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mmu_circTop3a_1031
Basic information of circular RNA
PanCircBase ID:
mmu_circTop3a_1031
mm39_Chr. Position ID:
chr11|60636642|60643191|-
Gene name:
Top3a
Transcript:
ENSMUST00000002891.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
16,15,14,13,12,11,10
Exon/intron offsets:
0,2049,2295,3349,3587,4759,6466
Genomic length:
6549
Exon/intron sizes in nt:
144,166,114,130,186,208,83
Flanking exon/introns:
chr11:60634881-60636642|chr11:60643191-60644712
Splice length:
1031
Other database IDs:
CIRCpedia: MMU_CIRCpedia_229808, circAtlas: mmu-Top3a_0010
Human Ortholog IDs:
Mature spliced Sequence:
GAGCTAGAGAAACTGGCATCTCGGAAATTGAGAATAAATGCCAAAGAAACCATGAGGATCGCGGAAAAGCTCTATACACAAGGGTACATCAGCTACCCCCGGACAGAAACAAACATCTTCCCCAAAGACTTAAACCTGGTTGCATTGGTAGAACAGCAGACCGTGGATCCACACTGGGGGGCTTTTGCTCAGACCATTCTAGAGCGAGGTGGCCCTACTCCCCGAAACGGGAGCAAGTCTGATCAAGCTCACCCTCCCATTCACCCCACCAAATACACCAGCGGCTTGCAGGGAGATGATCGGCGACTGTACGAGTTCATTGTTCGCCATTTCCTGGCTTGCTGCTCTCAGGACGCTCAGGGGCAAGAGACTACCGTAGAGATCGACATTGCCCAAGAGCGCTTTGTGGCCCACGGGCTCATCATTCTGGCCCGTAACTACCTAGATGTGTATCCGTATGATCACTGGAGTGACAAGCTCCTCCCCGTCTATGAACAAGGCTCCCACTTCCAGCCCAGCACTGTGGAAATGGTGGATGGAGAGACTAGCCCACCCCAACTGCTTACCGAAGCTGACCTCATCGCCCTCATGGAGAAACATGGGATCGGTACTGATGCAACTCATGCAGAACACATTGAGACCATCAAAGCCCGGATGTATGTGGGACTCACCTCAGACAAGCGGTTCCTGCCGGGGCACCTGGGCATGGGACTTGTAGAAGGTTACGATTCCATGGGTTATGAGATGTCCAAGCCTGACCTCCGTGCCGAGCTGGAAGCTGATCTCAAGCTGATCTGTGAGGGCAAGAAGGATAAGTTTCAAGTTCTAAGGCAGCAAGTGCAAAAATACAAGCAGGTTTTCATTGAAGCAGTGGCGAAGGCAAAGAAGTTGGATGAGGCTTTATCTCAGTACTTAGGAGAAAGAACAGAGATGGCCCAGCAAGAAGAGATCTACCCAGCCATGCCAGAGCCTGTTCGGAAGTGCCCACAGTGTAACAAGGATATGGTCCTCAAGACCAAGAAGAGTGGTGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGATCTACCCAGCCATGCC
59.96
AGCTTTTCCGCGATCCTCAT
59.82
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGATCTACCCAGCCATGCC
59.96
CCGCGATCCTCATGGTTTCT
60.18
150
PCR template sequence:
TGGCCCAGCAAGAAGAGATCTACCCAGCCATGCCAGAGCCTGTTCGGAAGTGCCCACAGTGTAACAAGGATATGGTCCTCAAGACCAAGAAGAGTGGTGGGAGCTAGAGAAACTGGCATCTCGGAAATTGAGAATAAATGCCAAAGAAACCATGAGGATCGCGGAAAAGCTCTATACACAAGGGTACATCAGCTACCCCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-322-5p(1), mmu-miR-351-5p(1), mmu-miR-676-3p(1), mmu-miR-483-5p(1), mmu-miR-1198-5p(1), mmu-miR-669d-5p(1), mmu-miR-188-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAAGAGTGGTGGGAGCTAGAGAAAC
siRNA sets
TTTCTCTAGCTCCCACCAC, TTCTCTAGCTCCCACCACT, TAGCTCCCACCACTCTTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTOP3A_1031_ORF_1
1.2538
0.386852941
0.996809937
987
ORF sequence:
ATGAGGATCGCGGAAAAGCTCTATACACAAGGGTACATCAGCTACCCCCGGACAGAAACAAACATCTTCCCCAAAGACTTAAACCTGGTTGCATTGGTAGAACAGCAGACCGTGGATCCACACTGGGGGGCTTTTGCTCAGACCATTCTAGAGCGAGGTGGCCCTACTCCCCGAAACGGGAGCAAGTCTGATCAAGCTCACCCTCCCATTCACCCCACCAAATACACCAGCGGCTTGCAGGGAGATGATCGGCGACTGTACGAGTTCATTGTTCGCCATTTCCTGGCTTGCTGCTCTCAGGACGCTCAGGGGCAAGAGACTACCGTAGAGATCGACATTGCCCAAGAGCGCTTTGTGGCCCACGGGCTCATCATTCTGGCCCGTAACTACCTAGATGTGTATCCGTATGATCACTGGAGTGACAAGCTCCTCCCCGTCTATGAACAAGGCTCCCACTTCCAGCCCAGCACTGTGGAAATGGTGGATGGAGAGACTAGCCCACCCCAACTGCTTACCGAAGCTGACCTCATCGCCCTCATGGAGAAACATGGGATCGGTACTGATGCAACTCATGCAGAACACATTGAGACCATCAAAGCCCGGATGTATGTGGGACTCACCTCAGACAAGCGGTTCCTGCCGGGGCACCTGGGCATGGGACTTGTAGAAGGTTACGATTCCATGGGTTATGAGATGTCCAAGCCTGACCTCCGTGCCGAGCTGGAAGCTGATCTCAAGCTGATCTGTGAGGGCAAGAAGGATAAGTTTCAAGTTCTAAGGCAGCAAGTGCAAAAATACAAGCAGGTTTTCATTGAAGCAGTGGCGAAGGCAAAGAAGTTGGATGAGGCTTTATCTCAGTACTTAGGAGAAAGAACAGAGATGGCCCAGCAAGAAGAGATCTACCCAGCCATGCCAGAGCCTGTTCGGAAGTGCCCACAGTGTAACAAGGATATGGTCCTCAAGACCAAGAAGAGTGGTGGGAGCTAG
Peptide sequence:
MRIAEKLYTQGYISYPRTETNIFPKDLNLVALVEQQTVDPHWGAFAQTILERGGPTPRNGSKSDQAHPPIHPTKYTSGLQGDDRRLYEFIVRHFLACCSQDAQGQETTVEIDIAQERFVAHGLIILARNYLDVYPYDHWSDKLLPVYEQGSHFQPSTVEMVDGETSPPQLLTEADLIALMEKHGIGTDATHAEHIETIKARMYVGLTSDKRFLPGHLGMGLVEGYDSMGYEMSKPDLRAELEADLKLICEGKKDKFQVLRQQVQKYKQVFIEAVAKAKKLDEALSQYLGERTEMAQQEEIYPAMPEPVRKCPQCNKDMVLKTKKSGGS
IRESfinder result
IRESfinder score
0.406352607
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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