1
	--------------------------------------------------------------------------------------------------------------------	Y105C5B.21b.1 Y105C5B.21 jac-1
celegans	.((((....((..(((((((((.((((((((((((((((....((((((...))))))....)))))).)))))))).....)).)))))))))..))....))))	1.000 -20.80

celegans

chromosome:IV:16026368:16026473:1

Opposite_strand|Intronic_non-coding|Y105C5B.21b.1|Y105C5B.21 ## Opposite_strand|Boundary_non-coding|Y105C5B.21b.2|Y105C5B.21 ## Opposite_strand|Intronic_coding|Y105C5B.21a|Y105C5B.21 ## Y105C5B.21|protein_coding|jac-1|jac-1 encodes the C. elegans p120 catenin orthologue. by homology, JAC-1 is predicted to be a component of the cadherin-catenin complex (CCC). although loss of jac-1 activity via RNAi does not result in obvious defects, jac-1(RNAi) does enhance embryonic morphogenesis defects produced by weak loss-of-function mutations in hmp-1/alpha-catenin, suggesting that JAC-1 positively regulates cadherin-catenin function in the embryo. JAC-1 likely regulates this function by promoting association between the actin cytoskeleton and the cadherin-catenin complex. a JAC-1 reporter fusion localizes to embryonic adherens junctions in a manner that is dependent upon the presence of HMR-1/cadherin, with which it specifically interacts in the yeast two-hybrid system. [Source: WormBase] ## {SimpF: WRM0613dE04 1 fosmid}

block6277 [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	0.711	no	no	0.24/0.24	21/21/1.00	0.0	0.0	1	0	1	0	3	17	3arm	1	nd	0.38	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------UAGAGUA----------------	1	novel
		len	cloning frequencies
			CE1
	-------------------------------------------------------------------GTAGAGTATTATTTTGAAACT---	21	1
celegans	accgtgactgagataacaccatagagtactgtatcgaacataacaggaccttcggacatcattttatGTAGAGTATTATTTTGAAACTgta
	*******************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<..................................	C30H6.2 C30H6.2 tag-141
celegans	((.((...((((((((.((((((((((..(((.(((((............))))))))..))))))))....)).))))))))..)).)).	0.970 -13.10

celegans

chromosome:IV:17366351:17366441:1

intergenic ## {SimpF: WRM0619bA10 1 fosmid,WRM0637cF11 1 fosmid,WRM0629dG02 1 fosmid,WRM0628dA12 1 fosmid,WRM0613aG09 1 fosmid,WRM0632cE07 1 fosmid,WRM0618bE06 1 fosmid}

block6573 [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	0.255	no	no	0.29/0.29	21/21/1.00	0.0	0.0	1	0	1	0	1	32	5arm	1	nd	0.43	5	1	1	na	na

		reads	miRBase family seed
seed	--AAUAUGA------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	-CAATATGATGTTATCCAAAGT-----------------------------------------------------------------------------------	21	1
celegans	aCAATATGATGTTATCCAAAGTtcttcgaaattctccacttcttttccgtgtcgcacaaccgaaggatcatgaacgaattattaagtttctggataaacattttg
	*********************************************************************************************************
	..........>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	W02D7.4 W02D7.4 W02D7.4
celegans	.(((.(((...(((((((.....(((...(((((.....(((...(((...(((......))).)))....))).)))))...)))....))))))).))).)))	0.750 -17.20

celegans

chromosome:V:8297402:8297506:-1

Same_strand|Boundary_non-coding|W02D7.4|W02D7.4 ## W02D7.4|protein_coding|W02D7.4|W02D7.4 [Source:RefSeq_peptide;Acc:NP_505142] ## {SimpF: WRM0630bG12 -1 fosmid,WRM068cD11 -1 fosmid,WRM0619bF11 -1 fosmid,WRM0627aB01 -1 fosmid,WRM0641cD02 -1 fosmid,WRM0610aB08 -1 fosmid,WRM0641aD03 -1 fosmid,WRM0629aF03 -1 fosmid,WRM063cD01 -1 fosmid,WRM0641aC12 -1 fosmid,W02D7.4 -1 Expression_profile,WRM0623dE08 -1 fosmid}

block6594 [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	0.568	no	no	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	1	26	3arm	3	nd	0.38	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------UUAGCGU--------------	1	novel
		len	cloning frequencies
			CE1
	------------------------------------------------------------------------------GTTAGCGTTAAGCCATGCCAG-	21	1
celegans	gactggatgtacaatgtgtccaaagtccgtgatttctaccaacctcccagacggaagaatatgtttcttggtctctggGTTAGCGTTAAGCCATGCCAGt
	****************************************************************************************************
celegans	.((((((((...(((((.((((.((.(((.((.((((.((............)).))))......)).))).)).))))...)))))....))).)))))	0.510 -22.90

celegans

chromosome:V:8840737:8840836:-1

intergenic ## {SimpF: WRM067dE11 -1 fosmid,WRM0615bG03 -1 fosmid,WRM0620bE07 -1 fosmid,WRM0612bC01 -1 fosmid,WRM067aB04 -1 fosmid,WRM0615dE07 -1 fosmid,WRM0620cD11 -1 fosmid,WRM0615bD11 -1 fosmid,WRM0639aE12 -1 fosmid,WRM0618aE10 -1 fosmid,WRM0626cH02 -1 fosmid}

block6604 [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	0.568	no	no	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	1	26	3arm	3	nd	0.38	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------UUAGCGU--------------	1	novel
		len	cloning frequencies
			CE1
	------------------------------------------------------------------------------GTTAGCGTTAAGCCATGCCAG-	21	1
celegans	gactggatgtacaatgtgtccaaagtccgtgatttctaccaacctcccagacggaagaatatgtttcttggtctctggGTTAGCGTTAAGCCATGCCAGt
	****************************************************************************************************
celegans	.((((((((...(((((.((((.((.(((.((.((((.((............)).))))......)).))).)).))))...)))))....))).)))))	0.510 -22.90

celegans

chromosome:V:8882832:8882931:-1

intergenic ## {SimpF: WRM0627bB06 -1 fosmid,WRM0611cD09 -1 fosmid,WRM0638aA04 -1 fosmid,WRM0625aH11 -1 fosmid,WRM0632cD08 -1 fosmid,WRM0614bC01 -1 fosmid,WRM0620dF01 -1 fosmid,WRM0632aF08 -1 fosmid,WRM0636aD03 -1 fosmid,WRM0630cG07 -1 fosmid,WRM0627cF05 -1 fosmid,WRM0628dF12 -1 fosmid,WRM0615bD11 -1 fosmid,WRM064dE05 -1 fosmid,WRM063bH07 -1 fosmid,WRM068aG12 -1 fosmid,WRM0614aB05 -1 fosmid}

block7635 [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	0.453	no	no	0.23/0.23	22/22/1.00	0.0	0.0	1	0	1	0	0	13	5arm	1	nd	0.36	4	1	1	na	na

		reads	miRBase family seed
seed	-UUUAUGA--------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	GTTTATGAAGACGATTATTATT------------------------------------------------------------	22	1
celegans	GTTTATGAAGACGATTATTATTatgaagaactggcgaatactattatgaagaaccggccaacgagtagtggtcgagtggacg
	**********************************************************************************
celegans	((((((...(((.((((((............((((.....................))))...)))))).)))..)))))).	0.810 -15.06

celegans

chromosome:X:1643930:1644011:-1

intergenic ## {Repeats: trf 37 47 0 class=trf} ## {SimpF: WRM0619cB06 -1 fosmid,WRM0637cC01 -1 fosmid,WRM0635bH10 -1 fosmid,WRM0634dF02 -1 fosmid,WRM061aG07 -1 fosmid,WRM0626bE10 -1 fosmid,WRM0626cF12 -1 fosmid,WRM0624cB10 -1 fosmid,WRM0641aB04 -1 fosmid,WRM0614bA02 -1 fosmid}

block4107 [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	0.171	no	no	0.54/0.54	24/24/1.00	0.0	0.0	1	0	1	0	1	31	5arm	1	nd	0.38	4	1	1	na	na

		reads	miRBase family seed
seed	--AGCAUUU-------------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	-GAGCATTTGAGCGAAGGGATGGTC---------------------------------------------------------------------------------------------	24	1
celegans	gGAGCATTTGAGCGAAGGGATGGTCtacagtaaagttgaggggtgcatcaagggattcacaagtccattttatttgctctccttttcgacatatccatatcccaatgtgaaggcgctt
	**********************************************************************************************************************
celegans	.((((.(((..(((..((((((.......((......((((((.(((.....((((......))))........))).))))))....)).......))))))..)))..))).))))	0.930 -30.86

celegans

chromosome:IV:3897069:3897186:-1

intergenic ## {SimpF: WRM0641bD04 -1 fosmid,WRM0634bC03 -1 fosmid,WRM0628dD05 -1 fosmid,WRM068aF02 -1 fosmid}

novel_lenNOK_shortStem_nonpairedHIGH (12 loci)

block1214 [novel_lenNOK_shortStem_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	0.609	no	no	0.12/0.12	25/25/0.00	0.0	0.0	1	0	1	0	3	6	5arm	1	nd	0.40	3	1	1	na	na

		reads	miRBase family seed
seed	----UUAGUUA-------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	---GTTAGTTATAATAATCAAATTTTTT--------------------------------------------	25	1
celegans	tatGTTAGTTATAATAATCAAATTTTTTcttccgtgactcgatagagaagaaggaatgtgtcggacccgtat
	************************************************************************
	......................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	H16D19.4 H16D19.4 H16D19.4
celegans	((((...(((...(((.((...((((((((..((.....))..))))))))..)).)))....))).)))).	0.520 -10.80

celegans

chromosome:I:12640710:12640781:1

Opposite_strand|Boundary_non-coding|H16D19.4|H16D19.4 ## H16D19.4|protein_coding|H16D19.4|H16D19.4 [Source:RefSeq_peptide;Acc:NP_493200] ## {SimpF: WRM066cD10 1 fosmid,WRM0629bB02 1 fosmid,WRM069aG07 1 fosmid,WRM0612aD06 1 fosmid}

block1542 [novel_lenNOK_shortStem_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	0.458	no	no	0.44/0.44	25/25/0.00	0.0	0.0	1	0	1	0	3	21	3arm	2	nd	0.36	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------UGUUGAU--------------------	1	novel
		len	cloning frequencies
			CE1
	------------------------------------------------------------------------GTGTTGATTGTTGGGTCCAAGTTTG---	25	1
celegans	agacttctttcctcctcggagtcggtttggggacgcttttttggtacaagttcatcttctgtgttttcaattGTGTTGATTGTTGGGTCCAAGTTTGgtc
	****************************************************************************************************
celegans	.((((.(((....((.(((((((((.(((..(((((.....(((.......)))......)))))..))).....)))))).)))))...)))...))))	0.870 -19.30

celegans

chromosome:II:2591007:2591106:-1

intergenic ## {SimpF: WRM0627bE01 -1 fosmid,WRM066aF05 -1 fosmid,WRM063cF01 -1 fosmid,WRM0627cD03 -1 fosmid}

block1543 [novel_lenNOK_shortStem_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	0.458	no	no	0.44/0.44	25/25/0.00	0.0	0.0	1	0	1	0	3	21	3arm	2	nd	0.36	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------UGUUGAU--------------------	1	novel
		len	cloning frequencies
			CE1
	------------------------------------------------------------------------GTGTTGATTGTTGGGTCCAAGTTTG---	25	1
celegans	agacttctttcctcctcggagtcggtttggggacgcttttttggtacaagttcatcttctgtgttttcaattGTGTTGATTGTTGGGTCCAAGTTTGgtc
	****************************************************************************************************
celegans	.((((.(((....((.(((((((((.(((..(((((.....(((.......)))......)))))..))).....)))))).)))))...)))...))))	0.870 -19.30