logoSmall RNA from different tissues of two rat strains.


miR classification

Alignments

other hairpins

novel_lenNOK_cloningOK_multiarm_DicerOK_5varHIGH_loopOverlap_bulgeHIGH (3 loci)

novel_lenNOK_cloningOK_multiarm_loopOverlap_randfoldOK (3 loci)

block2312064 [novel_lenNOK_cloningOK_multiarm_loopOverlap_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.002nono0.37/0.5219/26/0.620.3
0.0
0.0
0.0
0.3
0.0
13
3
1
0
0
0
5
1
1
0
0
0
38
27
22
-19
-1
11
5arm_loop_3arm
3arm
3arm
1
1
1
nd
nd
nd
0.53
0.28
0.42
4
3
7
265nana
  readsmiRBase family seed
seed-------------------------------------------CCCACAA--------------------------------------------------14novel
seed--------------------------------------------CCACAAC-------------------------------------------------4novel
seed------------------------------------------------AACUCAG---------------------------------------------3novel
seed------------------------------------------UCCCACA---------------------------------------------------2novel
seed------------------------------------------------------------UGCUCCA---------------------------------1novel
seed----------------------------------------GUUCCCA-----------------------------------------------------1novel
seed---------------------------------------UGUUCCC------------------------------------------------------1novel
  lencloning frequencies
   T1S2T2S1T3S2T5S1T5S2
 ------------------------------------------TCCCACAACTCAGTAAATTG--------------------------------------2011191
 -------------------------------------------CCCACAACTCAGTAAATTG--------------------------------------19---4-
 -----------------------------------------------CAACTCAGTAAATTGCTCCAGCCCCT---------------------------26---2-
 -----------------------------------------TTCCCACAACTCAGTAAAT----------------------------------------19---2-
 -----------------------------------------------CAACTCAGTAAATTGCTCCAGCCCC----------------------------25---1-
 ------------------------------------------TCCCACAACTCAGTAAATTGCTCC----------------------------------24---1-
 ---------------------------------------TGTTCCCACAACTCAGTAAATTG--------------------------------------23---1-
 -----------------------------------------------------------TTGCTCCAGCCCCTTTTTA----------------------19---1-
 --------------------------------------TTGTTCCCACAACTCAGTAAATTG--------------------------------------24---1-
rattagggatgggttttgctggggctggacctccccaaggcttgtTCCCACAACTCAGTAAATTGctccagcccctttttatgctttacccagcacctccctc 
 **************************************************************************************************** 
rat.((((((((((...((.(((((((((......(((.(((.(((.....)))..)))...))).))))))))).......))...))))).....))))).0.410 -33.60

ratchromosome:8:57742640:57742739:-1intergenic


sblock9740 [novel_lenNOK_cloningOK_multiarm_loopOverlap_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.003nono0.45/0.7018/23/0.450.0
0.0
0.0
0.0
0.0
0.0
1
1
7
0
0
0
1
1
5
0
0
0
0
6
41
28
19
-12
5arm
5arm
3arm_loop
1
1
1
nd
nd
nd
0.40
0.22
0.37
7
3
5
205nana
  readsmiRBase family seed
seed------------------------------------------CCUCAUU-------------------------------------------15novel
seed---------------------------------------------CAUUGUC----------------------------------------1novel
seed-CACCACC------------------------------------------------------------------------------------1novel
seed-------CGUGCAC------------------------------------------------------------------------------1novel
seed-------------------------------------------------GUCAGUG------------------------------------1novel
seed-----------------------------------------UCCUCAU--------------------------------------------1novel
  lencloning frequencies
   T1S1T1S2T2S2T3S2T5S1
 -----------------------------------------TCCTCATTGTCAGTGGTGA--------------------------------1921--7
 -----------------------------------------TCCTCATTGTCAGTGGTGAA-------------------------------20-1-1-
 -----------------------------------------TCCTCATTGTCAGTGGTGAAG------------------------------21--1--
 -----------------------------------------TCCTCATTGTCAGTGGTGAAGCT----------------------------23----1
 -----------------------------------------TCCTCATTGTCAGTGGTGAAGC-----------------------------22----1
 ------CCGTGCACTGTGTGGCCTGGACC---------------------------------------------------------------23----1
 TCACCACCGTGCACTGTGTG------------------------------------------------------------------------20----1
 ------------------------------------------------TGTCAGTGGTGAAGCTGC--------------------------181----
 --------------------------------------------TCATTGTCAGTGGTGAAGCT----------------------------20----1
 ----------------------------------------TTCCTCATTGTCAGTGGTGAAGC-----------------------------23----1
rattcaccaccgtgcactgtgtggcctggacctcctgccaccctTCCTCATTGTCAGTGGTGAagctgctggaggaaaggccacactgggttcac 
 ******************************************************************************************** 
rat........(((.((((((((((((...(((((.((....((((.((((.....)))).))))..)).)))))..)))))))))..))).)))0.990 -38.70

ratchromosome:5:79247627:79247718:1intergenic


sblock9742 [novel_lenNOK_cloningOK_multiarm_loopOverlap_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.001nono0.52/0.6519/25/0.330.0
0.0
0.0
0.0
0.0
2.3
0.0
0.0
2
3
1
4
0
0
0
0
1
2
1
2
0
0
0
0
29
38
11
4
10
-4
23
30
5arm
5arm_loop_3arm
3arm
3arm
1
1
1
1
nd
nd
nd
nd
0.60
0.30
0.26
0.26
7
4
3
3
123nana
  readsmiRBase family seed
seed----------------------------------------------------------------------------------------------ACAGCAC---------------5novel
seed---------------------------------------GAGAGCC----------------------------------------------------------------------3novel
seed------------------------------GGCAGCA-------------------------------------------------------------------------------2novel
seed-------------------------------------------------------------------------------------------CCUACAG------------------1novel
seed---------------------------------------------------------------------------------------GCCUCCU----------------------1novel
  lencloning frequencies
   T1S2T2S2T5S1
 ---------------------------------------------------------------------------------------------TACAGCACACAGCTGCCAG----191-4
 -----------------------------GGGCAGCACTGAGAGCCACT-------------------------------------------------------------------20--2
 --------------------------------------------------------------------------------------TGCCTCCTACAGCACACAG-----------19--1
 ------------------------------------------------------------------------------------------TCCTACAGCACACAGCTGCCAG----22--1
 --------------------------------------TGAGAGCCACTTCCCTTGAC----------------------------------------------------------20-1-
 --------------------------------------TGAGAGCCACTTCCCTTGACTGAGT-----------------------------------------------------25--1
 --------------------------------------TGAGAGCCACTTCCCTTGA-----------------------------------------------------------19--1
ratggggctgggcaaggtgctgtggagcagcaGGGCAGCACTGAGAGCCACTtcccttgactgagtggacaaggggcagcctccctttctgcctccTACAGCACACAGCTGCCAGccct 
 ******************************************************************************************************************** 
rat((((((((((...((((((((((((((.((((.......(((.((....(((((((.((....)).)))))))..))))))))).)))).))).)))))))...))..))))))))0.480 -56.41

ratchromosome:5:79248478:79248593:1intergenic


novel_lenNOK_cloningOK_multiarm_nonpairedHIGH (3 loci)

sblock12426 [novel_lenNOK_cloningOK_multiarm_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.484nono0.50/0.6718/19/0.000.0
0.0
0.2
0.0
12
1
0
0
3
1
0
0
8
37
14
-11
5arm
3arm_loop
2
2
nd
nd
0.42
0.67
3
10
164nana
  readsmiRBase family seed
seed---------CUCUGGG------------------------------------------------------------------------------------15miR-326/330
seed----------------------------------------------UUUCUGA-----------------------------------------------1novel
  lencloning frequencies
   T1S1T1S2T3S1T5S1
 --------CCTCTGGGCCCTTCCTTGT-------------------------------------------------------------------------1964-1
 --------CCTCTGGGCCCTTCCTTG--------------------------------------------------------------------------1821-1
 ---------------------------------------------CTTTCTGATTTGGGCTGG-------------------------------------18--1-
ratactgtccaCCTCTGGGCCCTTCCTTGTatcatcagtttcccttacctttctgatttgggctggttgatgatgacccagtgagagcgagtgtaagagacag 
 **************************************************************************************************** 
rat.(((((.(((((...((.((..((..(((((((((((.(((...............)))..)))))))))))....))..)).))))).))....)))))0.890 -24.76

ratchromosome:9:41763377:41763476:1intergenic


sblock4198 [novel_lenNOK_cloningOK_multiarm_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.248nono0.32/0.3918/19/0.000.0
0.0
0.0
0.0
21
1
0
0
3
1
0
0
31
8
5
25
5arm
3arm
1
1
nd
nd
0.39
0.39
3
4
234nana
  readsmiRBase family seed
seed--------------------------------CUUUAGA------------------------------------------------------------------------22novel
seed--------------------------------------------------------------------------------------GAAGUAG------------------1novel
  lencloning frequencies
   T1S1T1S2T4S2T5S2
 -------------------------------TCTTTAGAATGTGGAAGT--------------------------------------------------------------184512-
 -------------------------------------------------------------------------------------TGAAGTAGAGGTTTGAAG--------18---1
 -------------------------------TCTTTAGAATGTGGAAGTT-------------------------------------------------------------19--1-
ratagtgactcaataggaacaatcattttgggagTCTTTAGAATGTGGAAGTtgtgtgtagtgattcaaagtcacaaatgagctcttctgaagtagaggtttgaaggaagttat 
 *************************************************************************************************************** 
rat.(((((((.....((((..((((((..((((..((((...(((((...(((.((......)).)))..)))))..))))..))))..)))).)).))))....)).)))))0.970 -22.30

ratchromosome:14:15596630:15596740:1intergenic


sblock5704 [novel_lenNOK_cloningOK_multiarm_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.660nono0.22/0.4218/20/0.080.4
0.0
0.0
0.0
9
1
0
0
2
1
0
0
5
36
33
-2
5arm
3arm_loop
1
1
nd
nd
0.53
0.32
4
2
122nana
  readsmiRBase family seed
seed------UAAAGCU------------------------------------------------------------------------------------------------------6miR-9*
seed-------AAAGCUA-----------------------------------------------------------------------------------------------------5novel
seed-------------------------------------------------------------UGGGUUU-----------------------------------------------1novel
  lencloning frequencies
   T1S1T1S2
 ------TAAAGCTAGAATTAAAGG-------------------------------------------------------------------------------------------18-5
 -----TTAAAGCTAGAATTAAAGG-------------------------------------------------------------------------------------------1922
 ------------------------------------------------------------TTGGGTTTGGCTAAATCGT------------------------------------19-1
 -----TTAAAGCTAGAATTAAAG--------------------------------------------------------------------------------------------18-1
 -----TTAAAGCTAGAATTAAAGGT------------------------------------------------------------------------------------------201-
rataagagTTAAAGCTAGAATTAAAGGttggatacgcacgggattggtaaggctgaacttcagttgggtttggctaaatcgtatcatagcttcaccatccattcatgcaagggacctt 
 ******************************************************************************************************************* 
rat(((.(((...((..((((....((.(((....((....(((((((..(((..(((((.....)))))..)))..)))).)))...))....))).))))))..))....))))))0.490 -24.30

ratchromosome:18:75316334:75316448:1intergenic


novel_lenNOK_cloningOK_multiarm_shortStem (3 loci)

sblock2485 [novel_lenNOK_cloningOK_multiarm_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.296nono0.33/0.5618/18/0.000.0
0.0
0.0
0.0
18
1
0
0
2
1
0
0
1
32
36
8
5arm
3arm
1
1
nd
nd
0.22
0.17
3
2
193nana
  readsmiRBase family seed
seed--UUCCGUU------------------------------------------------------------------------------------------------------------18novel
seed--------------------------------------------------------------------UCCUUGC------------------------------------------1novel
  lencloning frequencies
   T2S1T4S1T4S2
 -TTTCCGTTAAAGAAGGAA--------------------------------------------------------------------------------------------------18-513
 -------------------------------------------------------------------TTCCTTGCCCGGTGCTTT--------------------------------181--
ratgTTTCCGTTAAAGAAGGAAggttgggccttagagaacagaggcgaaggagagtagattcctgagcatttccttgcccggtgctttgcagtgtctttttcccctccaagatggtaaac 
 ********************************************************************************************************************* 
rat(((((((((...((.((((((..(((((((((((.((...(((.(((((((.(((....)))....))))))))))..)).))))).)).))))))))))..))...))))).))))0.990 -33.30

ratchromosome:10:89582426:89582542:-1intergenic


sblock7889 [novel_lenNOK_cloningOK_multiarm_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.127nono0.33/0.3918/18/0.000.0
0.0
0.0
0.0
1
11
0
0
1
6
0
0
22
1
-3
21
5arm_loop
3arm
2
2
nd
nd
0.44
0.28
4
2
166nana
  readsmiRBase family seed
seed------------------------------------------------------------------UUUCCAA-----------15novel
seed-----------------------UUCCACA------------------------------------------------------1novel
  lencloning frequencies
   T1S1T2S1T3S1T3S2T4S2T5S2
 -----------------------------------------------------------------CTTTCCAATTAGCACTTG-18511116
 ----------------------TTTCCACATCCACAAATA--------------------------------------------181-----
ratgcaggctaccctggaataaagttttccacatccacaaataaagcttgaggaaatgctacaaaatcCTTTCCAATTAGCACTTGc 
 ************************************************************************************ 
rat((((((((...(((((....(((((.((..(((.(((.......))).)))..))....)))))...)))))..)))).)).))0.600 -14.30

ratchromosome:3:45835263:45835346:1intergenic


sblock9087 [novel_lenNOK_cloningOK_multiarm_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.159nono0.25/0.5618/24/0.240.0
0.0
1.0
0.0
0.0
0.0
0.0
0.0
0.0
0.2
0.0
0.0
0.0
0.0
14
1
4
1
1
1
1
0
0
0
0
0
0
0
3
1
1
1
1
1
1
0
0
0
0
0
0
0
4
16
46
36
24
8
0
29
16
-20
4
12
33
41
5arm
5arm
3arm_loop
3arm
3arm
3arm
3arm
1
1
1
1
1
1
2
nd
nd
nd
nd
nd
nd
nd
0.26
0.35
0.46
0.47
0.39
0.28
0.47
2
5
7
6
4
2
3
253nana
  readsmiRBase family seed
seed-----AGCAAUC----------------------------------------------------------------------------------------------------------16novel
seed-----------------------------------------------------AAAUCUA----------------------------------------------------------3novel
seed-----------------------------------------------------------------------------------------------------AGCUUUG----------1novel
seed---------------------------------------------------------------------------------------------AUGGUGA------------------1novel
seed-------------------------------------------------CGUUAAA--------------------------------------------------------------1novel
seed----------------------------------------------------------------AUCUCAG-----------------------------------------------1novel
seed-----------------UCCAUAU----------------------------------------------------------------------------------------------1novel
seed------------------------------------------------------------------------AUCAGCA---------------------------------------1novel
  lencloning frequencies
   T1S1T1S2T5S1
 ----TAGCAATCCTCTTTCCATA-----------------------------------------------------------------------------------------------191-14
 ----------------------------------------------------TAAATCTATGATATCTCAGT----------------------------------------------20--2
 ----------------------------------------------------TAAATCTATGATATCTCAG-----------------------------------------------19--1
 ---------------------------------------------------------------TATCTCAGTATCAGCACCA------------------------------------19--1
 ------------------------------------------------TCGTTAAATCTATGATATCTCAGT----------------------------------------------24--1
 ----TAGCAATCCTCTTTCCATAT----------------------------------------------------------------------------------------------20-1-
 ----------------TTCCATATATGATGCACCAT----------------------------------------------------------------------------------20--1
 --------------------------------------------------------------------------------------------TATGGTGATAGCTTTGTC--------18--1
 ----------------------------------------------------------------------------------------------------TAGCTTTGTCTCCCCACC181--
 -----------------------------------------------------------------------TATCAGCACCATATTGGAGCATA------------------------23--1
rataggtTAGCAATCCTCTTTCCATAtatgatgcaccatgggcgtgggctgtcgttaaatctatgatatctcagtatcagcaccatattggagcatatggtgatagctttgtctccccacc 
 ********************************************************************************************************************** 
rat.((..(((((..((.((.(((((.....(((.((((((((.((((.((((((.......)))))).))))......)).)))...))).)))))))).)).))..))).))..))...0.460 -29.30

ratchromosome:4:164256481:164256598:1intergenic


novel_lenNOK_gcHIGH_loopOverlap_randfoldOK (3 loci)

block87333 [novel_lenNOK_gcHIGH_loopOverlap_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.002nono0.94/0.9418/18/0.000.0
0.0
1
0
1
0
16
-2
3arm_loop
1
nd
0.28
2
11nana
  readsmiRBase family seed
seed     ----------------------------------AGGCGCC--------------------------     1novel
  lencloning frequencies
   T4S2
      ---------------------------------GAGGCGCCCCCCGGGGCC----------------     181
rat     cgtgccctccccctccagccccgggcggcccgcGAGGCGCCCCCCGGGGCCtcttaaagagacacgc      
      *******************************************************************      
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ENSRNOT00000004698 ENSRNOG00000003517 Tbx2
rat     ((((..(((........((((((((.(((((....)).))).))))))))........))).)))).     0.930 -37.29

ratchromosome:10:74082257:74082323:1Same_strand|Boundary_non-coding|ENSRNOT00000055832|ENSRNOG00000003517 ## Same_strand|Intronic_coding|ENSRNOT00000004698|ENSRNOG00000003517 ## ENSRNOG00000003517|protein_coding|Tbx2|T-box 2 Gene [Source:MGI (curated);Acc:Tbx2-001] ## {Repeats: GC_rich 1 34 1 class=Low_complexity,GC_rich 16 34 1 class=Low_complexity} ## {SimpF: oe = 0.72 1 CpG}


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