logoSmall RNA from different tissues of two rat strains.

miR-Intess™


Summary
Preprocessing
Mapping
Composition

miR classification
miR expression
Downloads
Table
Thresholds
Families
Clusters

Alignments

other non-annotated miRBase miRNAs

miRBaseNonMapped_lenNOK (4 loci)

rno-mir-292-as

Cloning frequencies
absoluteT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-292-as 5arm0000000001
normalizedT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-292-as 5arm0000000000.000
rno-mir-292-as relative cloning frequencies

block969944 (Antisense miRBase rno-mir-292-as) [miRBaseNonMapped_lenNOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBaseAS rno-mir-292-as0.179nono0.58/0.5819/19/0.000.0
0.0
1
0
1
0
23
10
5arm
1
nd
0.26
2
11nana
Clusters
Located in cluster 8: block969943_cand, rno-mir-292
block969944 hairpin
  readsmiRBase family seed
seed     ---------------------------------------CACUCAA------------------------------------------------------------------------------------------     1novel
  lencloning frequencies
   T5S2
      --------------------------------------ACACTCAAAACCTGGCGGC-------------------------------------------------------------------------------     191
rat     ------TTTGCAGCAG---------TTCTCAATCGGTAACACTCAAAACCTGGCGGCACTTTTCTTCCAAAGAAAACCCAAAAGAGCCCC--CAGTTTGAGTATCACAGGTTGGACGTCAAGGGTTAATGCGGGA-      
human     GGTATCTTCTCCGCAGG-TTGAGTCTTCTCAAGCGGTAACACTCAAAAGATGGCGGCACTTT-----CACCAGAGAGCAGAAAGTGCCCCCACAGTTTGAGTGCCACAGGCT-GAGGGGATGCGGCAAGGCGGCGA      
mouse     -----GTTCTTAGCCGTTTTGAG--TTCTCAACCGGTGACACTCAAAACCTGGCGGCACTTTTCTTCCGATGAAAATCCAAAAGAGCCCC--CAGTTTGAGTATCACAGGCTGGAGGTCAAGCTTAAGAAC-----      
            **    ** *         ******* **** **********  ************     *     * * *  **** *****  **********  ****** * ** *  * *    *   *           
 .....      ..........         ....<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<  <<<<<<<<<<<<<<<<<<<<<...................... .....ENSRNOT00000053618 ENSRNOG00000035495 rno-mir-292
rat           ((((((..((         ..(((((((.((...(((((((..((((.(((.(((((.(((....))).....))))).))).)  ))))))))))...)).))))).......))..))..)))))).      0.990 -30.41
human     .......((.((((..( (((.(((..(((.(((.((..((((((((...(((.((((((((     (...........))))))))).)))...))))))))..))..))) )))..))).))))...)))).))     0.994 -57.60
mouse          (((((((((....((((.  (((.((.((.((((.(((((((..((((.(((.(((((.....(((....))).))))).))).)  )))))))))).)))).)).))))).))))))).))))))          0.999 -46.10

ratchromosome:1:64274326:64274443:1Opposite_strand|Exonic_non-coding|ENSRNOT00000053618|ENSRNOG00000035495 ## ENSRNOG00000035495|miRNA|rno-mir-292|rno-mir-292 [Source:miRBase;Acc:MI0000966] ## {ASMIR: rno-mir-292-as}
humanchromosome:19:58982713:58982841:-1Opposite_strand|Boundary_non-coding|ENST00000362161|ENSG00000199031|miRNA|hsa-mir-371 [Source:miRBase;Acc:MI0000779] ## {ASMIR: hsa-mir-371-as}
mousechromosome:7:3219172:3219293:-1Opposite_strand|Boundary_non-coding|ENSMUST00000104847|ENSMUSG00000078041|miRNA|mmu-mir-292 [Source:miRBase;Acc:MI0000390] ## {ASMIR: mmu-mir-292-as}


rno-mir-129-1-as

Cloning frequencies
absoluteT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-129-1-as 3arm1000000000
normalizedT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-129-1-as 3arm0.000000000000
rno-mir-129-1-as relative cloning frequencies

block1543605 (Antisense miRBase rno-mir-129-1-as) [miRBaseNonMapped_lenNOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBaseAS rno-mir-129-1-as0.016nono0.53/0.5519/20/0.500.5
0.0
2
0
1
0
18
9
3arm
2
nd
0.20
2
21nana
Families
Member of family novel162 (seed AAGCCCA): rno-mir-129-2, rno-mir-129-1
block1543605 hairpin
  readsmiRBase family seed
seed     ----------------------------------------------------------------------------AAGCCCA--------------------------------------------------     1novel
seed     -----------------------------------------------------------------------------AGCCCAG-------------------------------------------------     1novel
  lencloning frequencies
   T1S1
      ---------------------------------------------------------------------------CAAGCCCAGACCGCAAAAAG--------------------------------------     201
      ----------------------------------------------------------------------------AAGCCCAGACCGCAAAAAG--------------------------------------     191
rat     -----------------AGCCTCCCGCAGATACTTTTTGGGGTAAGGGCTTCCTGACTACTGTGGAGA-GAACAGCAAGCCCAGACCGCAAAAAGACCCAAAGGAGACAGCTG--------------------      
human     GCCTCCCCTGTGGACAAGGCCTCCCGCAGATACTTTTTGGGGTAAGGGCTTCCTGACTACTGTTGAGAGGAACAGCAAGCCCAGACCGCAAAAAGATCCAAAGGAGACAGCAGCCATCCCATGGCAGGGGGGC      
mouse     --------------------------------CTTTTTGGGGTAAGGGCTTCCTGACTACTGTCGAGA-GAACAGCAAGCCCAGACCGCAAAAAG--------------------------------------      
                                      ******************************* **** **************************                                            
 .....                 ..........<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<.............                    .....ENSRNOT00000053721 ENSRNOG00000035598 rno-mir-129-1
rat                      (((((((........(((((((.(((..((((((.(((.((.((....))) )..))).))))))..))).))))))).......))))...))).                         0.990 -32.46
human     (((.((((((((((...(((((((....(((.(((((((.(((..((((((.(((.((.((....))))...))).))))))..))).))))))))))....))))......))).)))....))))))))))     0.963 -57.30
mouse                                     (((((((.(((..((((((.(((.......((.... )).))).))))))..))).)))))))                                           1.000 -26.20

ratchromosome:4:55892149:55892243:-1Opposite_strand|Exonic_non-coding|ENSRNOT00000053721|ENSRNOG00000035598 ## ENSRNOG00000035598|miRNA|rno-mir-129-1|rno-mir-129-1 [Source:miRBase;Acc:MI0000902] ## {ASMIR: rno-mir-129-1-as}
humanchromosome:7:127635127:127635259:-1Opposite_strand|Boundary_non-coding|ENST00000384972|ENSG00000207705|miRNA|hsa-mir-129-1 [Source:miRBase;Acc:MI0000252] ## {ASMIR: hsa-mir-129-1-as}
mousechromosome:6:28972586:28972720:-1Opposite_strand|Boundary_non-coding|ENSMUST00000083535|ENSMUSG00000065469|miRNA|mmu-mir-129-1 [Source:miRBase;Acc:MI0000222] ## {ASMIR: mmu-mir-129-1-as}


rno-mir-29a-as

Cloning frequencies
absoluteT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-29a-as 5arm0000000120
normalizedT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-29a-as 5arm00000000.0000.0000
rno-mir-29a-as relative cloning frequencies

block1641810 (Antisense miRBase rno-mir-29a-as) [miRBaseNonMapped_lenNOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBaseAS rno-mir-29a-as0.094nono0.43/0.4518/21/0.671.0
0.7
3
0
2
0
26
8
5arm
1
nd
0.22
3
32nana
Clusters
Located in cluster 56: rno-mir-29a, rno-mir-29b-1
block1641810 hairpin
  readsmiRBase family seed
seed     ---------------------------ACCGAUU------------------------------------------------------------------------------------     2novel
seed     ------------------------------GAUUUCA---------------------------------------------------------------------------------     1novel
  lencloning frequencies
   T4S2T5S1
      -----------------------------CGATTTCAGATGGTGCTA-----------------------------------------------------------------------     18-1
      --------------------------AACCGATTTCAGATGGTGCTA-----------------------------------------------------------------------     21-1
      --------------------------AACCGATTTCAGATGGTGCT------------------------------------------------------------------------     201-
rat     GCATGGTGCTTTTCCCCAATCATTATAACCGATTTCAGATGGTGCTAGAAAATTCTATTGACTCTGAACACCAAAAGAAATCAGTCATCCTCTAAGGGGTCACAAGAGGTCATGTGCA      
human     --------------------------AACCGATTTCAGATGGTGCTAGAAAATTATATTGACTCTGAACACCAAAAGAAATCAGTC--------------------------------      
mouse     --------------------------AACCGATTTCAGATGGTGCTAGAAAATTCTATTGACTCTGAACACCAAAAGAAATCAGTC--------------------------------      
                                **************************** *******************************                                      
 .................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<.......................ENSRNOT00000053581 ENSRNOG00000035458 rno-mir-29a
rat     (((((..((((((((((..........((.((((((...(((((.((((....((....)).))))..)))))...)))))).))..........)))).....))))))..))))).     0.820 -27.65
human                               ....((((((...(((((.((((.............))))..)))))...))))))....                                     1.000 -12.82
mouse                               ....((((((...(((((.((((....((....)).))))..)))))...))))))....                                     0.997 -13.20

ratchromosome:4:58107748:58107865:1Opposite_strand|Exonic_non-coding|ENSRNOT00000053581|ENSRNOG00000035458 ## ENSRNOG00000035458|miRNA|rno-mir-29a|rno-mir-29a [Source:miRBase;Acc:MI0000863] ## {ASMIR: rno-mir-29a-as}
humanchromosome:7:130211966:130212123:1Opposite_strand|Boundary_non-coding|ENST00000362111|ENSG00000198981|miRNA|hsa-mir-29a [Source:miRBase;Acc:MI0000087] ## {ASMIR: hsa-mir-29a-as}
mousechromosome:6:31012628:31012785:1Opposite_strand|Boundary_non-coding|ENSMUST00000083676|ENSMUSG00000065610|miRNA|mmu-mir-29a [Source:miRBase;Acc:MI0000576] ## {ASMIR: mmu-mir-29a-as}


miRBaseNonMapped_lenNOK_cloningHIGH_multiarm_DicerNOK_randfoldOK (3 loci)

rno-mir-344-5p

Cloning frequencies
absoluteT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-344-5p 5arm0.500000000000
rno-mir-344-5p 3arm239.500224010.500010.50020.500
normalizedT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-344-5p 5arm0.000000000000
rno-mir-344-5p 3arm0.0080.01000.0000.00000.0000.0000.0000.000
rno-mir-344-5p relative cloning frequencies

sblock653 (miRBaseNonMapped rno-mir-344-5p) [miRBaseNonMapped_lenNOK_cloningHIGH_multiarm_DicerNOK_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBaseNonMapped rno-mir-344-5p0.001nono0.44/0.5818/25/0.640.0
0.0
0.0
1.4
1
559
0
0
1
8
0
0
20
26
4
6
5arm
3arm
2
2
nd
nd
0.17
0.05
2
1
702824
Families
Member of family miR-344 (seed GAUCUAG): rno-mir-344, rno-mir-344
sblock653 hairpin
  readsmiRBase family seed
seed     -----------------------------------------------------------GAUCUAG-----------------------------------------     657miR-344
seed     ---------------------------------------------------------CUGAUCU-------------------------------------------     37novel
seed     ---------------------------------------------------------------UAGCCAA-------------------------------------     3novel
seed     --------------------------------------------------------CCUGAUC--------------------------------------------     2novel
seed     ------------------------------------------------------------AUCUAGC----------------------------------------     2novel
seed     ---------------------CAGGCUC-------------------------------------------------------------------------------     1miR-344/484
  lencloning frequencies
   T1S1T1S2T2S2T3S1T4S1T4S2T5S1T5S2
      ----------------------------------------------------------TGATCTAGCCAAAGCCTG-------------------------------     18911011-1-1-
      ----------------------------------------------------------TGATCTAGCCAAAGCCTGAC-----------------------------     2010281-11-2-
      ----------------------------------------------------------TGATCTAGCCAAAGCCTGACTG---------------------------     226736------
      ----------------------------------------------------------TGATCTAGCCAAAGCCTGACTGT--------------------------     231947------
      ----------------------------------------------------------TGATCTAGCCAAAGCCTGACT----------------------------     213425------
      ----------------------------------------------------------TGATCTAGCCAAAGCCTGA------------------------------     191724----11
      --------------------------------------------------------CCTGATCTAGCCAAAGCCTGAC-----------------------------     221161--1--
      --------------------------------------------------------CCTGATCTAGCCAAAGCC---------------------------------     1893------
      ----------------------------------------------------------TGATCTAGCCAAAGCCTGACTGTA-------------------------     24-3------
      --------------------------------------------------------CCTGATCTAGCCAAAGCCTG-------------------------------     2021------
      --------------------------------------------------------------CTAGCCAAAGCCTGACTGT--------------------------     1912------
      --------------------------------------------------------CCTGATCTAGCCAAAGCCT--------------------------------     192-------
      -----------------------------------------------------------GATCTAGCCAAAGCCTGACTG---------------------------     2111------
      --------------------TCAGGCTCCTGGCTAGATTC-------------------------------------------------------------------     201-------
      -------------------------------------------------------ACCTGATCTAGCCAAAGCCTGAC-----------------------------     23-1------
      -------------------------------------------------------ACCTGATCTAGCCAAAGCCT--------------------------------     20-1------
      ----------------------------------------------------------TGATCTAGCCAAAGCCTGACTGTAA------------------------     25-1------
      --------------------------------------------------------CCTGATCTAGCCAAAGCCTGA------------------------------     211-------
rno-miR-344-5p     --------------------TCAGGCTCCTGGCTAGATTCCAGG---------------------------------------------------------------     24--------
rat     GCAGCCAGGGTTTTTACCAGTCAGGCTCCTGGCTAGATTCCAGGTACCAACTGGTACCTGATCTAGCCAAAGCCTGACTGTAAGCTGTAAAAACAAAGGAAGACTGC      
mouse     -----CAGGGTTTTTACCAGTCAGGCTCCTGGCTAGATTCCAGGTACCAGCTGGTACCTGATCTAGCCAAAGCCTGACTGTAAGCCCTG------------------      
           ******************************************** ***********************************  *                         
 ...>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>................ENSRNOT00000053681 ENSRNOG00000035558
rat     ((((((...((((((((((((((((((..(((((((((..((((((((....))))))))))))))))).))))))))))......))))))))...))....))))     1.000 -57.10
mouse          ((((((((....((((((((((..(((((((((..((((((((....))))))))))))))))).)))))))))).))))))))                       1.000 -57.30

ratchromosome:1:115954563:115954669:-1Same_strand|Exonic_non-coding|ENSRNOT00000053681|ENSRNOG00000035558 ## ENSRNOG00000035558|miRNA||
mousechromosome:7:69022660:69022743:-1Same_strand|Exonic_non-coding|ENSMUST00000083634|ENSMUSG00000065568|miRNA|mmu-mir-344-1 [Source:miRBase;Acc:MI0000630] ## {MIR: mmu-mir-344-1}


rno-mir-203-as

Cloning frequencies
absoluteT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-203-as 5arm0021100011
rno-mir-203-as 3arm0022730300.500105.500152.500
normalizedT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-203-as 5arm000.0000.0000.0000000.0000.000
rno-mir-203-as 3arm000.0010.00400.00000.0000.0070.010
rno-mir-203-as relative cloning frequencies

sblock10183 (Antisense miRBase rno-mir-203-as) [miRBaseNonMapped_lenNOK_cloningHIGH_multiarm_DicerNOK_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBaseAS rno-mir-203-as0.001nono0.33/0.7218/25/0.600.0
0.2
0.0
0.0
2.8
1.4
1
5
266
0
0
0
1
4
6
0
0
0
16
29
25
21
0
8
5arm
5arm
3arm
1
1
1
nd
nd
nd
0.06
0.15
0.18
1
1
1
367761
sblock10183 hairpin
  readsmiRBase family seed
seed     ---------------------------------------------------------------------UGAACUG---------------------------------------     337novel
seed     ----------------------------------------------------------------------GAACUGU--------------------------------------     18novel
seed     --------------------------------------------------------------------UUGAACU----------------------------------------     6novel
seed     -------------------------------GUGGUCC-----------------------------------------------------------------------------     4novel
seed     ------------------------------AGUGGUC------------------------------------------------------------------------------     1novel
seed     -----------------GCGCGCC-------------------------------------------------------------------------------------------     1novel
  lencloning frequencies
   T2S1T2S2T3S1T3S2T4S2T5S1T5S2
      --------------------------------------------------------------------TTGAACTGTTAAGAACCACTG--------------------------     21719-1-2238
      --------------------------------------------------------------------TTGAACTGTTAAGAACCAC----------------------------     19518---2333
      --------------------------------------------------------------------TTGAACTGTTAAGAACCA-----------------------------     18112-1-2318
      --------------------------------------------------------------------TTGAACTGTTAAGAACCACTGG-------------------------     2219---829
      --------------------------------------------------------------------TTGAACTGTTAAGAACCACT---------------------------     2014---1219
      --------------------------------------------------------------------TTGAACTGTTAAGAACCACTGGAC-----------------------     2436-1-63
      --------------------------------------------------------------------TTGAACTGTTAAGAACCACTGGA------------------------     2331---36
      ---------------------------------------------------------------------TGAACTGTTAAGAACCAC----------------------------     182---123
      ---------------------------------------------------------------------TGAACTGTTAAGAACCACTG--------------------------     20-----22
      ---------------------------------------------------------------------TGAACTGTTAAGAACCACTGG-------------------------     21-3----1
      ------------------------------AGTGGTCCTAAACATTTCACAATTG------------------------------------------------------------     252------
      -------------------------------------------------------------------GTTGAACTGTTAAGAACCAC----------------------------     20-----11
      -------------------------------------------------------------------GTTGAACTGTTAAGAACCACTG--------------------------     22-1---1-
      ---------------------------------------------------------------------TGAACTGTTAAGAACCACT---------------------------     19-----1-
      ----------------TGCGCGCCGGGTCTAGTG---------------------------------------------------------------------------------     18--1----
      ---------------------------------------------------------------------TGAACTGTTAAGAACCACTGGAC-----------------------     23-----1-
      --------------------------------------------------------------------TTGAACTGTTAAGAACCACTGGACC----------------------     25------1
      -------------------------------------------------------------------GTTGAACTGTTAAGAACCACT---------------------------     21-----1-
      -----------------------------TAGTGGTCCTAAACATTTCA------------------------------------------------------------------     20------1
      ------------------------------AGTGGTCCTAAACATTTCACAA---------------------------------------------------------------     22-----1-
      ------------------------------AGTGGTCCTAAACATTTCAC-----------------------------------------------------------------     20-1-----
      -------------------------------------------------------------------GTTGAACTGTTAAGAACC------------------------------     18-----1-
rat     GCTGTCGCCGCTGCCGTGCGCGCCGGGTCTAGTGGTCCTAAACATTTCACAATTGCGCTACAGAACTGTTGAACTGTTAAGAACCACTGGACCAGGCGCGCCTGCACACAGAAGC      
human     ----------------------------CTAGTGGTCCTAAACATTTCACAATTGCGCTACAGAACTGTTGAACTGTTAAGAACCACTGG-------------------------      
mouse     ----------------------------CTAGTGGTCCTAAACATTTCACAATTGTGCTACAGAACTGTTGAACTGTCAAGAACCACTGG-------------------------      
                                  *************************** ********************* ************                               
 .........<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<...................ENSRNOT00000053612 ENSRNOG00000035489 rno-mir-203
rat     (((.((.....(((...(((((((.(((((((((((.((.((((.((((((.(((.....)))...))).))).)))).)).))))))))))).)))))))..)))....)))))     0.920 -49.30
human                                 ((((((((.((.((((.((((((.(((.....)))...))).))).)))).)).))))))))                              1.000 -17.80
mouse                                 ((((((((.((..(((.((((((.((.((...)).)).))).))).)))..)).))))))))                              0.997 -18.20

ratchromosome:6:136932075:136932189:-1Opposite_strand|Exonic_non-coding|ENSRNOT00000053612|ENSRNOG00000035489 ## ENSRNOG00000035489|miRNA|rno-mir-203|rno-mir-203 [Source:miRBase;Acc:MI0000945] ## {ASMIR: rno-mir-203-as}
humanchromosome:14:103653474:103653628:-1Opposite_strand|Boundary_non-coding|ENST00000384836|ENSG00000207568|miRNA|hsa-mir-203 [Source:miRBase;Acc:MI0000283] ## {SimpF: oe = 0.84 0 CpG,rank = 1 -1 FirstEF} ## {ASMIR: hsa-mir-203-as}
mousechromosome:12:113369053:113369207:-1Opposite_strand|Boundary_non-coding|ENSMUST00000083640|ENSMUSG00000065574|miRNA|mmu-mir-203 [Source:miRBase;Acc:MI0000246] ## {SimpF: oe = 0.89 1 CpG} ## {ASMIR: mmu-mir-203-as}


rno-mir-338-as

Cloning frequencies
absoluteT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-338-as 5arm32700440033
rno-mir-338-as 3arm11300030130
normalizedT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-338-as 5arm0.0010.000000.0000.000000.0000.000
rno-mir-338-as 3arm0.0000.0000000.00000.0000.0000
rno-mir-338-as relative cloning frequencies

sblock2905 (Antisense miRBase rno-mir-338-as) [miRBaseNonMapped_lenNOK_cloningHIGH_multiarm_DicerNOK_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBaseAS rno-mir-338-as0.001nono0.33/0.5218/26/0.490.0
0.0
1.4
2.1
28
21
0
0
6
5
0
0
20
20
4
2
5arm
3arm
1
1
nd
nd
0.16
0.11
1
1
747-13
Families
Member of family miR-7a* (seed CAACAAA): rno-mir-338, block2050959_cand
sblock2905 hairpin
  readsmiRBase family seed
seed     -----------------------------------------CAACAAA-------------------------------------------------------------------------------------------     50miR-7a*
seed     ---------------------------------------------------------------------------------CAGCACC---------------------------------------------------     21novel
seed     --------------------------------------------CAAAAUC----------------------------------------------------------------------------------------     3novel
  lencloning frequencies
   T1S1T1S2T3S1T3S2T4S2T5S1T5S2
      ----------------------------------------TCAACAAAATCACTGATGC--------------------------------------------------------------------------------     197531-1-
      ----------------------------------------TCAACAAAATCACTGATGCTG------------------------------------------------------------------------------     2111----11
      ----------------------------------------TCAACAAAATCACTGATGCT-------------------------------------------------------------------------------     2032-1-11
      ----------------------------------------TCAACAAAATCACTGATG---------------------------------------------------------------------------------     185-11---
      --------------------------------------------------------------------------------TCAGCACCAGGATATTGT-----------------------------------------     1821-11--
      --------------------------------------------------------------------------------TCAGCACCAGGATATTGTT----------------------------------------     191--1-2-
      --------------------------------------------------------------------------------TCAGCACCAGGATATTGTTGGG-------------------------------------     223----1-
      ----------------------------------------TCAACAAAATCACTGATGCTGG-----------------------------------------------------------------------------     221--1--1
      --------------------------------------------------------------------------------TCAGCACCAGGATATTGTTGGGG------------------------------------     232--1---
      --------------------------------------------------------------------------------TCAGCACCAGGATATTGTTGGGGA-----------------------------------     2421-----
      -------------------------------------------ACAAAATCACTGATGCTG------------------------------------------------------------------------------     183------
      ----------------------------------------TCAACAAAATCACTGATGCTGGAGTC-------------------------------------------------------------------------     262------
      --------------------------------------------------------------------------------TCAGCACCAGGATATTGTTG---------------------------------------     20-1-----
      --------------------------------------------------------------------------------TCAGCACCAGGATATTGTTGG--------------------------------------     211------
rat     --------------------GAGGCTGGCAGCTGCCCTCTTCAACAAAATCACTGATGCTGGAGTCA-CTGTGCACCCACTCAGCACCAGGATATTGTTGGGGAGGACGGCCTGGGCAGCGTCG---------------      
human     GGGCCCGGCAGGCAGGTCGGGAGGCTGGCAGCTGCCCTCTTCAACAAAATCACTGATGCTGGAGTCGCCTGAGTCATCACTCAGCACCAGGATATTGTTGGAGAGGACAGCC-GTGCGGCGTCTGGGGCTGACGGGGCC      
mouse     ------------------------------------CTCTTCAACAAAATCACTGATGCTGGAGTCA-CTGTGCACCCACTCAGCACCAGGATATTGTTGGGGAG----------------------------------      
                                          ******************************  *** *    ************************ ***                                        
 -----                    ----------------------------------------------- --------------------------------------------------------               -----ENSRNOT00000005839 ENSRNOG00000004392 LOC690853
 -----                    ----------------------------------------------- --------------------------------------------------------               -----ENSRNOT00000040443 ENSRNOG00000004392 LOC690853
 .....                    .................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<....................               .....ENSRNOT00000053588 ENSRNOG00000035465 rno-mir-338
rat                         ((.((((.((((((.((((..((((((.(((.(((.((((.((((.. ..........)))))))).)))))).))))))..)))).)))).))..)))).)).                    1.000 -47.90
human     ((.((((.....(((.((.(((.((((((.((((.((((((((((((.(((.(((.((((.((((.....((....)))))))))).)))))).)))))))))))).)))). )).)))).))).)).))).)))).))     0.940 -71.00
mouse                                         (((..((((((.(((.(((.((((.((((.. ..........)))))))).)))))).))))))..)))                                       0.998 -27.20

ratchromosome:10:109426975:109427077:1Opposite_strand|Exonic_non-coding|ENSRNOT00000053588|ENSRNOG00000035465 ## Opposite_strand|Intronic_coding|ENSRNOT00000005839|ENSRNOG00000004392 ## ENSRNOG00000004392|protein_coding|LOC690853| ## ENSRNOG00000035465|miRNA|rno-mir-338|rno-mir-338 [Source:miRBase;Acc:MI0000618] ## {ASMIR: rno-mir-338-as}
humanchromosome:17:76714241:76714378:1Opposite_strand|Intronic_coding|ENST00000326724|ENSG00000181409|protein_coding|Serine/threonine-protein kinase LMTK1 (EC 2.7.11.1)(Lemur tyrosine kinase 1)(Apoptosis-associated tyrosine kinase)(AATYK)(Brain apoptosis-associated tyrosine kinase)(CDK5-binding protein)(p35-binding protein)(p35BP) [Source:UniProtKB/Swiss-Prot;Acc:Q6ZMQ8] ## Opposite_strand|Boundary_non-coding|ENST00000390137|ENSG00000211563|miRNA|hsa-mir-338 [Source:miRBase;Acc:MI0000814] ## {Repeats: dust 0 class=dust} ## {ASMIR: hsa-mir-338-as}
mousechromosome:11:119876090:119876157:1Opposite_strand|Intronic_coding|ENSMUST00000064307|ENSMUSG00000025375|protein_coding|apoptosis-associated tyrosine kinase Gene [Source:MGI (curated);Acc:Aatk-001] ## Opposite_strand|Exonic_non-coding|ENSMUST00000083666|ENSMUSG00000065600|miRNA|mmu-mir-338 [Source:miRBase;Acc:MI0000619] ## {ASMIR: mmu-mir-338-as}


miRBaseNonMapped_Multihit_randfoldOK (2 loci)

block210143 (miRBaseNonMapped rno-mir-297) [miRBaseNonMapped_Multihit_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBaseNonMapped rno-mir-2970.001nono0.35/0.3923/23/1.00nd
0.0
nd
0.0
0
1
0
0
0
1
0
0
15
6
20
29
3arm
3arm
13
80
nd
nd
0.13
0.04
2
1
11nana
block210143 hairpin
  readsmiRBase family seed
seed--------------------------------------------------------------------------------------------GCAUGUA---------------------1novel
seed-----------------------------------------------------------------------------------UGUAUGU------------------------------0miR-297
  lencloning frequencies
   T3S1
 -------------------------------------------------------------------------------------------TGCATGTATGCATGTATGTATGT------231
rno-miR-297----------------------------------------------------------------------------------ATGTATGTGTGCATGTATGCATG---------------23-
ratatgcatgcatgtatgcatgtgtgaatgtatgcatgtgtgcatgtatgcatgtgtgcatgtatgtgtgtgcatgcatgcatgtATGTATGTGTGCATGTATGCATGTATGTATGTgtgcat 
 ************************************************************************************************************************ 
rat(((((((((((((((((((((((.(((((((((((..((((((((((((((..(((((....)))))..))))))))))))))..))))))))))).)))))))))))))))))))))))1.000 -73.60

ratchromosome:12:6886770:6886889:1intergenic ## {Repeats: (TATG)n 2 179 1 class=Simple_repeat,(TATG)n 103 135 1 class=Simple_repeat,trf 44 76 0 class=trf,trf 55 87 0 class=trf,dust 6886792 6886824 0 class=dust}


rno-mir-466b-2-as

Cloning frequencies
absoluteT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-466b-2-as 3arm00.00400000000
normalizedT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-466b-2-as 3arm00.00000000000
rno-mir-466b-2-as relative cloning frequencies

block675545 (Antisense miRBase rno-mir-466b-2-as) [miRBaseNonMapped_Multihit_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBaseAS rno-mir-466b-2-as0.001nono0.38/0.3821/21/1.000.0
0.0
1
0
1
0
20
9
3arm
268
nd
0.14
2
11nana
Families
Member of family miR-466b (seed AUGUGUG): mmu-mir-466b, rno-mir-466b, rno-mir-466b, rno-mir-466b-2, rno-mir-466b-1
block675545 hairpin
  readsmiRBase family seed
seed     -----------------------------------------------------------------------------ACACACA---------------------------------     1novel
  lencloning frequencies
   T1S2
      ----------------------------------------------------------------------------TACACACACACATATACACAC--------------------     211
rat     ttgccacttgtgtgtgtgtgcttgcgtatatgtgtatgtgtgtatgtatatgtataatcatatacacacatggacaTACACACACACATATACACACatgcacatacataggggcag      
      *********************************************************************************************************************      
 -------------------------------------------------------------------------------------------------------------------------------ENSRNOT00000042430 ENSRNOG00000029235 Sfmbt2
 .......................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<......................ENSRNOT00000063096 ENSRNOG00000041343 rno-mir-466b-2
rat     .((((.((((((((((((((..((.((((((((((..((((((((((.(((((..............))))).)))))))))))))))))))).))..)))))))))))))))))).     1.000 -57.44

ratchromosome:17:79288516:79288632:1Opposite_strand|Intronic_coding|ENSRNOT00000042430|ENSRNOG00000029235 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000051529|ENSRNOG00000029235 ## Opposite_strand|Exonic_non-coding|ENSRNOT00000063096|ENSRNOG00000041343 ## ENSRNOG00000041343|miRNA|rno-mir-466b-2|rno-mir-466b-2 [Source:miRBase;Acc:MI0006113] ## ENSRNOG00000029235|protein_coding|Sfmbt2|Scm-like with four mbt domains 2 Gene [Source:MGI (curated);Acc:Sfmbt2-001] ## {Repeats: (CA)n 1 50 1 class=Simple_repeat,dust 79288591 79288612 0 class=dust,trf 12 33 0 class=trf,trf 15 36 0 class=trf,(CA)n 18 39 1 class=Simple_repeat} ## {ASMIR: rno-mir-466b-2-as}


miRBaseNonMapped_lenNOK_cloningOK_multiarm_DicerNOK_randfoldOK (2 loci)

rno-mir-299-as

Cloning frequencies
absoluteT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-299-as 5arm32.5000000000.5000
rno-mir-299-as 3arm6.5002.500000.5000.5000001
normalizedT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-299-as 5arm0.0000.0000000000.0000
rno-mir-299-as 3arm0.0000.000000.0000.0000000.000
rno-mir-299-as relative cloning frequencies

sblock10170 (Antisense miRBase rno-mir-299-as) [miRBaseNonMapped_lenNOK_cloningOK_multiarm_DicerNOK_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBaseAS rno-mir-299-as0.001nono0.47/0.5618/21/0.240.3
0.6
0.6
0.7
9
16
0
0
3
5
0
0
32
35
0
2
5arm
3arm
2
2
nd
nd
0.00
0.00
0
0
25620
Families
Member of family miR-299 (seed GGUUUAC): rno-mir-299, rno-mir-299, block89547_cand
sblock10170 hairpin
  readsmiRBase family seed
seed     ----------------------------------------------------------------UAUGUGG-----------------------------------------------     10novel
seed     -----------------------------------------------------------------AUGUGGG----------------------------------------------     6novel
seed     ----------------------------------GUUUACC-----------------------------------------------------------------------------     6novel
seed     ---------------------------------GGUUUAC------------------------------------------------------------------------------     3miR-299
  lencloning frequencies
   T1S1T1S2T3S1T3S2T5S1T5S2
      ---------------------------------------------------------------GTATGTGGGACGGTAAACC------------------------------------     1912-1-2
      ---------------------------------GGTTTACCGTCCCACATAC------------------------------------------------------------------     1923----
      ----------------------------------------------------------------TATGTGGGACGGTAAACC------------------------------------     1821----
      ---------------------------------------------------------------GTATGTGGGACGGTAAACCA-----------------------------------     2021----
      ----------------------------------------------------------------TATGTGGGACGGTAAACCA-----------------------------------     193-----
      --------------------------------CGGTTTACCGTCCCACATAC------------------------------------------------------------------     201-----
      ---------------------------------------------------------------GTATGTGGGACGGTAAAC-------------------------------------     18--1---
      --------------------------------CGGTTTACCGTCCCACAT--------------------------------------------------------------------     18-1----
      ---------------------------------GGTTTACCGTCCCACATACAT----------------------------------------------------------------     21----1-
      --------------------------------CGGTTTACCGTCCCACATACA-----------------------------------------------------------------     211-----
rat     CGGACTGGATGGCTGGGCTGGATACCAAGAAGCGGTTTACCGTCCCACATACATACTCAAAATGTATGTGGGACGGTAAACCATTTCTTCAAGTACCGCGTGACAGCAGGGACAGCTG      
human     --------------------------------CGGTTTACCATCCCACATACATATTCAAAATGTATGTGGGACGGTAAACCA-----------------------------------      
mouse     --------------------------------CGGTTTACCGTCCCACATACATACTCAAAATGTATGTGGGACGGTAAACCA-----------------------------------      
                                      ********* ************* ***************************                                         
 ...............................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<..................................ENSRNOT00000053630 ENSRNOG00000035507 rno-mir-299
rat     (((.(((....((((.(((((.(((.((((((.(((((((((((((((((((((.......))))))))))))))))))))).))))))...)))))).))..)))).....))))))     1.000 -58.90
human                                     .((((((((.((((((((((((.......)))))))))))).)))))))).                                        1.000 -32.80
mouse                                     .(((((((((((((((((((((.......))))))))))))))))))))).                                        1.000 -38.50

ratchromosome:6:134389793:134389910:-1Opposite_strand|Exonic_non-coding|ENSRNOT00000053630|ENSRNOG00000035507 ## ENSRNOG00000035507|miRNA|rno-mir-299|rno-mir-299 [Source:miRBase;Acc:MI0000970] ## {ASMIR: rno-mir-299-as}
humanchromosome:14:100559835:100559992:-1Opposite_strand|Boundary_non-coding|ENST00000385016|ENSG00000207749|miRNA|hsa-mir-299 [Source:miRBase;Acc:MI0000744] ## {ASMIR: hsa-mir-299-as}
mousechromosome:12:110948799:110948956:-1Opposite_strand|Boundary_non-coding|ENSMUST00000083616|ENSMUSG00000065550|miRNA|mmu-mir-299 [Source:miRBase;Acc:MI0000399] ## {ASMIR: mmu-mir-299-as}


rno-mir-219-1-as

Cloning frequencies
absoluteT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-219-1-as 5arm0801410022
rno-mir-219-1-as 3arm0.500000000000
normalizedT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-219-1-as 5arm00.00000.0000.0000.000000.0000.000
rno-mir-219-1-as 3arm0.000000000000
rno-mir-219-1-as relative cloning frequencies

sblock6664 (Antisense miRBase rno-mir-219-1-as) [miRBaseNonMapped_lenNOK_cloningOK_multiarm_DicerNOK_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBaseAS rno-mir-219-1-as0.001nono0.39/0.6418/22/0.680.0
0.0
0.4
0.0
10
1
0
0
6
1
0
0
31
29
3
12
5arm
3arm
1
2
nd
nd
0.10
0.17
1
2
1971-2
Families
Member of family novel153 (seed GAAUUGC): rno-mir-219-1, rno-mir-219-2
sblock6664 hairpin
  readsmiRBase family seed
seed     ------------------------------------------------GACGUCC----------------------------------------------------------------------------------------------     17novel
seed     -------------------------------------------------ACGUCCA---------------------------------------------------------------------------------------------     1novel
seed     ----------------------------------------------------------------------------------------GAAUUGC------------------------------------------------------     1novel
  lencloning frequencies
   T1S1T1S2T2S2T3S1T3S2T5S1T5S2
      -----------------------------------------------GGACGTCCAGACGCAACTCTC---------------------------------------------------------------------------------     21-6--112
      -----------------------------------------------GGACGTCCAGACGCAACTC-----------------------------------------------------------------------------------     19-112---
      -----------------------------------------------GGACGTCCAGACGCAACTCTCG--------------------------------------------------------------------------------     22-1-1---
      -----------------------------------------------GGACGTCCAGACGCAACT------------------------------------------------------------------------------------     18---1---
      ------------------------------------------------GACGTCCAGACGCAACTCTC---------------------------------------------------------------------------------     20-----1-
      ---------------------------------------------------------------------------------------AGAATTGCGTTTGGACAA--------------------------------------------     181------
rat     ----------------CTCCCCCTCGAGGTTTGGGGGCGGCGGCTCGGGACGTCCAGACGCAACTCTCGGCCGGAGCCAGAGACTCGAGAATTGCGTTTGGACAATCAGGAGCCGCGGCCCGGGACAGGGAGAG---------------      
human     -----------------------------------------------GGACGTCCAGACTCAACTCTCGGCCGGAGCCATAGACTCGAGAATTGCGTTTGGACAATCA-----------------------------------------      
mouse     GCGCTCCGCCCGGCCTCTCCCCCTCGAGGTTTGGGGGCGGCGGCTCGGGACGTCCAGACGCAACTCTCGGCCGGAGCCAGAGACTCGAGAATTGCGTTTGGACAATCAGGAGCCGCGGCCCGGGACGGGGAGAGAAGCGCATCGGAGGC      
                                                     ************ ******************* ****************************                                               
 .....                ..<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<......               .....ENSRNOT00000053776 ENSRNOG00000035653 rno-mir-219-1
rat                     (((.((((....((((.((.((.(((((((..((.((((((((((((.(((((((....)))........)))).))))))))))))..))..))))))).)))).)))))))).)))                    0.820 -63.20
human                                                    ....((((((((.(((.(((((((....)))........)))).))).)))))))).....                                              1.000 -21.70
mouse     ((.(((((....((((((((((......((((.((.((.(((((((..((.((((((((((((.(((((((....)))........)))).))))))))))))..))..))))))).)))).))))))))))))..))....)))))))     0.815 -80.30

ratchromosome:20:4967795:4967912:-1Opposite_strand|Exonic_non-coding|ENSRNOT00000053776|ENSRNOG00000035653 ## ENSRNOG00000035653|miRNA|rno-mir-219-1|rno-mir-219-1 [Source:miRBase;Acc:MI0000959] ## {SimpF: oe = 0.97 -1 CpG} ## {ASMIR: rno-mir-219-1-as}
humanchromosome:6:33283564:33283721:-1Opposite_strand|Boundary_non-coding|ENST00000362166|ENSG00000199036|miRNA|hsa-mir-219-1 [Source:miRBase;Acc:MI0000296] ## {SimpF: rank = 1 1 FirstEF,oe = 1.00 0 CpG} ## {ASMIR: hsa-mir-219-1-as}
mousechromosome:17:34161910:34162058:1Opposite_strand|Boundary_non-coding|ENSMUST00000083621|ENSMUSG00000065555|miRNA|mmu-mir-219-1 [Source:miRBase;Acc:MI0000702] ## {SimpF: oe = 0.97 1 CpG, -1 Eponine} ## {ASMIR: mmu-mir-219-1-as}


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