logoC.briggsae small RNAs

miR-Intess™


Summary
Preprocessing
Mapping
Composition
miR classification

miR expression
Downloads
List
Heatmaps

cbr-mir-39

cbr-mir-39

Cloning frequencies
absoluteAF16
cbr-mir-39 3arm17
normalizedAF16
cbr-mir-39 3arm0.044
cbr-mir-39 relative cloning frequencies

block966 (miRBase cbr-mir-39) [miRNAknown_cloningOK_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-390.001nono0.50/0.5018/22/0.940.0
0.0
16
0
1
0
19
6
3arm
1
nd
0.23
2
171nana
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
block966 hairpin
  readsmiRBase family seed
seed     -----------------------------------------------------------------------------------------CACCGGG---------------------------------------------------     16miR-35/36/38/39/40/41
seed     ---------------------------------------------------------------------------------------------GGGUGAA-----------------------------------------------     1novel
  lencloning frequencies
   AF16
cbr-miR-39     ----------------------------------------------------------------------------------------TCACCGGGTGAAAAACGG--TTAG-----------------------------------     2216
      --------------------------------------------------------------------------------------------CGGGTGAAAAACGG--TTAG-----------------------------------     181
cbriggsae     ------------------CAGAGATGC-----AGGGAGCCCAACTGGTTC-TCACTGCAGTGAT------AAGCTATGTTACAGTCTATCACCGGGTGAAAAACGG--TTAGGCTCTTTA---------------AGCATCTCTGT-      
cremanei     -------------TCGGTCGGA----------TCGGACCTACACTGGTTT-TCGCTGCGGTGATACTTCGAGA--ATGA------TTATCACCGGGTGAAAATCAGG-GCAGGTCC-------------------GATTCCACCGA-      
celegans     CTACTGATTATTGAATTCCTGATATAC-----CGAGAGCCCAGCTGATT--TCGTCTTGGTAATA-----AGCTCGTCATTGAGATTATCACCGGGTGTAAATCAG--CTTGGCTCT------------------GGTGTCTCCGAA      
cbrenneri     GTTCATATTTTTCATATTCAGGGGTGGA----TCGGGCCTGTGCTGATTT-TTGCCGCTGTGATATTTCTAAGCCATGA------TTATCACCGGGCGAAAATTTGGCACAGGCC--------------------TCGTCCGCCCT-      
cjaponica     -----TGCAGTGGTCCCTCGGGGCAGAAGAGCCAGGACCTACATCAGTTTCTTTCCGCGGTAATAAA--TAATACATTA------TTATCACCGGGAGAAAAACTGGAGTAGGACCTGCGACTCGACTCGACCTTTATTCCGCTGTA      
ppacificus     -----------------TCTGAGTCCC-----TTCGATCGCCTCTGA----TCACTACGATGAAACT--GAGATAACGA-----GTTTTCACCGGGTGAACAGAAGCTGTTG-----------------------AAGATATCGGA-      
                        * *              *  *            *        * *       *               * ******** * * *   *     *                              *          
 -----                  ---------     ------------------ -------------      ------------------------------------  ------------               ----------- -----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 -45.60
cremanei                  (((((.(((          ((((((((...((((((( (((((.((((((((..((....  ..))      .)))))))))))))))))))). ..))))))                   ))))).)))))      1.000 -55.10
celegans     ...............(((..((.((((     (.((((((.((((((((  (((.((((((.(((     (.((((....)))).)))).)))))))).)))))))  )).))))))                  ))))).)).)))     0.957 -45.10
cbrenneri     ....................((((((((    (.(((((((((((((((( (((((...((((((..((........))      .))))))..)))))))))).))))))))))                    ).)))))))))      0.944 -57.20
cjaponica          ((((((((......((((..((.(((.((((.(((((..((((((.(((((.((((.((.((  (((....)))      )))).))))))))).))))))..))))).))))...)))...))..))))....))))))))     0.964 -52.50
ppacificus                      (((((....(     ((((((.((.((((.    (((((.((.(((((((  .........)     )))).)).))))))).)))).)).))))                       )))...)))))      1.000 -30.60

cbriggsaechromosome:chrII:7536042:7536140:1Opposite_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-39}
cremaneichromosome:chrUn:26787656:26787749:-1intergenic
celeganschromosome:chrII:11537983:11538097:1Opposite_strand|Intronic_coding|Y62F5A.9 ## {MIR: cel-mir-39}
cbrennerichromosome:chrUn:47821556:47821670:-1intergenic ## {SimpF: trf}
cjaponicachromosome:chrUn:117591701:117591834:-1Opposite_strand|Intronic_coding|NM_171042
ppacificuschromosome:chrUn:171595123:171595212:-1intergenic ## {Repeats: (GA)n 2 38 -1 class=Simple_repeat} ## {SimpF: trf}


©2008 InteRNA Genomics B.V.