logoSmall RNA from different tissues of two rat strains.


miR classification

Alignments

other hairpins

novel_loopOverlap_mirtron_randfoldOK_nonpairedHIGH_bulgeHIGH (2 loci)

block1489903 [novel_loopOverlap_mirtron_randfoldOK_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.007nono0.52/0.5223/23/1.000.0
0.0
1
0
1
0
8
-4
5arm_loop
1
0
0.39
5
11nana
  readsmiRBase family seed
seed     ---------ACAGACC--------------------------------------------     1novel
  lencloning frequencies
   T1S1
      --------CACAGACCTGACTTCTCTTCCAG-----------------------------     231
rat     gcttgccaCACAGACCTGACTTCTCTTCCAGacaggtggagtcactgtgtaggctgcagc      
      ************************************************************      
 ++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>ENSRNOT00000034201 ENSRNOG00000021249 RGD1561852_predicted
rat     ((..(((((((((...(((((((.(((......))).))))))))))))).))).))...     1.000 -25.20

ratchromosome:3:118918437:118918496:1Same_strand|Intronic_coding|ENSRNOT00000034201|ENSRNOG00000021249 ## ENSRNOG00000021249|protein_coding|RGD1561852_predicted|


novel_multiarm_5varHIGH_loopOverlap_randfoldOK (2 loci)

sblock11689 [novel_multiarm_5varHIGH_loopOverlap_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.001nono0.52/0.5519/24/0.831.2
0.0
2.4
0.0
5
1
0
0
2
1
0
0
18
0
-12
8
5arm_loop_3arm
3arm
1
1
nd
nd
0.26
0.17
5
2
62nana
  readsmiRBase family seed
seed----------------------GAGCUGG----------------------------------------3novel
seed-------------------GCUGAGC-------------------------------------------2novel
seed----------------------------------------------AGGAGGC----------------1novel
  lencloning frequencies
   T2S2T5S1
 ---------------------TGAGCTGGTGTCAGAAGCACTG--------------------------22-2
 ---------------------TGAGCTGGTGTCAGAAGCACTGT-------------------------231-
 ------------------TGCTGAGCTGGTGTCAGAA--------------------------------19-1
 ---------------------------------------------TAGGAGGCTGAGTAGGAAGAGGAG24-1
 ------------------TGCTGAGCTGGTGTCAGAAG-------------------------------20-1
rattccattcttgtcagcctcTGCTGAGCTGGTGTCAGAAGCACTGTtTAGGAGGCTGAGTAGGAAGAGGAG 
 ********************************************************************* 
rat(((.((((((((((((((..((((((.(((((.....))))))))))))))))))).))))))..))).1.000 -32.40

ratchromosome:8:57739018:57739086:-1intergenic


sblock7142 [novel_multiarm_5varHIGH_loopOverlap_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.002nono0.39/0.5219/23/0.780.0
1.0
2.3
0.0
2.0
2.7
3
3
3
0
0
0
1
2
1
0
0
0
26
19
8
-3
0
10
5arm_loop_3arm
3arm
3arm
1
1
1
nd
nd
nd
0.22
0.15
0.35
3
2
5
92nana
  readsmiRBase family seed
seed---------------------------CAAAGUU----------------------------------------------------------3novel
seed--------------------------------------------------UCCAGGU-----------------------------------2novel
seed-----------------------------------------------------AGGUCAG--------------------------------1novel
seed-----------------------------------------------------------------UUCUUCA--------------------1novel
seed--------------------------------------------------------------ACUUUCU-----------------------1novel
seed------------------------------------------------------------CGACUUU-------------------------1novel
  lencloning frequencies
   T1S1T5S1
 --------------------------TCAAAGTTTCTGATCTGGAGTCA-------------------------------------------23-3
 -------------------------------------------------TTCCAGGTCAGCGACTTTCTTC---------------------221-
 ----------------------------------------------------CAGGTCAGCGACTTTCTTCAG-------------------21-1
 -----------------------------------------------------------GCGACTTTCTTCAGCAGAA--------------19-1
 -------------------------------------------------TTCCAGGTCAGCGACTTTCT-----------------------20-1
 -------------------------------------------------------------GACTTTCTTCAGCAGAAAC------------19-1
 ----------------------------------------------------------------TTTCTTCAGCAGAAACGCTG--------20-1
rattggttttggtgggatgtttaataagaTCAAAGTTTCTGATCTGGAGTCATTCCAGGTCAGCGACTTTCTTCAGCAGAAACGCTGctctaact 
 ******************************************************************************************** 
rat.((((..(((((..(((((.....((..((((((.(((((((((((...))))))))))).))))))..)).....))))))))))..))))0.870 -30.50

ratchromosome:20:5541983:5542074:1intergenic


novel_multiarm_5varHIGH_mirtron (2 loci)

sblock822 [novel_multiarm_5varHIGH_mirtron]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.161nono0.45/0.5719/24/0.752.0
0.0
2.7
0.0
3
1
0
0
1
1
0
0
17
1
9
30
5arm
3arm
4
4
1
64
0.14
0.37
1
4
42nana
  readsmiRBase family seed
seed     ------------------GGCAGGU---------------------------------------------------------------------------------     2novel
seed     ---------------------------------------------------------------------------------------UUUCCAG------------     1novel
seed     ------------------------UUGGUAU---------------------------------------------------------------------------     1novel
  lencloning frequencies
   T3S2T5S2
      -----------------------GTTGGTATCCAGGTTACAAG---------------------------------------------------------------     201-
      --------------------------------------------------------------------------------------CTTTCCAGCAGGCACTAAC-     19-1
      -----------------GGGCAGGTTGGTATCCAGGTTACA-----------------------------------------------------------------     241-
      -----------------GGGCAGGTTGGTATCCAGGTT--------------------------------------------------------------------     211-
rat     gttggcgctgaggccctGGGCAGGTTGGTATCCAGGTTACAAGgtagctcctaagtagaagtttggtgcttggagacagaggtctgCTTTCCAGCAGGCACTAACt      
      **********************************************************************************************************      
 >>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ENSRNOT00000048969 ENSRNOG00000031230 HBB2_RAT
rat     (((((.(((...((...(((((((((.((.((((((.(((.....((((.((....)).))))..))))))))).))...)))))))))....)).))).))))).     0.880 -33.90

ratchromosome:1:161579284:161579389:-1Same_strand|Intronic_coding|ENSRNOT00000048969|ENSRNOG00000031230 ## Same_strand|Boundary_coding|ENSRNOT00000048969|ENSRNOG00000031230 ## ENSRNOG00000031230|protein_coding|HBB2_RAT|Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin) (Hemoglobin beta chain, minor-form). [Source:UniProtKB/Swiss-Prot;Acc:P11517]


sblock823 [novel_multiarm_5varHIGH_mirtron]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.161nono0.45/0.5719/24/0.752.0
0.0
2.7
0.0
3
1
0
0
1
1
0
0
17
1
9
30
5arm
3arm
4
4
1
64
0.14
0.37
1
4
42nana
  readsmiRBase family seed
seed     ------------------GGCAGGU---------------------------------------------------------------------------------     2novel
seed     ---------------------------------------------------------------------------------------UUUCCAG------------     1novel
seed     ------------------------UUGGUAU---------------------------------------------------------------------------     1novel
  lencloning frequencies
   T3S2T5S2
      -----------------------GTTGGTATCCAGGTTACAAG---------------------------------------------------------------     201-
      --------------------------------------------------------------------------------------CTTTCCAGCAGGCACTAAC-     19-1
      -----------------GGGCAGGTTGGTATCCAGGTTACA-----------------------------------------------------------------     241-
      -----------------GGGCAGGTTGGTATCCAGGTT--------------------------------------------------------------------     211-
rat     gttggcgctgaggccctGGGCAGGTTGGTATCCAGGTTACAAGgtagctcctaagtagaagtttggtgcttggagacagaggtctgCTTTCCAGCAGGCACTAACt      
      **********************************************************************************************************      
 >>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ENSRNOT00000041830 ENSRNOG00000029719 MGC72973
rat     (((((.(((...((...(((((((((.((.((((((.(((.....((((.((....)).))))..))))))))).))...)))))))))....)).))).))))).     0.880 -33.90

ratchromosome:1:161586010:161586115:-1Same_strand|Boundary_coding|ENSRNOT00000041830|ENSRNOG00000029719 ## Same_strand|Intronic_coding|ENSRNOT00000041830|ENSRNOG00000029719 ## ENSRNOG00000029719|protein_coding|MGC72973|Hemoglobin subunit beta-2 (Hemoglobin beta-2 chain) (Beta-2-globin) (Hemoglobin beta chain, minor-form). [Source:UniProtKB/Swiss-Prot;Acc:P11517]


novel_multiarm_DicerNOK_5varHIGH_loopOverlap_bulgeHIGH (2 loci)

sblock11672 [novel_multiarm_DicerNOK_5varHIGH_loopOverlap_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.356nono0.30/0.6019/23/0.783.3
0.0
4.0
0.5
7
2
0
0
2
1
0
0
40
14
-9
13
5arm_loop_3arm
3arm
1
1
nd
nd
0.45
0.24
4
4
92150
  readsmiRBase family seed
seed--------------------------------------------UGGCUUC----------------------------------------------------------3novel
seed---------------------------------------------------------------------------GGCAUCU---------------------------2novel
seed-----------------------------------------CUUUGGC-------------------------------------------------------------1novel
seed----------------------------------------------GCUUCUA--------------------------------------------------------1novel
seed-------------------------------------------UUGGCUU-----------------------------------------------------------1novel
seed------------------------------------------------UUCUAAG------------------------------------------------------1novel
  lencloning frequencies
   T4S2T5S1
 -------------------------------------------TTGGCTTCTAAGAGTAATTTCT--------------------------------------------2211
 --------------------------------------------------------------------------TGGCATCTGGGAGGGTGAAGT--------------21-1
 ---------------------------------------------GGCTTCTAAGAGTAATTTCT--------------------------------------------20-1
 ------------------------------------------TTTGGCTTCTAAGAGTAATTTCT--------------------------------------------23-1
 -----------------------------------------------CTTCTAAGAGTAATTTCTG-------------------------------------------19-1
 --------------------------------------------------------------------------TGGCATCTGGGAGGGTGAAG---------------20-1
 ----------------------------------------TCTTTGGCTTCTAAGAGTAA-------------------------------------------------20-1
 -------------------------------------------TTGGCTTCTAAGAGTAATT-----------------------------------------------19-1
ratgctgctccagagcaagtcctctttttctttcttccctcggTCTTTGGCTTCTAAGAGTAATTTCTGcccagcagTGGCATCTGGGAGGGTGAAGTtgcttgaaataagc 
 ************************************************************************************************************* 
rat(((......((((((........((((..(((((((...(((....(((....((((....))))....)))...)))....))))))).))))))))))......)))0.830 -28.50

ratchromosome:8:57732922:57733030:-1intergenic


sblock8061 [novel_multiarm_DicerNOK_5varHIGH_loopOverlap_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.017nono0.50/0.6118/24/0.832.5
0.0
0.0
0.0
0.5
0.0
0.0
0.0
2
1
1
2
0
0
0
0
1
1
1
2
0
0
0
0
2
18
28
21
15
0
-9
6
5arm
5arm
5arm_loop_3arm
3arm
1
1
1
1
nd
nd
nd
nd
0.29
0.30
0.32
0.41
4
6
4
5
630-2
  readsmiRBase family seed
seed----------------------------------------------------GCAAUGG-----------------------------------2novel
seed-------------------GGGGCAC--------------------------------------------------------------------1novel
seed---ACCUGAA------------------------------------------------------------------------------------1novel
seed-----------------------------GGAAAGU----------------------------------------------------------1novel
seed--------AACAUUG-------------------------------------------------------------------------------1novel
  lencloning frequencies
   T1S1T1S2T5S1
 ---------------------------------------------------TGCAATGGCTTTTCTCTCCCTC---------------------22-11
 -------GAACATTGGCCTGGGGCA---------------------------------------------------------------------18--1
 --TACCTGAACATTGGCCTGGGGCAC--------------------------------------------------------------------24--1
 ------------------TGGGGCACCATGGAAAGTCAGGC-----------------------------------------------------231--
 ----------------------------TGGAAAGTCAGGCATCTGCCAC--------------------------------------------22--1
ratttTACCTGAACATTGGCCTGGGGCACCATGGAAAGTCAGGCATCTGCCACcTGCAATGGCTTTTCTCTCCCTCcaggctcagtccagtgtgggt 
 ********************************************************************************************** 
rat((((((((...((((((((((((......((((((((((((....)))........))))))))).....)))))))).)))).))).))))).0.990 -34.10

ratchromosome:3:76970221:76970314:1intergenic


novel_multiarm_DicerNOK_5varHIGH_loopOverlap_randfoldOK_nonpairedHIGH (2 loci)

sblock11261 [novel_multiarm_DicerNOK_5varHIGH_loopOverlap_randfoldOK_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.004nono0.48/0.5220/25/0.750.0
0.0
2.0
0.0
0.0
2.5
1
1
2
0
0
0
1
1
2
0
0
0
18
28
6
6
-9
8
5arm
5arm_loop_3arm
3arm
1
1
1
nd
nd
nd
0.45
0.56
0.32
7
7
3
4343
  readsmiRBase family seed
seed     -----------------------------------------------------------CCUCUGU------------------------     1novel
seed     -----------------------------GCUAACU------------------------------------------------------     1novel
seed     ---------------------------------------------------------------UGUUCUC--------------------     1novel
seed     -------------------UGCAGAU----------------------------------------------------------------     1novel
  lencloning frequencies
   T2S1T3S1T4S2
      ------------------GTGCAGATTCAGCTAACTGC----------------------------------------------------     201--
      ----------------------------AGCTAACTGCGGCCCATTTTTCTGT-------------------------------------     251--
      ----------------------------------------------------------ACCTCTGTTCTCTGCATCTGC-----------     21-1-
      --------------------------------------------------------------CTGTTCTCTGCATCTGCAAGCA------     22--1
rat     agagagtgcagctgcgcaGTGCAGATTCAGCTAACTGCGGCCCATTTTTCTGTggccgACCTCTGTTCTCTGCATCTGCAAGCAtttctc      
      ******************************************************************************************      
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ENSRNOT00000031946 ENSRNOG00000026807 Q6P3V7_RAT
rat     .(((((....(((..((((((((((..(((.......(((((((......)).)))))....)))...)))))).)))).)))..)))))     0.830 -34.70

ratchromosome:7:23373135:23373224:1Same_strand|Intronic_coding|ENSRNOT00000031946|ENSRNOG00000026807 ## Same_strand|Boundary_non-coding|ENSRNOT00000059545|ENSRNOG00000026807 ## ENSRNOG00000026807|protein_coding|Q6P3V7_RAT|Gnn protein. [Source:UniProtKB/TrEMBL;Acc:Q6P3V7]


sblock11777 [novel_multiarm_DicerNOK_5varHIGH_loopOverlap_randfoldOK_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.010nono0.45/0.4520/22/1.000.0
2.5
0.0
1.5
1
2
0
0
1
2
0
0
10
14
3
-9
5arm
3arm_loop
1
1
nd
nd
0.35
0.35
4
3
330-12
  readsmiRBase family seed
seed-----------CUCACUU----------------------------------------------------------1novel
seed-------------------------------------------AUGGAAA--------------------------1novel
seed--------------------------------------ACCAUAU-------------------------------1novel
  lencloning frequencies
   T1S1T2S1T5S1
 ----------TCTCACTTTGAAACCCACCT----------------------------------------------20-1-
 ------------------------------------------TATGGAAAGGTGGGAGATAC--------------201--
 -------------------------------------TACCATATGGAAAGGTGGGAGA-----------------22--1
ratagcatgggccTCTCACTTTGAAACCCACCTttcatttTACCATATGGAAAGGTGGGAGATACgggagctttattgc 
 **************************************************************************** 
rat.(((.(((.(((((...((....((((((((((.............)))))))))).))...))))))))...)))0.940 -24.82

ratchromosome:8:72064297:72064372:-1intergenic


novel_multiarm_DicerNOK_5varHIGH_mirtron_randfoldOK (2 loci)

sblock8121 [novel_multiarm_DicerNOK_5varHIGH_mirtron_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.005nono0.62/0.6520/22/1.000.0
1.3
0.0
2.3
1
3
0
0
1
3
0
0
24
15
3
3
5arm
3arm
1
1
39
0
0.25
0.23
3
2
4402
  readsmiRBase family seed
seed     ----------------------------------------------------------GACAGGU---------------------------------     2novel
seed     --------------------------------------------------------------GGUACCC-----------------------------     1novel
seed     -------------------------AGGGGAG------------------------------------------------------------------     1novel
  lencloning frequencies
   T1S1T1S2T3S2T5S2
      ---------------------------------------------------------TGACAGGTACCCTCCCCCACA--------------------     21-1--
      ---------------------------------------------------------TGACAGGTACCCTCCCCCAC---------------------     20---1
      ------------------------CAGGGGAGGCAGACCTGTGA------------------------------------------------------     20--1-
      -------------------------------------------------------------AGGTACCCTCCCCCACATCCAG---------------     221---
rat     tgagtaagggtcagcagggtgaagCAGGGGAGGCAGACCTGTGActgacaggtacggTGACAGGTACCCTCCCCCACATCCAGactctgagagcacag      
      **************************************************************************************************      
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>ENSRNOT00000056349 ENSRNOG00000007018 NP_001102059.1
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>ENSRNOT00000009430 ENSRNOG00000007018 NP_001102059.1
rat     ((.((.((((((....(((((.....(((((((...((((((.((((.......)))).))))))..)))))))..))))).))))))....)).)).     0.970 -41.50

ratchromosome:3:106527752:106527849:1Same_strand|Intronic_coding|ENSRNOT00000009430|ENSRNOG00000007018 ## ENSRNOG00000007018|protein_coding|NP_001102059.1|mitogen activated protein kinase binding protein 1 [Source:RefSeq_peptide;Acc:NP_001102059]


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