logoC.elegans small RNAs

miR-Intess™


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cel-mir-40

cel-mir-40

Cloning frequencies
absoluteCE1
cel-mir-40 3arm5310
normalizedCE1
cel-mir-40 3arm3.709
cel-mir-40 relative cloning frequencies

block2593 (miRBase cel-mir-40) [miRNAknown_cloningHIGH_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cel-mir-400.001nono0.50/0.6118/24/0.900.0
0.0
4638
0
1
0
17
6
3arm
1
nd
0.15
1
53101nana
Clusters
Located in cluster 1: cel-mir-35, cel-mir-36, cel-mir-37, cel-mir-38, cel-mir-39, cel-mir-40, cel-mir-41
Families
Member of family miR-35/36/38/39/40/41 (seed CACCGGG): cel-mir-40, cel-mir-35, cel-mir-36, cel-mir-37, cel-mir-39, cel-mir-41, cel-mir-38
block2593 hairpin
  readsmiRBase family seed
seed     ---------------------------------------------------------------------------CACCGGG------------------------------------------------     5232miR-35/36/38/39/40/41
seed     ----------------------------------------------------------------------------ACCGGGU-----------------------------------------------     43miR-42
seed     -------------------------------------------------------------------------------GGGUGUA--------------------------------------------     32novel
seed     ------------------------------------------------------------------------UAUCACC---------------------------------------------------     2novel
seed     -------------------------------------------------------------------------AUCACCG--------------------------------------------------     1novel
  lencloning frequencies
   CE1
      --------------------------------------------------------------------------TCACCGGGTGTACATCAGCT------------------------------------     204638
      --------------------------------------------------------------------------TCACCGGGTGTACATCAGC-------------------------------------     19473
cel-miR-40     --------------------------------------------------------------------------TCACCGGGTGTACATCAGCTAA----------------------------------     2264
      ---------------------------------------------------------------------------CACCGGGTGTACATCAGCTA-----------------------------------     2033
      ------------------------------------------------------------------------------CGGGTGTACATCAGCTAA----------------------------------     1832
      --------------------------------------------------------------------------TCACCGGGTGTACATCAGCTAAG---------------------------------     2325
      --------------------------------------------------------------------------TCACCGGGTGTACATCAGCTA-----------------------------------     2125
      --------------------------------------------------------------------------TCACCGGGTGTACATCAG--------------------------------------     186
      ---------------------------------------------------------------------------CACCGGGTGTACATCAGCT------------------------------------     195
      ---------------------------------------------------------------------------CACCGGGTGTACATCAGC-------------------------------------     184
      -----------------------------------------------------------------------CTATCACCGGGTGTACATCAGC-------------------------------------     222
      ---------------------------------------------------------------------------CACCGGGTGTACATCAGCTAAG---------------------------------     221
      --------------------------------------------------------------------------TCACCGGGTGTACATCAGCTAAGG--------------------------------     241
      ------------------------------------------------------------------------TATCACCGGGTGTACATCAGCT------------------------------------     221
celegans     -----------TCCTGT--CCGCACCTCAGTGGATGTATGCCATGATGATAAGATA---TCAGAAA---TCCTATCACCGGGTGTACATCAGCTAAGGTGCGGGTACAGGT-------------------      
cbriggsae     ATCTCTGTATCCCCTGC--CCTCACCCCAGCGGGTTTTCATCGCAGTGATATGACGCATTCAAACCATTTCTTATCACCGGGTGTCAATCAGCTAGGGTGTGGGCGCGGGT-----ATCCACAGAGGT--      
cbrenneri     CTCCCT-----TCCTGAGGCGGGAACCGAGCTGATTTCTCCACTGGTGATAATTC----CAAGAATAGTGTTTATCACCGGGAGTAAATCTGCTCTGGTCCCGTCTCGGGACATTCAAACAAGGTGAG--      
cjaponica     -----------GCCCGC--CAGCACCCCAGCTGATGTTTTCCGTGGTGATACGATAC--ATATTTAGTCCACTATCACCGGGTTTACATCTGCTTGGGTGTATGGCTGGGT-------------------      
ppacificus     ------------TCTGAGTCCCTTCGATCGCCTCTGATCACTACGATGAAAC-------TGAGATAACGAGTTTTCACCGGGTGAACAGAAGCT--GTTGAAGATATCGGA-------------------      
cremanei     -TATCTTCAAACCCTGC--CCGTAACCTAGTTGATGTTCATCGCAGTGATATGACGCA-TCAGTACATTCCTTATCACCGGGTGTACATCAGCTAGGGTGCGGGTTCAGGTTCTTTATCATTGAAAGGTA      
                   * *   *         *    *           *** *          *          * ********     *   ***  * *         **                          
 -----           ------  -------------------------------------   -------   ------------------------------------------                   -----Y62F5A.9 Y62F5A.9 Y62F5A.9
celegans                .(((((  ((((((((.(((.((((((((((.((.(((((.(((.   ......)   )).))))).)))))))))))).))).))))))))..))))).                        1.000 -46.20
cbriggsae     ((((((((..(((.(((  ((.(((((.(((.((((..((((...((((((.((...............)).))))))..))))..)))).))).))))).))))).))).     ....))))))))       0.997 -50.76
cbrenneri     ((((((     ((((((((((((.(((((((.(((((((((...((((((((...    ............)))))))).)))).))))).)))).)))))))))))))))..........))).)))       0.994 -57.96
cjaponica                ((((((  ((((((((.(((.(((((...((.((((((((.(((..  .......)))...))))))))))...))))).))).)))))).)))).))))                        0.999 -46.60
ppacificus                 (((((....(((((((.((.((((.(((((.((.((((((       (.........))))).)).))))))).)))).)).  )))))))...)))))                        1.000 -30.60
cremanei      ((((((((((((..((  (((((.((((((((((((.((((...((((((((((... ...)).)).....))))))..)))).)))))))))))).)))))))...)))).........)))).))))     0.923 -46.80

celeganschromosome:II:11538100:11538191:1Opposite_strand|Intronic_coding|Y62F5A.9|Y62F5A.9 ## Y62F5A.9|protein_coding|Y62F5A.9|Y62F5A.9 [Source:RefSeq_peptide;Acc:NP_741048] ## {SimpF: Y62F5A.D 1 Expression_profile} ## {MIR: cel-mir-40}
cbriggsaechromosome:chrII:7536133:7536253:1Opposite_strand|Intronic_coding|NM_177732 ## Same_strand|Intronic_coding|NM_001101718 ## {MIR: cbr-mir-40}
cbrennerichromosome:chrUn:47822131:47822249:-1intergenic
cjaponicachromosome:chrUn:117591457:117591552:-1Opposite_strand|Intronic_coding|NM_171042
ppacificuschromosome:chrUn:171595123:171595212:-1intergenic ## {Repeats: (GA)n 2 38 -1 class=Simple_repeat} ## {SimpF: trf}
cremaneichromosome:chrUn:8778471:8778596:-1Same_strand|Intronic_coding|NM_001011005 ## Opposite_strand|Intronic_coding|NM_171042


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