top of page
mmu_circTop2a_1099
Basic information of circular RNA
PanCircBase ID:
mmu_circTop2a_1099
mm39_Chr. Position ID:
chr11|98884589|98890173|-
Gene name:
Top2a
Transcript:
ENSMUST00000068031.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
35,34,33,32,31,30,29,28
Exon/intron offsets:
0,443,1480,1917,2086,2965,4065,5398
Genomic length:
5584
Exon/intron sizes in nt:
1,72,20,01,35,44,12,41,00,00,000
Flanking exon/introns:
chr11:98884239-98884589|chr11:98890173-98891593
Splice length:
1099
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTTGTCGAGGCCAAGGAAAAGCAGGATGAACAAGTGGGCCTTCCTGGAAAGGCGGGGAAAGCAAAGGGGAAGAAAGCACAGATGTGTGCTGACGTCTTGCCTTCTCCTCGGGGCAAAAGAGTCATCCCCCAAGTGACTGTGGAGATGAAAGCTGAGGCAGAGAAGAAAATTAGGAAGAAAATTAAGAGTGAAAACGTTGAGGGTACCCCTGCTGAGGATGGTGCGGAACCAGGAAGCCTCCGGCAACGAATAGAGAAGAAGCAGAAGAAAGAGCCAGGTGCAAAGAAGCAGACTACATTGCCGTTTAAGCCTGTCAAAAAAGGGAGGAAGAAAAACCCCTGGTCTGACTCTGAGTCAGACGTGAGCAGTAATGAAAGTAACGTTGATGTCCCTCCTCGACAAAAAGAGCAAAGAAGTGCTGCAGCAAAAGCCAAATTCACAGTGGATTTAGACTCGGATGAAGATTTCTCAGGTTTGGATGAGAAGGATGAGGATGAAGATTTCCTCCCATTAGATGCTACTCCACCTAAGGCCAAAATCCCCCCAAAAAATACTAAAAAAGCACTGAAGACCCAGGGAAGCTCCATGTCGGTAGTTGATCTTGAAAGTGATGTTAAGGACAGTGTGCCAGCTTCTCCAGGCGTTCCTGCTGCTGACTTCCCAGCGGAAACTGAACAGTCAAAGCCATCCAAAAAGACCGTGGGAGTGAAGAAGACAGCAACCAAAAGCCAGTCTTCAGTCTCCACTGCTGGTACCAAAAAGAGAGCTGCGCCAAAGGGAACCAAATCAGATTCAGCCTTGAGTGCTCGTGTCTCGGAAAAACCTGCTCCTGCCAAAGCCAAGAACAGTCGCAAAAGGAAGCCATCTTCTTCTGATAGCTCTGACTCTGATTTTGAGAGAGCAATTTCTAAAGGTGCCACGAGCAAGAAAGCAAAGGGAGAGGAACAGGACTTCCCTGTGGACTTGGAAGACACGATAGCTCCTCGAGCCAAATCTGACCGGGCGAGGAAGCCAATTAAGTACCTGGAGGAGTCCGATGACGATGACGACCTCTTCTGAGGCAGAAGAGATTGTTTTAGGGATGGTTTTACGGAGCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGAGGAGTCCGATGACGATG
59.69
CTTTGCTTTCCCCGCCTTTC
60.04
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAGGAGTCCGATGACGATG
59.69
TCTTCCCCTTTGCTTTCCCC
59.89
147
PCR template sequence:
CGGGCGAGGAAGCCAATTAAGTACCTGGAGGAGTCCGATGACGATGACGACCTCTTCTGAGGCAGAAGAGATTGTTTTAGGGATGGTTTTACGGAGCCAGGTTGTCGAGGCCAAGGAAAAGCAGGATGAACAAGTGGGCCTTCCTGGAAAGGCGGGGAAAGCAAAGGGGAAGAAAGCACAGATGTGTGCTGACGTCTTGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(2), mmu-miR-149-5p(2), mmu-miR-16-5p(1), mmu-miR-34c-5p(1), mmu-miR-31-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-25-3p(1), mmu-miR-214-3p(1), mmu-miR-503-5p(1), mmu-miR-34b-5p(1), mmu-miR-207(1), mmu-miR-539-5p(1), mmu-miR-335-3p(1), mmu-miR-452-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTACGGAGCCAGGTTGTCGAGGCCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTOP2A_1099_ORF_1
1.2
0.303701262
0.998121734
1122
ORF sequence:
ATGACGATGACGACCTCTTCTGAGGCAGAAGAGATTGTTTTAGGGATGGTTTTACGGAGCCAGGTTGTCGAGGCCAAGGAAAAGCAGGATGAACAAGTGGGCCTTCCTGGAAAGGCGGGGAAAGCAAAGGGGAAGAAAGCACAGATGTGTGCTGACGTCTTGCCTTCTCCTCGGGGCAAAAGAGTCATCCCCCAAGTGACTGTGGAGATGAAAGCTGAGGCAGAGAAGAAAATTAGGAAGAAAATTAAGAGTGAAAACGTTGAGGGTACCCCTGCTGAGGATGGTGCGGAACCAGGAAGCCTCCGGCAACGAATAGAGAAGAAGCAGAAGAAAGAGCCAGGTGCAAAGAAGCAGACTACATTGCCGTTTAAGCCTGTCAAAAAAGGGAGGAAGAAAAACCCCTGGTCTGACTCTGAGTCAGACGTGAGCAGTAATGAAAGTAACGTTGATGTCCCTCCTCGACAAAAAGAGCAAAGAAGTGCTGCAGCAAAAGCCAAATTCACAGTGGATTTAGACTCGGATGAAGATTTCTCAGGTTTGGATGAGAAGGATGAGGATGAAGATTTCCTCCCATTAGATGCTACTCCACCTAAGGCCAAAATCCCCCCAAAAAATACTAAAAAAGCACTGAAGACCCAGGGAAGCTCCATGTCGGTAGTTGATCTTGAAAGTGATGTTAAGGACAGTGTGCCAGCTTCTCCAGGCGTTCCTGCTGCTGACTTCCCAGCGGAAACTGAACAGTCAAAGCCATCCAAAAAGACCGTGGGAGTGAAGAAGACAGCAACCAAAAGCCAGTCTTCAGTCTCCACTGCTGGTACCAAAAAGAGAGCTGCGCCAAAGGGAACCAAATCAGATTCAGCCTTGAGTGCTCGTGTCTCGGAAAAACCTGCTCCTGCCAAAGCCAAGAACAGTCGCAAAAGGAAGCCATCTTCTTCTGATAGCTCTGACTCTGATTTTGAGAGAGCAATTTCTAAAGGTGCCACGAGCAAGAAAGCAAAGGGAGAGGAACAGGACTTCCCTGTGGACTTGGAAGACACGATAGCTCCTCGAGCCAAATCTGACCGGGCGAGGAAGCCAATTAAGTACCTGGAGGAGTCCGATGACGATGACGACCTCTTCTGA
Peptide sequence:
MTMTTSSEAEEIVLGMVLRSQVVEAKEKQDEQVGLPGKAGKAKGKKAQMCADVLPSPRGKRVIPQVTVEMKAEAEKKIRKKIKSENVEGTPAEDGAEPGSLRQRIEKKQKKEPGAKKQTTLPFKPVKKGRKKNPWSDSESDVSSNESNVDVPPRQKEQRSAAAKAKFTVDLDSDEDFSGLDEKDEDEDFLPLDATPPKAKIPPKNTKKALKTQGSSMSVVDLESDVKDSVPASPGVPAADFPAETEQSKPSKKTVGVKKTATKSQSSVSTAGTKKRAAPKGTKSDSALSARVSEKPAPAKAKNSRKRKPSSSDSSDSDFERAISKGATSKKAKGEEQDFPVDLEDTIAPRAKSDRARKPIKYLEESDDDDDLF
IRESfinder result
IRESfinder score
0.317283693
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page