logoSmall RNA from different tissues of two rat strains.


miR classification

Alignments

other hairpins

novel_lenNOK_multiarm_Multihit_nonpairedHIGH_bulgeHIGH (13 loci)

sblock253 [novel_lenNOK_multiarm_Multihit_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.088nono0.35/0.5019/20/0.380.7
0.0
0.0
0.0
0.3
0.0
0.0
0.0
3
2
2
1
0
0
0
0
2
2
1
1
0
0
0
0
2
11
27
10
33
26
8
24
5arm
5arm
3arm
3arm
33
33
45
45
nd
nd
nd
nd
0.45
0.42
0.32
0.35
5
3
5
4
83nana
  readsmiRBase family seed
seed     ------------CCAGUAA---------------------------------------------------------------------------------------------------     2novel
seed     ---GUGCUAG------------------------------------------------------------------------------------------------------------     2novel
seed     -------------------------------------------------------------------------GGUGUUU--------------------------------------     2novel
seed     -----------------------------------------------------------------------------------------GAUAAAC----------------------     1novel
seed     -----GCUAGGA----------------------------------------------------------------------------------------------------------     1novel
  lencloning frequencies
   T1S1T2S2T5S1
      ------------------------------------------------------------------------TGGTGTTTTTAGAGTGTGA---------------------------     19--2
      -----------ACCAGTAACCTATGGAAGA----------------------------------------------------------------------------------------     191-1
      --TGTGCTAGGACCAGTAACCT------------------------------------------------------------------------------------------------     20--2
      ----TGCTAGGACCAGTAACCTA-----------------------------------------------------------------------------------------------     19-1-
      ----------------------------------------------------------------------------------------TGATAAACTTCAGGTGAATG----------     20--1
rat     tgTGTGCTAGGACCAGTAACCTATGGAAGActtcatgagctcataccactctccacctcactttgtggaagcTGGTGTTTTTAGAGTGTGATAAACTTCAGGTGAATGgatgcattca      
      **********************************************************************************************************************      
 --------------------------------------------------------------------------------------------------------------------------------ENSRNOT00000049496 ENSRNOG00000031160 LOC685793
 --------------------------------------------------------------------------------------------------------------------------------ENSRNOT00000042408 ENSRNOG00000031160 LOC685793
 --------------------------------------------------------------------------------------------------------------------------------ENSRNOT00000050327 ENSRNOG00000031160 LOC685793
 --------------------------------------------------------------------------------------------------------------------------------ENSRNOT00000040838 ENSRNOG00000031160 LOC685793
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ENSRNOT00000059958 ENSRNOG00000030545 LOC685793
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ENSRNOT00000049483 ENSRNOG00000030545 LOC685793
rat     ((.((((.....(((...((((...((((...((((..((((((((((((.(((((........))))))).)))))).....))))))))....))))))))...)))..)))).))     1.000 -32.60

ratchromosome:1:50133191:50133308:-1Same_strand|Intronic_non-coding|ENSRNOT00000049483|ENSRNOG00000030545 ## Same_strand|Intronic_coding|ENSRNOT00000059958|ENSRNOG00000030545 ## Same_strand|Boundary_non-coding|ENSRNOT00000039913|ENSRNOG00000030545 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000041575|ENSRNOG00000031160 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000042408|ENSRNOG00000031160 ## ENSRNOG00000030545|protein_coding|LOC685793| ## ENSRNOG00000031160|protein_coding|LOC685793|


sblock304 [novel_lenNOK_multiarm_Multihit_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.088nono0.35/0.5019/20/0.380.7
0.0
0.0
0.0
0.3
0.0
0.0
0.0
3
2
2
1
0
0
0
0
2
2
1
1
0
0
0
0
2
11
27
10
33
26
8
24
5arm
5arm
3arm
3arm
33
33
45
45
nd
nd
nd
nd
0.45
0.42
0.32
0.35
5
3
5
4
83nana
  readsmiRBase family seed
seed     ------------CCAGUAA---------------------------------------------------------------------------------------------------     2novel
seed     ---GUGCUAG------------------------------------------------------------------------------------------------------------     2novel
seed     -------------------------------------------------------------------------GGUGUUU--------------------------------------     2novel
seed     -----------------------------------------------------------------------------------------GAUAAAC----------------------     1novel
seed     -----GCUAGGA----------------------------------------------------------------------------------------------------------     1novel
  lencloning frequencies
   T1S1T2S2T5S1
      ------------------------------------------------------------------------TGGTGTTTTTAGAGTGTGA---------------------------     19--2
      -----------ACCAGTAACCTATGGAAGA----------------------------------------------------------------------------------------     191-1
      --TGTGCTAGGACCAGTAACCT------------------------------------------------------------------------------------------------     20--2
      ----TGCTAGGACCAGTAACCTA-----------------------------------------------------------------------------------------------     19-1-
      ----------------------------------------------------------------------------------------TGATAAACTTCAGGTGAATG----------     20--1
rat     tgTGTGCTAGGACCAGTAACCTATGGAAGActtcatgagctcataccactctccacctcactttgtggaagcTGGTGTTTTTAGAGTGTGATAAACTTCAGGTGAATGgatgcattca      
      **********************************************************************************************************************      
 --------------------------------------------------------------------------------------------------------------------------------ENSRNOT00000041575 ENSRNOG00000031160 LOC685793
rat     ((.((((.....(((...((((...((((...((((..((((((((((((.(((((........))))))).)))))).....))))))))....))))))))...)))..)))).))     1.000 -32.60

ratchromosome:1:50294081:50294198:-1Opposite_strand|Boundary_non-coding|ENSRNOT00000049496|ENSRNOG00000031160 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000041575|ENSRNOG00000031160 ## ENSRNOG00000031160|protein_coding|LOC685793|


sblock327 [novel_lenNOK_multiarm_Multihit_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.156nono0.35/0.5019/20/0.430.7
0.0
0.0
0.0
0.3
0.0
0.0
0.0
3
1
2
1
0
0
0
0
2
1
1
1
0
0
0
0
0
9
24
7
33
26
8
24
5arm
5arm
3arm
3arm
33
33
45
45
nd
nd
nd
nd
0.50
0.42
0.32
0.35
5
3
5
4
72nana
  readsmiRBase family seed
seed-GUGCUAG---------------------------------------------------------------------------------------------------------2novel
seed-----------------------------------------------------------------------GGUGUUU-----------------------------------2novel
seed---GCUAGGA-------------------------------------------------------------------------------------------------------1novel
seed----------CCAGUAA------------------------------------------------------------------------------------------------1novel
seed---------------------------------------------------------------------------------------GAUAAAC-------------------1novel
  lencloning frequencies
   T2S2T5S1
 ----------------------------------------------------------------------TGGTGTTTTTAGAGTGTGA------------------------19-2
 TGTGCTAGGACCAGTAACCT---------------------------------------------------------------------------------------------20-2
 --------------------------------------------------------------------------------------TGATAAACTTCAGGTGAATG-------20-1
 --TGCTAGGACCAGTAACCTA--------------------------------------------------------------------------------------------191-
 ---------ACCAGTAACCTATGGAAGC-------------------------------------------------------------------------------------19-1
ratTGTGCTAGGACCAGTAACCTATGGAAGCcttcatgagctcataccactctccacctcactttgtggaagcTGGTGTTTTTAGAGTGTGATAAACTTCAGGTGAATGgatgcag 
 ***************************************************************************************************************** 
rat..(((.....(((...((((...((((...((((..((((((((((((.(((((........))))))).)))))).....))))))))....))))))))...)))..))).1.000 -31.20

ratchromosome:1:50398870:50398982:-1intergenic


sblock6357 [novel_lenNOK_multiarm_Multihit_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.497nono0.56/0.6118/18/0.000.0
0.0
0.0
0.0
3
1
0
0
2
1
0
0
34
21
6
19
5arm
3arm
10
27
nd
nd
0.39
0.33
4
6
42nana
  readsmiRBase family seed
seed     -----------------------------------UUCUGUG------------------------------------------------------------------------------     3novel
seed     ----------------------------------------------------------------------------------UUCUGUG-------------------------------     1novel
  lencloning frequencies
   T2S1T2S2
      ----------------------------------GTTCTGTGTCACCTGGGG--------------------------------------------------------------------     1821
      ---------------------------------------------------------------------------------GTTCTGTGTCACCTGTGG---------------------     18-1
rat     gggggacagtgttctgtgtcacccatgggagagtGTTCTGTGTCACCTGGGGggagagtgttctgtgtcacccgtgggagtGTTCTGTGTCACCTGTGGgggagagtgttctgtgtcacc      
      ************************************************************************************************************************      
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ENSRNOT00000013218 ENSRNOG00000009851 RGD1311881
rat     ((((.((((....((...((.((((((((((((..((((....(((..(((.((..((....))...)).))))))))))..))))......))))))))))..))....)))).)).))     0.580 -33.80

ratchromosome:2:44107776:44107895:1Same_strand|Intronic_coding|ENSRNOT00000013218|ENSRNOG00000009851 ## ENSRNOG00000009851|protein_coding|RGD1311881|Putative uncharacterized protein RGD1311881. [Source:UniProtKB/TrEMBL;Acc:Q3B8Q3] ## {Repeats: trf 2145 2163 0 class=trf,trf 2045 2063 0 class=trf,trf 1816 1834 0 class=trf,trf 2192 2210 0 class=trf,trf 2095 2113 0 class=trf,trf 1738 1756 0 class=trf,trf 1968 1986 0 class=trf,trf 1994 2012 0 class=trf,trf 1942 1960 0 class=trf}


novel_lenNOK_multiarm_bulgeHIGH (13 loci)

sblock10926 [novel_lenNOK_multiarm_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.500nono0.17/0.3918/18/0.000.0
0.0
0.0
0.0
1
1
0
0
1
1
0
0
38
9
2
22
5arm
3arm
3
3
nd
nd
0.28
0.39
4
3
22nana
  readsmiRBase family seed
seed---------------------------------------UGGAAUA------------------------------------------------------------------1novel
seed--------------------------------------------------------------------------------------UGAAAGU-------------------1novel
  lencloning frequencies
   T1S2T3S2
 -------------------------------------------------------------------------------------TTGAAAGTTGTTGGGATC---------181-
 --------------------------------------TTGGAATAGTTTTAAAAT--------------------------------------------------------18-1
rataattaattgccaccttcaattagcaaatctaggaaatgTTGGAATAGTTTTAAAATagtatttctaaagagattatgccatgtgtTTGAAAGTTGTTGGGATCaaataattg 
 **************************************************************************************************************** 
rat(((((.(((...((..(((((..(((((.((........(((.((((((((....(((.....)))..)))))))).))))).)))))..)))))..))...))).))))).0.800 -17.50

ratchromosome:7:99239802:99239913:-1intergenic


sblock11338 [novel_lenNOK_multiarm_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.500nono0.17/0.3918/18/0.000.0
0.0
0.0
0.0
1
1
0
0
1
1
0
0
38
9
2
22
5arm
3arm
3
3
nd
nd
0.28
0.39
4
3
22nana
  readsmiRBase family seed
seed---------------------------------------UGGAAUA------------------------------------------------------------------1novel
seed--------------------------------------------------------------------------------------UGAAAGU-------------------1novel
  lencloning frequencies
   T1S2T3S2
 -------------------------------------------------------------------------------------TTGAAAGTTGTTGGGATC---------181-
 --------------------------------------TTGGAATAGTTTTAAAAT--------------------------------------------------------18-1
rataattaattgccaccttcaattagcaaatctaggaaatgTTGGAATAGTTTTAAAATagtatttctaaagagattatgccatgtgtTTGAAAGTTGTTGGGATCaaataattg 
 **************************************************************************************************************** 
rat(((((.(((...((..(((((..(((((.((........(((.((((((((....(((.....)))..)))))))).))))).)))))..)))))..))...))).))))).0.800 -17.50

ratchromosome:7:99460717:99460828:1intergenic


sblock12307 [novel_lenNOK_multiarm_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.157nono0.26/0.5018/23/0.670.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
1
2
2
1
0
0
0
0
1
1
2
1
0
0
0
0
0
30
20
9
34
2
13
28
5arm
3arm
3arm
3arm
2
2
2
2
nd
nd
nd
nd
0.68
0.26
0.50
0.67
6
4
9
8
63nana
  readsmiRBase family seed
seed------------------------------------------------------------------------------AUGUCUA----------------------------------2novel
seed-------------------------------------------------------------------ACAUUUG---------------------------------------------2novel
seed---------------------------------------------------------------------------------------------ACUGUCC-------------------1novel
seed-AAGAUCU---------------------------------------------------------------------------------------------------------------1novel
  lencloning frequencies
   T3S1T3S2T5S1
 ------------------------------------------------------------------CACATTTGGAATATGTCTACCAC------------------------------23--2
 -----------------------------------------------------------------------------TATGTCTACCACGTTTACTGTC--------------------221-1
 --------------------------------------------------------------------------------------------TACTGTCCTATGGCTGTC---------18-1-
 GAAGATCTCTTTGAAATTT----------------------------------------------------------------------------------------------------19--1
ratGAAGATCTCTTTGAAATTTaaagccatgcgtggcagcatgtgtataatgttgcaatctgaataagtCACATTTGGAATATGTCTACCACGTTTACTGTCCTATGGCTGTCtctcaatga 
 *********************************************************************************************************************** 
rat.......((.((((.......((((((((((((.(((((((....(((((.((...........)).)))))....))))).)).))))))..........)))))).....)))).))0.610 -27.20

ratchromosome:9:105174751:105174869:-1intergenic


sblock12322 [novel_lenNOK_multiarm_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.074nono0.43/0.6118/21/0.250.0
0.0
0.0
0.0
0.0
0.0
2
1
1
0
0
0
1
1
1
0
0
0
35
42
6
9
1
25
5arm
5arm
3arm
4
4
4
nd
nd
nd
0.39
0.21
0.52
6
4
10
42nana
  readsmiRBase family seed
seed     ------------------------------------CCCUCUG---------------------------------------------------------------------------     2novel
seed     --------------------------------------------------------------------------------------------UGUCUAC-------------------     1novel
seed     -------------------------------------------ACAGAAG--------------------------------------------------------------------     1novel
  lencloning frequencies
   T2S2T5S1
      -----------------------------------TCCCTCTGACAGAAGCGC-----------------------------------------------------------------     18-2
      ------------------------------------------GACAGAAGCGCTCCATGAT---------------------------------------------------------     19-1
      -------------------------------------------------------------------------------------------TTGTCTACTAAACTGCCTCAG------     211-
rat     tgaagaaagcctccatgttagtgcacttcagaaggTCCCTCTGACAGAAGCGCTCCATGATtttcaaatcagactgtgcttatctgttcctTTGTCTACTAAACTGCCTCAGcttcac      
      **********************************************************************************************************************      
 --------------------------------------------------------------------------------------------------------------------------------ENSRNOT00000047326 ENSRNOG00000037286 LOC367336
rat     (((((............((((((.((....(((((.......(((((((((((....(((((....)))))....)))))..))))))))))))).))))))..........))))).     0.550 -26.76

ratchromosome:9:105247364:105247481:-1Opposite_strand|Intronic_coding|ENSRNOT00000047326|ENSRNOG00000037286 ## ENSRNOG00000037286|protein_coding|LOC367336|


sblock12338 [novel_lenNOK_multiarm_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.096nono0.43/0.5319/21/0.500.0
0.0
0.0
0.0
1
1
0
0
1
1
0
0
26
2
1
25
5arm
3arm
4
4
nd
nd
0.21
0.38
4
3
22nana
  readsmiRBase family seed
seed---------------------------ACAGAAG----------------------------------------------------------------1novel
seed----------------------------------------------------------------------------UGUCUAC---------------1novel
  lencloning frequencies
   T2S2T5S1
 --------------------------GACAGAAGCGCTCCATGAT-----------------------------------------------------19-1
 ---------------------------------------------------------------------------TTGTCTACTAAACTGCCTCAG--211-
ratgttactgcacttcagaaggtccctctGACAGAAGCGCTCCATGATtttcaaatcagactgtgcttatctgttcctTTGTCTACTAAACTGCCTCAGct 
 ************************************************************************************************** 
rat(((...(((.((.((.(((.......(((((((((((....(((((....)))))....)))))..))))))......))).)).)).)))...))).0.540 -20.22

ratchromosome:9:105325930:105326027:-1intergenic


sblock12547 [novel_lenNOK_multiarm_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.074nono0.43/0.6118/21/0.250.0
0.0
0.0
0.0
0.0
0.0
2
1
1
0
0
0
1
1
1
0
0
0
35
42
6
9
1
25
5arm
5arm
3arm
4
4
4
nd
nd
nd
0.39
0.21
0.52
6
4
10
42nana
  readsmiRBase family seed
seed     ------------------------------------CCCUCUG---------------------------------------------------------------------------     2novel
seed     --------------------------------------------------------------------------------------------UGUCUAC-------------------     1novel
seed     -------------------------------------------ACAGAAG--------------------------------------------------------------------     1novel
  lencloning frequencies
   T2S2T5S1
      -----------------------------------TCCCTCTGACAGAAGCGC-----------------------------------------------------------------     18-2
      ------------------------------------------GACAGAAGCGCTCCATGAT---------------------------------------------------------     19-1
      -------------------------------------------------------------------------------------------TTGTCTACTAAACTGCCTCAG------     211-
rat     tgaagaaagcctccatgttagtgcacttcagaaggTCCCTCTGACAGAAGCGCTCCATGATtttcaaatcagactgtgcttatctgttcctTTGTCTACTAAACTGCCTCAGcttcac      
      **********************************************************************************************************************      
 --------------------------------------------------------------------------------------------------------------------------------ENSRNOT00000047066 ENSRNOG00000032758 Ndufv2
rat     (((((............((((((.((....(((((.......(((((((((((....(((((....)))))....)))))..))))))))))))).))))))..........))))).     0.550 -26.76

ratchromosome:9:104941947:104942064:1Opposite_strand|Boundary_non-coding|ENSRNOT00000046356|ENSRNOG00000032758 ## Opposite_strand|Intronic_coding|ENSRNOT00000047066|ENSRNOG00000032758 ## ENSRNOG00000032758|protein_coding|Ndufv2|NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquinone oxidoreductase 24 kDa subunit). [Source:UniProtKB/Swiss-Prot;Acc:P19234]


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