logoSmall RNA from different tissues of two rat strains.


miR classification

Alignments

other hairpins

novel_cloningOK_5varHIGH_loopOverlap (11 loci)

block1394369 [novel_cloningOK_5varHIGH_loopOverlap]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.621nono0.40/0.5818/23/0.743.6
2.4
19
0
2
0
9
-11
5arm_loop_3arm
1
nd
0.30
2
192nana
  readsmiRBase family seed
seed     ---------------ACCAGAC-----------------------------------------------     3novel
seed     ----------------------CAGGACU----------------------------------------     3novel
seed     ------------------AGACCAG--------------------------------------------     2novel
seed     --------------------ACCAGGA------------------------------------------     2novel
seed     --------------AACCAGA------------------------------------------------     2novel
seed     -----------------CAGACCA---------------------------------------------     2novel
seed     -----------AUAAACC---------------------------------------------------     1novel
seed     ------------UAAACCA--------------------------------------------------     1novel
seed     ----------AAUAAAC----------------------------------------------------     1novel
seed     ----------------CCAGACC----------------------------------------------     1novel
seed     -------------------GACCAGG-------------------------------------------     1novel
  lencloning frequencies
   T4S1T4S2
      ----------------CCAGACCAGGACTTGCAAC----------------------------------     1911
      -------------AAACCAGACCAGGACTTGCAACC---------------------------------     232-
      -----------------CAGACCAGGACTTGCAACCTAC------------------------------     222-
      --------------AACCAGACCAGGACTTGCAACC---------------------------------     2211
      ---------------------CCAGGACTTGCAACCTACA-----------------------------     19-2
      ------------------AGACCAGGACTTGCAACC---------------------------------     181-
      -------------------GACCAGGACTTGCAACCTAC------------------------------     201-
      ---------AAATAAACCAGACCAGGACT----------------------------------------     201-
      -----------ATAAACCAGACCAGGACTTG--------------------------------------     20-1
      ---------------------CCAGGACTTGCAACCTACAA----------------------------     201-
      ----------AATAAACCAGACCAGGACTTGC-------------------------------------     22-1
      ---------------ACCAGACCAGGACTTGCAACCT--------------------------------     22-1
      --------------AACCAGACCAGGACTTGCAACCT--------------------------------     231-
      -------------------GACCAGGACTTGCAACCTACA-----------------------------     211-
rat     ttgctttatAAATAAACCAGACCAGGACTTGCAACCTACAAaagcccgtcttctttcttgtgtgagtag      
      *********************************************************************      
 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.....................................ENSRNOT00000011773 ENSRNOG00000008536 Actc1
rat     .(((((....((.(((..((((..((.(((...........))))).))))..))).))....))))).     1.000 -9.20

ratchromosome:3:99900990:99901058:-1Same_strand|Boundary_non-coding|ENSRNOT00000011773|ENSRNOG00000008536 ## ENSRNOG00000008536|protein_coding|Actc1|Actin, alpha cardiac muscle 1 (Alpha-cardiac actin). [Source:UniProtKB/Swiss-Prot;Acc:P68035]


block1499941 [novel_cloningOK_5varHIGH_loopOverlap]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.568nono0.26/0.4219/24/0.752.1
1.1
10
0
2
0
11
-2
3arm
2
nd
0.30
2
202nana
  readsmiRBase family seed
seed--------------------------------------------------------------GUAGAAU------------------------6novel
seed-----------------------------------------------------------UUUGUAG---------------------------5novel
seed--------------------------------------------------------CCUUUUG------------------------------3novel
seed----------------------------------------------------------------AGAAUUG----------------------2novel
seed-----------------------------------------------------------------GAAUUGU---------------------1miR-219
seed-------------------------------------------------------------UGUAGAA-------------------------1novel
seed---------------------------------------------------------------UAGAAUU-----------------------1novel
seed------------------------------------------------------------UUGUAGA--------------------------1novel
  lencloning frequencies
   T1S1T5S1
 -------------------------------------------------------------TGTAGAATTGTAACTGCCAC------------20-5
 ----------------------------------------------------------TTTTGTAGAATTGTAACTGCCACT-----------2413
 ---------------------------------------------------------------TAGAATTGTAACTGCCACT-----------1911
 -------------------------------------------------------CCCTTTTGTAGAATTGTAACTG----------------22-2
 --------------------------------------------------------------GTAGAATTGTAACTGCCAC------------19-1
 ----------------------------------------------------------------AGAATTGTAACTGCCACTA----------19-1
 ------------------------------------------------------------TTGTAGAATTGTAACTGCCAC------------21-1
 -------------------------------------------------------------TGTAGAATTGTAACTGCCACT-----------21-1
 -------------------------------------------------------CCCTTTTGTAGAATTGTAACT-----------------21-1
 -----------------------------------------------------------TTTGTAGAATTGTAACTGCCACT-----------23-1
 ----------------------------------------------------------TTTTGTAGAATTGTAACTG----------------19-1
ratgtgcaaaagattaatgatatgaatgtggtgtcgagtttatgaaggtgttctttctCCCTTTTGTAGAATTGTAACTGCCACTatagtctgcat 
 ********************************************************************************************* 
rat((((...((((((...........((((((((((.((((..((((............))))..)))).)))..)).)))))..))))))))))0.710 -15.92

ratchromosome:3:141759977:141760069:1intergenic


block2428655 [novel_cloningOK_5varHIGH_loopOverlap]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.226nono0.61/0.7618/25/0.758.8
11.6
16
0
8
0
20
-5
3arm
1
nd
0.20
1
168nana
  readsmiRBase family seed
seed----------------------------------------------------------UGCUCGG----------------------------------------3novel
seed------------------------------------------------------GGCAUGC--------------------------------------------3novel
seed-----------------------------------------------GGAACUG---------------------------------------------------2novel
seed--------------------------------------------------------CAUGCUC------------------------------------------2novel
seed---------------------------------------------------------AUGCUCG-----------------------------------------1novel
seed-------------------------------------------------AACUGGG-------------------------------------------------1novel
seed-------------------------------------------------------GCAUGCU-------------------------------------------1novel
seed-----------------------------------------------------------------UGUCGCC---------------------------------1novel
seed---------------------------------------------------------------GGUGUCG-----------------------------------1novel
seed-------------------------------------------------------------UCGGUGU-------------------------------------1novel
  lencloning frequencies
   T1S1T2S1T2S2T3S1T3S2T4S1T4S2T5S2
 ---------------------------------------------------------ATGCTCGGTGTCGCCGCAGC----------------------------201---1---
 -------------------------------------------------------GCATGCTCGGTGTCGCCGCA------------------------------20----1--1
 --------------------------------------------------------CATGCTCGGTGTCGCCGCAG-----------------------------20-------1
 ----------------------------------------------------------------GTGTCGCCGCAGCCTTGGGTC--------------------21-----1--
 ------------------------------------------------------------CTCGGTGTCGCCGCAGCCTT-------------------------20----1---
 -----------------------------------------------------GGGCATGCTCGGTGTCGCC---------------------------------19---1----
 ------------------------------------------------------GGCATGCTCGGTGTCGCCG--------------------------------19------1-
 -----------------------------------------------------GGGCATGCTCGGTGTCGCCGCA------------------------------22---1----
 --------------------------------------------------------------CGGTGTCGCCGCAGCCTTGGGTC--------------------23--1-----
 ----------------------------------------------AGGAACTGGGCATGCTCGGTGTC------------------------------------23--1-----
 ---------------------------------------------------------ATGCTCGGTGTCGCCGCAGCCT--------------------------22------1-
 -----------------------------------------------------GGGCATGCTCGGTGTCGCCGCAGCC---------------------------25---1----
 ----------------------------------------------AGGAACTGGGCATGCTCG-----------------------------------------18-1------
 ------------------------------------------------GAACTGGGCATGCTCGGTGTC------------------------------------21---1----
ratgccgtagcctataaaatccggagcgcggcgcgcggagcggcaggcgAGGAACTGGGCATGCTCGGTGTCGCCGCAGCCTTGGGTCgcaagtaggaagcccgtgca 
 ********************************************************************************************************* 
rat((((...(((((...(((((..(((((((((((.(((((.(((........)))....))))).))).)))))).))..))))).....))))).....)).)).0.930 -44.50

ratchromosome:8:82724176:82724280:1intergenic


block2057990 [novel_cloningOK_5varHIGH_loopOverlap]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.384nono0.55/0.6319/25/0.771.3
0.0
7
0
5
0
16
-3
3arm
1
nd
0.30
3
135nana
  readsmiRBase family seed
seed---------------------------------------------GCGCUGC----------------------------6novel
seed------------------------------------------CCUGCGC-------------------------------4novel
seed----------------------------------------CUCCUGC---------------------------------2novel
seed-------------------------------------CUUCUCC------------------------------------1miR-207
  lencloning frequencies
   T1S1T1S2T2S2T4S2T5S1
 --------------------------------------------TGCGCTGCTCTTGAAACCCA----------------20-1-14
 -----------------------------------------TCCTGCGCTGCTCTTGAAACCCA----------------23-1--3
 ---------------------------------------TCTCCTGCGCTGCTCTTGAAACCCA----------------251-1--
 ------------------------------------CCTTCTCCTGCGCTGCTCT-------------------------19----1
ratgtttgttgggtaaaggagtcgatgaacagccaatcgccttcTCCTGCGCTGCTCTTGAAACCCAtttgtcctttacaagg 
 ******************************************************************************** 
rat.(((((.((..(((((..((((.((.((((((............)).)))).))))))...)).)))..))...))))).0.990 -19.00

ratchromosome:6:122583846:122583925:1intergenic


block2247728 [novel_cloningOK_5varHIGH_loopOverlap]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.035nono0.47/0.5218/25/0.711.3
1.1
9
0
2
0
36
-2
5arm_loop
1
nd
0.25
2
142nana
  readsmiRBase family seed
seed-------------------------------------------GCGAUGC----------------------------------------------------------------------9novel
seed-------------------------------------CAGGAUG----------------------------------------------------------------------------3novel
seed-----------------------------------CUCAGGA------------------------------------------------------------------------------1novel
seed----------------------------------------------AUGCUAA-------------------------------------------------------------------1novel
  lencloning frequencies
   T4S1T5S1
 ------------------------------------------TGCGATGCTAATGAGCCAGAGA--------------------------------------------------------22-5
 ------------------------------------------TGCGATGCTAATGAGCCAGAG---------------------------------------------------------2112
 ------------------------------------TCAGGATGCGATGCTAATGAGCCA------------------------------------------------------------24-2
 ------------------------------------TCAGGATGCGATGCTAATGAGCCAG-----------------------------------------------------------25-1
 ----------------------------------TCTCAGGATGCGATGCTA--------------------------------------------------------------------18-1
 ------------------------------------------TGCGATGCTAATGAGCCA------------------------------------------------------------18-1
 ---------------------------------------------GATGCTAATGAGCCAGAGA--------------------------------------------------------19-1
ratttggttgaatctgttatggagatggtggggggattcTCAGGATGCGATGCTAATGAGCCAGAGAtagtctggagtgttcatagcagtgtctgagcttccactaacactccacactcacca 
 ************************************************************************************************************************ 
rat.(((.(((...(((...((((.(((((((((....((((((.(((.(((..((((..(((((.....)))))..))))))).)))...)))))))))))))))...))))))).))))))0.990 -39.70

ratchromosome:7:112744754:112744873:1intergenic


block2325294 [novel_cloningOK_5varHIGH_loopOverlap]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.528nono0.32/0.6118/24/0.733.6
0.0
1.0
0.0
5
5
0
0
2
1
0
0
9
24
-4
-13
5arm_loop
5arm_loop
1
1
nd
nd
0.25
0.59
2
11
112nana
  readsmiRBase family seed
seed-------------------------GGUGCUC---------------------------------------------------6novel
seed----------------CCCCACC------------------------------------------------------------3novel
seed----------GACUCUC------------------------------------------------------------------2novel
  lencloning frequencies
   T4S2T5S1
 ------------------------TGGTGCTCTAAGATATAAAAAG-------------------------------------22-5
 ---------TGACTCTCCCCACCATGGTGCTCT--------------------------------------------------24-2
 ---------------TCCCCACCATGGTGCTCTA-------------------------------------------------19-1
 ------------------------TGGTGCTCTAAGATATAAA----------------------------------------19-1
 ---------------TCCCCACCATGGTGCTCTAAGA----------------------------------------------22-1
 ---------------TCCCCACCATGGTGCTCT--------------------------------------------------181-
rattccttggccTGACTCTCCCCACCATGGTGCTCTAAGATATAAAAAGagatagaatgagaaggggacctgggtactgtgctgga 
 *********************************************************************************** 
rat(((..(((...(((((((((..(((..((((((...........)))).))..)))....)))))...)))).....))))))0.960 -18.30

ratchromosome:8:72081122:72081204:-1intergenic


block1060470 [novel_cloningOK_5varHIGH_loopOverlap]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.272nono0.50/0.6818/24/0.803.3
4.8
10
0
2
0
28
-8
5arm_loop_3arm
1
nd
0.15
2
102nana
  readsmiRBase family seed
seed-----------------------------------AGGCCUG---------------------------------------------------------------------------3novel
seed-----------------------------------------GGUUCGU---------------------------------------------------------------------3novel
seed-------------------------------------GCCUGGU-------------------------------------------------------------------------2novel
seed------------------------------GGAAUAG--------------------------------------------------------------------------------1novel
seed-----------------------------AGGAAUA---------------------------------------------------------------------------------1novel
  lencloning frequencies
   T1S1T5S1
 ----------------------------------TAGGCCTGGTTCGTGAGTCT---------------------------------------------------------------20-2
 ----------------------------------------TGGTTCGTGAGTCTCCCCTGAG-------------------------------------------------------22-2
 ----------------------------TAGGAATAGGCCTGGTTC-----------------------------------------------------------------------18-1
 ------------------------------------GGCCTGGTTCGTGAGTCTCCCCTG---------------------------------------------------------24-1
 ------------------------------------GGCCTGGTTCGTGAGTCTCCCC-----------------------------------------------------------22-1
 ----------------------------------------TGGTTCGTGAGTCTCCCCTGAGA------------------------------------------------------23-1
 ----------------------------------TAGGCCTGGTTCGTGAGT-----------------------------------------------------------------18-1
 -----------------------------AGGAATAGGCCTGGTTCGTGAG------------------------------------------------------------------221-
rattgaccggagcagccactcctggggcggcTAGGAATAGGCCTGGTTCGTGAGTCTCCCCTGAGAtaagtgacttaggtttagtttaatacctgggaagcctctgtgatgctggggcag 
 ********************************************************************************************************************* 
rat((.((..((((..(((....(((((..(((((..(((((((((.((((..(((((....)))))..)))).)))))))))........)))))...))))).))).))))..)))).0.910 -39.70

ratchromosome:20:5506134:5506250:-1intergenic


block1094153 [novel_cloningOK_5varHIGH_loopOverlap]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.157nono0.40/0.4619/26/0.717.1
7.6
14
0
2
0
15
-14
5arm_loop_3arm
1
nd
0.27
2
142nana
  readsmiRBase family seed
seed--------------------------GGCUACA------------------------------------------------4novel
seed----------------------AGUUGGC----------------------------------------------------3novel
seed-----------------------------------AGUAGAU---------------------------------------2novel
seed------------------------------ACAGAAG--------------------------------------------1novel
seed--------------------------------------AGAUAGU------------------------------------1novel
seed-------------------------------------UAGAUAG-------------------------------------1novel
seed----------------GGCAGUA----------------------------------------------------------1novel
seed----------------------------------AAGUAGA----------------------------------------1novel
  lencloning frequencies
   T1S1T5S1
 ---------------------TAGTTGGCTACAGAAGTAGA----------------------------------------20-3
 -------------------------TGGCTACAGAAGTAGATAGTGTG---------------------------------23-2
 ----------------------------------AAGTAGATAGTGTGTGACTC---------------------------201-
 -----------------------------TACAGAAGTAGATAGTGTGTGACTC---------------------------25-1
 ------------------------------------GTAGATAGTGTGTGACTCT--------------------------19-1
 ----------------------------------AAGTAGATAGTGTGTGACTCTG-------------------------22-1
 -------------------------TGGCTACAGAAGTAGATAGT------------------------------------20-1
 -------------------------TGGCTACAGAAGTAGATAGTG-----------------------------------21-1
 ---------------------------------GAAGTAGATAGTGTGTGACTC---------------------------21-1
 ---------------TGGCAGTAGTTGGCTACAGAAGTAGA----------------------------------------26-1
 -------------------------------------TAGATAGTGTGTGACTCTG-------------------------19-1
ratgttcagagacaacctTGGCAGTAGTTGGCTACAGAAGTAGATAGTGTGTGACTCTGgtgtcccctgctgctctggctgagc 
 ********************************************************************************* 
rat((((((......((..((((((((..(((..((((..((.((...)).))..))))..)))..))))))))..))))))))0.990 -26.60

ratchromosome:20:5561438:5561518:1intergenic


block1766678 [novel_cloningOK_5varHIGH_loopOverlap]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.015nono0.35/0.3923/25/0.731.4
1.0
11
0
3
0
28
-9
5arm_loop_3arm
1
nd
0.26
2
113nana
  readsmiRBase family seed
seed------------------------------CCACAUC---------------------------------------------------------------------6novel
seed-----------------------------UCCACAU----------------------------------------------------------------------4novel
seed--------------------------------------GUAUCUU-------------------------------------------------------------1novel
  lencloning frequencies
   T1S1T1S2T5S1
 -----------------------------TCCACATCTGTATCTTATCTGTCA-----------------------------------------------------24-13
 ----------------------------TTCCACATCTGTATCTTATCTGTCA-----------------------------------------------------25--3
 -----------------------------TCCACATCTGTATCTTATCTGTC------------------------------------------------------23--2
 ----------------------------TTCCACATCTGTATCTTATCTGT-------------------------------------------------------231--
 -------------------------------------TGTATCTTATCTGTCATAGCAGA----------------------------------------------23--1
ratttgacagaggctctagtacattctgtatTTCCACATCTGTATCTTATCTGTCATAGCAGAttttagggcaggtgtcagaggctggatgtggtagcttttcactcag 
 ********************************************************************************************************** 
rat.(((..((((..(((.(((((((.((......((((((((.(((.((((((....))))))...))))))))))).....)).))))))).)))..))))..))).0.980 -32.60

ratchromosome:5:114526142:114526247:-1intergenic


novel_cloningOK_loopOverlap (11 loci)

block212283 [novel_cloningOK_loopOverlap]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.567nono0.50/0.7518/20/0.900.0
0.0
0.0
0.0
1
6
0
0
1
3
0
0
19
27
3
-5
5arm
5arm_loop
1
1
nd
nd
0.25
0.45
2
6
104nana
  readsmiRBase family seed
seed     ----------------------------GGCAGGC----------------------------------------------------------------------     6novel
seed     ------------------------------CAGGCUA--------------------------------------------------------------------     2novel
seed     --------------------------------GGCUACG------------------------------------------------------------------     1novel
seed     --------------------CCAGGCU------------------------------------------------------------------------------     1novel
  lencloning frequencies
   T2S1T2S2T3S1T5S2
      ---------------------------CGGCAGGCTACGTTTACCTC----------------------------------------------------------     20---6
      -----------------------------GCAGGCTACGTTTACCTCAC--------------------------------------------------------     2011--
      -------------------CCCAGGCTCGGCAGGCTACG------------------------------------------------------------------     20--1-
      -------------------------------AGGCTACGTTTACCTCAC--------------------------------------------------------     181---
rat     tgccggtccctttgctagtcccaggctCGGCAGGCTACGTTTACCTCacagcttctcacagagcgaagcgccgcaaagttttgacattttggcaacggagacgca      
      *********************************************************************************************************      
 ................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>ENSRNOT00000060843 ENSRNOG00000001007 Baiap2l1
rat     .((..(((((.(((((((((..(((((((((..(((.(((((..................))))).)))))))...))))).)))....)))))).)).))))).     0.580 -28.47

ratchromosome:12:10584722:10584826:1Same_strand|Boundary_non-coding|ENSRNOT00000001335|ENSRNOG00000001007 ## ENSRNOG00000001007|protein_coding|Baiap2l1|Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 (BAI1-associated protein 2-like protein 1). [Source:UniProtKB/Swiss-Prot;Acc:Q3KR97]


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