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mmu_circPde6c_967
Basic information of circular RNA
PanCircBase ID:
mmu_circPde6c_967
mm39_Chr. Position ID:
chr19|38150338|38169380|+
Gene name:
Pde6c
Transcript:
ENSMUST00000112329.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
12,13,14,15,16,17,18,19,20
Exon/intron offsets:
0,383,870,7486,13744,16157,16367,18280,18885
Genomic length:
19042
Exon/intron sizes in nt:
1,47,10,81,10,88,10,11,00,00,00,000
Flanking exon/introns:
chr19:38148229-38150338|chr19:38169380-38172125
Splice length:
967
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AAGGAGGACTTGCCGGACCCGAGAACAGCAGACCTGTACGAGTTCTGTTTCAGCGACTTCCCCATTACGGAGCACGAGTTGGTTAAATGCGGGCTGAGGCTGTTTTTGGAGATAAACGTGGTGGAGAAATTCAAAGTCCCTGTAGAGGTTCTTACAAGGTGGATGTACACAGTCCGGAAAGGGTACCGTCCTGTCACCTACCACAACTGGCGGCACGGATTCAACGTGGGGCAGACCATGTTCACTTTGTTAATGACAGGAAGACTAAAGAAATACTATACAGACCTTGAAGCCTTTGCCATGCTCGCTGCTGCTTTCTGCCATGACATTGACCACAGAGGCACCAATAACTTGTACCAAATGAAGTCCACATCTCCACTTGCAAGGCTTCATGGGACTTCCATTTTAGAGCGACATCACCTGGAATATAGCAAGACTCTCTTGCAGGATGAGAGTTTAAACATCTTCCAGAATCTAAACAAGCGGCAGTTTGAAACGGTGATCCATTTGTTCGAGGTTGCAATAATAGCAACTGACCTGGCACTCTATTTCAAGAAGAGAACCATGTTTCAAAAGATCGTTGATACCTGCGAGCAGATGCAAAGTGAAGAAGAAACCATCAAATACGTAACCTCCGACCCGACCAAAAAGGAAGTCATCATGGCCATGATGATGACTGCCTGTGACCTGTCTGCCATCACCAAGCCCTGGGAGGTGCAGAGTCAGCCTATGATGGACAGAAGCAAAAAGGATGAACTCCCGAAACTTCAAGTGGGATTTATTGATTTTGTTTGTACTTTCGTATATAAGGAGTTCTCTCGGTTTCATGGAGAGATCACACCCATGCTGAACGGCCTTCAGAATAACAGGGTGGAATGGAAATCCCTGGCGGAGGAGTACGAGGCGAAGGTGAAGGTGACTGAAGAAGAGGCGGGAAAGCAGGAAGAAGAAGCCTCAGATGGAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AATGGAAATCCCTGGCGGAG
60.11
GGGGAAGTCGCTGAAACAGA
59.97
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCGAAGGTGAAGGTGACTGA
59.97
AACTCGTGCTCCGTAATGGG
60.11
144
PCR template sequence:
AGGGTGGAATGGAAATCCCTGGCGGAGGAGTACGAGGCGAAGGTGAAGGTGACTGAAGAAGAGGCGGGAAAGCAGGAAGAAGAAGCCTCAGATGGAAAAGAAGGAGGACTTGCCGGACCCGAGAACAGCAGACCTGTACGAGTTCTGTTTCAGCGACTTCCCCATTACGGAGCACGAGTTGGTTAAATGCGGGCTGAGGC
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-15b-5p(1), mmu-miR-10a-5p(1), mmu-miR-503-5p(1), mmu-miR-541-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCAGATGGAAAAGAAGGAGGACTTGC
siRNA sets
CAAGTCCTCCTTCTTTTCC, AAGTCCTCCTTCTTTTCCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDE6C_967_ORF_1
1.0826
0.296486618
0.993125678
975
ORF sequence:
ATGGAAAAGAAGGAGGACTTGCCGGACCCGAGAACAGCAGACCTGTACGAGTTCTGTTTCAGCGACTTCCCCATTACGGAGCACGAGTTGGTTAAATGCGGGCTGAGGCTGTTTTTGGAGATAAACGTGGTGGAGAAATTCAAAGTCCCTGTAGAGGTTCTTACAAGGTGGATGTACACAGTCCGGAAAGGGTACCGTCCTGTCACCTACCACAACTGGCGGCACGGATTCAACGTGGGGCAGACCATGTTCACTTTGTTAATGACAGGAAGACTAAAGAAATACTATACAGACCTTGAAGCCTTTGCCATGCTCGCTGCTGCTTTCTGCCATGACATTGACCACAGAGGCACCAATAACTTGTACCAAATGAAGTCCACATCTCCACTTGCAAGGCTTCATGGGACTTCCATTTTAGAGCGACATCACCTGGAATATAGCAAGACTCTCTTGCAGGATGAGAGTTTAAACATCTTCCAGAATCTAAACAAGCGGCAGTTTGAAACGGTGATCCATTTGTTCGAGGTTGCAATAATAGCAACTGACCTGGCACTCTATTTCAAGAAGAGAACCATGTTTCAAAAGATCGTTGATACCTGCGAGCAGATGCAAAGTGAAGAAGAAACCATCAAATACGTAACCTCCGACCCGACCAAAAAGGAAGTCATCATGGCCATGATGATGACTGCCTGTGACCTGTCTGCCATCACCAAGCCCTGGGAGGTGCAGAGTCAGCCTATGATGGACAGAAGCAAAAAGGATGAACTCCCGAAACTTCAAGTGGGATTTATTGATTTTGTTTGTACTTTCGTATATAAGGAGTTCTCTCGGTTTCATGGAGAGATCACACCCATGCTGAACGGCCTTCAGAATAACAGGGTGGAATGGAAATCCCTGGCGGAGGAGTACGAGGCGAAGGTGAAGGTGACTGAAGAAGAGGCGGGAAAGCAGGAAGAAGAAGCCTCAGATGGAAAA
Peptide sequence:
MEKKEDLPDPRTADLYEFCFSDFPITEHELVKCGLRLFLEINVVEKFKVPVEVLTRWMYTVRKGYRPVTYHNWRHGFNVGQTMFTLLMTGRLKKYYTDLEAFAMLAAAFCHDIDHRGTNNLYQMKSTSPLARLHGTSILERHHLEYSKTLLQDESLNIFQNLNKRQFETVIHLFEVAIIATDLALYFKKRTMFQKIVDTCEQMQSEEETIKYVTSDPTKKEVIMAMMMTACDLSAITKPWEVQSQPMMDRSKKDELPKLQVGFIDFVCTFVYKEFSRFHGEITPMLNGLQNNRVEWKSLAEEYEAKVKVTEEEAGKQEEEASDGK
IRESfinder result
IRESfinder score
0.49548404
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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