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mmu_circTop2a_1621
Basic information of circular RNA
PanCircBase ID:
mmu_circTop2a_1621
mm39_Chr. Position ID:
chr11|98900415|98909767|-
Gene name:
Top2a
Transcript:
ENSMUST00000068031.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
16,15,14,13,12,11,10,9,8,7,6,5
Exon/intron offsets:
0,203,438,884,1316,2431,4825,5098,5296,6438,6840,9206
Genomic length:
9352
Exon/intron sizes in nt:
11,01,06,11,11,26,15,80,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr11:98900148-98900415|chr11:98909767-98912536
Splice length:
1621
Other database IDs:
circBase: hsa_circ_0106819, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_20602
Human Ortholog IDs:
Mature spliced Sequence:
AGAAAATAATGTAATTAGCATCTGGAATAATGGGAAAGGAATCCCTGTTGTTGAACACAAAGTTGAGAAAATATATGTCCCAGCTCTCATATTTGGACAACTCCTGACCTCCAGTAACTATGACGACGATGAGAAGAAAGTGACAGGTGGTCGAAATGGCTATGGAGCTAAACTGTGTAACATATTCAGCACCAAATTTACTGTGGAAACAGCCAGTAGAGAGTACAAGAAAATGTTCAAACAGACGTGGATGGATAACATGGGGAGAGCTGGTGACATGGAACTCAAGCCCTTTAGTGGAGAAGATTATACATGTATCACCTTCCAGCCTGACTTATCTAAGTTTAAAATGCAAAGCCTGGACAAAGATATTGTTGCACTGATGGTCAGAAGAGCATATGATATCGCTGGCTCCACTAAAGATGTCAAAGTCTTTCTTAATGGAAATAGTCTGCCAGTGAAAGGATTCCGCAGTTACGTGGATTTGTATTTGAAGGATAAGGTAGATGAAACTGGGAATTCACTGAAGGTGATACATGAACAGGTCAATCCCCGGTGGGAAGTGTGCTTAACAATGAGCGAGAGAGGCTTCCAGCAGATTAGCTTCGTCAACAGCATTGCGACTTCTAAGGGCGGCAGACATGTCGATTATGTAGCTGATCAGATTGTGAGCAAACTCGTTGATGTGGTGAAAAAGAAGAACAAGGGCGGGGTTGCAGTGAAGGCTCATCAGGTGAAAAATCACATGTGGATTTTTGTAAATGCCTTAATTGAAAACCCAACCTTTGACTCTCAAACAAAAGAAAACATGACTTTACAAGCCAAGAGCTTTGGATCAACATGTCAATTAAGTGAAAAGTTCATCAAAGCTGCAATTGGTTGTGGTATTGTGGAAAGCATACTAAACTGGGTGAAGTTCAAGGCTCAAATCCAACTGAACAAGAAGTGTTCAGCTGTAAAACATACCAAAATCAAGGGAATCCCCAAACTTGATGATGCCAACGATGCAGGGAGCCGAAACTCTACTGAATGCACACTTATCCTGACTGAGGGAGACTCAGCAAAAACTCTAGCCGTTTCAGGCCTTGGAGTGGTTGGAAGAGACAAATATGGGGTGTTCCCTCTTAGAGGAAAGATACTCAATGTGCGAGAAGCCTCTCATAAACAGATCATGGAAAATGCTGAAATTAACAATATCATCAAGATTGTGGGTCTCCAGTACAAGAAAAACTATGAAGATGAAGATTCATTGAAAACTCTTCGTTATGGGAAGATCATGATTATGACAGATCAGGACCAAGATGGTTCCCACATCAAAGGCTTGCTGATCAATTTTATCCATCACAATTGGCCATCTCTTCTGCGACATCGTTTTCTAGAAGAATTTATCACTCCCATTGTAAAGGTGTCCAAAAATAAGCAAGAAATAGCATTCTATAGTCTTCCCGAGTTTGAAGAATGGAAAAGTTCGACTCCGAATCATAAAAAGTGGAAAGTCAAATACTACAAAGGTTTGGGCACCAGCACATCAAAGGAAGCTAAGGAATATTTTGCAGATATGAAACGACATCGTATTCAGTTCAAATACTCTGGCCCTGAAGATGATGCTGCGATCAGCCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCACATCAAAGGAAGCTAAGGA
59.99
TGTGTTCAACAACAGGGATTCC
59.04
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTTCAAATACTCTGGCCCTGA
59.09
TCCAAATATGAGAGCTGGGACA
58.89
141
PCR template sequence:
CAGCACATCAAAGGAAGCTAAGGAATATTTTGCAGATATGAAACGACATCGTATTCAGTTCAAATACTCTGGCCCTGAAGATGATGCTGCGATCAGCCTGAGAAAATAATGTAATTAGCATCTGGAATAATGGGAAAGGAATCCCTGTTGTTGAACACAAAGTTGAGAAAATATATGTCCCAGCTCTCATATTTGGACAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-7b-5p(2), mmu-miR-103-3p(1), mmu-miR-221-3p(1), mmu-miR-152-3p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-7a-5p(1), mmu-miR-138-5p(1), mmu-miR-130b-3p(1), mmu-miR-301b-3p(1), mmu-miR-541-5p(1), mmu-miR-107-3p(1), mmu-miR-301a-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGCGATCAGCCTGAGAAAATAATGTA
siRNA sets
TACATTATTTTCTCAGGCT, TATTTTCTCAGGCTGATCG, TTATTTTCTCAGGCTGATC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTOP2A_1621_ORF_1
1.0918
0.176740879
0.999459534
1398
ORF sequence:
ATGTTCAAACAGACGTGGATGGATAACATGGGGAGAGCTGGTGACATGGAACTCAAGCCCTTTAGTGGAGAAGATTATACATGTATCACCTTCCAGCCTGACTTATCTAAGTTTAAAATGCAAAGCCTGGACAAAGATATTGTTGCACTGATGGTCAGAAGAGCATATGATATCGCTGGCTCCACTAAAGATGTCAAAGTCTTTCTTAATGGAAATAGTCTGCCAGTGAAAGGATTCCGCAGTTACGTGGATTTGTATTTGAAGGATAAGGTAGATGAAACTGGGAATTCACTGAAGGTGATACATGAACAGGTCAATCCCCGGTGGGAAGTGTGCTTAACAATGAGCGAGAGAGGCTTCCAGCAGATTAGCTTCGTCAACAGCATTGCGACTTCTAAGGGCGGCAGACATGTCGATTATGTAGCTGATCAGATTGTGAGCAAACTCGTTGATGTGGTGAAAAAGAAGAACAAGGGCGGGGTTGCAGTGAAGGCTCATCAGGTGAAAAATCACATGTGGATTTTTGTAAATGCCTTAATTGAAAACCCAACCTTTGACTCTCAAACAAAAGAAAACATGACTTTACAAGCCAAGAGCTTTGGATCAACATGTCAATTAAGTGAAAAGTTCATCAAAGCTGCAATTGGTTGTGGTATTGTGGAAAGCATACTAAACTGGGTGAAGTTCAAGGCTCAAATCCAACTGAACAAGAAGTGTTCAGCTGTAAAACATACCAAAATCAAGGGAATCCCCAAACTTGATGATGCCAACGATGCAGGGAGCCGAAACTCTACTGAATGCACACTTATCCTGACTGAGGGAGACTCAGCAAAAACTCTAGCCGTTTCAGGCCTTGGAGTGGTTGGAAGAGACAAATATGGGGTGTTCCCTCTTAGAGGAAAGATACTCAATGTGCGAGAAGCCTCTCATAAACAGATCATGGAAAATGCTGAAATTAACAATATCATCAAGATTGTGGGTCTCCAGTACAAGAAAAACTATGAAGATGAAGATTCATTGAAAACTCTTCGTTATGGGAAGATCATGATTATGACAGATCAGGACCAAGATGGTTCCCACATCAAAGGCTTGCTGATCAATTTTATCCATCACAATTGGCCATCTCTTCTGCGACATCGTTTTCTAGAAGAATTTATCACTCCCATTGTAAAGGTGTCCAAAAATAAGCAAGAAATAGCATTCTATAGTCTTCCCGAGTTTGAAGAATGGAAAAGTTCGACTCCGAATCATAAAAAGTGGAAAGTCAAATACTACAAAGGTTTGGGCACCAGCACATCAAAGGAAGCTAAGGAATATTTTGCAGATATGAAACGACATCGTATTCAGTTCAAATACTCTGGCCCTGAAGATGATGCTGCGATCAGCCTGAGAAAATAA
Peptide sequence:
MFKQTWMDNMGRAGDMELKPFSGEDYTCITFQPDLSKFKMQSLDKDIVALMVRRAYDIAGSTKDVKVFLNGNSLPVKGFRSYVDLYLKDKVDETGNSLKVIHEQVNPRWEVCLTMSERGFQQISFVNSIATSKGGRHVDYVADQIVSKLVDVVKKKNKGGVAVKAHQVKNHMWIFVNALIENPTFDSQTKENMTLQAKSFGSTCQLSEKFIKAAIGCGIVESILNWVKFKAQIQLNKKCSAVKHTKIKGIPKLDDANDAGSRNSTECTLILTEGDSAKTLAVSGLGVVGRDKYGVFPLRGKILNVREASHKQIMENAEINNIIKIVGLQYKKNYEDEDSLKTLRYGKIMIMTDQDQDGSHIKGLLINFIHHNWPSLLRHRFLEEFITPIVKVSKNKQEIAFYSLPEFEEWKSSTPNHKKWKVKYYKGLGTSTSKEAKEYFADMKRHRIQFKYSGPEDDAAISLRK
IRESfinder result
IRESfinder score
0.512865415
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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