logoSmall RNA from different tissues of two rat strains.


miR classification

Alignments

other hairpins

novel_lenNOK_cloningHIGH_multiarm_loopOverlap_nonpairedHIGH (5 loci)

sblock5446 [novel_lenNOK_cloningHIGH_multiarm_loopOverlap_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.015nono0.32/0.4418/19/0.000.0
0.0
0.0
0.1
8
22
0
0
7
8
0
0
11
29
30
-1
5arm
3arm
2
2
nd
nd
0.56
0.33
5
3
529nana
  readsmiRBase family seed
seed     -----------------------------------------------------------------GUAAACA----------------------------------------     34miR-30a/30b/30c/30d/30e/384
seed     ------------GUAAACA---------------------------------------------------------------------------------------------     16miR-30a/30b/30c/30d/30e/384
seed     ------------------------------------------------------------------UAAACAU---------------------------------------     1novel
seed     -------------UAAACAU--------------------------------------------------------------------------------------------     1novel
  lencloning frequencies
   T1S1T1S2T2S1T2S2T3S2T4S1T4S2T5S1T5S2
      ----------------------------------------------------------------TGTAAACATCCTTGAGGA------------------------------     1872--134-5
      ----------------------------------------------------------------TGTAAACATCCTTGAGGAC-----------------------------     1922-11-312
      -----------TGTAAACATCCTTGAAGA-----------------------------------------------------------------------------------     18212---114
      -----------TGTAAACATCCTTGAAGAA----------------------------------------------------------------------------------     19-11-1-1-1
      -----------------------------------------------------------------GTAAACATCCTTGAGGAC-----------------------------     18---1-----
      ------------GTAAACATCCTTGAAGAA----------------------------------------------------------------------------------     181--------
rat     gcaggctgtgtTGTAAACATCCTTGAAGAagagctcagaagaaaagtcctgggttgtactgtgtTGTAAACATCCTTGAGGACcagctctgcaggagaataatgctgcctgc      
      ****************************************************************************************************************      
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ENSRNOT00000036306 ENSRNOG00000028703 Slc39a6
rat     ((((((.(((((((.....(((.((....((((((..........(((((((((..(((......)))...))))...))))).)))))).)))))..))))))).))))))     0.730 -36.90

ratchromosome:18:16371446:16371557:-1Same_strand|Intronic_coding|ENSRNOT00000036306|ENSRNOG00000028703 ## ENSRNOG00000028703|protein_coding|Slc39a6|Zinc transporter ZIP6 precursor (Zrt- and Irt-like protein 6) (ZIP-6) (Solute carrier family 39 member 6). [Source:UniProtKB/Swiss-Prot;Acc:Q4V887]


novel_lenNOK_cloningHIGH_randfoldOK_bulgeHIGH (5 loci)

block1189274 [novel_lenNOK_cloningHIGH_randfoldOK_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.001nono0.44/0.4718/19/0.000.0
0.2
45
0
8
0
12
2
5arm
1
nd
0.26
4
618nana
  readsmiRBase family seed
seed     -------------UCCAGUU------------------------------------------------     61miR-145
  lencloning frequencies
   T1S2T2S2T3S1T3S2T4S1T4S2T5S1T5S2
      ------------GTCCAGTTTTCCCACAAA--------------------------------------     182375101622
      ------------GTCCAGTTTTCCCACAAAC-------------------------------------     19-17122-1
rat     agtgaaaacaagGTCCAGTTTTCCCACAAACtttgaggtaagtttaagaaagctgactaggtttttgc      
      ********************************************************************      
 ------------------------------------------------------------------------------ENSRNOT00000015887 ENSRNOG00000028169 NP_001101151.1
rat     .((((((((..(((.((((((((....((((((......))))))..)))))))))))..))))))))     1.000 -20.70

ratchromosome:2:159532326:159532393:-1Opposite_strand|Intronic_coding|ENSRNOT00000015887|ENSRNOG00000028169 ## ENSRNOG00000028169|protein_coding|NP_001101151.1|protein phosphatase 1 (formerly 2C)-like [Source:RefSeq_peptide;Acc:NP_001101151]


block1434364 [novel_lenNOK_cloningHIGH_randfoldOK_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.007nono0.61/0.6318/19/0.000.0
0.0
124
0
10
0
5
9
5arm
1
nd
0.22
4
19610nana
  readsmiRBase family seed
seed------CUCCCAG------------------------------------------------------------------196novel
  lencloning frequencies
   T1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
 -----TCTCCCAGCCCTTGTACC--------------------------------------------------------1847598638151754
 -----TCTCCCAGCCCTTGTACCC-------------------------------------------------------19----33----
ratttgacTCTCCCAGCCCTTGTACCccacaggccttcagggctctcatgagacaaagggtctggcctttaaagggagtcag 
 ******************************************************************************* 
rat.(((((((((((((((((((........((((.....))))........)))).))).))))........)))))))).0.910 -29.49

ratchromosome:3:4090171:4090249:1intergenic


block1542680 [novel_lenNOK_cloningHIGH_randfoldOK_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.010nono0.42/0.4818/23/0.090.0
0.4
158
0
5
0
16
0
3arm
1
nd
0.22
4
1765nana
  readsmiRBase family seed
seed-----------------------------------AAGGCAU---------------------------176novel
  lencloning frequencies
   T1S2T2S1T3S1T4S1T4S2
 ----------------------------------TAAGGCATAAAGCCTTGGT----------------191114549
 ----------------------------------TAAGGCATAAAGCCTTGG-----------------18---3034
 ----------------------------------TAAGGCATAAAGCCTTGGTG---------------20---75
 ----------------------------------TAAGGCATAAAGCCTTGGTGC--------------21---11
 ----------------------------------TAAGGCATAAAGCCTTGGTGCAG------------23----1
rattgtagaagtgagatattaagatatgccttgagggTAAGGCATAAAGCCTTGGTgcagtcttgtgctgcg 
 ********************************************************************* 
rat.((((...((((((((((((.(((((((((....)))))))))....))))))...))))))..)))).0.740 -19.90

ratchromosome:4:53851940:53852008:-1intergenic


block1839923 [novel_lenNOK_cloningHIGH_randfoldOK_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.001nono0.58/0.6118/19/0.000.0
0.0
120
0
10
0
17
17
3arm
2
nd
0.22
4
17010nana
  readsmiRBase family seed
seed----------------------------------------------------------------------------------AGCAGCA---------------------------170miR-15b/16/195/322/497
  lencloning frequencies
   T1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
 ---------------------------------------------------------------------------------CAGCAGCACACTGTGACC-----------------182195151512193898
 ---------------------------------------------------------------------------------CAGCAGCACACTGTGACCT----------------1932-314-4-2
ratgtcagctgagaagccagcatacagtgaagtccctgtaaatgctgctgggtgaatggaagcctgtggtgactccagtcacacCAGCAGCACACTGTGACCtctggcctctctggaca 
 ******************************************************************************************************************** 
rat(((....((((.(((((..(((((((.............(((((((((((((.((((.(((...)))...)))).)))).))))))))))))))))....))))).))))..))).0.830 -54.11

ratchromosome:5:62887977:62888092:1intergenic


block2183527 [novel_lenNOK_cloningHIGH_randfoldOK_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.007nono0.67/0.6718/18/0.000.0
0.0
38
0
8
0
20
11
3arm
1
nd
0.28
4
628nana
  readsmiRBase family seed
seed--------------------------------------------------------------------------------GGGUCCC------------------------------62novel
  lencloning frequencies
   T1S1T1S2T2S1T2S2T3S1T3S2T5S1T5S2
 -------------------------------------------------------------------------------AGGGTCCCTGGTAGCTCC--------------------181545181028
ratctgaactcaccacaatcatcccaggagtttgtgacctgggccgggaccccctgtggtcacacatccctccattcatgcaAGGGTCCCTGGTAGCTCCagttcatggctccagttcag 
 ********************************************************************************************************************* 
rat(((((((................((((.((((((.((((((((((((((...((((............))))........))))))).)))....)))).)))))))))))))))))0.410 -39.49

ratchromosome:7:10920552:10920668:1intergenic


novel_lenNOK_cloningOK_5varHIGH_loopOverlap_randfoldOK (5 loci)

block1767268 [novel_lenNOK_cloningOK_5varHIGH_loopOverlap_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.008nono0.36/0.5319/25/0.428.0
4.8
34
0
3
0
6
-22
3arm
1
nd
0.16
2
433nana
  readsmiRBase family seed
seed-------------------------------------ACACACA------------------------------------11novel
seed--------------------------------------------------CUGCUUU-----------------------11novel
seed---------------------------------------------GGUAUCU----------------------------9novel
seed----------------------------------------------------GCUUUUC---------------------6novel
seed------------------------------------------------AUCUGCU-------------------------4novel
seed-----------------------------------------------UAUCUGC--------------------------2novel
  lencloning frequencies
   T1S1T3S1T5S1
 -------------------------------------------------TCTGCTTTTCAGCCTGAAG------------19--10
 ------------------------------------AACACACATGGTATCTGCTTTTCAG-------------------25--10
 --------------------------------------------TGGTATCTGCTTTTCAGCCTGA--------------22315
 ---------------------------------------------------TGCTTTTCAGCCTGAAGCCTCAG------231-3
 -----------------------------------------------TATCTGCTTTTCAGCCTGA--------------191-3
 ----------------------------------------------GTATCTGCTTTTCAGCCTGA--------------20--2
 ---------------------------------------------------TGCTTTTCAGCCTGAAGCCTC--------21--1
 -------------------------------------------------TCTGCTTTTCAGCCTGAAGCCTC--------23--1
 ------------------------------------AACACACATGGTATCTGCTTTT----------------------22--1
 ---------------------------------------------------TGCTTTTCAGCCTGAAGCC----------19-1-
ratggcctcttctgaagtgtcaacacaggctgagagcggAACACACATGGTATCTGCTTTTCAGCCTGAAGCCTCAGcccgcc 
 ******************************************************************************** 
rat(((.....((((.((.......(((((((((((((((((.......)).)))))))).)))))))..)).))))...)))0.490 -28.70

ratchromosome:5:114565099:114565178:-1intergenic


block959483 [novel_lenNOK_cloningOK_5varHIGH_loopOverlap_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.001nono0.42/0.4519/25/0.231.4
1.2
1.0
1.0
9
4
0
0
4
2
0
0
13
0
-6
6
3arm
3arm
4
4
nd
nd
0.05
0.12
1
2
134nana
  readsmiRBase family seed
seed----------------------------------------------------CACCUAU------------------------6novel
seed-----------------------------------------------GUCAUCA-----------------------------2novel
seed-----------------------------------------------------------GUGACUG-----------------2miR-134
seed-------------------------------------------------------------GACUGUU---------------1novel
seed-------------------------------------------------CAUCACC---------------------------1novel
seed--------------------------------------------------------------ACUGUUA--------------1novel
  lencloning frequencies
   T1S2T3S2T4S2T5S1
 ---------------------------------------------------TCACCTATGTGACTGTTAG-------------191113
 ----------------------------------------------------------TGTGACTGTTAGCCCATATCTGTGA25---2
 ----------------------------------------------TGTCATCACCTATGTGACTGT----------------21-1-1
 ------------------------------------------------TCATCACCTATGTGACTGT----------------19---1
 ------------------------------------------------------------TGACTGTTAGCCCATATCT----191---
 -------------------------------------------------------------GACTGTTAGCCCATATCTGTGA22---1
rattcatagggatttgggaaccacttacagtcttcattgagcatgggtgTGTCATCACCTATGTGACTGTTAGCCCATATCTGTGA 
 *********************************************************************************** 
rat(((((((....((((.....((.((((((........(((((((((......))))))))))))))).))))))..)))))))0.970 -30.70

ratchromosome:1:47968706:47968788:1intergenic


block204044 [novel_lenNOK_cloningOK_5varHIGH_loopOverlap_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.005nono0.53/0.6218/26/0.328.3
0.0
4.1
0.0
10
6
0
0
4
4
0
0
30
22
-23
13
3arm
3arm
3
3
nd
nd
0.21
0.32
2
6
196nana
  readsmiRBase family seed
seed------------------------------------------------------------------------CAUCACA---------------------------------7novel
seed----------------------------------------------------GCCUCUG-----------------------------------------------------5novel
seed----------------------------------------------------------GCUCACC-----------------------------------------------2novel
seed----------------------------------------------------------------------CUCAUCA-----------------------------------2novel
seed---------------------------------------------GUCCUUU------------------------------------------------------------1novel
seed-------------------------------------------------------------CACCACA--------------------------------------------1novel
seed---------------------------------------------------UGCCUCU------------------------------------------------------1novel
  lencloning frequencies
   T1S1T2S2T3S1T3S2T5S1T5S2
 -----------------------------------------------------------------------TCATCACACTCTCTCCCTG----------------------192-1-4-
 ---------------------------------------------------TGCCTCTGCTCACCACACCCTCA--------------------------------------23---11-
 ---------------------------------------------------TGCCTCTGCTCACCACAC-------------------------------------------18-1--1-
 ---------------------------------------------------------------------CCTCATCACACTCTCTCCC------------------------19-----1
 ---------------------------------------------------------------------CCTCATCACACTCTCTCCCTG----------------------21----1-
 --------------------------------------------------TTGCCTCTGCTCACCACACCC-----------------------------------------21----1-
 ---------------------------------------------------------TGCTCACCACACCCTCATCACACTC------------------------------25----1-
 --------------------------------------------AGTCCTTTGCCTCTGCTCACCACACC------------------------------------------26-1----
 ---------------------------------------------------TGCCTCTGCTCACCACACCCT----------------------------------------21----1-
 ------------------------------------------------------------TCACCACACCCTCATCACAC--------------------------------20-----1
 ---------------------------------------------------------TGCTCACCACACCCTCATC------------------------------------19----1-
ratcggtttcctcaaattgaaagccgagggagaggtgggggagtgggagtcctttgcctctgctcaccacacccTCATCACACTCTCTCCCTGcccttcacccctcctcacccgg 
 **************************************************************************************************************** 
rat(((...........((((.((..(((((((((((((((.((((((((...........)))).)))).)))))))......))))))))))..))))...........))).0.530 -39.55

ratchromosome:12:44296838:44296949:-1intergenic


block233551 [novel_lenNOK_cloningOK_5varHIGH_loopOverlap_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.010nono0.55/0.6218/26/0.508.3
4.1
10
0
4
0
33
-23
3arm
3
nd
0.21
2
104nana
  readsmiRBase family seed
seed     ---------------------------------------------------------GCCUCUG--------------------------------------------------------     5novel
seed     ---------------------------------------------------------------GCUCACC--------------------------------------------------     2novel
seed     --------------------------------------------------------UGCCUCU---------------------------------------------------------     1novel
seed     --------------------------------------------------GUCCUUU---------------------------------------------------------------     1novel
seed     ------------------------------------------------------------------CACCACA-----------------------------------------------     1novel
  lencloning frequencies
   T2S2T3S2T5S1T5S2
      --------------------------------------------------------TGCCTCTGCTCACCACACCCTCA-----------------------------------------     23-11-
      --------------------------------------------------------TGCCTCTGCTCACCACAC----------------------------------------------     181-1-
      --------------------------------------------------------------TGCTCACCACACCCTCATCACACTC---------------------------------     25--1-
      -------------------------------------------------------TTGCCTCTGCTCACCACACCC--------------------------------------------     21--1-
      -----------------------------------------------------------------TCACCACACCCTCATCACAC-----------------------------------     20---1
      -------------------------------------------------AGTCCTTTGCCTCTGCTCACCACACC---------------------------------------------     261---
      --------------------------------------------------------------TGCTCACCACACCCTCATC---------------------------------------     19--1-
      --------------------------------------------------------TGCCTCTGCTCACCACACCCT-------------------------------------------     21--1-
rat     gatcttggtttcctcaaattgaaagccgagggagaggtgggggagtgggAGTCCTTTGCCTCTGCTCACCACACCCTCATCACACTCtctccctgcccttcacccctcctcacccggtcc      
      ************************************************************************************************************************      
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ENSRNOT00000056932 ENSRNOG00000037566 RGD1560398_predicted
rat     ((((..(((..........((((.((..(((((((((((((((.((((((((...........)))).)))).)))))))......))))))))))..)))).........))).)))).     0.420 -40.91

ratchromosome:12:43046181:43046300:1Same_strand|Intronic_non-coding|ENSRNOT00000056932|ENSRNOG00000037566 ## ENSRNOG00000037566|protein_coding|RGD1560398_predicted|


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