logoC.briggsae small RNAs

miR-Intess™


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Composition
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cbr-mir-35

cbr-mir-35

Cloning frequencies
absoluteAF16
cbr-mir-35 3arm827
normalizedAF16
cbr-mir-35 3arm2.156
cbr-mir-35 relative cloning frequencies

block973 (miRBase cbr-mir-35) [miRNAknown_cloningHIGH_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-350.001nono0.48/0.5318/23/0.600.0
1.2
792
0
1
0
32
6
3arm
1
nd
0.09
1
8271nana
Clusters
Located in cluster 3: cbr-mir-36, cbr-mir-38, cbr-mir-39, cbr-mir-40, block969_novel, cel-mir-35, cbr-mir-41, cbr-mir-35
Families
Member of family miR-35/36/38/39/40/41 (seed CACCGGG): cel-mir-35, cel-mir-35, cel-mir-36, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cbr-mir-39, cbr-mir-35, cbr-mir-36, cbr-mir-40, cbr-mir-41, cbr-mir-38, block969_novel, block5129_cand
block973 hairpin
  readsmiRBase family seed
seed     -----------------------------------------------------------------------------CACCGGG----------------------------------------------------     810miR-35/36/38/39/40/41
seed     ---------------------------------------------------------------------------------GGGUGAA------------------------------------------------     12novel
seed     ----------------------------------------------------------------------------UCACCGG-----------------------------------------------------     5novel
  lencloning frequencies
   AF16
cbr-miR-35     ----------------------------------------------------------------------------TCACCGGGTGAAAA------CTTGCAAG--------------------------------     22486
      ----------------------------------------------------------------------------TCACCGGGTGAAAA------CTTGC-----------------------------------     19306
      ----------------------------------------------------------------------------TCACCGGGTGAAAA------CTTG------------------------------------     1812
      --------------------------------------------------------------------------------CGGGTGAAAA------CTTGCAAG--------------------------------     1812
      ----------------------------------------------------------------------------TCACCGGGTGAAAA------CTTGCAAGT-------------------------------     236
      ---------------------------------------------------------------------------ATCACCGGGTGAAAA------CTTGCAAG--------------------------------     233
      ---------------------------------------------------------------------------ATCACCGGGTGAAAA------CTTGC-----------------------------------     202
cbriggsae     -----------------TAGTCCAGTTCTGGACATTCGCGGGTTTTTTCCTTCGGTGATATTCGA-AGAATCGCTATCACCGGGTGAAAA------CTTGCAAGTGTCTTGCTTCGACTGGTCATTTTGCTTGTAT      
cremanei     -------------------GGTCGGATCGGCCCTCC-ACTGGTTTTCGCC-TCGGTCATATTTCA-AGTATGATTATCACCGGGTGAAAA------TCAGAGCAGGGCCGATTCCACC------------------      
celegans     TTCCCAACTATTATTCTCGGATCAGATCGAGCCATT-GCTGGTTTCTTCC-ACAGTGGTACTTTCCATTAGAACTATCACCGGGTGGAAA------CTAGCAGTGGCTCGATCTTTTCC-----------------      
cbrenneri     GTTCTCTATTATTCTATTCGGCCGGATCGGACCTAT-GCTGGTTTTCACC-GCGGTTATACTTCTAACAATAATTATCACCGGGTTAAAA------CTTGCAGAGGTCCGGTCCGGCC------------------      
cjaponica     ----------------------------------CTGGCTGGTATCCGCG-ATGGTGTTACACTACTGTAATG-TATCACCGGGTGGAAA------CTTGCAAG--------------------------------      
ppacificus     ------TCTGAGTCCCTTCGATCGCCTCTGATCACT---------------ACGATGAAACTGAGATAACGAGTTTTCACCGGGTGAACAGAAGCTGTTGAAGATATCGGA-------------------------      
                                                             *   *              * *********  * *         *                                          
 -----                 ------------------------------------------------ ------------------------      ---------------------------------------------NM_177732
 -----                 ------------------------------------------------ ------------------------      ---------------------------------------------NM_214509
 -----                 ------------------------------------------------ ------------------------      ---------------------------------------------NM_207243
 -----                 ------------------------------------------------ ------------------------      ---------------------------------------------NM_207243
 -----                 ------------------------------------------------ ------------------------      ---------------------------------------------NM_207243
 -----                 ------------------------------------------------ ------------------------      ---------------------------------------------NM_207243
 -----                 ------------------------------------------------ ------------------------      ---------------------------------------------NM_207243
 -----                 ------------------------------------------------ ------------------------      ---------------------------------------------NM_207243
 -----                 ------------------------------------------------ ------------------------      ---------------------------------------------NM_207243
 -----                 ------------------------------------------------ ------------------------      ---------------------------------------------NM_207243
 -----                 ------------------------------------------------ ------------------------      ---------------------------------------------NM_207243
 -----                 ------------------------------------------------ ------------------------      ---------------------------------------------NM_207243
 -----                 ------------------------------------------------ ------------------------      ---------------------------------------------NM_207243
 -----                 ------------------------------------------------ ------------------------      ---------------------------------------------NM_001030843
 +++++                 ++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++      +++++++++++++++++++++++++++++++++++++++++++++NM_001101718
 +++++                 ++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++      +++++++++++++++++++++++++++++++++++++++++++++NM_001011629
 -----                 ------------------------------------------------ ------------------------      ---------------------------------------------NM_207243
 -----                 ------------------------------------------------ ------------------------      ---------------------------------------------NM_207243
 -----                 ------------------------------------------------ ------------------------      ---------------------------------------------NM_207243
 -----                 ------------------------------------------------ ------------------------      ---------------------------------------------NM_207243
 -----                 ------------------------------------------------ ------------------------      ---------------------------------------------NM_207243
 -----                 ------------------------------------------------ ------------------------      ---------------------------------------------NM_171042
cbriggsae                      ..(.((((((..(((((((.((((((((((.((..((((((((..((( ....))).)))))))))).)))))      ))))).)))))))......)))))).).............     1.000 -42.60
cremanei                        (((.(((((((((((.. .(((((((((((( .((((.(((..((( ....))).))).))))))))))))      ))))...))))))))))).)))                       1.000 -49.80
celegans     ..................(((..((((((((((((( (((((((((..(( ...((((((.(((......))).))))))..))..))))      ))))))))))))))))))..)))                      0.989 -54.00
cbrenneri     ...................(((((((((((((((.( ((.((((((.((( .((((.(((.((........)).))).))))))).))))      )).))).)))))))))))))))                       0.989 -52.20
cjaponica                                       ...((.(((.(((((. .(((((.((((.........)) )).))))).))))).)      )).))...                                     1.000 -21.90
ppacificus           (((((....(((((((.((.((((.(((((               .((.(((((((.........))))).)).))))))).)))).)).)))))))...)))))                              1.000 -30.60

cbriggsaechromosome:chrII:7536620:7536731:1Opposite_strand|Intronic_non-coding|NM_177732|Slc35d1 ## Opposite_strand|Intronic_coding|NM_214509|COLP1alpha ## Same_strand|Intronic_coding|NM_001101718|LOC100009540 ## Same_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## {Repeats: no} ## {MIR: cbr-mir-35}
cremaneichromosome:chrUn:26788069:26788158:-1intergenic ## {SimpF: trf}
celeganschromosome:chrII:11537510:11537620:1Opposite_strand|Intronic_coding|Y62F5A.9 ## {MIR: cel-mir-35}
cbrennerichromosome:chrUn:47823952:47824061:-1intergenic
cjaponicachromosome:chrUn:117591190:117591341:-1Opposite_strand|Intronic_coding|NM_171042
ppacificuschromosome:chrUn:171595123:171595212:-1intergenic ## {Repeats: (GA)n 2 38 -1 class=Simple_repeat} ## {SimpF: trf}


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