logoSmall RNA from different tissues of two rat strains.


miR classification

Alignments

other non-annotated miRBase miRNAs

miRBaseNonMapped_lenNOK_multiarm_DicerNOK_randfoldOK (1 loci)

miRBaseNonMapped_lenNOK_randfoldOK_bulgeHIGH (1 loci)

rno-mir-342-as

Cloning frequencies
absoluteT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-342-as 5arm0001000000
normalizedT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-342-as 5arm0000.000000000
rno-mir-342-as relative cloning frequencies

block1980627 (Antisense miRBase rno-mir-342-as) [miRBaseNonMapped_lenNOK_randfoldOK_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBaseAS rno-mir-342-as0.001nono0.53/0.5319/19/0.000.0
0.0
1
0
1
0
28
8
5arm
1
nd
0.21
4
11nana
block1980627 hairpin
  readsmiRBase family seed
seed     -----------------------------GGUGCGA------------------------------------------------------------------------     1novel
  lencloning frequencies
   T2S2
      ----------------------------GGGTGCGATTTCTGTGTGA-------------------------------------------------------------     191
rat     GGGGTGGTGCTCAGCAGGCCAAGGTGACGGGTGCGATTTCTGTGTGAGACAATTCCATTGACCATGTCCCTCAATCACAGATAGCACCCCTCACCTTGAGCCCATTTT      
human     ----------------------------GGGTGCGATTTCTGTGTGAGACAATTCCATTAACCATGTCCCTCAATCACAGATAGCACCC-------------------      
mouse     ----------------------------GGGTGCGATTTCTGTGTGAGACAATTCCATTGACCATGTCCCTCAATCACAGATAGCACCC-------------------      
                                  ******************************* *****************************                         
 ----------------------------------------------------------------------------------------------------------------------ENSRNOT00000032757 ENSRNOG00000014476 Evl
 ----------------------------------------------------------------------------------------------------------------------ENSRNOT00000019583 ENSRNOG00000014476 Evl
 ...............<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<....ENSRNOT00000053735 ENSRNOG00000035612 rno-mir-342
rat     .((((((.(((((........((((((.((((((....(((((((((((((..((....))...))))..)))..))))))..)))))).))))))))))))))))).     0.440 -44.40
human                                 ((((((....(((((((((((((.............))))..)))..))))))..))))))                        1.000 -21.42
mouse                                 ((((((....(((((((((((((..((....))...))))..)))..))))))..))))))                        0.994 -21.80

ratchromosome:6:132990798:132990905:-1Opposite_strand|Intronic_coding|ENSRNOT00000019583|ENSRNOG00000014476 ## Opposite_strand|Exonic_non-coding|ENSRNOT00000053735|ENSRNOG00000035612 ## ENSRNOG00000035612|miRNA|rno-mir-342|rno-mir-342 [Source:miRBase;Acc:MI0000626] ## ENSRNOG00000014476|protein_coding|Evl|Ena/VASP-like protein (Ena/vasodilator-stimulated phosphoprotein- like). [Source:UniProtKB/Swiss-Prot;Acc:O08719] ## {ASMIR: rno-mir-342-as}
humanchromosome:14:99645726:99645873:-1Opposite_strand|Intronic_coding|ENST00000355449|ENSG00000196405|protein_coding|Ena/VASP-like protein (Ena/vasodilator-stimulated phosphoprotein-like) [Source:UniProtKB/Swiss-Prot;Acc:Q9UI08] ## Opposite_strand|Boundary_non-coding|ENST00000362212|ENSG00000199082|miRNA|hsa-mir-342 [Source:miRBase;Acc:MI0000805] ## {ASMIR: hsa-mir-342-as}
mousechromosome:12:109896811:109896958:-1Opposite_strand|Intronic_coding|ENSMUST00000109854|ENSMUSG00000021262|protein_coding|Ena-vasodilator stimulated phosphoprotein Gene [Source:MGI Symbol;Acc:MGI:1194884] ## Opposite_strand|Boundary_non-coding|ENSMUST00000083502|ENSMUSG00000065436|miRNA|mmu-mir-342 [Source:miRBase;Acc:MI0000627] ## {Repeats: trf 0 class=trf} ## {ASMIR: mmu-mir-342-as}


miRBaseNonMapped_rep_Multihit_randfoldOK (1 loci)

rno-mir-466b-1-as

Cloning frequencies
absoluteT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-466b-1-as 5arm0000.012000000.012
normalizedT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-466b-1-as 5arm0000.000000000.000
rno-mir-466b-1-as relative cloning frequencies

block675546 (Antisense miRBase rno-mir-466b-1-as) [miRBaseNonMapped_rep_Multihit_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBaseAS rno-mir-466b-1-as0.001noLTR/ERVK,SINE0.50/0.5020/20/1.000.0
0.0
2
0
2
0
19
16
5arm
85
nd
0.05
1
22nana
Families
Member of family miR-466b (seed AUGUGUG): mmu-mir-466b, rno-mir-466b, rno-mir-466b, rno-mir-466b-2, rno-mir-466b-1
block675546 hairpin
  readsmiRBase family seed
seed     --------------------CACGUGU---------------------------------------------------------------------------------------------     2novel
  lencloning frequencies
   T2S2T5S2
      -------------------GCACGTGTGTGTATGTGTGT---------------------------------------------------------------------------------     2011
rat     cattcctgtgtgtgtgcttGCACGTGTGTGTATGTGTGTgtgtatgtatattcatatacacacatggacatacacacacacatatatacacatgcaaatatatagagacatcacatgaat      
      ************************************************************************************************************************      
 ----------------------------------------------------------------------------------------------------------------------------------ENSRNOT00000042430 ENSRNOG00000029235 Sfmbt2
 .............<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<...............................ENSRNOT00000062970 ENSRNOG00000041217 rno-mir-466b-1
rat     .((((.((((((((((.(((((.((((((((((((((((((((((((....((((........)))))))))))))))))))))))))))).))))).)))))).......)))).))))     0.960 -52.61

ratchromosome:17:79291556:79291675:1Opposite_strand|Intronic_coding|ENSRNOT00000042430|ENSRNOG00000029235 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000051529|ENSRNOG00000029235 ## Opposite_strand|Exonic_non-coding|ENSRNOT00000062970|ENSRNOG00000041217 ## ENSRNOG00000041217|miRNA|rno-mir-466b-1|rno-mir-466b-1 [Source:miRBase;Acc:MI0006112] ## ENSRNOG00000029235|protein_coding|Sfmbt2|Scm-like with four mbt domains 2 Gene [Source:MGI (curated);Acc:Sfmbt2-001] ## {Repeats: (TA)n 1 80 1 class=Simple_repeat,dust 79291570 79291590 0 class=dust,RMER12 850 851 -1 class=LTR/ERVK,ID_B1 -17 207 -1 class=SINE} ## {ASMIR: rno-mir-466b-1-as}


miRBaseNonMapped_rep_lenNOK_multiarm_DicerNOK_5varHIGH_randfoldOK (1 loci)

rno-mir-378-as

Cloning frequencies
absoluteT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-378-as 5arm000.333100010.3331
rno-mir-378-as 3arm0000000020
normalizedT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-378-as 5arm000.0000.0000000.0000.0000.000
rno-mir-378-as 3arm000000000.0000
rno-mir-378-as relative cloning frequencies

sblock5677 (Antisense miRBase rno-mir-378-as) [miRBaseNonMapped_rep_lenNOK_multiarm_DicerNOK_5varHIGH_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBaseAS rno-mir-378-as0.001noSINE,SINE/MIR0.55/0.6118/23/0.570.0
3.3
0.0
1.0
0.7
0.0
2
3
2
0
0
0
2
3
1
0
0
0
15
24
28
16
5
6
5arm
5arm
3arm
1
3
3
nd
nd
nd
0.05
0.14
0.22
1
1
3
7514
Families
Member of family novel168 (seed UGACUCC): rno-mir-378, block1384022_cand
sblock5677 hairpin
  readsmiRBase family seed
seed     -----------------------------------------------------------------------------------CACAGGA------------------------------------------------------     2novel
seed     --------------------------------------------------UGACUCC---------------------------------------------------------------------------------------     2novel
seed     ------------------------------------CCACUCA-----------------------------------------------------------------------------------------------------     2novel
seed     ---------------------------------------------CCUUCUG--------------------------------------------------------------------------------------------     1novel
  lencloning frequencies
   T2S1T2S2T4S2T5S1T5S2
      -------------------------------------------------CTGACTCCAAGTCCAGTG-----------------------------------------------------------------------------     181--1-
      ----------------------------------------------------------------------------------ACACAGGACCTGGAGTCAGGAGC---------------------------------------     23---2-
      -----------------------------------TCCACTCAGGCCTTCTGACTC----------------------------------------------------------------------------------------     21--1--
      --------------------------------------------GCCTTCTGACTCCAAGTCCAGT------------------------------------------------------------------------------     22----1
      -----------------------------------TCCACTCAGGCCTTCTGAC------------------------------------------------------------------------------------------     19-1---
rat     --------------------AGCGGGGAAGGTGACTCCACTCAGGCCTTCTGACTCCAAGTCCAGTGCTATTTCGAGGTAACACACAGGACCTGGAGTCAGGAGCCCTGGGTGGCTCTGTCACCCCCTGGCTG-----------      
human     -----------------------------------TCCACTCAGGCCTTCTGACTCCAAGTCCAGTGCTATTTCTAGGTAACACACAGGACCTGGAGTCAGGAGCCCTGGGTGGC-----------------------------      
mouse     CCAGGATCACCCAGCCAGAGAGCGGGGAAGGTGACTCCACTCAGGCCTTCTGACTCCAAGTCCAGTGCTATTTCGAGGTAACACACAGGACCTGGAGTCAGGAGCCCTGGGTGGCTCTGTCACCCCCTGGCTGAGTGGTCGTGG      
                                         *************************************** ****************************************                                   
 -----                    -----------------------------------------------------------------------------------------------------------------           -----ENSRNOT00000023661 ENSRNOG00000017503 Ppargc1b
 .....                    ......................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<.........................           .....ENSRNOT00000053640 ENSRNOG00000035517 rno-mir-378
rat                         (((.(((..((((((.(((((((((.((((((((((((.((((.(((.((((....)))).)))...)))).)))))))))))).)))))))))....)))))).))).))).                1.000 -66.80
human                                        .(((((((((.((((((((((((.((((.(((.((((....)))).)))...)))).)))))))))))).))))))))).                                  1.000 -47.90
mouse     (((.((((((.(((((.......((((..((((((.(((((((((.((((((((((((.((((.(((.((((....)))).)))...)))).)))))))))))).)))))))))....))))))))))))))).)))))).)))     0.991 -84.41

ratchromosome:18:57377783:57377895:1Opposite_strand|Boundary_non-coding|ENSRNOT00000053640|ENSRNOG00000035517 ## Opposite_strand|Intronic_coding|ENSRNOT00000023661|ENSRNOG00000017503 ## Opposite_strand|Exonic_non-coding|ENSRNOT00000053640|ENSRNOG00000035517 ## ENSRNOG00000017503|protein_coding|Ppargc1b|Peroxisome proliferator-activated receptor gamma coactivator 1-beta (PPAR-gamma coactivator 1-beta) (PPARGC-1-beta) (PGC-1-beta). [Source:UniProtKB/Swiss-Prot;Acc:Q811R2] ## ENSRNOG00000035517|miRNA|rno-mir-378|rno-mir-378 [Source:miRBase;Acc:MI0003719] ## {Repeats: MIR 27 50 1 class=SINE/MIR,MIR -62 146 -1 class=SINE,MIR 30 62 -1 class=SINE/MIR,MIR 20 149 1 class=SINE} ## {ASMIR: rno-mir-378-as}
humanchromosome:5:149092536:149092688:-1Opposite_strand|Boundary_non-coding|ENST00000403750|ENSG00000155846|protein_coding|Peroxisome proliferator-activated receptor gamma coactivator 1-beta (PPAR-gamma coactivator 1-beta)(PPARGC-1-beta)(PGC-1-beta)(PGC-1-related estrogen receptor alpha coactivator) [Source:UniProtKB/Swiss-Prot;Acc:Q86YN6] ## Opposite_strand|Intronic_coding|ENST00000309241|ENSG00000155846|protein_coding|Peroxisome proliferator-activated receptor gamma coactivator 1-beta (PPAR-gamma coactivator 1-beta)(PPARGC-1-beta)(PGC-1-beta)(PGC-1-related estrogen receptor alpha coactivator) [Source:UniProtKB/Swiss-Prot;Acc:Q86YN6] ## {Repeats: MIRb 1 class=SINE/MIR,MIRb -1 class=SINE/MIR} ## {SimpF: rank = 1 -1 FirstEF} ## {ASMIR: hsa-mir-378-as}
mousechromosome:18:61557447:61557590:1Opposite_strand|Intronic_coding|ENSMUST00000063307|ENSMUSG00000033871|protein_coding|peroxisome proliferative activated receptor, gamma, coactivator 1 beta Gene [Source:MGI (curated);Acc:Ppargc1b-001] ## Opposite_strand|Boundary_non-coding|ENSMUST00000083601|ENSMUSG00000065535|miRNA|mmu-mir-378 [Source:miRBase;Acc:MI0000795] ## {Repeats: MIR -1 class=SINE/MIR,MIRb 1 class=SINE/MIR} ## {ASMIR: mmu-mir-378-as}


miRBaseNonMapped_rep_lenNOK_multiarm_DicerNOK_loopOverlap_randfoldOK (1 loci)

rno-mir-151-as

Cloning frequencies
absoluteT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-151-as 5arm0000200000
rno-mir-151-as 3arm00.33300000001
normalizedT1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
rno-mir-151-as 5arm00000.00000000
rno-mir-151-as 3arm00.00000000000.000
rno-mir-151-as relative cloning frequencies

sblock11350 (Antisense miRBase rno-mir-151-as) [miRBaseNonMapped_rep_lenNOK_multiarm_DicerNOK_loopOverlap_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBaseAS rno-mir-151-as0.001noLINE,LINE/L20.48/0.6118/23/0.250.0
1.0
0.0
1.5
2
2
0
0
1
2
0
0
19
38
12
-1
5arm
3arm
1
3
nd
nd
0.17
0.17
1
3
43-14-9
Families
Member of family miR-339 (seed CCCUGUC): rno-mir-339, rno-mir-151, block1084584_cand, block2837956_cand
sblock11350 hairpin
  readsmiRBase family seed
seed     ----------------------------------------CCCUGUC-----------------------------------------------------------------------------------------------------------------     2miR-339
seed     ---------------------------------------------------------------------------------UACUAGA------------------------------------------------------------------------     1novel
seed     -----------------------------------------------------------------------------------CUAGACU----------------------------------------------------------------------     1novel
  lencloning frequencies
   T1S2T3S1T5S2
      ---------------------------------------TCCCTGTCCTCAAGGAGC-------------------------------------------------------------------------------------------------------     18-2-
      --------------------------------------------------------------------------------ATACTAGACTGTGAGCTCCTCGA---------------------------------------------------------     23--1
      ----------------------------------------------------------------------------------ACTAGACTGTGAGCTCCT------------------------------------------------------------     181--
rat     ----------------CGG----GAGGTGAGTATGACGATCCCTGTCCTCAAGGAGCCTCAGTCTAGTA-GGGAGGAGACATACTAGACTGTGAGCTCCTCGAGGGCAGG-AAAGCGCTCCA-TCATCTGTGCTCCA-TGCCCA----------------      
human     GGCCTGGAGGTTTGGGCAACACCGAGGTGAGTATGACCATCCCTGTCCTCAAGGAGCTTCAGTCTAGTAGGGGATGAGACATACTAGACTGTGAGCTCCTCGAGGGCAGGAAAAGTGTTTTAGTCATCTTTGCCCCAGTGACTAGCACCAGGCT------      
mouse     TGCACTGTGCTCCTGGCAG----GAGGTGAGTATGACGATCCCTGTCCTCAAGGAGCCTCAGTCTAGTA-GGGAGGAGACATACTAGACTGTGAGCTCCTCGAGGGCAGG-AAAGCGCTCCA-TCATCTGTGCTCCA-TGCCCAGGACCTGAGCAGTCCA      
                      *      ************** ******************* *********** **** *********************************** **** * *  * ****** *** *** ** * *                      
 -----                ---    ---------------------------------------------- ---------------------------------------- ----------- -------------- ------                -----ENSRNOT00000011219 ENSRNOG00000007916 Ptk2
 -----                ---    ---------------------------------------------- ---------------------------------------- ----------- -------------- ------                -----ENSRNOT00000046362 ENSRNOG00000007916 Ptk2
 .....                <<<    <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< <<<<<<<<... .............. ......                .....ENSRNOT00000053580 ENSRNOG00000035457 rno-mir-151
rat                     .((    (....((((((((((...(((((((((.((((((..(((((((((( ...........))))))))))...)))))).))))))))) ....)).)).. ......)))))).. ..))).                     0.580 -55.40
human     (((((((.((((.(((((.....(((((((.((.(((....(((((((((.((((((((((((((((((............)))))))))).)))))))).)))))))))......))).)).))))))))))))....))))....)))))))           0.919 -76.80
mouse     ((.(((((..(((((((((    (((((((....((((...(((((((((.((((((..(((((((((( ...........))))))))))...)))))).))))))))) ....)).)).. )))).....)))). )))).)))).....))))).))     0.967 -69.00

ratchromosome:7:110979296:110979415:1Opposite_strand|Intronic_coding|ENSRNOT00000011219|ENSRNOG00000007916 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000010896|ENSRNOG00000007916 ## Opposite_strand|Exonic_non-coding|ENSRNOT00000053580|ENSRNOG00000035457 ## ENSRNOG00000035457|miRNA|rno-mir-151|rno-mir-151 [Source:miRBase;Acc:MI0000647] ## ENSRNOG00000007916|protein_coding|Ptk2|Focal adhesion kinase 1 (EC 2.7.10.2) (FADK 1) (pp125FAK). [Source:UniProtKB/Swiss-Prot;Acc:O35346] ## {Repeats: L2 -94 3325 -1 class=LINE,L2 3255 3284 1 class=LINE,L2 3149 3169 1 class=LINE/L2,L2 3180 3180 -1 class=LINE/L2,L2 3202 3219 -1 class=LINE/L2} ## {ASMIR: rno-mir-151-as}
humanchromosome:8:141811822:141811975:1Opposite_strand|Boundary_non-coding|ENST00000342207|ENSG00000169398|protein_coding|Focal adhesion kinase 1 (FADK 1)(EC 2.7.10.2)(pp125FAK)(Protein-tyrosine kinase 2) [Source:UniProtKB/Swiss-Prot;Acc:Q05397] ## Opposite_strand|Intronic_coding|ENST00000354438|ENSG00000169398|protein_coding|Focal adhesion kinase 1 (FADK 1)(EC 2.7.10.2)(pp125FAK)(Protein-tyrosine kinase 2) [Source:UniProtKB/Swiss-Prot;Acc:Q05397] ## {Repeats: L2 -1 class=LINE/L2,L2 1 class=LINE/L2} ## {ASMIR: hsa-mir-151-as}
mousechromosome:15:73085208:73085359:1Opposite_strand|Intronic_non-coding|ENSMUST00000068756|ENSMUSG00000022607|protein_coding|PTK2 protein tyrosine kinase 2 Gene [Source:MGI Symbol;Acc:MGI:95481] ## Opposite_strand|Intronic_coding|ENSMUST00000080736|ENSMUSG00000022607|protein_coding|PTK2 protein tyrosine kinase 2 Gene [Source:MGI Symbol;Acc:MGI:95481] ## Opposite_strand|Boundary_non-coding|ENSMUST00000083678|ENSMUSG00000065612|miRNA|mmu-mir-151 [Source:miRBase;Acc:MI0000173] ## {Repeats: L2 -1 class=LINE/L2,L2 1 class=LINE/L2} ## {ASMIR: mmu-mir-151-as}


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