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mmu_circTop1_459
Basic information of circular RNA
PanCircBase ID:
mmu_circTop1_459
mm39_Chr. Position ID:
chr2|160524570|160535722|+
Gene name:
Top1
Transcript:
ENSMUST00000109468.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
4,5,6,7,8
Exon/intron offsets:
0,1797,4997,7626,11045
Genomic length:
11152
Exon/intron sizes in nt:
1,24,56,96,76,107
Flanking exon/introns:
chr2:160512122-160524570|chr2:160535722-160540043
Splice length:
459
Other database IDs:
circAtlas: mmu-Top1_0011
circAtlas: hsa-TOP1_0011, CIRCpedia: HSA_CIRCpedia_133579
Human Ortholog IDs:
Mature spliced Sequence:
TGAACATAAAGATTCTGAAAAGAAACACAAAGAGAAAGAGAAAACCAAACACAAAGATGGCAGCTCAGAAAAACATAAAGACAAACATAAAGACAGAGACAAGGAAAGACGAAAGGAGGAAAAGATTAGAGCTGCTGGGGATGCAAAAATAAAGAAGGAAAAGGAAAATGGCTTCTCTAGTCCGCCACGAATTAAAGATGAACCTGAGGATGATGGCTATTTTGCTCCTCCAAAAGAGGATATTAAGCCATTGAAGAGGCTTCGAGATGAAGATGATGCTGATTATAAACCTAAGAAAATTAAGACAGAAGATATCAAGAAGGAGAAGAAAAGAAAATCAGAAGAGGAAGAGGATGGTAAACTTAAAAAGCCCAAGAATAAAGATAAAGATAAAAAAGTTGCTGAGCCAGATAATAAGAAAAAGAAGCCGAAAAAGGAAGAGGAACAGAAGTGGAAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAAAAGTTGCTGAGCCAGAT
55.83
TGTTTTTCTGAGCTGCCATCT
58.13
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAAAAGTTGCTGAGCCAGAT
55.83
TGTTTTTCTGAGCTGCCATCTT
58.77
142
PCR template sequence:
AACTTAAAAAGCCCAAGAATAAAGATAAAGATAAAAAAGTTGCTGAGCCAGATAATAAGAAAAAGAAGCCGAAAAAGGAAGAGGAACAGAAGTGGAAATGTGAACATAAAGATTCTGAAAAGAAACACAAAGAGAAAGAGAAAACCAAACACAAAGATGGCAGCTCAGAAAAACATAAAGACAAACATAAAGACAGAGAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(1), mmu-miR-324-5p(1), mmu-miR-149-5p(1), mmu-miR-129-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAAGTGGAAATGTGAACATAAAGAT
siRNA sets
TTATGTTCACATTTCCACT,TTTATGTTCACATTTCCAC,TCTTTATGTTCACATTTCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTOP1_459_ORF_1
1.1354
-0.126252767
0.235112285
345
ORF sequence:
ATGAAGATGATGCTGATTATAAACCTAAGAAAATTAAGACAGAAGATATCAAGAAGGAGAAGAAAAGAAAATCAGAAGAGGAAGAGGATGGTAAACTTAAAAAGCCCAAGAATAAAGATAAAGATAAAAAAGTTGCTGAGCCAGATAATAAGAAAAAGAAGCCGAAAAAGGAAGAGGAACAGAAGTGGAAATGTGAACATAAAGATTCTGAAAAGAAACACAAAGAGAAAGAGAAAACCAAACACAAAGATGGCAGCTCAGAAAAACATAAAGACAAACATAAAGACAGAGACAAGGAAAGACGAAAGGAGGAAAAGATTAGAGCTGCTGGGGATGCAAAAATAA
Peptide sequence:
MKMMLIINLRKLRQKISRRRRKENQKRKRMVNLKSPRIKIKIKKLLSQIIRKRSRKRKRNRSGNVNIKILKRNTKRKRKPNTKMAAQKNIKTNIKTETRKDERRKRLELLGMQK
IRESfinder result
IRESfinder score
0.230496762
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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