logoC.elegans small RNAs


miR classification

Alignments

other hairpins

novel_lenNOK_nonpairedHIGH_bulgeHIGH (22 loci)

block2127 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.684nono0.56/0.5825/26/0.000.0
0.5
2
0
1
0
17
11
3arm
1
nd
0.38
4
21nana
  readsmiRBase family seed
seed-----------------------------------------------------------------------UGUGUGG-----------------------------------2novel
  lencloning frequencies
   CE1
 ----------------------------------------------------------------------GTGTGTGGCGGCACGGTAACTGTTT------------------251
 ----------------------------------------------------------------------GTGTGTGGCGGCACGGTAACTGTTTC-----------------261
celeganscacattgaaataatccaaagcgaaactgacagttttacatttgatggtgagttgttcgatcaaatatctaGTGTGTGGCGGCACGGTAACTGTTTCggatttcggagcattgt 
 ***************************************************************************************************************** 
celegans.(((.((....(((((.(((((..((((...((..((((((.((((.(((.........)))..)))).))))))..))....))))...))))).)))))......)).)))0.900 -23.50

celeganschromosome:II:842769:842881:1intergenic ## {SimpF: WRM068cE11 1 fosmid,WRM0622dC12 1 fosmid,F28A10.9 1 Expression_profile,WRM0627cG11 1 fosmid,WRM062cB08 1 fosmid,WRM0638dH08 1 fosmid,WRM0629aG02 1 fosmid,WRM067dE12 1 fosmid,WRM0626dF08 1 fosmid,WRM066aC01 1 fosmid,WRM0636cH07 1 fosmid,WRM061aB10 1 fosmid}


block2378 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.970nono0.39/0.3918/18/0.000.0
0.0
1
0
1
0
22
15
5arm
1
nd
0.44
4
11nana
  readsmiRBase family seed
seed-----------------------UGAAUAA---------------------------------------------------------------------------------------1novel
  lencloning frequencies
   CE1
 ----------------------GTGAATAAGTGATGACAG-----------------------------------------------------------------------------181
celegansgtctagtgaaggcgtaaaagtgGTGAATAAGTGATGACAGctttttcttcttgtctgattgatttgattcgaattgttgtaaagaccatctgccatctgaacttgtcgaggtgtgac 
 ********************************************************************************************************************* 
celegans(((.......((((....((((((..((..((....(((((..(((..((..(((.....)))..))...)))..)))))....)).))..)))).)).....)))).......)))0.760 -20.44

celeganschromosome:II:7493774:7493890:1intergenic ## {SimpF: WRM0619cF06 1 fosmid,WRM0613dH09 1 fosmid,WRM0621bG05 1 fosmid,WRM0621dE08 1 fosmid,WRM0611cE04 1 fosmid,WRM0633aE12 1 fosmid}


block3061 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.638nono0.47/0.4719/19/0.000.0
0.0
1
0
1
0
34
0
3arm
1
nd
0.37
4
11nana
  readsmiRBase family seed
seed--------------------------------------------------------------GAUGAGU---------------------------------------------1novel
  lencloning frequencies
   CE1
 -------------------------------------------------------------GGATGAGTAGGAGTTGAAG----------------------------------191
celeganstctctcggttttcgggcactctcgctgctgtcggagctggagccataactgtatttggattGGATGAGTAGGAGTTGAAGatcctgatagttttgaaggtgcggcttttaggga 
 ****************************************************************************************************************** 
celegans(((((.((((.....((((..(((..(((((((((.((..(((....(((.(((((.....))))))))....)))..)).))).))))))..)))..))))))))...)))))0.460 -29.30

celeganschromosome:III:6905840:6905953:-1intergenic ## {SimpF: T07E3.3 -1 Expression_profile,WRM0619bC05 -1 fosmid,WRM0631dH02 -1 fosmid,WRM0641dA07 -1 fosmid,WRM0626cC01 -1 fosmid,WRM0614bF02 -1 fosmid,WRM0627bE11 -1 fosmid,WRM0627bD12 -1 fosmid}


block3076 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.141nono0.33/0.3318/18/0.000.0
0.0
1
0
1
0
15
0
5arm
1
nd
0.33
4
11nana
  readsmiRBase family seed
seed     ----------------GAUGACG------------------------------------------------------     1novel
  lencloning frequencies
   CE1
      ---------------GGATGACGACATTAATAT--------------------------------------------     181
celegans     ggaatcggattcactGGATGACGACATTAATATaaaaaactaaaagtgtaaatgttctttccatcattccccacccc      
      *****************************************************************************      
 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<.......................................................T20H4.2 T20H4.2 T20H4.2
celegans     ((....(((.....((((....((((((.((((............)))).))))))...))))....)))....)).     0.990 -11.80

celeganschromosome:III:7241269:7241345:-1Opposite_strand|Boundary_non-coding|T20H4.2|T20H4.2 ## T20H4.2|protein_coding|T20H4.2|T20H4.2 [Source:RefSeq_peptide;Acc:NP_498597] ## {SimpF: WRM0613bC02 -1 fosmid,WRM069cD05 -1 fosmid,WRM0622aE05 -1 fosmid,WRM061aF10 -1 fosmid}


block4017 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.274nono0.50/0.5018/18/0.000.0
0.0
1
0
1
0
24
2
5arm
1
nd
0.39
4
11nana
  readsmiRBase family seed
seed-------------------------AUAACAG--------------------------------------------------------------1novel
  lencloning frequencies
   CE1
 ------------------------GATAACAGGAAGGTTGGG----------------------------------------------------181
celeganscatctgaataataataataatatgGATAACAGGAAGGTTGGGaaaagcttcgaacaaccggtcgggaattcacagtgaatttgttggggggtgc 
 ********************************************************************************************** 
celegans(((((...((((((........(((((....((..(((((.(((....)))...)))))..))....)))))........))))))..))))).0.780 -17.29

celeganschromosome:IV:1296739:1296832:-1intergenic ## {SimpF: WRM0612cE01 -1 fosmid}


block4145 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.162nono0.62/0.6319/21/0.500.0
1.0
2
0
1
0
12
5
5arm
1
nd
0.52
4
21nana
  readsmiRBase family seed
seed     -------------CGCCGAG--------------------------------------------------------------     2novel
  lencloning frequencies
   CE1
      ------------CCGCCGAGTTCTTGACCACAC-------------------------------------------------     211
      ------------CCGCCGAGTTCTTGACCAC---------------------------------------------------     191
celegans     gtagcgtagacgCCGCCGAGTTCTTGACCACACttttgcaaattttaaaggaaatgtgaagttttaaggtgtccgtgcctac      
      **********************************************************************************      
 --------------------------------------------------------------------------------------------ZK185.2 ZK185.2 ZK185.2
celegans     ((((((..((((((....((..(((.((....((((((.......))))))....)).)))..))..))))))..))).)))     0.860 -21.10

celeganschromosome:IV:4538650:4538731:-1Opposite_strand|Intronic_coding|ZK185.2|ZK185.2 ## ZK185.2|protein_coding|ZK185.2|ZK185.2 encodes an ortholog of human SLC41A1 (OMIM:610801) and bacterial MgtE. like its orthologs, ZK185.2 is predicted to transport Mg(2+) into cells. ZK185.2 is paralogous to K07H8.2 and ZK1053.6, and has no obvious function in mass RNAi assays. [Source: WormBase] ## {SimpF: WRM0619bB07 -1 fosmid}


block4477 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.047nono0.27/0.2726/26/0.000.0
0.0
1
0
1
0
10
0
3arm
1
nd
0.38
4
11nana
  readsmiRBase family seed
seed     -----------------------------------------------------CAAAUGA----------------------------     1novel
  lencloning frequencies
   CE1
      ----------------------------------------------------GCAAATGATTTGAATTCTTGATTCTT----------     261
celegans     tgattcagcagtttcacaacttttttgatcaggtgttttcattattttatatGCAAATGATTTGAATTCTTGATTCTTctgatcttca      
      ****************************************************************************************      
 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<...................................................W08D2.8 W08D2.8 kin-21
celegans     .((.((((.((..(((......(((.(((((..(((................)))..))))).)))....)))..)).))))...)).     0.840 -14.79

celeganschromosome:IV:9832863:9832950:-1intergenic ## {SimpF: WRM0637cA06 -1 fosmid,WRM0625dA07 -1 fosmid,WRM067bF08 -1 fosmid,WRM0621bB05 -1 fosmid}


block5360 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.284nono0.28/0.2818/18/0.000.0
0.0
1
0
1
0
11
28
5arm
1
nd
0.44
5
11nana
  readsmiRBase family seed
seed     ------------AUUUCUU----------------------------------------------------------------------------------------------     1novel
  lencloning frequencies
   CE1
      -----------TATTTCTTCTCAAGTTTC------------------------------------------------------------------------------------     181
celegans     aaaaagcttatTATTTCTTCTCAAGTTTCaaataaacagtttcaataaaaagatacccattgtggtatatgttaaattgtgtataattatcttgtgaaaatgttgaatttttt      
      *****************************************************************************************************************      
 ---------------------------------------------------------------------------------------------------------------------------H06H21.10a H06H21.10 tat-2
 ---------------------------------------------------------------------------------------------------------------------------H06H21.10b H06H21.10 tat-2
celegans     ((((((.(((.((((..(((.((((......(((.(((((((.((((.....(((((......))))).))))))))))).)))......)))).))))))).))).))))))     1.000 -16.40

celeganschromosome:IV:4830193:4830305:1Opposite_strand|Intronic_coding|H06H21.10a|H06H21.10 ## H06H21.10|protein_coding|tat-2|H06H21.10a [Source:RefSeq_peptide;Acc:NP_001023252] ## {SimpF: H06H21.10 1 Expression_profile,WRM0631cB02 1 fosmid}


block5409 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.207nono0.48/0.5221/25/0.330.0
0.0
0.0
0.0
2
1
0
0
1
1
0
0
2
12
7
1
5arm
5arm
2
2
nd
nd
0.36
0.33
3
4
31nana
  readsmiRBase family seed
seed---CAGCAAA--------------------------------------------------------------------2novel
seed-------------ACAUGCA----------------------------------------------------------1novel
  lencloning frequencies
   CE1
 --GCAGCAAAGTGACATGCAGATAGTC---------------------------------------------------252
 ------------GACATGCAGATAGTCCAACGG---------------------------------------------211
celegansgaGCAGCAAAGTGACATGCAGATAGTCCAACGGgctcatcatatttccgtcgttttgtcgcgtttatacgatgtgctt 
 ****************************************************************************** 
celegans(((((.((..(((..((((.(((((....(((((...........)))))....)))))))))...)))..)))))))0.500 -17.60

celeganschromosome:IV:5217597:5217674:1intergenic ## {SimpF: WRM0616bF04 1 fosmid,WRM0632cH10 1 fosmid,yk578d4 1 RNAi,WRM067dF01 1 fosmid}


block5826 [novel_lenNOK_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.402nono0.28/0.2825/25/0.000.0
0.0
2
0
1
0
7
0
5arm
2
nd
0.32
4
21nana
  readsmiRBase family seed
seed--------AUUUGUG--------------------------------------------------2novel
  lencloning frequencies
   CE1
 -------GATTTGTGATTGTAAACGAAAATTG---------------------------------252
celegansttgccacGATTTGTGATTGTAAACGAAAATTGatagtaatgaatgtttttcacactgattgtcga 
 ***************************************************************** 
celegans.....(((((((((((....(((((...((((....))))...))))).)))))..))))))...0.800 -9.70

celeganschromosome:IV:13433997:13434061:1intergenic


Back to summary page other hairpins: Page 1 Jump 10 pages back Previous page Page 18 Next page Jump 10 pages forward Page 45
©2008 InteRNA Genomics B.V.