logoSmall RNA from different tissues of two rat strains.


miR classification

Alignments

other hairpins

novel_lenNOK_Multihit_loopOverlap_randfoldOK_bulgeHIGH (18 loci)

block963058 [novel_lenNOK_Multihit_loopOverlap_randfoldOK_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.001nono0.40/0.4719/20/0.250.8
0.5
4
0
1
0
22
-2
3arm_loop
20
nd
0.26
4
41nana
  readsmiRBase family seed
seed     -------------------------------------------------GCAGAAC---------------------------------     3novel
seed     ----------------------------------------------AUUGCAG------------------------------------     1novel
  lencloning frequencies
   T5S1
      ------------------------------------------------TGCAGAACCTACAGTGTTG----------------------     193
      ---------------------------------------------TATTGCAGAACCTACAGTGT------------------------     201
rat     tctgttgatgcaggatctccactttcactgttctagcaaaccaacTATTGCAGAACCTACAGTGTTGgaacaactgcattgtatcagga      
      *****************************************************************************************      
 ---------------------------------------------------------------------------------------------------ENSRNOT00000059938 ENSRNOG00000039174 RGD1563865_predicted
rat     ((((.((((((((....((((....(((((((((.((((........)))))))....)))))).))))....))))))))...)))).     1.000 -28.40

ratchromosome:1:51600640:51600728:1Opposite_strand|Boundary_non-coding|ENSRNOT00000059936|ENSRNOG00000039174 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000059938|ENSRNOG00000039174 ## ENSRNOG00000039174|protein_coding|RGD1563865_predicted|


block963957 [novel_lenNOK_Multihit_loopOverlap_randfoldOK_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.001nono0.40/0.4719/20/0.250.8
0.5
4
0
1
0
22
-2
3arm_loop
20
nd
0.26
4
41nana
  readsmiRBase family seed
seed     -------------------------------------------------GCAGAAC---------------------------------     3novel
seed     ----------------------------------------------AUUGCAG------------------------------------     1novel
  lencloning frequencies
   T5S1
      ------------------------------------------------TGCAGAACCTACAGTGTTG----------------------     193
      ---------------------------------------------TATTGCAGAACCTACAGTGT------------------------     201
rat     tctgttgatgcaggatctccactttcactgttctagcaaaccaacTATTGCAGAACCTACAGTGTTGgaacaactgcattgtatcagga      
      *****************************************************************************************      
 ---------------------------------------------------------------------------------------------------ENSRNOT00000048246 ENSRNOG00000039174 RGD1563865_predicted
rat     ((((.((((((((....((((....(((((((((.((((........)))))))....)))))).))))....))))))))...)))).     1.000 -28.40

ratchromosome:1:52003428:52003516:1Opposite_strand|Boundary_non-coding|ENSRNOT00000059936|ENSRNOG00000039174 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000048246|ENSRNOG00000039174 ## ENSRNOG00000039174|protein_coding|RGD1563865_predicted|


block964157 [novel_lenNOK_Multihit_loopOverlap_randfoldOK_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.001nono0.40/0.4719/20/0.250.8
0.5
4
0
1
0
22
-2
3arm_loop
20
nd
0.26
4
41nana
  readsmiRBase family seed
seed     -------------------------------------------------GCAGAAC---------------------------------     3novel
seed     ----------------------------------------------AUUGCAG------------------------------------     1novel
  lencloning frequencies
   T5S1
      ------------------------------------------------TGCAGAACCTACAGTGTTG----------------------     193
      ---------------------------------------------TATTGCAGAACCTACAGTGT------------------------     201
rat     tctgttgatgcaggatctccactttcactgttctagcaaaccaacTATTGCAGAACCTACAGTGTTGgaacaactgcattgtatcagga      
      *****************************************************************************************      
 ---------------------------------------------------------------------------------------------------ENSRNOT00000048246 ENSRNOG00000039174 RGD1563865_predicted
rat     ((((.((((((((....((((....(((((((((.((((........)))))))....)))))).))))....))))))))...)))).     1.000 -28.40

ratchromosome:1:52047802:52047890:1Opposite_strand|Boundary_non-coding|ENSRNOT00000059936|ENSRNOG00000039174 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000048246|ENSRNOG00000039174 ## ENSRNOG00000039174|protein_coding|RGD1563865_predicted|


block964389 [novel_lenNOK_Multihit_loopOverlap_randfoldOK_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.007nono0.40/0.4719/20/0.250.8
0.5
4
0
1
0
35
-2
3arm_loop
20
nd
0.26
4
41nana
  readsmiRBase family seed
seed     --------------------------------------------------------------GCAGAAC----------------------------------------------     3novel
seed     -----------------------------------------------------------AUUGCAG-------------------------------------------------     1novel
  lencloning frequencies
   T5S1
      -------------------------------------------------------------TGCAGAACCTACAGTGTTG-----------------------------------     193
      ----------------------------------------------------------TATTGCAGAACCTACAGTGT-------------------------------------     201
rat     ctgtcaaaggacctctgttgatgcgggatctccactttcactgttctagcaaaccaacTATTGCAGAACCTACAGTGTTGgaacaactgcattgtatcaggacatttactttgca      
      *******************************************************************************************************************      
 -----------------------------------------------------------------------------------------------------------------------------ENSRNOT00000048246 ENSRNOG00000039174 RGD1563865_predicted
rat     .((.(((((....((((.((((((((....((((....(((((((((.((((........)))))))....)))))).))))....))))))))...)))).......)))))))     0.960 -31.00

ratchromosome:1:52235128:52235242:1Opposite_strand|Boundary_non-coding|ENSRNOT00000059936|ENSRNOG00000039174 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000048246|ENSRNOG00000039174 ## ENSRNOG00000039174|protein_coding|RGD1563865_predicted|


block964936 [novel_lenNOK_Multihit_loopOverlap_randfoldOK_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.005nono0.40/0.4719/20/0.250.8
0.5
4
0
1
0
22
-2
3arm_loop
20
nd
0.26
4
41nana
  readsmiRBase family seed
seed     -------------------------------------------------GCAGAAC---------------------------------     3novel
seed     ----------------------------------------------AUUGCAG------------------------------------     1novel
  lencloning frequencies
   T5S1
      ------------------------------------------------TGCAGAACCTACAGTGTTG----------------------     193
      ---------------------------------------------TATTGCAGAACCTACAGTGT------------------------     201
rat     tctgttgatgcgggatctccactttcactgttctagcaaaccaacTATTGCAGAACCTACAGTGTTGgaacaactgcattgtatcagga      
      *****************************************************************************************      
 ---------------------------------------------------------------------------------------------------ENSRNOT00000059909 ENSRNOG00000030267 RGD1561185_predicted
rat     ((((.((((((((....((((....(((((((((.((((........)))))))....)))))).))))....))))))))...)))).     1.000 -27.70

ratchromosome:1:52651328:52651416:1Opposite_strand|Boundary_non-coding|ENSRNOT00000048991|ENSRNOG00000030267 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000059909|ENSRNOG00000030267 ## ENSRNOG00000030267|protein_coding|RGD1561185_predicted|


block965207 [novel_lenNOK_Multihit_loopOverlap_randfoldOK_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.002nono0.40/0.4719/20/0.250.8
0.5
4
0
1
0
22
-2
3arm_loop
20
nd
0.21
4
41nana
  readsmiRBase family seed
seed     -------------------------------------------------GCAGAAC---------------------------------     3novel
seed     ----------------------------------------------AUUGCAG------------------------------------     1novel
  lencloning frequencies
   T5S1
      ------------------------------------------------TGCAGAACCTACAGTGTTG----------------------     193
      ---------------------------------------------TATTGCAGAACCTACAGTGT------------------------     201
rat     tctgttgatgcaggatctccacttacactgttctagcaaaccaacTATTGCAGAACCTACAGTGTTGgaacaactgcattgtatcagga      
      *****************************************************************************************      
 ---------------------------------------------------------------------------------------------------ENSRNOT00000059909 ENSRNOG00000030267 RGD1561185_predicted
 ---------------------------------------------------------------------------------------------------ENSRNOT00000059908 ENSRNOG00000030267 RGD1561185_predicted
rat     ((((.((((((((....((((...((((((((((.((((........)))))))....)))))))))))....))))))))...)))).     1.000 -29.70

ratchromosome:1:52751927:52752015:1Opposite_strand|Intronic_non-coding|ENSRNOT00000059908|ENSRNOG00000030267 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000048991|ENSRNOG00000030267 ## ENSRNOG00000030267|protein_coding|RGD1561185_predicted|


block965453 [novel_lenNOK_Multihit_loopOverlap_randfoldOK_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.001nono0.40/0.4719/20/0.250.8
0.5
4
0
1
0
22
-2
3arm_loop
20
nd
0.26
4
41nana
  readsmiRBase family seed
seed     -------------------------------------------------GCAGAAC---------------------------------     3novel
seed     ----------------------------------------------AUUGCAG------------------------------------     1novel
  lencloning frequencies
   T5S1
      ------------------------------------------------TGCAGAACCTACAGTGTTG----------------------     193
      ---------------------------------------------TATTGCAGAACCTACAGTGT------------------------     201
rat     tctgttgatgcaggatctccactttcactgttctagcaaaccaacTATTGCAGAACCTACAGTGTTGgaacaactgcattgtatcagga      
      *****************************************************************************************      
 ---------------------------------------------------------------------------------------------------ENSRNOT00000059908 ENSRNOG00000030267 RGD1561185_predicted
rat     ((((.((((((((....((((....(((((((((.((((........)))))))....)))))).))))....))))))))...)))).     1.000 -28.40

ratchromosome:1:52820180:52820268:1Opposite_strand|Intronic_non-coding|ENSRNOT00000059908|ENSRNOG00000030267 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000059909|ENSRNOG00000030267 ## ENSRNOG00000030267|protein_coding|RGD1561185_predicted|


block965659 [novel_lenNOK_Multihit_loopOverlap_randfoldOK_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.001nono0.40/0.4719/20/0.250.8
0.5
4
0
1
0
24
-2
3arm_loop
20
nd
0.21
4
41nana
  readsmiRBase family seed
seed-----------------------------------------------------GCAGAAC-----------------------------------3novel
seed--------------------------------------------------AUUGCAG--------------------------------------1novel
  lencloning frequencies
   T5S1
 ----------------------------------------------------TGCAGAACCTACAGTGTTG------------------------193
 -------------------------------------------------TATTGCAGAACCTACAGTGT--------------------------201
ratgacctctgttgatgcaggatctccacttacactgttctagcaaaccaacTATTGCAGAACCTACAGTGTTGgaacaactgcattgtatcaggtca 
 *********************************************************************************************** 
rat(((((....((((((((....((((...((((((((((.((((........)))))))....)))))))))))....))))))))....))))).1.000 -34.40

ratchromosome:1:52863794:52863888:1intergenic


novel_lenNOK_cloningHIGH_multiarm_DicerNOK_loopOverlap (18 loci)

block1671650 [novel_lenNOK_cloningHIGH_multiarm_DicerNOK_loopOverlap]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.521nono0.26/0.4718/25/0.150.0
0.0
0.0
0.0
1.0
0.0
0.0
0.0
2
35
1
1
0
0
0
0
2
4
1
1
0
0
0
0
26
28
20
15
-2
-5
2
8
5arm_loop
3arm_loop
3arm
3arm
3
4
4
4
nd
nd
nd
nd
0.17
0.37
0.35
0.42
1
4
4
5
59500
  readsmiRBase family seed
seed--------------------------------------------------GUGAAAU---------------------------------------43novel
seed---------------------------------GGACUUA--------------------------------------------------------4novel
seed---------------------------------------ACGUUGU--------------------------------------------------3novel
seed--------------------------------------------GUUAAUG---------------------------------------------2novel
seed---------------------------GAGUGUG--------------------------------------------------------------2novel
seed---------------------------------------------------------GUGAAUG--------------------------------1novel
seed-------------------------------------------------UGUGAAA----------------------------------------1novel
seed---------------------------------------------------------------GUUGGCC--------------------------1novel
seed----------------------------------------------------GAAAUGU-------------------------------------1novel
seed---------------------------------------------------UGAAAUG--------------------------------------1miR-203
  lencloning frequencies
   T1S1T1S2T3S1T4S1T5S1
 -------------------------------------------------TGTGAAATGTGAATGTTGG----------------------------192-1135
 -------------------------------------------------TGTGAAATGTGAATGTTG-----------------------------18----3
 --------------------------------TGGACTTACGTTGTTAATGTGAAA----------------------------------------24----2
 --------------------------------------TACGTTGTTAATGTGAAATG--------------------------------------20----1
 --------------------------------------TACGTTGTTAATGTGAAATGTGA-----------------------------------23----1
 --------------------------------TGGACTTACGTTGTTAATGTGA------------------------------------------22----1
 -------------------------------------------TGTTAATGTGAAATGTGAA----------------------------------19----1
 --------------------------------------------------GTGAAATGTGAATGTTGGC---------------------------19----1
 -------------------------------------------TGTTAATGTGAAATGTGAATGTTGG----------------------------25----1
 --------------------------------------TACGTTGTTAATGTGAAAT---------------------------------------19----1
 -------------------------------------------------TGTGAAATGTGAATGTTGGC---------------------------201----
 ------------------------------------------------ATGTGAAATGTGAATGTTG-----------------------------19----1
 ---------------------------------------------------TGAAATGTGAATGTTGGCC--------------------------19----1
 --------------------------------TGGACTTACGTTGTTAATGTG-------------------------------------------21----1
 --------------------------TGAGTGTGGACTTACGTT----------------------------------------------------18-1---
 --------------------------------------------------------TGTGAATGTTGGCCTTGAAG--------------------20----1
 --------------------------------------------------------------TGTTGGCCTTGAAGGAACA---------------19----1
 --------------------------TGAGTGTGGACTTACGTTGT--------------------------------------------------20----1
ratctggcttatggtgtggcaggtggtggtgagtgtggacttacgttgttaaTGTGAAATGTGAATGTTGGccttgaaggaacaagcttagagaggcag 
 ************************************************************************************************ 
rat(((.(((.......(((..((.....((((.((.((((((((((..........)))))))..))).)))))).....))..)))....))).)))0.830 -19.40

ratchromosome:4:119377014:119377109:1intergenic


block1575017 [novel_lenNOK_cloningHIGH_multiarm_DicerNOK_loopOverlap]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.521nono0.26/0.4718/25/0.150.0
0.0
0.0
0.0
1.0
0.0
0.0
0.0
2
35
1
1
0
0
0
0
2
4
1
1
0
0
0
0
26
28
20
15
-2
-5
2
8
5arm_loop
3arm_loop
3arm
3arm
3
4
4
4
nd
nd
nd
nd
0.17
0.37
0.35
0.42
1
4
4
5
59500
  readsmiRBase family seed
seed     --------------------------------------------------GUGAAAU---------------------------------------     43novel
seed     ---------------------------------GGACUUA--------------------------------------------------------     4novel
seed     ---------------------------------------ACGUUGU--------------------------------------------------     3novel
seed     --------------------------------------------GUUAAUG---------------------------------------------     2novel
seed     ---------------------------GAGUGUG--------------------------------------------------------------     2novel
seed     ---------------------------------------------------------GUGAAUG--------------------------------     1novel
seed     -------------------------------------------------UGUGAAA----------------------------------------     1novel
seed     ---------------------------------------------------------------GUUGGCC--------------------------     1novel
seed     ----------------------------------------------------GAAAUGU-------------------------------------     1novel
seed     ---------------------------------------------------UGAAAUG--------------------------------------     1miR-203
  lencloning frequencies
   T1S1T1S2T3S1T4S1T5S1
      -------------------------------------------------TGTGAAATGTGAATGTTGG----------------------------     192-1135
      -------------------------------------------------TGTGAAATGTGAATGTTG-----------------------------     18----3
      --------------------------------TGGACTTACGTTGTTAATGTGAAA----------------------------------------     24----2
      --------------------------------------TACGTTGTTAATGTGAAATG--------------------------------------     20----1
      --------------------------------------TACGTTGTTAATGTGAAATGTGA-----------------------------------     23----1
      --------------------------------TGGACTTACGTTGTTAATGTGA------------------------------------------     22----1
      -------------------------------------------TGTTAATGTGAAATGTGAA----------------------------------     19----1
      --------------------------------------------------GTGAAATGTGAATGTTGGC---------------------------     19----1
      -------------------------------------------TGTTAATGTGAAATGTGAATGTTGG----------------------------     25----1
      --------------------------------------TACGTTGTTAATGTGAAAT---------------------------------------     19----1
      -------------------------------------------------TGTGAAATGTGAATGTTGGC---------------------------     201----
      ------------------------------------------------ATGTGAAATGTGAATGTTG-----------------------------     19----1
      ---------------------------------------------------TGAAATGTGAATGTTGGCC--------------------------     19----1
      --------------------------------TGGACTTACGTTGTTAATGTG-------------------------------------------     21----1
      --------------------------TGAGTGTGGACTTACGTT----------------------------------------------------     18-1---
      --------------------------------------------------------TGTGAATGTTGGCCTTGAAG--------------------     20----1
      --------------------------------------------------------------TGTTGGCCTTGAAGGAACA---------------     19----1
      --------------------------TGAGTGTGGACTTACGTTGT--------------------------------------------------     20----1
rat     ctggcttatggtgtggcaggtggtggtgagtgtggacttacgttgttaaTGTGAAATGTGAATGTTGGccttgaaggaacaagcttagagaggcag      
      ************************************************************************************************      
 ----------------------------------------------------------------------------------------------------------ENSRNOT00000057552 ENSRNOG00000037879
rat     (((.(((.......(((..((.....((((.((.((((((((((..........)))))))..))).)))))).....))..)))....))).)))     0.830 -19.40

ratchromosome:4:119286191:119286286:-1Opposite_strand|Intronic_coding|ENSRNOT00000057552|ENSRNOG00000037879 ## ENSRNOG00000037879|protein_coding||


Back to summary page other hairpins: Page 1 Jump 10 pages back Previous page Page 30846 Next page Jump 10 pages forward Page 31204
©2008 InteRNA Genomics B.V.