miR-Intess: classification

noncloned miRBase miRNAs

miRNAknown_rep_shortStem_randfoldOK (2 loci)

cel-mir-1833

block4872 (miRBase cel-mir-1833) [miRNAknown_rep_shortStem_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
miRBase cel-mir-1833	0.001	no	DNA,UNKNOWN	0.52/0.52	23/23/1.00	nd	nd	0	0	0	0	0	13	3arm	1	nd	0.14	2	0	0	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------GAGGCUU---------------	0	novel
		len	cloning frequencies

cel-miR-1833	--------------------------------------------------------------------------------CGAGGCTTGCGAAATAAGTGTGC	23
celegans	ACGCTTACTTCGCAA--------------GCCTCGCGCGTTTTCTTTT----------CAAGA------GAAAAAGCGTGCGAGGCTTGCGAAATAAGTGTGC
cbriggsae	GGCCAGATCTCCCACAAGTCTAGCACAAGTCTCCGAGCACATTATTCTATGTATTAGCTAAGACTTGTGGGAGGCTTGTGCAAGACTTGTGGAAGACTTGTCC
ppacificus	-----GCCTTTCTAC--------------TTTCCGAGC-CCTCATTCGCCAT------CAAAC----TGGGAACGGTGTGTGAGGCTTAAAAAATA-GAATGC
	* * * * * * * * * *
	++++++++++++++++++++ +++++++++++++++++++ +++++ +++++++++++++++++++++++++++++++++++++++	Y41E3.4 Y41E3.4 ers-1
celegans	(((((((.((((((( (((((((((((((((((.. ...)) ))))..)))))))))))))))))).)))))))..	1.000 -47.70
cbriggsae	(((.((.(((.((((((((((.((((((((((((...((((....(((..((....))..)))..)))))))))))))))).)))))))))).))))).))).	0.984 -49.70
ppacificus	((..(((((. (((..(((. ((((((.((((.( (.... ...))..)))).)))))))))..))).)) ))).))	1.000 -21.10

celegans	chromosome:IV:15012308:15012380:-1	Same_strand\|Intronic_coding\|Y41E3.4\|Y41E3.4 ## Y41E3.4\|protein_coding\|ers-1\|ers-1 encodes a glutaminyl (Q) tRNA synthetase that affects growth and embryonic and larval viability in large-scale RNAi screens. it is predicted to be mitochondrial. [Source: WormBase] ## {Repeats: trf 13 36 0 class=trf,Ce000253 114 137 1 class=UNKNOWN} ## {SimpF: Y41E3.4 -1 Expression_profile,oe = 1.03 0 CpG} ## {MIR: cel-mir-1833}
cbriggsae	chromosome:chrV:15256935:15257037:1	Same_strand\|Intronic_coding\|NM_065290 ## {Repeats: DNA2-10_CB 1 1355 1 class=DNA} ## {SimpF: trf,trf}
ppacificus	chromosome:chrUn:74025648:74025719:1	intergenic

miRBaseNonMapped_loopOverlap_randfoldOK (1 loci)

block4071 (miRBaseNonMapped cel-mir-1832) [miRBaseNonMapped_loopOverlap_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
miRBaseNonMapped cel-mir-1832	0.001	no	UNKNOWN	0.57/0.57	21/21/1.00	nd	nd	0	0	0	0	26	-2	3arm_loop	3	nd	0.19	2	0	0	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------GGGCGGA---------------------------------------	0	novel
		len	cloning frequencies

cel-miR-1832	--------------------------------------------------------TGGGCGGAGCGAATCGATGAT--------------------------	21
celegans	TCTCCCTCCAAAATATGAACTCTCCGACCAATCAGCGCAGTTGAACTCTGCTAAAGTGGGCGGAGCGAATCGATGATTGGTCGAAGTTCAAATTTTGGAAGAA
cbriggsae	-----------------------------CACCACCAGAGGCTCTCACCACAAAAGTGGGCGGAGCCAAGGGATGGCT-------------------------
cbrenneri	-------------------CTATTTTTTCACTTTTCTCAGC---------CGACAGGGGGCGGAGCGAAGTGAAAAATGG-----------------------
cjaponica	-------GCAAGATAACAA-----AAAAAACATACCGAAAGAAGTCTCCACGCCTGTGGGCGGAGCTTATGCGGTATTCCCATCCAACAATCCTCTCGC----
	* * * * ********* * *
	-----------------------------------------------------------------------------------------------------------------	Y54G2A.2a Y54G2A.2 Y54G2A.2
	-----------------------------------------------------------------------------------------------------------------	Y54G2A.2b Y54G2A.2 Y54G2A.2
celegans	(((...((((((((.((((((...((((((((((.((...(((..(((((((......))))))))))..)).)))))))))).)))))).))))))))))).	1.000 -43.70
cbriggsae	..(((((...((((((..((((....))))..))))))...)).)))..	1.000 -22.80
cbrenneri	(((.(((((((((((.(((.(( (.......))).))).))))))))))))))	1.000 -20.40
cjaponica	((.(((...... .......((((((....(((.((((..(((....))))))))))...))))))................))).))	0.978 -19.85

celegans	chromosome:IV:2794097:2794199:-1	Opposite_strand\|Intronic_coding\|Y54G2A.2a\|Y54G2A.2 ## Y54G2A.2\|protein_coding\|Y54G2A.2\|Y54G2A.2a [Source:RefSeq_peptide;Acc:NP_001023492] ## {Repeats: Ce000170 88 109 1 class=UNKNOWN}
cbriggsae	chromosome:chrII:8445808:8445950:-1	Same_strand\|Intronic_coding\|NM_001047975 ## Opposite_strand\|Intronic_coding\|NM_001011629
cbrenneri	chromosome:chrUn:142150396:142150447:1	intergenic
cjaponica	chromosome:chrUn:85818211:85818297:1	Opposite_strand\|Boundary_coding\|NM_001027993 ## Opposite_strand\|Intronic_coding\|NM_001002841

miRBaseNonMapped_randfoldOK (1 loci)

cel-mir-1832

block2229 (miRBaseNonMapped cel-mir-1832) [miRBaseNonMapped_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
miRBaseNonMapped cel-mir-1832	0.001	no	Unknown	0.57/0.57	21/21/1.00	nd	nd	0	0	0	0	8	10	3arm	3	nd	0.10	1	0	0	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------------------GGGCGGA-----------------------------------	0	novel
		len	cloning frequencies

cel-miR-1832	------------------------------------------------------------------------------------------T--GGGCGGAGCGAATCGATGAT----------------------	21
celegans	--------------------CCGACCAATCAGCGTTTTC-------------GAACTCCGCCCAATCC----ATCTAATTGGTTGGAAAGT--GGGCGGAGCGAATCGATGATTGGTCGGG--------------
cremanei	AGATACTGTTCCACAACGTCTCCATCAATCAGATTTCTC-------------GCATTCCGCCCGTTTA-------CAATCGGTTGGGCGGGACGGGCGGAACGAGCT--CCTTTGATATGGAGACCAGCTATCT-
cbriggsae	----------------------AGCCAAAAATT-------------------AGGCTCCGCCCATTTT--------------TTTTAAAGT--GGGCGGAGCCTATT-----TTAAAGT----------------
cjaponica	----------------------GATTGACAGTTGTTTTTGGTGTTTGCGAACAAGCTCCGCCTACTTTTTGATTTTCAATTTTTTAAATGT--GGGCGGAGCTTGTC--CGATTAGATTAAGGTATTGTGTTTTC
ppacificus	----------------------GAGAGAGTGGCGCTCTC-------------GCACCCCTCGTCAGCC--------AATGAGCTTGATAGG--GGGCGGAGACGCCA--CTGTTAG-------------------
	* ** * * * *****
	----- ------------------- ---------------- ------------------- ---------------------------- -----	C01F1.6 C01F1.6 C01F1.6
celegans	(((((((((((.((..((( (..(((((((((.((( (.((....)).))))...) )))))))))))).)).))))))))))).	1.000 -48.80
cremanei	((((((((.........((((((((..((((((...((( (..((((((((((((. (((....)))....)))))))))))))))).. ..))))))))))))))))).)))))	0.954 -45.30
cbriggsae	......(((.( (((((((((((((((( ....))))) )))))))))))).) )).....	1.000 -32.50
cjaponica	.....(((((...(((((((.....((.(((((((((((((((..(((((...........))))).)) ))))))))))))). )).....))))))).)))))......	0.995 -37.80
ppacificus	..((.((((((((((.( ((.(((((.((((((. .....))).)))))) )))))))).))))) )).))..	1.000 -39.00

celegans	chromosome:II:4284441:4284522:1	Opposite_strand\|Intronic_coding\|C01F1.6\|C01F1.6 ## C01F1.6\|protein_coding\|C01F1.6\|C01F1.6 [Source:RefSeq_peptide;Acc:NP_494753] ## {Repeats: CEREP20 49 70 1 class=Unknown} ## {SimpF: C01F1.6 1 Expression_profile,WRM0624aB08 1 fosmid}
cremanei	chromosome:chrUn:65023130:65023241:1	Opposite_strand\|Exonic_coding\|NM_067756
cbriggsae	chromosome:chrIII:10673025:10673146:1	Same_strand\|Intronic_coding\|NM_170975 ## Opposite_strand\|Intronic_coding\|NM_075402
cjaponica	chromosome:chrUn:110151886:110151994:1	Same_strand\|Intronic_coding\|NM_064565
ppacificus	chromosome:chrUn:65000043:65000164:-1	intergenic

miRNAknown_RNA_shortStem_loopOverlap_nonpairedHIGH_bulgeHIGH (1 loci)

cel-mir-1831

block1747 (miRBase cel-mir-1831) [miRNAknown_RNA_shortStem_loopOverlap_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
miRBase cel-mir-1831	0.056	snRNA	no	0.64/0.64	22/22/1.00	nd	nd	0	0	0	0	0	-1	5arm_loop	1	nd	0.32	4	0	0	na	na

		reads	miRBase family seed
seed	---------------------CCUGGCU-------------------------------------------------------	0	novel
		len	cloning frequencies

cel-miR-1831	--------------------ACCTGGCTGGGGGTATCTCGTG-----------------------------------------	22
celegans	--------------------ACCTGGCTGGGGGTATCTCGTGATCATGAAGACGGGATCCCCATGGTGA--------------
cbriggsae	--------------------ACCTGGCTGGGGGTATTCCGTGATCATGAAGACGGAATCCCCATGGCGAGGC-----------
ppacificus	--GCAGCTCCTCATAAACTTACCTGGCTGGGGGTCTCTCGTGATCATGAAGACGGGAACCCTACGGTGAGGCGTGACCATTGC
cjaponica	GCTCGACGACTCATAAACTTACCTGGCTGGGGGTATCTCGCGATCAACAAGGCGGGATCCCCATGGTGAGGCCTGTCTATTGC
cbrenneri	----GGCGACTCATAAACTTACCTGGCTGGGGGTATTTCGCGATCATCAAGGCGGAATCCCCATGGTGAGGCCTGCC------
cremanei	-----GCGACTCATAAACTTACCTGGCTGGGGGTATTCTGTGATCATCAAGGCAGAATCCCCATGGCGAGGCCTTTCCATTGC
	************** * * *** * * * * *** *
	+++++ +++++++++++++++++++++++++++++++++++++++++++++++++ +++++	C15F1.5b C15F1.5 C15F1.5
	+++++ +++++++++++++++++++++++++++++++++++++++++++++++++ +++++	C15F1.5a C15F1.5 C15F1.5
	>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>	C15F1.9 C15F1.9 sup-39
celegans	.....((((((((.(((((((..........))))))))))).))))..	1.000 -17.60
cbriggsae	.(((.((((((((.(((((((..........))))))))))).)))).))).	1.000 -25.80
ppacificus	((((....((((...((((((......(((((.((((((..........)))))))))))..))))))..))))...))))	0.979 -24.80
cjaponica	.......(((.......((((((......((((.(((((((..........)))))))))))..))))))....)))......	0.950 -27.70
cbrenneri	(((..........((((((......((((.(((((((..........)))))))))))..)))))))))....	0.857 -24.60
cremanei	................(((.((((((((.(((((((..........))))))))))).)))).)))............	0.990 -24.20

celegans	chromosome:II:6968442:6968490:-1	Same_strand\|Intronic_coding\|C15F1.5a\|C15F1.5 ## Same_strand\|Exonic_non-coding\|C15F1.9\|C15F1.9 ## C15F1.5\|protein_coding\|C15F1.5\|C15F1.5b [Source:RefSeq_peptide;Acc:NP_001040742] ## C15F1.9\|snRNA\|sup-39\|C15F1.9, snRNA [Source:RefSeq_dna;Acc:NR_002616] ## {SimpF: WRM0638bC12 -1 fosmid,WRM069aH05 -1 fosmid,WRM061cD05 -1 fosmid,WRM0635cG12 -1 fosmid,WRM0618aC01 -1 fosmid,WRM0625bE07 -1 fosmid,C15F1.D -1 Expression_profile,WRM0637cD07 -1 fosmid,CEOP2272 1 Operon} ## {MIR: cel-mir-1831}
cbriggsae	chromosome:chrV:12177554:12177642:1	Opposite_strand\|Intronic_coding\|NM_074155 ## Same_strand\|Intronic_coding\|NM_001113262
ppacificus	chromosome:chrUn:15658487:15658567:-1	Opposite_strand\|Intronic_coding\|NM_028737
cjaponica	chromosome:chrUn:125685895:125685977:1	intergenic
cbrenneri	chromosome:chrUn:68563240:68563312:-1	Same_strand\|Intronic_coding\|NM_063029
cremanei	chromosome:chrUn:132231022:132231099:1	Same_strand\|Intronic_coding\|NM_001047277 ## Opposite_strand\|Intronic_coding\|NM_205265

miRNAknown_lenNOK_loopOverlap_nonpairedHIGH_bulgeHIGH (1 loci)

cel-mir-261

block2317 (miRBase cel-mir-261) [miRNAknown_lenNOK_loopOverlap_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
miRBase cel-mir-261	0.889	no	no	0.32/0.32	19/19/0.00	nd	nd	0	0	0	0	15	-9	3arm_loop	1	nd	0.42	4	0	0	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------AGCUUUU------------------------------------	0	novel
		len	cloning frequencies

cel-miR-261	--------------------------------------------------------------------TAGCTTTT-TAGT--TTTCACG----------------------	19
celegans	TGATGGCTTTTCTGGATTTGTTCCCTTCACGTGTAGAAAGAAACGAGCAAAAAAAATCTTAGTGT---TAGCTTTT-TAGT--TTTCACGGTGAATATGGATATT-------
cbrenneri	GGATGAATGCAAAGAAAAGTTGCCGACTAT-----CGAAGAAGCGACAAAAATGCATTATCAACTGAACAGCTTTTTTGATTGTTTCTCGATTGCTGCTGATATTGCCCACC
cjaponica	CGAAAA-------AAATTGGT----------------ACAAAACTTTCAAAAAAAA-----AATTGCAGAGCTTTTGTTGT--TTTTTCG----------------------
	** * * * ** * **** * * ******* * * *
	<<<<<<................................................................ ........ .... ...................... .....	B0034.4 B0034.4 B0034.4
celegans	.....(((((((((.((.((.......)).)).)))))......))))........((...(((. .((((... .))) )..)))...))...........	1.000 -14.50
cbrenneri	((.((...((((.....(((.((.....(( ((.((((((((((((((.((....((....))...)).)))))).)))))))))))).)).)))....)))).))))	0.988 -24.50
cjaponica	(((((( ((...... (((((((((((((...... ..))).)))).))))))..) )))))))	0.999 -11.10

celegans	chromosome:II:5969021:5969119:1	intergenic ## {SimpF: WRM0628aH10 1 fosmid,WRM0627cF01 1 fosmid,WRM0634dD10 1 fosmid,WRM0632bD02 1 fosmid,WRM0612dB10 1 fosmid,WRM0624cG04 1 fosmid,WRM0634aB06 1 fosmid,WRM0614aH11 1 fosmid,WRM0622dH03 1 fosmid} ## {MIR: cel-mir-261}
cbrenneri	chromosome:chrUn:84845634:84845740:1	Opposite_strand\|Intronic_coding\|NM_001022802
cjaponica	chromosome:chrUn:14565971:14566109:-1	Same_strand\|Boundary_coding\|NM_001029165

miRNAknown_lenNOK_multiarm_DicerNOK_shortStem_mirtron (1 loci)

cel-mir-1019

sblock9 (miRBase cel-mir-1019) [miRNAknown_lenNOK_multiarm_DicerNOK_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
miRBase cel-mir-1019	0.029	no	no	0.36/0.42	24/25/0.50	nd nd	nd nd	0 0	0 0	0 0	0 0	0 0	3 7	5arm 3arm	1 1	1 0	0.20 0.35	2 5	0	0	3	0

		reads	miRBase family seed
seed	--------------UGAGCAU---------------------------------------------------------------------------------------------------	0	novel
seed	--------------------------------------------------------------------------------UGUAAU-----U----------------------------	0	novel
		len	cloning frequencies

cel-miR-1019	-------------------------------------------------------------------------------CTGTAAT-----TCCACATTG----------CTTTCCAG--	24
cel-miR-1019*	-------------GTGAGCATTGTT---------------------CGAGTTTCATTTT-------------------------------------------------------------	25
celegans	-------------GTGAGCATTGTT---------------------CGAGTTTCATTTTTAATAAAATTTATTTAAAAACTGTAAT-----TCCACATTG----------CTTTCCAG--
cremanei	-------------GTGAGCATTGTA---------------------TGAGCCA-----------------ATCTGAAAAAACCTAC-----TTCAGGTTGAGAATACAGTTTTAA-----
cjaponica	-------------GTGAGCATAGTT---------------------CGAGTTACAGTA------------ATCCAATGACTACTGT--ATCTCCACTTTG----------CTTTC-----
cbrenneri	-------------GTGAGCATCGTT---------------------GGATTTATAGTTTTTTT-------TTCAAAAAATTCTAACTATAATCCACTTTG----------CTTAA-----
ppacificus	TTGTTGAAGAACTGTGAGCATTATTGATCTTTGATCTTTTGAATTGTGAATCATATTTCGGAC-------ACCTGATCAGTCTAAT--TAGTGCTTTTGG----------TTTACAATGA
	******** * ** * * * * * * **
	>>>>> ++++++++++++ ++++++++++++++++++++++++++++++++++++++++ +++++++++ ++++++++ >>>>>	M04C9.5 M04C9.5 dyf-5
celegans	..(((((.(((. .(((((.(((((((((..........))))))).)).))) )).))).)) ))).....	1.000 -13.10
cremanei	.((((.(((((( (....(( (((((((......... )))))))))...))))))))))).	1.000 -14.80
cjaponica	..(((((.(((. .(((.((((((( .((....)).)))))) ).))).))).)) )))..	1.000 -19.40
cbrenneri	.((((((..((. (((.((((((((..((( (....))))....)))))))))))))..)) )))).	1.000 -17.10
ppacificus	((((((..((((((.((((((((.......((((((.((((((.((((...)))).)))))). ....))))))...... )))))))).))) ))).))))))	0.996 -23.82

celegans	chromosome:I:9361588:9361656:1	Same_strand\|Intronic_coding\|M04C9.5\|M04C9.5 ## Same_strand\|Boundary_coding\|M04C9.5\|M04C9.5 ## M04C9.5\|protein_coding\|dyf-5\|dyf-5 encodes a putative MAP kinase orthologous to human MAK/ICK (OMIM:154235), Chlamydomonas reinhardtii LF4, and Leishmania mexicana MPK9. DYF-5 negatively regulates cilial length, restricts KAP-1 to middle ciliary segments, is required for normal localization of six IFT components, and is required for OSM-3 to comigrate normally with IFT particles. DYF-5 is also required for dye-filling of amphid and phasmid neurons and for normal chemotaxis, dauer formation, and male mating. DYF-5 is expressed in head neurons (including amphid neurons), tail neurons (including phasmid neurons), CAN cells, excretory canal neurons, posterior lateral ganglion neurons and in many male tail cells. dyf-5 mutant cilia are abnormally elongated, either failing to enter the amphid channel or accumulating IFT proteins at their distal ends, whereas DYF-5 overexpression results in truncated cilia. the dyf-5 promoter region contains an X-box, predicted to be bound and transcriptionally activated by DAF-19, and dyf-5 is regulated by DAF-19 in vivo. dyf-5 animals are slightly shorter than normal. [Source: WormBase] ## {SimpF: WRM0625aB10 1 fosmid,WRM0632bF02 1 fosmid,WRM0612aC09 1 fosmid,WRM064dG06 1 fosmid} ## {MIR: cel-mir-1019}
cremanei	chromosome:chrUn:17538323:17538431:1	Opposite_strand\|Intronic_coding\|NM_059002
cjaponica	chromosome:chrUn:95002809:95002917:-1	Opposite_strand\|Intronic_coding\|NM_007674 ## Same_strand\|Boundary_coding\|NM_060092 ## Same_strand\|Boundary_non-coding\|NM_199946
cbrenneri	chromosome:chrUn:140316700:140316808:-1	Same_strand\|Boundary_coding\|NM_060092 ## Same_strand\|Boundary_non-coding\|NM_199946
ppacificus	chromosome:chrUn:64451867:64451967:1	Opposite_strand\|Intronic_coding\|NM_132581 ## Same_strand\|Intronic_coding\|NM_203770

miRNAknown_lenNOK_randfoldOK (1 loci)

cel-mir-1820

block5575 (miRBase cel-mir-1820) [miRNAknown_lenNOK_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
miRBase cel-mir-1820	0.001	no	no	0.28/0.28	25/25/0.00	nd	nd	0	0	0	0	22	3	5arm	1	nd	0.16	2	0	0	na	na

		reads	miRBase family seed
seed	-----------------------------------------UUUGAUU----------------------------------------------------------------------------------------------------------	0	novel
		len	cloning frequencies

cel-miR-1820	----------------------------------------TTTTGATTG-TTTTTCGATG-ATGTTC---------------------------------------------------------------------------------------	25
celegans	------------------TTCAAAAATTGCATTTTCCATCTTTTGATTG-TTTTTCGATG-ATGTTCGTTAAATCGGTATAAG---CGAACCATTGTAAA---CAATCAAAGAATGGAGAATCAATTTATGAT---------------------
cremanei	TCTGGTATTTTTCTGATATTTTTCTGATCTCATTTCCATTTTTTGATTG-TTATTCGATG--ATGTCGTCGAATGGAATTGT----CGAACCATTGAAAA---TAATCAAAAAATGGAGAGAGATTCAAGTTTTGAATTGGTAAGAAGTCCAGA
cbriggsae	----------------------------------------TTTTGATTGATTTTTCGGTT--TTGTTATCTATTTTCGGCAT----AGAAACTCTGAAAAACGCAATTTTAA------------------------------------------
cbrenneri	---------------------------------CCGTTCTTTTTGATTGTTTTTACTAGG-ATCTGAATTCTTTT-----------CAGGACCTCCACAA---TAATCAGA-------------------------------------------
cjaponica	GTGTCAATGCTTACTATACTCGCGGAGGCTTGTCGCCGTCTTTTGATTG-TTATTCGATG-ATGTTCGACGTTTTTGTGAATACGTCGAACCATTGAAAA---CTGTCAAAACATGACGATTGTGCCGAAATTTGTCAGGTTTGTGGCC-----
ppacificus	----------------------------------------GTTTGATTG-TTTGTCGATGCATTGTTATCAGATCACG--------AGAGACATTGAAGAGA-CAATTGAAA------------------------------------------
	****** * * * * * *
celegans	.(((.((((((.(((((((((..(((((((( (((..((((( ..(((((((...........)) )))))))))).))) ))))))))..))))))))))))))).))).	1.000 -39.90
cremanei	(((((..((((((((((......((((((((.((((((((((((((((( ((.((((((( ...(((.(((......))). )))..))))))))) )))))))))))))))))))))))..))......))))).)))))..)))))	0.921 -50.00
cbriggsae	....(((((.((((((((.. ..(((.(((((.......)) )))))).))))))))..)))))....	1.000 -11.70
cbrenneri	........((((((((((......((( .((((((.....)) )))).)))....)) ))))))))	0.999 -15.30
cjaponica	..((((..((((((........(((..((..((((.(((.(((((((.( ((.((((((( ..(((((((((.((....)).)))))))))))))))))) ).))))))).))).)))).)).)))......)).))))...)))).	0.930 -44.84
ppacificus	.((..(((( (((.((((((..((((.........))) )....))))))..))) ))))..)).	0.962 -14.50

celegans	chromosome:IV:7767444:7767550:1	intergenic ## {SimpF: WRM068dD06 1 fosmid,WRM067dH10 1 fosmid,WRM0640dD07 1 fosmid} ## {MIR: cel-mir-1820}
cremanei	chromosome:chrUn:43869115:43869258:-1	Opposite_strand\|Intronic_coding\|NM_200104
cbriggsae	chromosome:chrIV:13380242:13380388:1	Same_strand\|Intronic_coding\|NM_067049 ## Opposite_strand\|Intronic_coding\|NM_064726
cbrenneri	chromosome:chrUn:116745940:116746002:1	Same_strand\|UTR_coding\|NM_068392
cjaponica	chromosome:chrUn:64052439:64052582:1	intergenic
ppacificus	chromosome:chrUn:3495593:3495739:-1	Opposite_strand\|Intronic_coding\|NM_001045347 ## Same_strand\|Intronic_coding\|NM_001001910

miRNAknown_lenNOK_randfoldOK_nonpairedHIGH_bulgeHIGH (1 loci)

cel-mir-1021

block5106 (miRBase cel-mir-1021) [miRNAknown_lenNOK_randfoldOK_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
miRBase cel-mir-1021	0.001	no	no	0.44/0.44	25/25/0.00	nd	nd	0	0	0	0	14	3	5arm	1	nd	0.32	4	0	0	na	na

		reads	miRBase family seed
seed	---------------AGUGAGA---------------------------------------------------------------------------	0	novel
		len	cloning frequencies

cel-miR-1021	--------------AAGTGAGATCATGTGAAATCCTCGG----------------------------------------------------------	25
celegans	tactgttttgaaacAAGTGAGATCATGTGAAATCCTCGGagctcggagctttgaattttccaaatattcatatttaaattatttgtttcaaacagta
	*************************************************************************************************
celegans	((((((((.(((((((((((....(((((((....(((((((.....)))))))............))))))).....)))))))))))))))))))	1.000 -28.69

celegans

chromosome:IV:16473044:16473140:-1

intergenic ## {SimpF: WRM0621bE04 -1 fosmid} ## {MIR: cel-mir-1021}

miRNAknown_nonpairedHIGH_bulgeHIGH (1 loci)

cel-mir-262

block7527 (miRBase cel-mir-262) [miRNAknown_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
miRBase cel-mir-262	0.592	no	no	0.35/0.35	20/20/1.00	nd	nd	0	0	0	0	15	3	3arm	1	nd	0.45	5	0	0	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------UUUCUCG---------------------------	0	novel
		len	cloning frequencies

cel-miR-262	-------------------------------------------------------------------------GTTTCTCGATGTTTTCTGAT---------------	20
celegans	gtgcaaaattgtattaaaataaactttattggattacaaaaaaaatgtatcaatttttctttttcatttttacGTTTCTCGATGTTTTCTGATactgttgctagcagt
	************************************************************************************************************
celegans	(((((....))))).......(((..(((..((..(((....(((((((.....................))))))).....)))..))..)))..))).........	1.000 -13.40

celegans

chromosome:V:18736648:18736755:1

intergenic ## {SimpF: WRM0620bC12 1 fosmid} ## {MIR: cel-mir-262}

miRNAknown_randfoldOK_bulgeHIGH (1 loci)

cel-mir-353

block825 (miRBase cel-mir-353) [miRNAknown_randfoldOK_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
miRBase cel-mir-353	0.001	no	no	0.38/0.38	21/21/1.00	nd	nd	0	0	0	0	8	11	5arm	1	nd	0.29	4	0	0	na	na

		reads	miRBase family seed
seed	---------AAUUGCC-------------------------------------------------------------------	0	novel
		len	cloning frequencies

cel-miR-353	--------CAATTGCCATGTGTTGGTATT------------------------------------------------------	21
celegans	GACGGGCACAATTGCCATGTGTTGGTATTATTGCTTCAAGTTATTT--GAAGCTGTAATATCAATAAGCATGTCTCGT-----
cremanei	--------CAATTGCCAAATACGGTGCCCGCCTCCACAATATATTTCGGAGACTGGAA-------------GTCCCGTTGTTG
	********* * * * * * * * *
	+++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++++++ +++++	D1007.12.2 D1007.12 rpl-24.1
	+++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++++++ +++++	D1007.12.1 D1007.12 rpl-24.1
celegans	.(((((.(((..(((....((((((((((((.((((((((...))) ))))).)))))))))))).)))))))))))	0.750 -29.20
cremanei	.......(((..((((.(((((.((((............))))..))).. )).))))..)))	0.562 -11.60

celegans	chromosome:I:4585899:4585974:1	Same_strand\|Intronic_coding\|D1007.12.1\|D1007.12 ## D1007.12\|protein_coding\|rpl-24.1\|rpl-24.1 encodes a large ribosomal subunit L24 protein. [Source: WormBase] ## {SimpF: CEOP1188 1 Operon,WRM067cA07 1 fosmid,D1007.12 1 Expression_profile} ## {MIR: cel-mir-353}
cremanei	chromosome:chrUn:104979613:104979728:-1	Opposite_strand\|Boundary_coding\|NM_061183

Back to summary page

noncloned miRBase miRNAs:

Page 1

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Page 5

miR-Intess™

cel-mir-1833

block4872 (miRBase cel-mir-1833) [miRNAknown_rep_shortStem_randfoldOK]

block4071 (miRBaseNonMapped cel-mir-1832) [miRBaseNonMapped_loopOverlap_randfoldOK]

cel-mir-1832

block2229 (miRBaseNonMapped cel-mir-1832) [miRBaseNonMapped_randfoldOK]

cel-mir-1831

block1747 (miRBase cel-mir-1831) [miRNAknown_RNA_shortStem_loopOverlap_nonpairedHIGH_bulgeHIGH]

cel-mir-261

block2317 (miRBase cel-mir-261) [miRNAknown_lenNOK_loopOverlap_nonpairedHIGH_bulgeHIGH]

cel-mir-1019

sblock9 (miRBase cel-mir-1019) [miRNAknown_lenNOK_multiarm_DicerNOK_shortStem_mirtron]

cel-mir-1820

block5575 (miRBase cel-mir-1820) [miRNAknown_lenNOK_randfoldOK]

cel-mir-1021

block5106 (miRBase cel-mir-1021) [miRNAknown_lenNOK_randfoldOK_nonpairedHIGH_bulgeHIGH]

cel-mir-262

block7527 (miRBase cel-mir-262) [miRNAknown_nonpairedHIGH_bulgeHIGH]

cel-mir-353

block825 (miRBase cel-mir-353) [miRNAknown_randfoldOK_bulgeHIGH]