other hairpins
novel_gcHIGH_nonpairedHIGH (2 loci)
block2173264 [novel_gcHIGH_nonpairedHIGH]
| miRNA | randfold | RNA | rep | GC min/max | len min/max/mir_range | 5'var | 3'var | reads | reads edited | libs | libs edited | base distance | loop distance | position | locations | exon distance | unpaired | max bulge | total reads | total libs | dicer | drosha |
| no | 0.325 | no | no | 0.91/0.91 | 22/22/1.00 | 0.0 | 0.0 | 1 | 0 | 1 | 0 | 10 | 25 | 3arm | 1 | 25 | 0.36 | 3 | 1 | 1 | na | na |
| reads | miRBase family seed | ||
| seed | -----------------------------------------------------------------------------------GCCCGCU------------------------ | 1 | novel |
| len | cloning frequencies | ||
| T1S1 | |||
| ----------------------------------------------------------------------------------CGCCCGCTCGCCCGCCCTCCGG---------- | 22 | 1 | |
| rat | cgcccgacgccgggacctcggggctctgcggccttccttcccccgccctcccctccaggtgagtcaggcggggaagccggctCGCCCGCTCGCCCGCCCTCCGGccgcggacgc | ||
| ****************************************************************************************************************** | |||
| >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ | ENSRNOT00000017096 ENSRNOG00000012499 LOC685072 | ||
| rat | ((.(((..((((((....((((((...((((((...(((.((((((((((.((....)).)))...))))))))))..))).)))..))...))))...))))))..))).)). | 0.950 -55.30 |
| rat | chromosome:7:141013776:141013889:-1 | Same_strand|Intronic_non-coding|ENSRNOT00000017096|ENSRNOG00000012499 ## Same_strand|Boundary_non-coding|ENSRNOT00000016801|ENSRNOG00000012499 ## ENSRNOG00000012499|protein_coding|LOC685072| |
novel_gcHIGH_shortStem_randfoldOK (2 loci)
block1414586 [novel_gcHIGH_shortStem_randfoldOK]
| miRNA | randfold | RNA | rep | GC min/max | len min/max/mir_range | 5'var | 3'var | reads | reads edited | libs | libs edited | base distance | loop distance | position | locations | exon distance | unpaired | max bulge | total reads | total libs | dicer | drosha |
| no | 0.010 | no | no | 0.91/0.91 | 22/22/1.00 | 0.0 | 0.0 | 1 | 0 | 1 | 0 | 1 | 13 | 3arm | 1 | nd | 0.18 | 1 | 1 | 1 | na | na |
| reads | miRBase family seed | ||
| seed | -----------------------------------------------------------CCGCCCU--------------- | 1 | novel |
| len | cloning frequencies | ||
| T1S2 | |||
| ----------------------------------------------------------CCCGCCCTGCCTGCGCCCCCGC- | 22 | 1 | |
| rat | gcagggaaccctgccaggcaggatcgggctggcagctggtgtcctgcccctgtcatgaCCCGCCCTGCCTGCGCCCCCGCa | ||
| ********************************************************************************* | |||
| rat | ((.(((......((((((((((..((((.((((((..(((.....))).))))))...)))).)))))))).))))).)). | 0.520 -40.60 |
| rat | chromosome:3:142525747:142525827:-1 | intergenic |
block2221953 [novel_gcHIGH_shortStem_randfoldOK]
| miRNA | randfold | RNA | rep | GC min/max | len min/max/mir_range | 5'var | 3'var | reads | reads edited | libs | libs edited | base distance | loop distance | position | locations | exon distance | unpaired | max bulge | total reads | total libs | dicer | drosha |
| no | 0.005 | no | no | 0.91/0.91 | 23/23/1.00 | 0.0 | 0.0 | 1 | 0 | 1 | 0 | 3 | 12 | 5arm | 1 | nd | 0.22 | 3 | 1 | 1 | na | na |
| reads | miRBase family seed | ||
| seed | ----CCGGGGC-------------------------------------------------------------------------- | 1 | novel |
| len | cloning frequencies | ||
| T5S1 | |||
| ---CCCGGGGCCCCCCGCACCCCCCA----------------------------------------------------------- | 23 | 1 | |
| rat | gcgCCCGGGGCCCCCCGCACCCCCCAcccgggccggccatgcagggggaatcacggggggcggggcgggaagggcgcagggcgca | ||
| ************************************************************************************* | |||
| ----------------------------------------------------------------------------------------------- | ENSRNOT00000006800 ENSRNOG00000005034 D10Ertd610e | ||
| rat | ((((((...(((((((((.((((((.((((..((..((.....)).)).....))))))).))))))))..))))...)))))). | 0.990 -55.70 |
| rat | chromosome:7:67142856:67142940:1 | Opposite_strand|Intronic_coding|ENSRNOT00000006800|ENSRNOG00000005034 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000043994|ENSRNOG00000005034 ## ENSRNOG00000005034|protein_coding|D10Ertd610e|Guanine nucleotide exchange factor GEFT (RhoA/Rac/Cdc42 guanine nucleotide exchange factor GEFT)(Rac/Cdc42/Rho exchange factor GEFT)(p63RhoGEF) [Source:UniProtKB/Swiss-Prot;Acc:Q9CWR0] ## {Repeats: dust 67142846 67142869 0 class=dust,GC_rich 4 27 1 class=Low_complexity,GC_rich 1 39 1 class=Low_complexity} |
novel_lenNOK_5varHIGH_loopOverlap_randfoldOK_nonpairedHIGH (2 loci)
block1093438 [novel_lenNOK_5varHIGH_loopOverlap_randfoldOK_nonpairedHIGH]
| miRNA | randfold | RNA | rep | GC min/max | len min/max/mir_range | 5'var | 3'var | reads | reads edited | libs | libs edited | base distance | loop distance | position | locations | exon distance | unpaired | max bulge | total reads | total libs | dicer | drosha |
| no | 0.005 | no | no | 0.54/0.58 | 19/24/0.67 | 3.0 | 2.0 | 6 | 0 | 2 | 0 | 33 | -18 | 3arm_loop | 1 | nd | 0.32 | 3 | 6 | 2 | na | na |
| reads | miRBase family seed | |||
| seed | -----------------------------------------GGCAGAC---------------------------------------------------- | 4 | novel | |
| seed | ---------------------------------------GUGGCAG------------------------------------------------------ | 1 | novel | |
| seed | -------------------------------------------------CGACUUC-------------------------------------------- | 1 | novel | |
| len | cloning frequencies | |||
| T4S2 | T5S1 | |||
| ----------------------------------------TGGCAGACTCGACTTCCTCA---------------------------------------- | 20 | 1 | 1 | |
| ----------------------------------------TGGCAGACTCGACTTCCTC----------------------------------------- | 19 | - | 1 | |
| ------------------------------------------------TCGACTTCCTCAAAGGGGC--------------------------------- | 19 | - | 1 | |
| ----------------------------------------TGGCAGACTCGACTTCCTCAAAGG------------------------------------ | 24 | - | 1 | |
| --------------------------------------TGTGGCAGACTCGACTTCCTCA---------------------------------------- | 22 | - | 1 | |
| rat | gaggggggtataacacaaggaaagctgctcagacccttTGTGGCAGACTCGACTTCCTCAAAGGGGCtgagctgggccgttccctgctaggctgacctca | |||
| **************************************************************************************************** | ||||
| rat | ((((..(((......((.((((.(((((((((.(((((((.((.((......)).)).))))))).))))))..)))..)))).))....)))..)))). | 1.000 -43.50 | ||
| rat | chromosome:20:5535350:5535449:1 | intergenic |
block1349709 [novel_lenNOK_5varHIGH_loopOverlap_randfoldOK_nonpairedHIGH]
| miRNA | randfold | RNA | rep | GC min/max | len min/max/mir_range | 5'var | 3'var | reads | reads edited | libs | libs edited | base distance | loop distance | position | locations | exon distance | unpaired | max bulge | total reads | total libs | dicer | drosha |
| no | 0.009 | no | no | 0.42/0.45 | 18/20/0.25 | 1.8 | 0.5 | 4 | 0 | 3 | 0 | 14 | -5 | 3arm | 1 | nd | 0.33 | 3 | 4 | 3 | na | na |
| reads | miRBase family seed | ||||
| seed | ---------------------------------------------UCAGAAC------------------------ | 1 | novel | ||
| seed | -----------------------------------------AACAUCA---------------------------- | 1 | novel | ||
| seed | -------------------------------------------CAUCAGA-------------------------- | 1 | novel | ||
| seed | ------------------------------------------ACAUCAG--------------------------- | 1 | novel | ||
| len | cloning frequencies | ||||
| T1S1 | T4S2 | T5S1 | |||
| ----------------------------------------GAACATCAGAACTAGAGCAC---------------- | 20 | - | - | 1 | |
| -----------------------------------------AACATCAGAACTAGAGCAC---------------- | 19 | 1 | - | - | |
| --------------------------------------------ATCAGAACTAGAGCACTG-------------- | 18 | - | 1 | - | |
| ------------------------------------------ACATCAGAACTAGAGCAC---------------- | 18 | - | 1 | - | |
| rat | gacctggaggggtgcagatctatactgaggacacagctaaGAACATCAGAACTAGAGCACTGcaagccctccgtgt | ||||
| **************************************************************************** | |||||
| ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ | ENSRNOT00000061548 ENSRNOG00000019322 NOTC1_RAT | ||||
| rat | .((.(((((((.(((((.((((..((((.................))))...))))...)))))..))))))).)) | 0.980 -26.03 | |||
| rat | chromosome:3:4704644:4704719:-1 | Same_strand|Boundary_non-coding|ENSRNOT00000019137|ENSRNOG00000019322 ## Same_strand|Intronic_non-coding|ENSRNOT00000061548|ENSRNOG00000019322 ## ENSRNOG00000019322|protein_coding|NOTC1_RAT|Neurogenic locus notch homolog protein 1 precursor (Notch 1) [Contains: Notch 1 extracellular truncation; Notch 1 intracellular domain]. [Source:UniProtKB/Swiss-Prot;Acc:Q07008] |
novel_lenNOK_5varHIGH_mirtron_nonpairedHIGH_bulgeHIGH (2 loci)
block1043112 [novel_lenNOK_5varHIGH_mirtron_nonpairedHIGH_bulgeHIGH]
| miRNA | randfold | RNA | rep | GC min/max | len min/max/mir_range | 5'var | 3'var | reads | reads edited | libs | libs edited | base distance | loop distance | position | locations | exon distance | unpaired | max bulge | total reads | total libs | dicer | drosha |
| no | 0.706 | no | no | 0.72/0.75 | 18/20/0.33 | 2.0 | 0.7 | 3 | 0 | 3 | 0 | 5 | 7 | 3arm | 1 | 4 | 0.50 | 4 | 3 | 3 | na | na |
| reads | miRBase family seed | ||||
| seed | ------------------------------------------------CCGCAGG--------------- | 2 | novel | ||
| seed | ---------------------------------------------GGGCCGC------------------ | 1 | novel | ||
| len | cloning frequencies | ||||
| T3S1 | T5S1 | T5S2 | |||
| -----------------------------------------------GCCGCAGGCGAAGAACCG----- | 18 | 1 | - | 1 | |
| --------------------------------------------CGGGCCGCAGGCGAAGAACC------ | 20 | - | 1 | - | |
| rat | cgtgactgtcggccgagctccggggcagccatcttcagttttccCGGGCCGCAGGCGAAGAACCGtccgg | ||||
| ********************************************************************** | |||||
| -------------------------------------------------------------------------------- | ENSRNOT00000054761 ENSRNOG00000012536 Tmem23 | ||||
| +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>+++++++++++ | ENSRNOT00000054760 ENSRNOG00000036605 2700046G09Rik | ||||
| rat | ((.(((..((.(((..((.((((((.(((........))).))))))))....)))...))...))))). | 0.980 -25.00 | |||
| rat | chromosome:1:236396219:236396288:1 | Opposite_strand|Boundary_non-coding|ENSRNOT00000016737|ENSRNOG00000012536 ## Same_strand|Boundary_coding|ENSRNOT00000054760|ENSRNOG00000036605 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000054761|ENSRNOG00000012536 ## ENSRNOG00000036605|protein_coding|2700046G09Rik|RIKEN cDNA 2700046G09 gene Gene [Source:MGI Symbol;Acc:MGI:1914438] ## ENSRNOG00000012536|protein_coding|Tmem23|Phosphatidylcholine:ceramide cholinephosphotransferase 1 (EC 2.7.8.27) (Sphingomyelin synthase 1) (Transmembrane protein 23) (Protein Mob). [Source:UniProtKB/Swiss-Prot;Acc:Q7TSX5] ## {SimpF: oe = 0.92 1 CpG} |
block1316926 [novel_lenNOK_5varHIGH_mirtron_nonpairedHIGH_bulgeHIGH]
| miRNA | randfold | RNA | rep | GC min/max | len min/max/mir_range | 5'var | 3'var | reads | reads edited | libs | libs edited | base distance | loop distance | position | locations | exon distance | unpaired | max bulge | total reads | total libs | dicer | drosha |
| no | 0.198 | no | no | 0.48/0.50 | 22/25/0.40 | 0.0 1.5 | 0.0 0.8 | 1 4 | 0 0 | 1 2 | 0 0 | 23 8 | 8 17 | 3arm 3arm | 1 1 | 11 1 | 0.45 0.41 | 4 4 | 5 | 2 | na | na |
| reads | miRBase family seed | |||
| seed | ---------------------------------------------------------------------------CAAACUC---------------------------- | 3 | novel | |
| seed | ------------------------------------------------------------------CCCAUCU------------------------------------- | 1 | novel | |
| seed | ---------------------------------------------------------------------------------CCCACCU---------------------- | 1 | novel | |
| len | cloning frequencies | |||
| T3S1 | T4S1 | |||
| --------------------------------------------------------------------------ACAAACTCCCACCTTCCTTCCTAGA----------- | 25 | 3 | - | |
| --------------------------------------------------------------------------------TCCCACCTTCCTTCCTAGATCT-------- | 22 | - | 1 | |
| -----------------------------------------------------------------ACCCATCTAACAAACTCCCACC----------------------- | 22 | 1 | - | |
| rat | gctggtgagtgaggagggaagagaaatagttgcttgggtgcaaagtcagtgcctcctctaacacaACCCATCTAACAAACTCCCACCTTCCTTCCTAGATCTatgttagt | |||
| ************************************************************************************************************** | ||||
| >>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>> | ENSRNOT00000028793 ENSRNOG00000021201 Txnip | |||
| rat | (((((.((...((((((((((.((....((((..(((((.....((.((........)).))...)))))..))))....))....))))))))))...))....))))) | 0.970 -28.00 | ||
| rat | chromosome:2:191358707:191358816:1 | Same_strand|Boundary_coding|ENSRNOT00000028793|ENSRNOG00000021201 ## ENSRNOG00000021201|protein_coding|Txnip|Thioredoxin-interacting protein (Vitamin D3 up-regulated protein 1). [Source:UniProtKB/Swiss-Prot;Acc:Q5M7W1] |
novel_lenNOK_Multihit_5varHIGH_loopOverlap_bulgeHIGH (2 loci)
block964092 [novel_lenNOK_Multihit_5varHIGH_loopOverlap_bulgeHIGH]
| miRNA | randfold | RNA | rep | GC min/max | len min/max/mir_range | 5'var | 3'var | reads | reads edited | libs | libs edited | base distance | loop distance | position | locations | exon distance | unpaired | max bulge | total reads | total libs | dicer | drosha |
| no | 0.076 | no | no | 0.59/0.61 | 18/22/0.50 | 2.0 | 0.0 | 2 | 0 | 2 | 0 | 12 | -5 | 3arm | 25 | nd | 0.28 | 4 | 2 | 2 | na | na |
| reads | miRBase family seed | |||
| seed | -----------------------------------------AGCUGCC-------------------------- | 1 | miR-22 | |
| seed | ---------------------------------------------GCCUCUU---------------------- | 1 | novel | |
| len | cloning frequencies | |||
| T2S1 | T5S1 | |||
| ----------------------------------------AAGCTGCCTCTTCTGACACCCC------------ | 22 | - | 1 | |
| --------------------------------------------TGCCTCTTCTGACACCCC------------ | 18 | 1 | - | |
| rat | ctgtcatcccatagttcagattgacttttattaagaggctAAGCTGCCTCTTCTGACACCCCacagtgagcagg | |||
| ************************************************************************** | ||||
| ------------------------------------------------------------------------------------ | ENSRNOT00000048246 ENSRNOG00000039174 RGD1563865_predicted | |||
| rat | (((((((......(((((((.............((((((......))))))))))).))......)))).))). | 0.700 -18.41 | ||
| rat | chromosome:1:52044554:52044627:1 | Opposite_strand|Boundary_non-coding|ENSRNOT00000059936|ENSRNOG00000039174 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000048246|ENSRNOG00000039174 ## ENSRNOG00000039174|protein_coding|RGD1563865_predicted| |
block1424765 [novel_lenNOK_Multihit_5varHIGH_loopOverlap_bulgeHIGH]
| miRNA | randfold | RNA | rep | GC min/max | len min/max/mir_range | 5'var | 3'var | reads | reads edited | libs | libs edited | base distance | loop distance | position | locations | exon distance | unpaired | max bulge | total reads | total libs | dicer | drosha |
| no | 0.061 | no | no | 0.61/0.68 | 18/24/0.60 | 0.0 1.0 3.5 | 0.0 2.0 3.0 | 1 2 2 | 0 0 0 | 1 2 2 | 0 0 0 | 16 21 27 | 19 9 -2 | 5arm 5arm 5arm_loop | 2 9 11 | 39 32 21 | 0.53 0.29 0.41 | 5 4 4 | 5 | 5 | na | na |
| reads | miRBase family seed | ||||||
| seed | -----------------------------------UGGCAGC------------------------------------------------------------- | 1 | novel | ||||
| seed | ----------------------------CGCAAGA-------------------------------------------------------------------- | 1 | novel | ||||
| seed | ------------------------GCGACGC------------------------------------------------------------------------ | 1 | novel | ||||
| seed | ----------------------CAGCGAC-------------------------------------------------------------------------- | 1 | novel | ||||
| seed | -----------------AGCGACA------------------------------------------------------------------------------- | 1 | novel | ||||
| len | cloning frequencies | ||||||
| T1S1 | T2S1 | T3S2 | T5S1 | T5S2 | |||
| -----------------------AGCGACGCAAGATGGCAG-------------------------------------------------------------- | 18 | - | - | - | - | 1 | |
| ---------------------ACAGCGACGCAAGATGGCAGCCAC---------------------------------------------------------- | 24 | - | 1 | - | - | - | |
| ----------------------------------ATGGCAGCCACCACAGGCTCGG----------------------------------------------- | 22 | - | - | 1 | - | - | |
| ----------------GAGCGACAGCGACGCAAGA-------------------------------------------------------------------- | 19 | 1 | - | - | - | - | |
| ---------------------------ACGCAAGATGGCAGCCACCACAG----------------------------------------------------- | 23 | - | - | - | 1 | - | |
| rat | gaaggggccggccttcGAGCGACAGCGACGCAAGATGGCAGCCACCACAGGCTCGGgtgagcgggggcgccgggcgtgctggcagacggagcgcgggctgctt | ||||||
| ******************************************************************************************************* | |||||||
| +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ | ENSRNOT00000002504 ENSRNOG00000025580 LOC679539 | ||||||
| .......................................>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++ | ENSRNOT00000035048 ENSRNOG00000025580 LOC679539 | ||||||
| rat | .(((.((((.(((((((.....((((.((((....((((.(((.((....((((....)))).))))))))).)))))))).....))))).)).)))).))) | 1.000 -52.40 | |||||
| rat | chromosome:3:158768615:158768717:-1 | Same_strand|Boundary_non-coding|ENSRNOT00000013962|ENSRNOG00000025580 ## Same_strand|Intronic_coding|ENSRNOT00000002504|ENSRNOG00000025580 ## ENSRNOG00000025580|protein_coding|LOC679539|ubiquitin-conjugating enzyme E2 variant 1 [Source:RefSeq_peptide;Acc:NP_001103815] ## {SimpF: 1 Eponine} |
novel_lenNOK_Multihit_5varHIGH_randfoldOK_bulgeHIGH (2 loci)
block668544 [novel_lenNOK_Multihit_5varHIGH_randfoldOK_bulgeHIGH]
| miRNA | randfold | RNA | rep | GC min/max | len min/max/mir_range | 5'var | 3'var | reads | reads edited | libs | libs edited | base distance | loop distance | position | locations | exon distance | unpaired | max bulge | total reads | total libs | dicer | drosha |
| no | 0.009 | no | no | 0.42/0.47 | 19/23/0.33 | 2.3 | 3.7 | 3 | 0 | 3 | 0 | 16 | 8 | 5arm | 136 | nd | 0.26 | 4 | 3 | 3 | na | na |
| reads | miRBase family seed | ||||
| seed | -----------------CAUCCAU---------------------------------------------------------------------------------------------- | 2 | novel | ||
| seed | ------------------------GACAACU--------------------------------------------------------------------------------------- | 1 | novel | ||
| len | cloning frequencies | ||||
| T1S2 | T3S1 | T3S2 | |||
| -----------------------TGACAACTTTGGCATCGTG---------------------------------------------------------------------------- | 19 | - | 1 | - | |
| ----------------TCATCCATGACAACTTTGGCATC------------------------------------------------------------------------------- | 23 | 1 | - | - | |
| ----------------TCATCCATGACAACTTTGG----------------------------------------------------------------------------------- | 19 | - | - | 1 | |
| rat | gcccccctggccaaggTCATCCATGACAACTTTGGCATCGTGgaagggctcatgaccacagtccatgtcatcactgccactcagaagaccgtggatgacccctctggctaactgtggc | ||||
| ********************************************************************************************************************** | |||||
| rat | (((....((((((.(((((((((((....((.(((((..((((..(((((.........)))))...))))...)))))...)).....)))))))))))....)))))).....))) | 0.620 -41.20 | |||
| rat | chromosome:17:62876952:62877069:1 | intergenic |
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