logoSmall RNA from different tissues of two rat strains.


miR classification

Alignments

other hairpins

novel_lenNOK_cloningHIGH_shortStem (67 loci)

block2595323 [novel_lenNOK_cloningHIGH_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.080nono0.39/0.4218/19/0.000.0
0.0
45
0
9
0
1
5
3arm
1
nd
0.26
2
549nana
  readsmiRBase family seed
seed----------------------------------UUCUUAG------------54novel
  lencloning frequencies
   T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
 ---------------------------------ATTCTTAGGTGTCTTGGAC-195921113585
 ---------------------------------ATTCTTAGGTGTCTTGGA--18-----3-11
rattgttcatactcaaagagctcttcacaaggaagcATTCTTAGGTGTCTTGGACa 
 ***************************************************** 
rat.(((((.((((.(((((..((((.....))))..))))).)).))..))))).1.000 -12.40

ratchromosome:9:45531540:45531592:1intergenic


block2619454 [novel_lenNOK_cloningHIGH_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.448nono0.37/0.4018/20/0.010.0
0.0
217
0
4
0
2
18
3arm
1
nd
0.22
2
2344nana
  readsmiRBase family seed
seed---------------------------------------------------------CCUCACA------------234novel
  lencloning frequencies
   T2S1T2S2T4S2T5S2
 --------------------------------------------------------ACCTCACACTGTATTTGT--181209711
 --------------------------------------------------------ACCTCACACTGTATTTGTT-1976--
 --------------------------------------------------------ACCTCACACTGTATTTGTTG2011--
ratcagcatttgggaagtggaggcagaaactcagcctttataggaagacagaagccaagACCTCACACTGTATTTGTtg 
 **************************************************************************** 
rat(((((..((...((((((((.......((..(((....)))..))............)))).)))).))..)))))0.630 -14.61

ratchromosome:9:75282024:75282099:1intergenic


novel_lenNOK_cloningOK_multiarm_DicerNOK (67 loci)

sblock10598 [novel_lenNOK_cloningOK_multiarm_DicerNOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.208nono0.16/0.3819/23/0.200.5
0.0
0.0
0.5
0.0
0.0
2
1
4
0
0
0
2
1
2
0
0
0
4
21
9
22
2
16
5arm
3arm
3arm
4
4
7
nd
nd
nd
0.26
0.24
0.21
3
2
2
103-6-5
  readsmiRBase family seed
seed------------------------------------------------------------------GUCACUA--------------------4novel
seed------------------------------------------------------------------------AUUUGCA--------------2novel
seed--------------------------------------------------------------------CACUAUU------------------1novel
seed-----GGAUAUU---------------------------------------------------------------------------------1novel
seed------GAUAUUC--------------------------------------------------------------------------------1novel
seed----------------------------------------------------AGUAAUU----------------------------------1novel
  lencloning frequencies
   T1S1T1S2T5S1
 -----------------------------------------------------------------TGTCACTATTTGCACAAAT---------19--4
 -----------------------------------------------------------------------TATTTGCACAAATATTTTT---191-1
 ----AGGATATTCTGGTGTTTAT----------------------------------------------------------------------19-1-
 -----GGATATTCTGGTGTTTATG---------------------------------------------------------------------19--1
 ---------------------------------------------------CAGTAATTTATGGCTGTCACT---------------------21--1
 -------------------------------------------------------------------TCACTATTTGCACAAATATTTTT---23--1
ratgctgaggatattctggtgtttatgtctgcacagaccaagttaaggctatgtcagtaatttatggcTGTCACTATTTGCACAAATatttttgcc 
 ********************************************************************************************* 
rat((.(((((((((...((((..(((..((.((((.((((((((.(((...)))..)))))..))))))))).)))..)))).))))))))))).0.550 -20.40

ratchromosome:7:17109216:17109308:-1intergenic


sblock10607 [novel_lenNOK_cloningOK_multiarm_DicerNOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.507nono0.26/0.4718/23/0.360.0
0.0
0.0
0.0
0.2
0.0
0.0
0.0
1.5
0.4
2
1
1
2
5
0
0
0
0
0
1
1
1
1
2
0
0
0
0
0
4
47
42
12
5
26
-15
-5
21
31
5arm
5arm_loop_3arm
3arm_loop
3arm
3arm
2
4
4
4
4
nd
nd
nd
nd
nd
0.38
0.47
0.42
0.35
0.16
4
8
4
7
2
113-7-3
  readsmiRBase family seed
seed--------------------------------------------------------------------------------------------GUGACGA----------------4novel
seed-----CUGUUUC-------------------------------------------------------------------------------------------------------2novel
seed---------------------------------------------------------------------------------CUUAAUC---------------------------2novel
seed------------------------------------------------CCAGCAU------------------------------------------------------------1miR-338
seed-------------------------------------------------------GAAAUGG-----------------------------------------------------1novel
seed-------------------------------------------------------------------------------------------UGUGACG-----------------1novel
  lencloning frequencies
   T1S1T1S2T5S1
 -------------------------------------------------------------------------------------------TGTGACGAGTGATATGCCT-----191-3
 ----TCTGTTTCATATTGTCCACTG------------------------------------------------------------------------------------------21--2
 ------------------------------------------------------TGAAATGGATGTAATTTGA------------------------------------------19-1-
 --------------------------------------------------------------------------------TCTTAATCAGTTGTGACGAG---------------20--1
 ------------------------------------------------------------------------------------------TTGTGACGAGTGATATGC-------181--
 -----------------------------------------------TCCAGCATGAAATGGATGT-------------------------------------------------19--1
 --------------------------------------------------------------------------------TCTTAATCAGTTGTGACGAGTGA------------23--1
rataatcTCTGTTTCATATTGTCCACTGcgtccagtagactgcttcatacTCCAGCATGAAATGGATGTAATTTGAaatgctaTCTTAATCAGTTGTGACGAGTGATATGCCTaggat 
 ******************************************************************************************************************* 
rat.(((.(((...(((((....((((.(((((((.(((..(((((((((((((........)))).)))...))))..))..))).......))).)))))))))))))..))))))0.640 -22.60

ratchromosome:7:17113635:17113749:-1intergenic


sblock10630 [novel_lenNOK_cloningOK_multiarm_DicerNOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.208nono0.16/0.3819/23/0.200.5
0.0
0.0
0.5
0.0
0.0
2
1
4
0
0
0
2
1
2
0
0
0
4
21
9
22
2
16
5arm
3arm
3arm
4
4
7
nd
nd
nd
0.26
0.24
0.21
3
2
2
103-6-5
  readsmiRBase family seed
seed------------------------------------------------------------------GUCACUA--------------------4novel
seed------------------------------------------------------------------------AUUUGCA--------------2novel
seed--------------------------------------------------------------------CACUAUU------------------1novel
seed-----GGAUAUU---------------------------------------------------------------------------------1novel
seed------GAUAUUC--------------------------------------------------------------------------------1novel
seed----------------------------------------------------AGUAAUU----------------------------------1novel
  lencloning frequencies
   T1S1T1S2T5S1
 -----------------------------------------------------------------TGTCACTATTTGCACAAAT---------19--4
 -----------------------------------------------------------------------TATTTGCACAAATATTTTT---191-1
 ----AGGATATTCTGGTGTTTAT----------------------------------------------------------------------19-1-
 -----GGATATTCTGGTGTTTATG---------------------------------------------------------------------19--1
 ---------------------------------------------------CAGTAATTTATGGCTGTCACT---------------------21--1
 -------------------------------------------------------------------TCACTATTTGCACAAATATTTTT---23--1
ratgctgaggatattctggtgtttatgtctgcacagaccaagttaaggctatgtcagtaatttatggcTGTCACTATTTGCACAAATatttttgcc 
 ********************************************************************************************* 
rat((.(((((((((...((((..(((..((.((((.((((((((.(((...)))..)))))..))))))))).)))..)))).))))))))))).0.550 -20.40

ratchromosome:7:17362033:17362125:-1intergenic


sblock10638 [novel_lenNOK_cloningOK_multiarm_DicerNOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.507nono0.26/0.4718/23/0.360.0
0.0
0.0
0.0
0.2
0.0
0.0
0.0
1.5
0.4
2
1
1
2
5
0
0
0
0
0
1
1
1
1
2
0
0
0
0
0
4
47
42
12
5
26
-15
-5
21
31
5arm
5arm_loop_3arm
3arm_loop
3arm
3arm
2
4
4
4
4
nd
nd
nd
nd
nd
0.38
0.47
0.42
0.35
0.16
4
8
4
7
2
113-7-3
  readsmiRBase family seed
seed--------------------------------------------------------------------------------------------GUGACGA----------------4novel
seed-----CUGUUUC-------------------------------------------------------------------------------------------------------2novel
seed---------------------------------------------------------------------------------CUUAAUC---------------------------2novel
seed------------------------------------------------CCAGCAU------------------------------------------------------------1miR-338
seed-------------------------------------------------------GAAAUGG-----------------------------------------------------1novel
seed-------------------------------------------------------------------------------------------UGUGACG-----------------1novel
  lencloning frequencies
   T1S1T1S2T5S1
 -------------------------------------------------------------------------------------------TGTGACGAGTGATATGCCT-----191-3
 ----TCTGTTTCATATTGTCCACTG------------------------------------------------------------------------------------------21--2
 ------------------------------------------------------TGAAATGGATGTAATTTGA------------------------------------------19-1-
 --------------------------------------------------------------------------------TCTTAATCAGTTGTGACGAG---------------20--1
 ------------------------------------------------------------------------------------------TTGTGACGAGTGATATGC-------181--
 -----------------------------------------------TCCAGCATGAAATGGATGT-------------------------------------------------19--1
 --------------------------------------------------------------------------------TCTTAATCAGTTGTGACGAGTGA------------23--1
rataatcTCTGTTTCATATTGTCCACTGcgtccagtagactgcttcatacTCCAGCATGAAATGGATGTAATTTGAaatgctaTCTTAATCAGTTGTGACGAGTGATATGCCTaggat 
 ******************************************************************************************************************* 
rat.(((.(((...(((((....((((.(((((((.(((..(((((((((((((........)))).)))...))))..))..))).......))).)))))))))))))..))))))0.640 -22.60

ratchromosome:7:17374994:17375108:-1intergenic


sblock10876 [novel_lenNOK_cloningOK_multiarm_DicerNOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.360nono0.42/0.5618/25/0.420.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
1
2
4
1
4
0
0
0
0
0
1
1
2
1
3
0
0
0
0
0
0
4
23
20
2
29
24
4
15
33
5arm
5arm
5arm
3arm
3arm
1
1
1
1
1
nd
nd
nd
nd
nd
0.53
0.40
0.19
0.53
0.42
6
3
2
8
3
1931917
  readsmiRBase family seed
seed--------------------------------------------------------------------------------------AGGCACG-------------7novel
seed------------------------AUAGCGU---------------------------------------------------------------------------4novel
seed--------------------GACUAUA-------------------------------------------------------------------------------3novel
seed-----GACUGUC----------------------------------------------------------------------------------------------2novel
seed----------------------------------------------------------------------------------------GCACGAU-----------1novel
seed--------------------------------------------------------------------CUAACGG-------------------------------1novel
seed-UGGAGAC--------------------------------------------------------------------------------------------------1novel
  lencloning frequencies
   T1S1T3S1T5S1
 -------------------------------------------------------------------------------------TAGGCACGATGGGACAGAA--191-4
 -----------------------TATAGCGTTTCAGCTCTCCTG--------------------------------------------------------------21--4
 ----AGACTGTCTGGGTGTTGACT----------------------------------------------------------------------------------20--2
 -------------------------------------------------------------------------------------TAGGCACGATGGGACAGA---18-11
 -------------------TGACTATAGCGTTTCAGCTCTCCTG--------------------------------------------------------------25--1
 TTGGAGACTGTCTGGGTGT---------------------------------------------------------------------------------------19--1
 -------------------TGACTATAGCGTTTCAGCTCT------------------------------------------------------------------21--1
 -------------------TGACTATAGCGTTTCAGCTCTCCT---------------------------------------------------------------241--
 -------------------------------------------------------------------ACTAACGGCAAGGGATTAT--------------------19--1
 ---------------------------------------------------------------------------------------GGCACGATGGGACAGAATA19--1
ratttggAGACTGTCTGGGTGTTGACTATAGCGTTTCAGCTCTCCTGggctagacagaagggagggagggactaacggcaagggattaTAGGCACGATGGGACAGAAta 
 ********************************************************************************************************** 
rat.......((((((...(((...((((((((((((..(((((((...((....))..)))))))...))..))))........))))))..)))...))))))....0.930 -26.60

ratchromosome:7:96036667:96036772:-1intergenic


sblock10993 [novel_lenNOK_cloningOK_multiarm_DicerNOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.100nono0.39/0.6018/25/0.590.0
0.0
0.0
0.0
0.0
1.8
0.0
0.0
1
5
7
2
0
0
0
0
1
1
2
1
0
0
0
0
17
18
10
5
4
7
19
26
5arm
3arm
3arm
3arm
1
1
1
1
nd
nd
nd
nd
0.15
0.23
0.33
0.32
1
3
2
2
172910
  readsmiRBase family seed
seed-----------------------------------------------------------------GGCUAAU-----------------------9novel
seed-----------------------------------------------------CAGCACC-----------------------------------5novel
seed------------------------------------------------------------------------CUACAUU----------------2novel
seed------------------AGGAGGA----------------------------------------------------------------------1novel
  lencloning frequencies
   T5S1T5S2
 ----------------------------------------------------------------TGGCTAATCTACATTCTGCTC----------2171
 ----------------------------------------------------TCAGCACCAAGTTGGCTAATCTACA------------------253-
 -----------------------------------------------------------------------TCTACATTCTGCTCGGCTG-----192-
 ----------------------------------------------------TCAGCACCAAGTTGGCTAATCT---------------------221-
 -----------------TAGGAGGACCAGTGGTGCTG----------------------------------------------------------201-
 ----------------------------------------------------------------TGGCTAATCTACATTCTG-------------181-
 ----------------------------------------------------TCAGCACCAAGTTGGCTAA------------------------191-
ratgcaatagcctgtatatataggaggaccagtggtgctggacttggtggtctccTCAGCACCAAGTTGGCTAATCTACATTCTGCTCggctgcagcc 
 *********************************************************************************************** 
rat((..(((((.(((.((.((((.((.(((.((((((((((((....))))....))))))))...)))))..)))).))..)))..)))))..)).0.940 -30.90

ratchromosome:7:116624297:116624391:-1intergenic


sblock11167 [novel_lenNOK_cloningOK_multiarm_DicerNOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.322nono0.32/0.5318/19/0.000.0
0.0
0.0
0.0
0.0
0.0
4
1
6
0
0
0
1
1
3
0
0
0
10
15
11
14
17
20
5arm
3arm
3arm
4
6
7
nd
nd
nd
0.26
0.33
0.37
2
4
4
1332-1
  readsmiRBase family seed
seed---------------------------------------------------------------------CCUAUCU----------------------8novel
seed-----------CGUUUGU--------------------------------------------------------------------------------4novel
seed------------------------------------------------------------------ACUCCUA-------------------------1novel
  lencloning frequencies
   T1S1T3S2T5S1
 --------------------------------------------------------------------TCCTATCTCTACACAAATA-----------19116
 ----------TCGTTTGTCAGACAGGGTC---------------------------------------------------------------------19--4
 -----------------------------------------------------------------TACTCCTATCTCTACACA---------------18--1
rattgaactttgcTCGTTTGTCAGACAGGGTCcctcagaactggacataatgtacagattctatcagatacTCCTATCTCTACACAAATAtctccaagtca 
 ************************************************************************************************** 
rat.((.(((.....((((((.(((.(((((..((.(((((((.((.....)).))).))))...))..)).))).)))....))))))......))))).0.830 -15.50

ratchromosome:7:17181313:17181410:1intergenic


sblock11272 [novel_lenNOK_cloningOK_multiarm_DicerNOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.315nono0.37/0.5618/19/0.000.0
0.0
0.1
0.0
0.0
0.1
1
1
8
0
0
0
1
1
5
0
0
0
43
30
19
-10
7
17
5arm_loop
3arm
3arm
1
1
1
nd
nd
nd
0.72
0.47
0.26
11
7
2
10600
  readsmiRBase family seed
seed---------------------------------------------------------------------------------GGCAACA------------------------------7novel
seed--------------------------------------------GGCAGUC-------------------------------------------------------------------1novel
seed----------------------------------------------------------------------CCAUAGU-----------------------------------------1novel
seed--------------------------------------------------------------------------------AGGCAAC-------------------------------1novel
  lencloning frequencies
   T1S2T2S2T3S1T3S2T5S1T5S2
 --------------------------------------------------------------------------------AGGCAACAGCTGAATGTG--------------------181-2111
 ---------------------------------------------------------------------TCCATAGTAAAAGGCAACA------------------------------19---1--
 -------------------------------------------AGGCAGTCCGCTGTAGAA---------------------------------------------------------18-1----
 --------------------------------------------------------------------------------AGGCAACAGCTGAATGTGT-------------------19----1-
 -------------------------------------------------------------------------------AAGGCAACAGCTGAATGTG--------------------19--1---
ratgcaggctatttttaacccaacacacaaaaacactgggtcttggAGGCAGTCCGCTGTAGAAtgaaagtcTCCATAGTAAAAGGCAACAGCTGAATGTGTtttggatgtcacggcgtgt 
 ********************************************************************************************************************** 
rat(((.(((.........((((.(((((....(((((.(((((((((((..((...........))..))))))).......))))..))).))..))))).)))).......))).)))0.720 -28.60

ratchromosome:7:34782317:34782434:1intergenic


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