logoSmall RNA from different tissues of two rat strains.


miR classification

Alignments

other hairpins

novel_lenNOK_multiarm_DicerNOK_Multihit_5varHIGH_loopOverlap_nonpairedHIGH_bulgeHIGH (4 loci)

sblock8609 [novel_lenNOK_multiarm_DicerNOK_Multihit_5varHIGH_loopOverlap_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.405nono0.58/0.7519/25/0.671.3
0.0
2.0
1.0
0.0
0.5
3
1
2
0
0
0
2
1
2
0
0
0
7
25
11
12
-5
11
5arm
3arm_loop
3arm
28
30
31
nd
nd
nd
0.46
0.44
0.45
5
4
4
65020
  readsmiRBase family seed
seed--------CCAGCGA------------------------------------------------------------------------------------2novel
seed----------------------------------------------------------------------GCAGUGU----------------------1novel
seed------------------------------------------------------------------CUCUGCA--------------------------1novel
seed------------CGACCCC--------------------------------------------------------------------------------1novel
seed--------------------------------------------------AACCCCG------------------------------------------1novel
  lencloning frequencies
   T1S1T2S1T3S2T5S1T5S2
 -------GCCAGCGACCCCAGAGGACCCCAG--------------------------------------------------------------------24--2--
 ---------------------------------------------------------------------TGCAGTGTCCCGTGGACAT-----------191----
 -------------------------------------------------CAACCCCGAACGATGGACTCTGCAG-------------------------25-1---
 -----------GCGACCCCAGAGGACCCCAGCAC-----------------------------------------------------------------23----1
 -----------------------------------------------------------------ACTCTGCAGTGTCCCGTGGACA------------22---1-
ratcagtcctGCCAGCGACCCCAGAGGACCCCAGCACgactctcttcggtgtCAACCCCGAACGATGGACTCTGCAGTGTCCCGTGGACATtctggaagact 
 *************************************************************************************************** 
rat.((((...((((.....(((..((((....(((.((.(((((((((........))))).))..)).)))))...))))..))).....))))..))))0.890 -28.40

ratchromosome:4:150453571:150453669:-1intergenic


sblock8624 [novel_lenNOK_multiarm_DicerNOK_Multihit_5varHIGH_loopOverlap_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.392nono0.58/0.7519/25/0.671.3
0.0
2.0
1.0
0.0
0.5
3
1
2
0
0
0
2
1
2
0
0
0
14
32
18
12
-5
11
5arm
3arm_loop
3arm
28
30
31
nd
nd
nd
0.46
0.44
0.45
5
4
4
65020
  readsmiRBase family seed
seed---------------CCAGCGA-------------------------------------------------------------------------------------------2novel
seed---------------------------------------------------------AACCCCG-------------------------------------------------1novel
seed-------------------------------------------------------------------------CUCUGCA---------------------------------1novel
seed-----------------------------------------------------------------------------GCAGUGU-----------------------------1novel
seed-------------------CGACCCC---------------------------------------------------------------------------------------1novel
  lencloning frequencies
   T1S1T2S1T3S2T5S1T5S2
 --------------GCCAGCGACCCCAGAGGACCCCAG---------------------------------------------------------------------------24--2--
 --------------------------------------------------------CAACCCCGAACGATGGACTCTGCAG--------------------------------25-1---
 ----------------------------------------------------------------------------TGCAGTGTCCCGTGGACAT------------------191----
 ------------------GCGACCCCAGAGGACCCCAGCAC------------------------------------------------------------------------23----1
 ------------------------------------------------------------------------ACTCTGCAGTGTCCCGTGGACA-------------------22---1-
ratggtgctgcagtcctGCCAGCGACCCCAGAGGACCCCAGCACgactctcttcggtgtCAACCCCGAACGATGGACTCTGCAGTGTCCCGTGGACATtctggaagactttgtacc 
 ***************************************************************************************************************** 
rat(((((...((((...((((.....(((..((((....(((.((.(((((((((........))))).))..)).)))))...))))..))).....))))..))))..)))))0.830 -35.30

ratchromosome:4:150577181:150577293:-1intergenic


sblock8659 [novel_lenNOK_multiarm_DicerNOK_Multihit_5varHIGH_loopOverlap_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.340nono0.50/0.7518/25/0.601.3
0.0
0.0
1.0
0.0
0.0
3
1
1
0
0
0
2
1
1
0
0
0
14
35
0
12
-5
37
5arm
3arm_loop
3arm
28
30
30
nd
nd
nd
0.33
0.44
0.41
4
4
3
54020
  readsmiRBase family seed
seed---------------CCAGCGA----------------------------------------------------------------------------------------------2novel
seed---------------------------------------------------------AACCCCG----------------------------------------------------1novel
seed-------------------CGACCCC------------------------------------------------------------------------------------------1novel
seed---------------------------------------------------------------------------------------------------GAAGACU----------1novel
  lencloning frequencies
   T2S1T2S2T3S2T5S2
 --------------GCCAGCGACCCCAGAGGACCCCAG------------------------------------------------------------------------------24--2-
 --------------------------------------------------------------------------------------------------GGAAGACTTTGTACCCTC18-1--
 ------------------GCGACCCCAGAGGACCCCAGCAC---------------------------------------------------------------------------23---1
 --------------------------------------------------------CAACCCCGAACGATGGACTCTGCAG-----------------------------------251---
ratggtgctgcagtcctGCCAGCGACCCCAGAGGACCCCAGCACgactctcttcggtgtCAACCCCGAACGATGGACTCTGCAGtgtcccgtggacgttctGGAAGACTTTGTACCCTC 
 ******************************************************************************************************************** 
rat(((((...((((...((((.(((.(((..((((....(((.((.(((((((((........))))).))..)).)))))...))))..)))..)))))))..))))..)))))...0.990 -37.60

ratchromosome:4:150641424:150641539:-1intergenic


novel_lenNOK_multiarm_DicerNOK_Multihit_randfoldOK_nonpairedHIGH (4 loci)

sblock100 [novel_lenNOK_multiarm_DicerNOK_Multihit_randfoldOK_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.001nono0.41/0.5319/22/0.500.0
0.0
0.0
0.0
1
1
0
0
1
1
0
0
34
0
5
34
5arm
3arm
4
17
nd
nd
0.37
0.43
3
5
210-20
  readsmiRBase family seed
seed     -----------------------------------AGCCUUU----------------------------------------------------------------------------     1novel
seed     -------------------------------------------------------------------------------------------------AGGUUGU--------------     1novel
  lencloning frequencies
   T5S1
      ------------------------------------------------------------------------------------------------TAGGTTGTCTTCTGTGTTCTCA     221
      ----------------------------------AAGCCTTTTGGATGGCCAC-----------------------------------------------------------------     191
rat     aggacatttttttttatttcttgttccatccttaAAGCCTTTTGGATGGCCACtactggggacagtgttgccctctccttaggcacagaggaataaTAGGTTGTCTTCTGTGTTCTCA      
      **********************************************************************************************************************      
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ENSRNOT00000043239 ENSRNOG00000033820
 --------------------------------------------------------------------------------------------------------------------------------ENSRNOT00000043702 ENSRNOG00000034080 RGD1563490_predicted
rat     (((((((........((..((((((...(((((...((((...(((.(((.((.((((....)))))).)))...)))..))))...)))))..))))))..)).....)))))))..     0.920 -36.82

ratchromosome:1:47790502:47790619:-1Opposite_strand|Intronic_non-coding|ENSRNOT00000043702|ENSRNOG00000034080 ## Same_strand|Intronic_coding|ENSRNOT00000043239|ENSRNOG00000033820 ## ENSRNOG00000033820|protein_coding|| ## ENSRNOG00000034080|protein_coding|RGD1563490_predicted|


sblock1253 [novel_lenNOK_multiarm_DicerNOK_Multihit_randfoldOK_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.001nono0.41/0.5319/22/0.500.0
0.0
0.0
0.0
1
1
0
0
1
1
0
0
34
0
5
34
5arm
3arm
4
17
nd
nd
0.37
0.43
3
5
210-20
  readsmiRBase family seed
seed-----------------------------------AGCCUUU----------------------------------------------------------------------------1novel
seed-------------------------------------------------------------------------------------------------AGGUUGU--------------1novel
  lencloning frequencies
   T5S1
 ------------------------------------------------------------------------------------------------TAGGTTGTCTTCTGTGTTCTCA221
 ----------------------------------AAGCCTTTTGGATGGCCAC-----------------------------------------------------------------191
rataggacatttttttttatttcttgttccatccttaAAGCCTTTTGGATGGCCACtactggggacagtgttgccctctccttaggcacagaggaataaTAGGTTGTCTTCTGTGTTCTCA 
 ********************************************************************************************************************** 
rat(((((((........((..((((((...(((((...((((...(((.(((.((.((((....)))))).)))...)))..))))...)))))..))))))..)).....)))))))..0.920 -36.82

ratchromosome:1:47741241:47741358:1intergenic


sblock132 [novel_lenNOK_multiarm_DicerNOK_Multihit_randfoldOK_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.003nono0.41/0.5319/22/0.500.0
0.0
0.0
0.0
1
1
0
0
1
1
0
0
32
0
5
34
5arm
3arm
4
17
nd
nd
0.37
0.43
3
5
210-20
  readsmiRBase family seed
seed-----------------------------------------------------------------------------------------------AGGUUGU--------------1novel
seed---------------------------------AGCCUUU----------------------------------------------------------------------------1novel
  lencloning frequencies
   T5S1
 ----------------------------------------------------------------------------------------------TAGGTTGTCTTCTGTGTTCTCA221
 --------------------------------AAGCCTTTTGGATGGCCAC-----------------------------------------------------------------191
rataggacatttttttatttcttgttccatccttaAAGCCTTTTGGATGGCCACtactggggacagtgttgccctctccttaggcacagaggaataaTAGGTTGTCTTCTGTGTTCTCA 
 ******************************************************************************************************************** 
rat(((((((......((..((((((...(((((...((((...(((.(((.((.((((....)))))).)))...)))..))))...)))))..))))))..)).....)))))))..0.980 -38.00

ratchromosome:1:48341086:48341201:-1intergenic


sblock1405 [novel_lenNOK_multiarm_DicerNOK_Multihit_randfoldOK_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.004nono0.45/0.5919/25/0.560.0
0.0
0.2
0.2
0.0
0.0
4
1
4
0
0
0
1
1
2
0
0
0
2
20
15
17
-1
9
5arm
3arm
3arm
24
24
24
nd
nd
nd
0.32
0.48
0.53
3
5
5
93-8-13
  readsmiRBase family seed
seed---CCAGUGU--------------------------------------------------------------------------------4miR-199a
seed---------------------------------------------------------GGACCUU--------------------------3novel
seed--------------------------------------------------------AGGACCU---------------------------1novel
seed----------------------------------------------CCAGUGU-------------------------------------1miR-199a
  lencloning frequencies
   T1S1T4S2T5S1
 --------------------------------------------------------AGGACCTTCTCACTAACAG---------------19--3
 --TCCAGTGTGGCTTCTGTCCCAGT-----------------------------------------------------------------23--3
 --TCCAGTGTGGCTTCTGTCCCAG------------------------------------------------------------------22--1
 ---------------------------------------------TCCAGTGTCGTAGGACCTTCTCACT--------------------25-1-
 -------------------------------------------------------TAGGACCTTCTCACTAACAG---------------201--
ratgtTCCAGTGTGGCTTCTGTCCCAGTacctccactatcactggaccTCCAGTGTCGTAGGACCTTCTCACTAACAGcggctgcattgtgaa 
 ****************************************************************************************** 
rat.((((((((..(((.((((...((....(((((...((((((....))))))..)).)))....)).....)))).)))..))))).)))0.980 -31.90

ratchromosome:1:51031104:51031193:1intergenic


novel_lenNOK_multiarm_DicerNOK_loopOverlap_mirtron (4 loci)

sblock2571 [novel_lenNOK_multiarm_DicerNOK_loopOverlap_mirtron]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.540nono0.55/0.6719/21/0.500.0
0.0
0.0
0.0
0.0
0.0
1
2
1
0
0
0
1
2
1
0
0
0
17
34
18
8
-8
21
5arm
5arm_loop_3arm
3arm
1
1
1
54
37
1
0.25
0.37
0.48
2
6
5
4405
  readsmiRBase family seed
seed     -----------------------------------UGGCGGC---------------------------------------------------------------------     2novel
seed     ------------------GUGGUUG--------------------------------------------------------------------------------------     1novel
seed     -------------------------------------------------------------------------UGAGUCC-------------------------------     1novel
  lencloning frequencies
   T2S1T2S2T3S1T5S2
      ----------------------------------ATGGCGGCTGTGAGTCTGC----------------------------------------------------------     191--1
      ------------------------------------------------------------------------GTGAGTCCTGGCCACCAGAGC------------------     21-1--
      -----------------GGTGGTTGGGTGGTAAGATG--------------------------------------------------------------------------     20--1-
rat     gctgcccgtgcggcggcGGTGGTTGGGTGGTAAGATGGCGGCTGTGAGTCTGCggctcggcgacttggtgtgGTGAGTCCTGGCCACCAGAGCtgaacgaaagacggcgcg      
      ***************************************************************************************************************      
 ............................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++ENSRNOT00000004159 ENSRNOG00000003065 RGD1309459
rat     ((.((((((.((((...((((((..((((.((((.((.(((((((......))))).)).)).)))).))........))..))))))...)))).)))......))))).     0.650 -43.60

ratchromosome:10:10648048:10648158:1Same_strand|Exonic_non-coding|ENSRNOT00000004159|ENSRNOG00000003065 ## Same_strand|Boundary_non-coding|ENSRNOT00000004159|ENSRNOG00000003065 ## Same_strand|Boundary_coding|ENSRNOT00000004159|ENSRNOG00000003065 ## ENSRNOG00000003065|protein_coding|RGD1309459|Nuclear protein NP60. [Source:UniProtKB/Swiss-Prot;Acc:Q5RKH0] ## {SimpF: oe = 0.89 1 CpG}


sblock11403 [novel_lenNOK_multiarm_DicerNOK_loopOverlap_mirtron]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.271nono0.59/0.6518/23/0.600.7
0.0
0.0
3.7
0.0
0.0
3
1
1
0
0
0
3
1
1
0
0
0
25
39
31
4
-1
9
5arm
3arm
3arm
1
1
1
41
12
4
0.17
0.35
0.17
3
3
2
53-8-15
  readsmiRBase family seed
seed     ---------------------------GCACAGG-----------------------------------------------------------------------------------     2novel
seed     ---------------------------------------------------------------------CCCUGUG-----------------------------------------     1novel
seed     --------------------------UGCACAG------------------------------------------------------------------------------------     1novel
seed     -----------------------------------------------------------AGCCAAA---------------------------------------------------     1novel
  lencloning frequencies
   T1S1T1S2T5S2
      ----------------------------------------------------------CAGCCAAAGCCCCCTGTGGT---------------------------------------     20-1-
      -------------------------GTGCACAGGGTTTGGACC--------------------------------------------------------------------------     18-1-
      --------------------------------------------------------------------CCCCTGTGGTCCTCTTGT-------------------------------     18--1
      --------------------------TGCACAGGGTTTGGACCGAGAG---------------------------------------------------------------------     221--
      --------------------------TGCACAGGGTTTGGACCGAGAGC--------------------------------------------------------------------     23--1
rat     taggcctgtggaacaggaaagggagGTGCACAGGGTTTGGACCGAGAGCggctccactCAGCCAAAGCCCCCTGTGGTCCTCTTGTgcagtcgatcctgaccatcagtttgtcctac      
      *********************************************************************************************************************      
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>ENSRNOT00000042610 ENSRNOG00000029941 Grina
rat     ((((.((((((..(((((..((....(((((((((...((((((((.((((((......))))...))...)).))))))))))))))).))..))))).))).))).....)))).     0.620 -39.60

ratchromosome:7:114279108:114279224:1Same_strand|Intronic_coding|ENSRNOT00000042610|ENSRNOG00000029941 ## ENSRNOG00000029941|protein_coding|Grina|glutamate receptor, ionotropic, N-methyl D-asparate-associated protein 1 (glutamate binding) [Source:RefSeq_peptide;Acc:NP_695220]


sblock4712 [novel_lenNOK_multiarm_DicerNOK_loopOverlap_mirtron]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.419nono0.63/0.7519/20/0.500.0
0.0
0.0
0.0
1
1
0
0
1
1
0
0
23
29
15
-2
5arm
3arm_loop
1
1
42
0
0.21
0.25
1
2
22-14-13
  readsmiRBase family seed
seed     ------------------------UGGGGUG----------------------------------------------------------------------------------     1novel
seed     -----------------------------------------------------------------CGCGCCC-----------------------------------------     1novel
  lencloning frequencies
   T1S2T3S2
      ----------------------------------------------------------------CCGCGCCCTGTCTCCTGCAG-----------------------------     20-1
      -----------------------TTGGGGTGCAGGGTAGCAG-----------------------------------------------------------------------     191-
rat     cccaatggcctaggagttagactTTGGGGTGCAGGGTAGCAGgaggaagccccgcgctcacgtcCCGCGCCCTGTCTCCTGCAGcgctggccgcgaaatgagcccgaggcggg      
      *****************************************************************************************************************      
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>ENSRNOT00000019052 ENSRNOG00000014205 Klf2_predicted
rat     (((....((((.((.(((....((((.(((.(((.((.(((((((..((....((((.........)))).))..))))))).)).)))))).))))...))))).)))))))     1.000 -48.00

ratchromosome:16:17943302:17943414:-1Same_strand|Intronic_coding|ENSRNOT00000019052|ENSRNOG00000014205 ## ENSRNOG00000014205|protein_coding|Klf2_predicted|Krueppel-like factor 2 (Lung krueppel-like factor). [Source:UniProtKB/Swiss-Prot;Acc:Q9ET58] ## {SimpF: oe = 0.82 -1 CpG}


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