logoC.elegans small RNAs

miR-Intess™


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Composition
miR classification

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cel-mir-238

cel-mir-238

Cloning frequencies
absoluteCE1
cel-mir-238 3arm1131
normalizedCE1
cel-mir-238 3arm0.790
cel-mir-238 relative cloning frequencies

block3156 (miRBase cel-mir-238) [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-2380.001nono0.42/0.5018/23/0.980.0
0.8
1086
0
1
0
16
8
3arm
1
nd
0.18
3
11311nana
Families
Member of family miR-239a (seed UUGUACU): cel-mir-238, cel-mir-239a
block3156 hairpin
  readsmiRBase family seed
seed--------------------------------------------------------------------------------------UUGUACU-----------------------------------------1099miR-239a
seed---------------------------------------------------------------------------------------UGUACUC----------------------------------------23novel
seed-------------------------------------------------------------------------------------UUUGUAC------------------------------------------7novel
seed------------------------------------------------------------------------------------------ACUCCGA-------------------------------------1novel
seed----------------------------------------------------------------------------------------GUACUCC---------------------------------------1novel
  lencloning frequencies
   CE1
 -------------------------------------------------------------------------------------TTTGTACTCCGATGCCATTC-----------------------------20669
 -------------------------------------------------------------------------------------TTTGTACTCCGATGCCATTCAG---------------------------22417
 --------------------------------------------------------------------------------------TTGTACTCCGATGCCATTC-----------------------------1913
 -------------------------------------------------------------------------------------TTTGTACTCCGATGCCATT------------------------------197
 --------------------------------------------------------------------------------------TTGTACTCCGATGCCATTCAG---------------------------217
cel-miR-238-------------------------------------------------------------------------------------TTTGTACTCCGATGCCATTCAGA--------------------------235
 ------------------------------------------------------------------------------------CTTTGTACTCCGATGCCATTCAG---------------------------234
 ------------------------------------------------------------------------------------CTTTGTACTCCGATGCCATTC-----------------------------213
 --------------------------------------------------------------------------------------TTGTACTCCGATGCCATTCAGA--------------------------222
 -------------------------------------------------------------------------------------TTTGTACTCCGATGCCAT-------------------------------181
 ---------------------------------------------------------------------------------------TGTACTCCGATGCCATTC-----------------------------181
 --------------------------------------------------------------------------------------TTGTACTCCGATGCCATTCAGAT-------------------------231
 -----------------------------------------------------------------------------------------TACTCCGATGCCATTCAGA--------------------------191
celegans----------------TCTCCATTG-----ACTGTTTGGATGTTCTCGGACGTTCAAAGCTACATCC--AACAAATT--GGTAGCTTTGTACTCCGATGCCATTCAGATAGTTATGAGCCATG----------- 
cbriggsaeCCAAAACTTCTTCTTATCCTCATGAATATGACTGTTTGGGTGTCCTTGGATGTAAAAAGCTATAAATCTGTTAA-----GATTGCTTTGTACTCCGATGCCATCCACATGGTCTGACGACAAGAAGATATGG-- 
cjaponica-----------------CCTCA--------ACCGTTTGGACGTGATTGGATGTTCAAAGCCAGCGCCATATCGAAATATGGCAGCTTTGTACTCCGATGCCGTTCAGAGGGT---------------------- 
cbrenneri--------GACCAGGTTCCAGG--------ACCGTCTGGATGTGATCGGGTGTAAAAAGCTATCCACGAAG--------AATCGCTTTGTACTCCGATGCCATTCAGAGGGTTTTCCAA---------ATGGTC 
cremaneiTCAAAGTCAACGTGGACCACTGTGA----TACCATTTGGGTGGACACGGACGTAAAAAGCTATGCCCGTGGTTAGGTA-TTTAGCTTTGTACTCCGATGCCATTCAAATGGTTGTGTGGTTTTGGATTGTGG-- 
                  *            **  * ***  *     **  **  ***** *                     ****************** * ** *  **                       
celegans                .(((...((     ((((((((((((...(((((.((.((((((((...((  ((....))  )))))))))).)))))))...)))))))))))))).))).....           1.000 -38.40
cbriggsae(((.....(((((((.((.(((.......((((((.((((((...(((((.(((.(((((....(((((....)     ))))))))).))))))))...)))))).))))))))).)).)))))))..)))  0.997 -38.61
cjaponica                 .....        (((.((((((((..((((((.((.((((((....(((((((....))))))).)))))).))))))))..)))))))).)))                      1.000 -38.80
cbrenneri        (((((......(((        (((.((((((((..((((((.(((.(((((..((......)        )...))))).)))))))))..)))))))).))))))....         .)))))0.998 -40.40
cremanei.((.((((.....(((((((.....    .(((((((((((((.((((((.(((.(((((((((((........)))) ..))))))).))))))).)))))))))))))))...)))))))..)))).)).  1.000 -50.80

celeganschromosome:III:8867235:8867332:-1intergenic ## {SimpF: WRM0637aD12 -1 fosmid,WRM0622dD10 -1 fosmid} ## {MIR: cel-mir-238}
cbriggsaechromosome:chrIII:13410775:13410901:-1Opposite_strand|Intronic_coding|NM_001026518 ## Same_strand|Intronic_coding|NM_070558
cjaponicachromosome:chrUn:4625393:4625479:1Same_strand|Intronic_coding|NM_080787 ## Opposite_strand|Intronic_coding|NM_078517
cbrennerichromosome:chrUn:17763342:17763442:-1Same_strand|Intronic_coding|NM_209159
cremaneichromosome:chrUn:98387127:98387253:-1intergenic


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