logoSmall RNA from different tissues of two rat strains.


miR classification

Alignments

other hairpins

novel_lenNOK_cloningOK_multiarm_loopOverlap_bulgeHIGH (11 loci)

block1848529 [novel_lenNOK_cloningOK_multiarm_loopOverlap_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.121nono0.48/0.7218/22/0.370.3
0.0
2.0
0.5
0.0
0.5
15
1
2
0
0
0
6
1
1
0
0
0
22
30
17
-8
-14
-21
5arm_loop_3arm
5arm_loop_3arm
3arm
1
1
1
nd
nd
nd
0.26
0.33
0.37
4
4
5
306nana
  readsmiRBase family seed
seed------------------------GGUUUAU------------------------------------------18novel
seed-----------------------UGGUUUA-------------------------------------------7novel
seed--------------------------------------GCCUGGG----------------------------1novel
seed--------------------------UUUAUGG----------------------------------------1novel
seed-------------------------------GGUCCCU-----------------------------------1novel
seed------------------GAACUUG------------------------------------------------1novel
seed----------------------------------CCCUGCC--------------------------------1novel
  lencloning frequencies
   T1S1T1S2T4S1T4S2T5S1T5S2
 -----------------------TGGTTTATGGTCCCTGCC--------------------------------18----8-
 -----------------------TGGTTTATGGTCCCTGCCT-------------------------------191--13-
 -----------------------TGGTTTATGGTCCCTGCCTG------------------------------20-21-11
 ----------------------TTGGTTTATGGTCCCTGCCT-------------------------------20----4-
 ----------------------TTGGTTTATGGTCCCTGC---------------------------------18-2----
 -----------------GGAACTTGGTTTATGGTCCCT-----------------------------------21----1-
 ----------------------TTGGTTTATGGTCCCTGCC--------------------------------19----1-
 -------------------------GTTTATGGTCCCTGCCTGG-----------------------------19----1-
 ------------------------------TGGTCCCTGCCTGGGCCT-------------------------18----1-
 -------------------------------------TGCCTGGGCCTTGTGTCTA-----------------19----1-
 ---------------------------------TCCCTGCCTGGGCCTTGTGTCT------------------22----1-
ratcatcctgtgtgctcaggggaacTTGGTTTATGGTCCCTGCCTgggccttgtgtctatccttgggcagctgtgt 
 ************************************************************************* 
rat(((...((.((((((((((.((..((((((.(((....)))))))))..)).....)))))))))))).))).0.990 -24.00

ratchromosome:5:79247435:79247507:1intergenic


sblock12372 [novel_lenNOK_cloningOK_multiarm_loopOverlap_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.047nono0.39/0.5318/24/0.170.5
0.0
0.0
0.3
1.0
0.0
0.0
0.7
4
4
1
3
0
0
0
0
2
2
1
1
0
0
0
0
35
43
34
21
-8
-11
11
22
5arm_loop_3arm
5arm_loop_3arm
3arm
3arm
1
1
1
1
nd
nd
nd
nd
0.26
0.42
0.39
0.44
4
4
5
4
123nana
  readsmiRBase family seed
seed--------------------------------------------GUCAAGG-------------------------------------------------------------------4novel
seed------------------------------------------------------------------------------GUGAAGA---------------------------------2novel
seed------------------------------------AACAAAG---------------------------------------------------------------------------2novel
seed-------------------------------------ACAAAGU--------------------------------------------------------------------------2novel
seed-------------------------------------------------------------------------------UGAAGAA--------------------------------1novel
seed-------------------------------------------------------------------AGCACCA--------------------------------------------1miR-29a/29b/29c
  lencloning frequencies
   T1S1T4S2T5S1
 -------------------------------------------TGTCAAGGCAGTCCCTGAA--------------------------------------------------------19-13
 -----------------------------------------------------------------------------TGTGAAGAACTAAGAAGC-----------------------18--2
 ------------------------------------AACAAAGTGTCAAGGCAGT---------------------------------------------------------------19--2
 ------------------------------------------------------------------TAGCACCACTTTGTGAAG----------------------------------18--1
 ------------------------------------------------------------------------------GTGAAGAACTAAGAAGCCA---------------------19--1
 -----------------------------------TAACAAAGTGTCAAGGCAGT---------------------------------------------------------------20--1
 -----------------------------------TAACAAAGTGTCAAGGCAGTCCCT-----------------------------------------------------------241--
ratggtaagtcaagcgctcatggtcagctatcaagctcTAACAAAGTGTCAAGGCAGTCCCTGAAtccaTAGCACCACTTTGTGAAGAACTAAGAAGCCAaccttgagggaccactcaccc 
 ********************************************************************************************************************** 
rat(((.(((......((((.(((..(((....((.(((.(((((((((((.((....)).)))...........))))))))..))).))....)))..))).)))).....))).))).0.960 -28.00

ratchromosome:9:7094761:7094878:1intergenic


sblock7138 [novel_lenNOK_cloningOK_multiarm_loopOverlap_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.240nono0.50/0.5819/25/0.460.0
1.0
0.0
0.0
2.0
2.2
1
2
9
0
0
0
1
1
2
0
0
0
16
24
34
11
-1
-8
5arm
5arm_loop
3arm_loop
1
1
1
nd
nd
nd
0.36
0.29
0.60
4
4
8
132nana
  readsmiRBase family seed
seed--------------------------------------------------GAGAUCU---------------------------------------------------10novel
seed---------------------------CAACUCU--------------------------------------------------------------------------1novel
seed-----------------AGUCACC------------------------------------------------------------------------------------1novel
seed-------------------------AGCAACU----------------------------------------------------------------------------1novel
  lencloning frequencies
   T1S1T5S1
 -------------------------------------------------TGAGATCTGGGCTGCTCTT----------------------------------------19-4
 -------------------------------------------------TGAGATCTGGGCTGCTCTTAACTCC----------------------------------25-3
 -------------------------------------------------TGAGATCTGGGCTGCTCTTA---------------------------------------2021
 --------------------------GCAACTCTCCAGTCGGAGTGCTCT----------------------------------------------------------24-1
 ----------------CAGTCACCTAGCAACTCTCCAG----------------------------------------------------------------------22-1
 ------------------------TAGCAACTCTCCAGTCGGAGTG--------------------------------------------------------------22-1
ratgggaccaggctgggtccagtcacctagcaactctccagtcggagtgctcTGAGATCTGGGCTGCTCTTAACTCCggccatgagctgggaggcggctgcctcggcaccc 
 ************************************************************************************************************ 
rat(((.....((((((..(((((.(((..((.(((....((((((((((((........))))........))))))))...))).))..))).))))).)))))).)))0.410 -43.70

ratchromosome:20:5540678:5540785:1intergenic


novel_lenNOK_mirtron_randfoldOK_nonpairedHIGH (11 loci)

block25311 [novel_lenNOK_mirtron_randfoldOK_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.006nono0.68/0.6819/19/0.000.0
0.0
2
0
1
0
16
10
3arm
2
4
0.32
3
21nana
  readsmiRBase family seed
seed     -----------------------------------------------------------------CAGCAGC---------------------------     2novel
  lencloning frequencies
   T1S2
      ----------------------------------------------------------------CCAGCAGCCTCCTCACCTG----------------     192
rat     tttgggtctggtgcgggggcctcctgtgtcaacttgctgatcctctcccaccattcagaaggtaCCAGCAGCCTCCTCACCTGccttccctgcccaaaa      
      ***************************************************************************************************      
 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++ENSRNOT00000020818 ENSRNOG00000015430 Nlgn2
 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++ENSRNOT00000056872 ENSRNOG00000015430 Nlgn2
 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++ENSRNOT00000056871 ENSRNOG00000015430 Nlgn2
rat     (((((((..((((.((((((...(((.((..((((.((((..............)))).)))))))))..)))))).))))..........))))))).     0.870 -33.24

ratchromosome:10:56668594:56668692:-1Same_strand|Intronic_coding|ENSRNOT00000056871|ENSRNOG00000015430 ## ENSRNOG00000015430|protein_coding|Nlgn2|Neuroligin-2 precursor. [Source:UniProtKB/Swiss-Prot;Acc:Q62888]


block25369 [novel_lenNOK_mirtron_randfoldOK_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.009nono0.42/0.4219/19/0.000.0
0.0
1
0
1
0
13
21
3arm
1
0
0.32
3
11nana
  readsmiRBase family seed
seed     --------------------------------------------------------------------------GUGCUUC------------------------     1novel
  lencloning frequencies
   T3S2
      -------------------------------------------------------------------------TGTGCTTCATTTTTCCCAG-------------     191
rat     cagccttgggcaaggggcgcagtggagcagaagggacgtcactggggtgatgaccactggtggtattctctccTGTGCTTCATTTTTCCCAGcttctcaagctgg      
      *********************************************************************************************************      
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>ENSRNOT00000021357 ENSRNOG00000015674 NP_001099266.1
rat     (((.((((((.((((((...(((((((((((..(((..((((((((((....))).)))))))..)))..))...)))))))))...)))..)))))))))))).     0.790 -43.00

ratchromosome:10:56735608:56735712:-1Same_strand|Intronic_coding|ENSRNOT00000021357|ENSRNOG00000015674 ## ENSRNOG00000015674|protein_coding|NP_001099266.1|centaurin, beta 1 [Source:RefSeq_peptide;Acc:NP_001099266]


block52862 [novel_lenNOK_mirtron_randfoldOK_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.004nono0.42/0.4319/23/0.500.5
1.5
2
0
1
0
23
2
3arm
1
1
0.37
3
21nana
  readsmiRBase family seed
seed     -------------------------------------------------------ACUAAAU--------------------------------------     1novel
seed     --------------------------------------------------------CUAAAUG-------------------------------------     1novel
  lencloning frequencies
   T3S2
      ------------------------------------------------------GACTAAATGAGCTCTGTTCCCTA-----------------------     231
      -------------------------------------------------------ACTAAATGAGCTCTGTTCC--------------------------     191
rat     aggagccgaagggctcttagctcagaagggatgggacacatagaatataatagtGACTAAATGAGCTCTGTTCCCTAggcatggagtcctgtggcatcca      
      ****************************************************************************************************      
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>ENSRNOT00000054976 ENSRNOG00000036701 Actg1
rat     .(((((((.((((((((..(((....(((((.(((.((..(((.((......))..)))..))..)))...))))).)))..)))))))).)))).))).     0.910 -35.70

ratchromosome:10:109774600:109774699:-1Same_strand|Intronic_coding|ENSRNOT00000054976|ENSRNOG00000036701 ## ENSRNOG00000036701|protein_coding|Actg1|Actin, cytoplasmic 2 (Gamma-actin). [Source:UniProtKB/Swiss-Prot;Acc:P63259]


block80333 [novel_lenNOK_mirtron_randfoldOK_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.006nono0.61/0.6118/18/0.000.0
0.0
1
0
1
0
25
4
5arm
1
3
0.33
3
11nana
  readsmiRBase family seed
seed     --------------------------GCUGUGA----------------------------------------------------------------------------------     1novel
  lencloning frequencies
   T4S1
      -------------------------TGCTGTGAGTATCCCCCC------------------------------------------------------------------------     181
rat     ttggttctgggctggcgctcatgggTGCTGTGAGTATCCCCCCtgccttgctggtttcctagggagagggaagtcactaactgcctgtgaggagcatgctgagcccagaacacag      
      *******************************************************************************************************************      
 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ENSRNOT00000026156 ENSRNOG00000019208 P2rx5
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ENSRNOT00000056463 ENSRNOG00000019208 P2rx5
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ENSRNOT00000056462 ENSRNOG00000019208 P2rx5
rat     .(((((((((((((((((((((((((...((((...(((((((((((.....))).....))))...))))..)))).....))))))))).....)))).)))))))))).)).     0.940 -50.50

ratchromosome:10:60043212:60043326:1Same_strand|Intronic_coding|ENSRNOT00000056463|ENSRNOG00000019208 ## Same_strand|Boundary_coding|ENSRNOT00000026156|ENSRNOG00000019208 ## ENSRNOG00000019208|protein_coding|P2rx5|P2X purinoceptor 5 (ATP receptor) (P2X5) (Purinergic receptor). [Source:UniProtKB/Swiss-Prot;Acc:P51578]


block221554 [novel_lenNOK_mirtron_randfoldOK_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.005nono0.72/0.7218/18/0.000.0
0.0
1
0
1
0
7
17
5arm
2
4
0.33
2
11nana
  readsmiRBase family seed
seed     --------GGGGGUU------------------------------------------------------------------------     1novel
  lencloning frequencies
   T4S2
      -------GGGGGGTTGGGGGGGTTT--------------------------------------------------------------     181
rat     tgctgggGGGGGGTTGGGGGGGTTTgttttgttgttttgttttaggtgggtgggggtgggagggccatctcttcactctgcttcagt      
      ***************************************************************************************      
 -------------------------------------------------------------------------------------------------ENSRNOT00000059227 ENSRNOG00000001457 Rfc2
 ++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>ENSRNOT00000001996 ENSRNOG00000001470 Limk1
rat     .(((((((.((((.((..(((((..(((((.((..((..(((.....)))..))...)).))))).)))))..)))))).)))))))     0.950 -25.80

ratchromosome:12:23125457:23125543:1Opposite_strand|Boundary_non-coding|ENSRNOT00000001989|ENSRNOG00000001457 ## Same_strand|Boundary_non-coding|ENSRNOT00000001996|ENSRNOG00000001470 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000059227|ENSRNOG00000001457 ## ENSRNOG00000001457|protein_coding|Rfc2|replication factor C 2 [Source:RefSeq_peptide;Acc:NP_446238] ## ENSRNOG00000001470|protein_coding|Limk1|LIM domain kinase 1 (EC 2.7.11.1) (LIMK-1). [Source:UniProtKB/Swiss-Prot;Acc:P53669] ## {Repeats: dust 23125461 23125476 0 class=dust}


block266957 [novel_lenNOK_mirtron_randfoldOK_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.004nono0.26/0.2619/19/0.000.0
0.0
1
0
1
0
31
0
3arm
1
4
0.32
3
11nana
  readsmiRBase family seed
seed     -------------------------------------------------------------AAAGGUA------------------------------------------     1novel
  lencloning frequencies
   T5S1
      ------------------------------------------------------------TAAAGGTAAAAATTTCCAG-------------------------------     191
rat     tgcaggtcctgagatatttcgactatgttttcacaggagtgtttacctttgagatggtgaTAAAGGTAAAAATTTCCAGagaaaatatgggatctggatttcagttgtat      
      **************************************************************************************************************      
 ++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++ENSRNOT00000003869 ENSRNOG00000002863 Cacna1e
 ++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++ENSRNOT00000003928 ENSRNOG00000002863 Cacna1e
rat     (((((...(((((((.......((((((((((...((((..((((((((((.........))))))))))...))))...)))))))))).......)))))))))))).     0.940 -31.84

ratchromosome:13:69433026:69433135:-1Same_strand|Boundary_coding|ENSRNOT00000003869|ENSRNOG00000002863 ## ENSRNOG00000002863|protein_coding|Cacna1e|Voltage-dependent R-type calcium channel subunit alpha-1E (Voltage- gated calcium channel subunit alpha Cav2.3) (Calcium channel, L type, alpha-1 polypeptide, isoform 6) (RBE-II) (RBE2) (Brain calcium channel II) (BII). [Source:UniProtKB/Swiss-Prot;Acc:Q07652]


block848738 [novel_lenNOK_mirtron_randfoldOK_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.010nono0.53/0.5319/19/0.000.0
0.0
1
0
1
0
13
26
3arm
1
3
0.37
3
11nana
  readsmiRBase family seed
seed     ------------------------------------------------------------------------------------CCUGAGC------------------------     1novel
  lencloning frequencies
   T3S1
      -----------------------------------------------------------------------------------ACCTGAGCTTCTTCTCTCC-------------     191
rat     tctggagttcagagaagggttcttggcttgacagcatccatgcagtgtcctcagttcctagcttttgggtgttatcagaaccaACCTGAGCTTCTTCTCTCCcagaaaacccaga      
      *******************************************************************************************************************      
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>ENSRNOT00000019934 ENSRNOG00000014667 Dll1
rat     (((((..(((((((((((((((((((.((((.((((((((.((((............)).))...)))))))).))))..))))...))))).)))))))....)))...)))))     0.990 -36.50

ratchromosome:1:54246371:54246485:-1Same_strand|Intronic_coding|ENSRNOT00000019934|ENSRNOG00000014667 ## ENSRNOG00000014667|protein_coding|Dll1|Delta-like protein 1 precursor (Drosophila Delta homolog 1) (Delta1). [Source:UniProtKB/Swiss-Prot;Acc:P97677]


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