logoSmall RNA from different tissues of two rat strains.

miR-Intess™


Summary
Preprocessing
Mapping
Composition
miR classification

miR expression
Downloads
List
Heatmaps

rno-let-7f

rno-let-7f

Cloning frequencies
absoluteT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-let-7f 5arm40980260772590526493308342682715598257891187512008
rno-let-7f 3arm3372942552603351407815420082.500
normalizedT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-let-7f 5arm1.3621.1381.4031.5711.5022.0331.2131.3570.7830.799
rno-let-7f 3arm0.0110.0130.0140.0150.0160.0110.0060.0080.0130.005
rno-let-7f relative cloning frequencies

sblock12788 (miRBase rno-let-7f-2) [miRNAknown_cloningHIGH_multiarm_DicerOK_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase rno-let-7f-20.001nono0.28/0.4318/24/0.810.0
0.0
1.0
0.4
181154
671
0
0
10
10
0
0
7
5
6
5
5arm
3arm
2
2
nd
nd
0.10
0.10
2
2
2410571021
Clusters
Located in cluster 96: rno-let-7f, rno-mir-98
Families
Member of family let-7a/7b/7c/7d/7e/7f/7i/miR-98 (seed GAGGUAG): rno-let-7a, rno-let-7f, rno-let-7e, rno-let-7a, rno-let-7f, rno-let-7d, rno-let-7c, rno-let-7b, rno-mir-98, rno-let-7c, rno-let-7i, block113823_cand, block2634835_cand
sblock12788 hairpin
  readsmiRBase family seed
seed     ---------------------------GAGGUAG-----------------------------------------------------------------------------------------------     239011let-7a/7b/7c/7d/7e/7f/7i/miR-98
seed     ----------------------------AGGUAGU----------------------------------------------------------------------------------------------     1047miR-196a/196b/196c
seed     -----------------------------------------------------------------------------------UAUACAG---------------------------------------     925novel
seed     -----------------------------GGUAGUA---------------------------------------------------------------------------------------------     33novel
seed     ------------------------------GUAGUAG--------------------------------------------------------------------------------------------     17novel
seed     --------------------------UGAGGUA------------------------------------------------------------------------------------------------     12novel
seed     -------------------------------UAGUAGA-------------------------------------------------------------------------------------------     10novel
seed     ---------------------------------------------------------------------------------ACUAUAC-----------------------------------------     1novel
seed     --------------------------------------------------------------------------------AACUAUA------------------------------------------     1novel
  lencloning frequencies
   T1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
      --------------------------TGAGGTAGTAGATTGTATAG-----------------------------------------------------------------------------------     2011759793270217462880173854620754731283395
rno-let-7f     --------------------------TGAGGTAGTAGATTGTATAGTT---------------------------------------------------------------------------------     2210831726671927314692769303734638128683186
      --------------------------TGAGGTAGTAGATTGTATAGT----------------------------------------------------------------------------------     219665569566336068772070453960661328952751
      --------------------------TGAGGTAGTAGATTGTAT-------------------------------------------------------------------------------------     184789271126352862386428921645270413951279
      --------------------------TGAGGTAGTAGATTGTATA------------------------------------------------------------------------------------     1929581770165520392807197711911903946892
      --------------------------TGAGGTAGTAGATTGTATAGTTT--------------------------------------------------------------------------------     23441271376400314273223282223172
      ----------------------------------------------------------------------------------CTATACAGTCTACTGTCTTTC--------------------------     21106976443774427597022
      ---------------------------GAGGTAGTAGATTGTATAG-----------------------------------------------------------------------------------     1956424752465535333133
      --------------------------TGAGGTAGTAGATTGTATAGTTTT-------------------------------------------------------------------------------     2469893348401817313122
      ---------------------------GAGGTAGTAGATTGTATAGTT---------------------------------------------------------------------------------     2146383319343515371428
      ---------------------------GAGGTAGTAGATTGTATAGT----------------------------------------------------------------------------------     2028302517302412341515
      ----------------------------------------------------------------------------------CTATACAGTCTACTGTCT-----------------------------     18344510132718111187
      ----------------------------------------------------------------------------------CTATACAGTCTACTGTCTT----------------------------     1993246111049122
      ---------------------------GAGGTAGTAGATTGTATA------------------------------------------------------------------------------------     1814787753894
      ---------------------------GAGGTAGTAGATTGTATAGTTT--------------------------------------------------------------------------------     22-32-1522--
      ----------------------------AGGTAGTAGATTGTATAGTT---------------------------------------------------------------------------------     2011312212--
      ----------------------------------------------------------------------------------CTATACAGTCTACTGTCTTTCCC------------------------     23-4-11--411
      ----------------------------------------------------------------------------------CTATACAGTCTACTGTCTTTCC-------------------------     22124111-2--
      -----------------------------GGTAGTAGATTGTATAGTT---------------------------------------------------------------------------------     1922231--11-
      ------------------------------GTAGTAGATTGTATAGTT---------------------------------------------------------------------------------     18-123---31-
      ----------------------------AGGTAGTAGATTGTATAGT----------------------------------------------------------------------------------     193-2-1111--
      ----------------------------------------------------------------------------------CTATACAGTCTACTGTCTTT---------------------------     2011122---11
      ----------------------------AGGTAGTAGATTGTATAG-----------------------------------------------------------------------------------     1822-1-11-11
      -------------------------ATGAGGTAGTAGATTGTATAG-----------------------------------------------------------------------------------     211-1-1-2-1-
      -----------------------------GGTAGTAGATTGTATAGT----------------------------------------------------------------------------------     18-11----111
      ----------------------------AGGTAGTAGATTGTATAGTTT--------------------------------------------------------------------------------     21---1---1--
      -------------------------ATGAGGTAGTAGATTGTA--------------------------------------------------------------------------------------     18-1-----1--
      -------------------------ATGAGGTAGTAGATTGTATAGTT---------------------------------------------------------------------------------     23-1-1------
      -------------------------ATGAGGTAGTAGATTGTAT-------------------------------------------------------------------------------------     19---1-1----
      -------------------------------------------------------------------------------TAACTATACAGTCTACTGTCTTT---------------------------     231---------
      ---------------------------GAGGTAGTAGATTGTATAGTTTT-------------------------------------------------------------------------------     23-1--------
      --------------------------------------------------------------------------------AACTATACAGTCTACTGTCTTTC--------------------------     23--------1-
rat     ------------------TGT-GGGATGAGGTAGTAGATTGTATAGTTTTAGGG------TCATACCCCATCTTGGAGATAACTATACAGTCTACTGTCTTTCCCACG---------------------      
human     CACCAAGACCGACTGCCCTTT-GGGGTGAGGTAGTAGGTTGTATAGTT-TGGGG------CTCTGCCCTG-CTATGGGATAACTATACAATCTACTGTCTTTCCTGAAGTGGCTGTAATATCTGCGGTG      
mouse     CAGAAGAAAAACTTGCTCTATCAGAGTGAGGTAGTAGATTGTATAGTTGTGGGGTAGTGATTTTACCCTGTTTAGGAGATAACTATACAATCTATTGCCTTCCCTGAGG-------AGTAGACTTGCTG      
                        * *  *  *********** ********** * ***         * ***    *  * ************ **** ** *** **                               
 +++++                  +++ ++++++++++++++++++++++++++++++++      ++++++++++++++++++++++++++++++++++++++++++++++++                     +++++ENSRNOT00000003882 ENSRNOG00000002877 HUWE1_RAT
 +++++                  +++ ++++++++++++++++++++++++++++++++      ++++++++++++++++++++++++++++++++++++++++++++++++                     +++++ENSRNOT00000004064 ENSRNOG00000002877 HUWE1_RAT
 .....                  >>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>      >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>                     .....ENSRNOT00000053587 ENSRNOG00000035464 rno-let-7f-2
rat                       .(( ((((.(((..((((((((((((((((...(((      .....))).(((.....)))))))))))))))))))..))))))))).                          1.000 -40.70
human     ((((.(((...((.((((((. .(((.(((..(((((((((((((((( (((((      (...)))))) .........))))))))))))))))..))))))..))).))).))....)))..))))     0.910 -54.30
mouse     ............(((((((.((((...((((((((((((((((((((((((((((((.....))))))).........)))))))))))))))))))))))..))))))       )))))........     0.974 -49.60

ratchromosome:X:41376943:41377025:1Same_strand|Intronic_coding|ENSRNOT00000003882|ENSRNOG00000002877 ## Same_strand|Boundary_non-coding|ENSRNOT00000053587|ENSRNOG00000035464 ## Same_strand|Exonic_non-coding|ENSRNOT00000053587|ENSRNOG00000035464 ## Same_strand|Intronic_non-coding|ENSRNOT00000004064|ENSRNOG00000002877 ## ENSRNOG00000035464|miRNA|rno-let-7f-2|rno-let-7f-2 [Source:miRBase;Acc:MI0000834] ## ENSRNOG00000002877|protein_coding|HUWE1_RAT|E3 ubiquitin-protein ligase HUWE1 (EC 6.3.2.-) (HECT, UBA and WWE domain-containing protein 1) (URE-B1) (Upstream regulatory element- binding protein 1) (Fragment). [Source:UniProtKB/Swiss-Prot;Acc:P51593] ## {MIR: rno-let-7f-2}
humanchromosome:22:44887271:44887390:1Same_strand|Boundary_non-coding|ENST00000362116|ENSG00000198986|miRNA|hsa-let-7a-3 [Source:miRBase;Acc:MI0000062] ## {MIR: hsa-let-7a-3}
mousechromosome:13:48633184:48633305:-1Same_strand|Boundary_non-coding|ENSMUST00000083583|ENSMUSG00000065517|miRNA|mmu-let-7f-1 [Source:miRBase;Acc:MI0000562] ## {MIR: mmu-let-7f-1}


sblock5323 (miRBase rno-let-7f-1) [miRNAknown_cloningHIGH_multiarm_DicerOK_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase rno-let-7f-10.001nono0.21/0.4118/26/0.810.0
0.0
0.0
1.0
0.0
0.7
181154
1
618
0
0
0
10
1
10
0
0
0
7
37
5
9
-22
20
5arm
5arm_loop_3arm
3arm
2
2
2
nd
nd
nd
0.05
0.61
0.06
1
9
1
2401921021
Clusters
Located in cluster 33: rno-let-7a, rno-let-7f
Families
Member of family let-7b* (seed UAUACAA): rno-let-7a, rno-let-7f, rno-let-7c, rno-let-7b, rno-let-7f-1
sblock5323 hairpin
  readsmiRBase family seed
seed     ---------------------------GAGGUAG----------------------------------------------------------------------------------------     237854let-7a/7b/7c/7d/7e/7f/7i/miR-98
seed     -----------------------------------------------------------------------------------UAUACAA--------------------------------     1098let-7b*
seed     ----------------------------AGGUAGU---------------------------------------------------------------------------------------     1045miR-196a/196b/196c
seed     ---------------------------------------------------------------------------------ACUAUAC----------------------------------     41novel
seed     ----------------------------------------------------------------------------------CUAUACA---------------------------------     39novel
seed     -----------------------------GGUAGUA--------------------------------------------------------------------------------------     36novel
seed     ------------------------------------------------------------------------------------AUACAAU-------------------------------     25novel
seed     --------------------------UGAGGUA-----------------------------------------------------------------------------------------     18novel
seed     ------------------------------GUAGUAG-------------------------------------------------------------------------------------     17novel
seed     -------------------------------UAGUAGA------------------------------------------------------------------------------------     11novel
seed     -----------------------------------------------------------------------------GAUAACU--------------------------------------     3novel
seed     --------------------------------------------------------------------------------AACUAUA-----------------------------------     1novel
seed     -------------------------GUGAGGU------------------------------------------------------------------------------------------     1novel
seed     ------------------------------------------------------------------------------AUAACUA-------------------------------------     1novel
seed     ---------------------------------------------------------UGAUUUU----------------------------------------------------------     1novel
seed     -------------------------------------------------------------------------------UAACUAU------------------------------------     1novel
  lencloning frequencies
   T1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
      --------------------------TGAGGTAGTAGATTGTATAG----------------------------------------------------------------------------     2011759793270217462880173854620754731283395
rno-let-7f     --------------------------TGAGGTAGTAGATTGTATAGTT--------------------------------------------------------------------------     2210831726671927314692769303734638128683186
      --------------------------TGAGGTAGTAGATTGTATAGT---------------------------------------------------------------------------     219665569566336068772070453960661328952751
      --------------------------TGAGGTAGTAGATTGTAT------------------------------------------------------------------------------     184789271126352862386428921645270413951279
      --------------------------TGAGGTAGTAGATTGTATA-----------------------------------------------------------------------------     1929581770165520392807197711911903946892
      --------------------------TGAGGTAGTAGATTGTATAGTTG-------------------------------------------------------------------------     232501771961691631348214399108
      --------------------------TGAGGTAGTAGATTGTATAGTTGT------------------------------------------------------------------------     245230352269405257206114
      ----------------------------------------------------------------------------------CTATACAATCTATTGCCTTCC-------------------     2198638581922410215517
      ---------------------------GAGGTAGTAGATTGTATAG----------------------------------------------------------------------------     1956424752465535333133
      ---------------------------GAGGTAGTAGATTGTATAGTT--------------------------------------------------------------------------     2146383319343515371428
      ----------------------------------------------------------------------------------CTATACAATCTATTGCCT----------------------     18291642544817791813
      ---------------------------GAGGTAGTAGATTGTATAGT---------------------------------------------------------------------------     2028302517302412341515
      ----------------------------------------------------------------------------------CTATACAATCTATTGCCTTCCC------------------     22219252127569196
      ----------------------------------------------------------------------------------CTATACAATCTATTGCCTTC--------------------     20133814221221197
      ---------------------------GAGGTAGTAGATTGTATA-----------------------------------------------------------------------------     1814787753894
      ----------------------------------------------------------------------------------CTATACAATCTATTGCCTT---------------------     1945851411414
      -----------------------------------------------------------------------------------TATACAATCTATTGCCTTCC-------------------     203-354--12-
      --------------------------TGAGGTAGTAGATTGTATAGTTGTG-----------------------------------------------------------------------     2542-111-142
      --------------------------------------------------------------------------------AACTATACAATCTATTGCCTTCC-------------------     2322-13152--
      ---------------------------------------------------------------------------------ACTATACAATCTATTGCCTTCCC------------------     2331-333--1-
      ----------------------------AGGTAGTAGATTGTATAGTT--------------------------------------------------------------------------     2011312212--
      --------------------------------------------------------------------------------AACTATACAATCTATTGCC-----------------------     1922--1-3121
      ---------------------------------------------------------------------------------ACTATACAATCTATTGCC-----------------------     1861-1-1-3--
      -----------------------------GGTAGTAGATTGTATAGTT--------------------------------------------------------------------------     1922231--11-
      ------------------------------GTAGTAGATTGTATAGTT--------------------------------------------------------------------------     18-123---31-
      ----------------------------AGGTAGTAGATTGTATAG----------------------------------------------------------------------------     1822-1-11-11
      ----------------------------AGGTAGTAGATTGTATAGT---------------------------------------------------------------------------     193-2-1111--
      -------------------------GTGAGGTAGTAGATTGTATAGTT--------------------------------------------------------------------------     2322--1211--
      ---------------------------GAGGTAGTAGATTGTATAGTTG-------------------------------------------------------------------------     22-1--11--22
      ---------------------------GAGGTAGTAGATTGTATAGTTGT------------------------------------------------------------------------     231---1--122
      ---------------------------------------------------------------------------------ACTATACAATCTATTGCCTTCC-------------------     22-2-1-1-2--
      --------------------------------------------------------------------------------AACTATACAATCTATTGCCTTCCC------------------     2422-1------
      --------------------------------------------------------------------------------AACTATACAATCTATTGCCT----------------------     201-----13--
      -----------------------------GGTAGTAGATTGTATAGT---------------------------------------------------------------------------     18-11----111
      ----------------------------AGGTAGTAGATTGTATAGTTGT------------------------------------------------------------------------     2211--1---11
      -----------------------------------------------------------------------------------TATACAATCTATTGCCTTCCC------------------     21---4--1---
      ---------------------------------------------------------------------------------ACTATACAATCTATTGCCT----------------------     19-2-----2--
      -------------------------GTGAGGTAGTAGATTGTATAG----------------------------------------------------------------------------     212--1------
      ----------------------------------------------------------------------------------CTATACAATCTATTGCCTTCCCT-----------------     23-1--2-----
      -------------------------GTGAGGTAGTAGATTGTA-------------------------------------------------------------------------------     18--1-1--1--
      -------------------------GTGAGGTAGTAGATTGTATAGT---------------------------------------------------------------------------     22---1--1---
      --------------------------------------------------------------------------------AACTATACAATCTATTGCCTT---------------------     21-2--------
      ----------------------------------------------------------------------------AGATAACTATACAATCTAT---------------------------     19-----2----
      ---------------------------------------------------------------------------------ACTATACAATCTATTGCCTTC--------------------     2111--------
      --------------------------TGAGGTAGTAGATTGTATAGTTGTGG----------------------------------------------------------------------     261-1-------
      -------------------------GTGAGGTAGTAGATTGTAT------------------------------------------------------------------------------     191---------
      ---------------------------------------------------------------------------------ACTATACAATCTATTGCCTT---------------------     20--1-------
      ------------------------------GTAGTAGATTGTATAGTTGT------------------------------------------------------------------------     20--1-------
      -----------------------------------------------------------------------------------TATACAATCTATTGCCTTC--------------------     19---1------
      ------------------------AGTGAGGTAGTAGATTGTA-------------------------------------------------------------------------------     191---------
      -----------------------------------------------------------------------------GATAACTATACAATCTATTG-------------------------     20-1--------
      ------------------------------------------------------------------------------ATAACTATACAATCTATTGCCTTC--------------------     24-------1--
      --------------------------------------------------------------------------------AACTATACAATCTATTGCCTTC--------------------     22---1------
      ----------------------------------------------------------------------------AGATAACTATACAATCTATTGCC-----------------------     23---------1
      --------------------------------------------------------GTGATTTTACCCTGTTTAGGAGA-------------------------------------------     23--------1-
      -------------------------------------------------------------------------------TAACTATACAATCTATTGCCT----------------------     21---1------
      -----------------------------------------------------------------------------------TATACAATCTATTGCCTT---------------------     18---------1
rat     -------------------ATCAGAGTGAGGTAGTAGATTGTATAGTTGTGGGGTAGTGATTTTACCCTGTTTAGGAGATAACTATACAATCTATTGCCTTCCCTGAG--------------      
human     CAGAAGAAAACATTGCTCTATCAGAGTGAGGTAGTAGATTGTATAGTTGTGGGGTAGTGATTTTACCCTGTTCAGGAGATAACTATACAATCTATTGCCTTCCCTGAGGAGTAGACTTGCTG      
mouse     CAGAAGAAAAACTTGCTCTATCAGAGTGAGGTAGTAGATTGTATAGTTGTGGGGTAGTGATTTTACCCTGTTTAGGAGATAACTATACAATCTATTGCCTTCCCTGAGGAGTAGACTTGCTG      
                         ***************************************************** ***********************************                    
 .....                   >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>              .....ENSRNOT00000053661 ENSRNOG00000035538 rno-let-7f-1
rat                        .((((.(..(((((((((((((((((((((((((((((.....))))))).........))))))))))))))))))))))..))))).                   1.000 -44.40
human     ............(((((((.((((...((((((((((((((((((((((((((((((.....))))))).........)))))))))))))))))))))))..)))))))))))........     0.900 -49.80
mouse     ............(((((((.((((...((((((((((((((((((((((((((((((.....))))))).........)))))))))))))))))))))))..)))))))))))........     0.974 -49.60

ratchromosome:17:22120135:22120223:1Same_strand|Exonic_non-coding|ENSRNOT00000053661|ENSRNOG00000035538 ## ENSRNOG00000035538|miRNA|rno-let-7f-1|rno-let-7f-1 [Source:miRBase;Acc:MI0000833] ## {MIR: rno-let-7f-1}
humanchromosome:9:95978430:95978551:1Same_strand|Boundary_non-coding|ENST00000362202|ENSG00000199072|miRNA|hsa-let-7f-1 [Source:miRBase;Acc:MI0000067] ## {MIR: hsa-let-7f-1}
mousechromosome:13:48633184:48633305:-1Same_strand|Boundary_non-coding|ENSMUST00000083583|ENSMUSG00000065517|miRNA|mmu-let-7f-1 [Source:miRBase;Acc:MI0000562] ## {MIR: mmu-let-7f-1}


©2008 InteRNA Genomics B.V.