top of page
mmu_circTop1_238
Basic information of circular RNA
PanCircBase ID:
mmu_circTop1_238
mm39_Chr. Position ID:
chr2|160540043|160544743|+
Gene name:
Top1
Transcript:
ENSMUST00000109468.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
9,10
Exon/intron offsets:
0,4578
Genomic length:
4700
Exon/intron sizes in nt:
1,16,122
Flanking exon/introns:
chr2:160535722-160540043|chr2:160544743-160545491
Splice length:
238
Other database IDs:
CIRCpedia: HSA_CIRCpedia_168544
Human Ortholog IDs:
Mature spliced Sequence:
GTGGGAAGAAGAACGTTATCCAGAAGGCATCAAATGGAAATTCCTAGAGCATAAAGGGCCTGTCTTCGCTCCACCATATGAGCCTCTGCCAGAGAGTGTCAAGTTTTACTATGATGGTAAAGTTATGAAGCTGAGTCCTAAAGCAGAAGAAGTAGCTACATTCTTTGCAAAAATGCTTGACCACGAATATACTACTAAGGAAATATTCAGGAAAAATTTCTTTAAAGATTGGAGAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCAAAAATGCTTGACCACGA
59.59
GAGCGAAGACAGGCCCTTTA
59.75
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCAAAAATGCTTGACCACGA
59.59
GGCAGAGGCTCATATGGTGG
60.25
163
PCR template sequence:
TAAAGCAGAAGAAGTAGCTACATTCTTTGCAAAAATGCTTGACCACGAATATACTACTAAGGAAATATTCAGGAAAAATTTCTTTAAAGATTGGAGAAAGGTGGGAAGAAGAACGTTATCCAGAAGGCATCAAATGGAAATTCCTAGAGCATAAAGGGCCTGTCTTCGCTCCACCATATGAGCCTCTGCCAGAGAGTGTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
NA
Interacting miRNAs (#binding sites)
NA
siRNAs for circular RNA silencing
Junction sequence
AGATTGGAGAAAGGTGGGAAGAAGAA
siRNA sets
TTCTTCCCACCTTTCTCCA, CTTCTTCCCACCTTTCTCC, TTCTTCTTCCCACCTTTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTOP1_238_ORF_1
0.6427
-0.171939418
0.027930443
168
ORF sequence:
ATGAAGCTGAGTCCTAAAGCAGAAGAAGTAGCTACATTCTTTGCAAAAATGCTTGACCACGAATATACTACTAAGGAAATATTCAGGAAAAATTTCTTTAAAGATTGGAGAAAGGTGGGAAGAAGAACGTTATCCAGAAGGCATCAAATGGAAATTCCTAGAGCATAA
Peptide sequence:
MKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKVGRRTLSRRHQMEIPRA
IRESfinder result
IRESfinder score
0.71212312
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page