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mmu_circCdc42bpa_504
Basic information of circular RNA
PanCircBase ID:
mmu_circCdc42bpa_504
mm39_Chr. Position ID:
chr1|179896861|179912070|+
Gene name:
Cdc42bpa
Transcript:
ENSMUST00000097453.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
9,10,11,12
Exon/intron offsets:
0,3048,5273,15075
Genomic length:
15209
Exon/intron sizes in nt:
80,16,71,23,134
Flanking exon/introns:
chr1:179894964-179896861|chr1:179912070-179921508
Splice length:
504
Other database IDs:
CIRCpedia: MMU_CIRCpedia_226777, circAtlas: mmu-Cdc42bpa_0056
Human Ortholog IDs:
Mature spliced Sequence:
GAAACAATGCCCCCACCAACACATACTGCATTTTCTGGCCATCATCTACCATTTGTTGGTTTTACATATACTAGTAGCTGTGTTCTTTCTGATCGGAGCTGTTTAAGAGTCACAGCAGGCCCCACCTCATTGGACCTTGATGTCAGTGTCCAGAGGACTCTAGACAATAACTTAGCAACTGAGGCTTATGAAAGGAGAATTAAGCGGCTTGAGCAGGAAAAGCTTGAACTGACTAGAAAACTTCAAGAGTCAACACAGACTGTTCAAGCTCTGCAATATTCAACTGTTGATGGTCCACTAACGGCAAGCAAAGATTTAGAAATTAAAAGTCTGAAAGAAGAGATTGAAAAACTAAGGAAACAAGTAGCAGAAGTGAATCATTTGGAACAACAACTTGAAGAAGCTAATTCTGTGAGACGAGAACTAGATGATGCTTTCAGGCAAATCAAAGCTTCTGAAAAACAAATCAAAACTTTGCAGCAGGAAAGAGAAGAACTAAATAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTTTCAGGCAAATCAAAGCT
57.96
TCCGATCAGAAAGAACACAGCT
59.7
169
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTTTCAGGCAAATCAAAGCT
57.96
AGCTCCGATCAGAAAGAACACA
59.7
172
PCR template sequence:
TAATTCTGTGAGACGAGAACTAGATGATGCTTTCAGGCAAATCAAAGCTTCTGAAAAACAAATCAAAACTTTGCAGCAGGAAAGAGAAGAACTAAATAAGGAAACAATGCCCCCACCAACACATACTGCATTTTCTGGCCATCATCTACCATTTGTTGGTTTTACATATACTAGTAGCTGTGTTCTTTCTGATCGGAGCT
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-382-5p(1), mmu-miR-383-5p(1), mmu-miR-1198-5p(1), mmu-miR-3061-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAACTAAATAAGGAAACAATGCCCC
siRNA sets
ATTGTTTCCTTATTTAGTT, TTGTTTCCTTATTTAGTTC, CATTGTTTCCTTATTTAGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDC42BPA_504_ORF_1
1.0816
-0.003345361
0.98132678
1002
ORF sequence:
ATGCCCCCACCAACACATACTGCATTTTCTGGCCATCATCTACCATTTGTTGGTTTTACATATACTAGTAGCTGTGTTCTTTCTGATCGGAGCTGTTTAAGAGTCACAGCAGGCCCCACCTCATTGGACCTTGATGTCAGTGTCCAGAGGACTCTAGACAATAACTTAGCAACTGAGGCTTATGAAAGGAGAATTAAGCGGCTTGAGCAGGAAAAGCTTGAACTGACTAGAAAACTTCAAGAGTCAACACAGACTGTTCAAGCTCTGCAATATTCAACTGTTGATGGTCCACTAACGGCAAGCAAAGATTTAGAAATTAAAAGTCTGAAAGAAGAGATTGAAAAACTAAGGAAACAAGTAGCAGAAGTGAATCATTTGGAACAACAACTTGAAGAAGCTAATTCTGTGAGACGAGAACTAGATGATGCTTTCAGGCAAATCAAAGCTTCTGAAAAACAAATCAAAACTTTGCAGCAGGAAAGAGAAGAACTAAATAAGGAAACAATGCCCCCACCAACACATACTGCATTTTCTGGCCATCATCTACCATTTGTTGGTTTTACATATACTAGTAGCTGTGTTCTTTCTGATCGGAGCTGTTTAAGAGTCACAGCAGGCCCCACCTCATTGGACCTTGATGTCAGTGTCCAGAGGACTCTAGACAATAACTTAGCAACTGAGGCTTATGAAAGGAGAATTAAGCGGCTTGAGCAGGAAAAGCTTGAACTGACTAGAAAACTTCAAGAGTCAACACAGACTGTTCAAGCTCTGCAATATTCAACTGTTGATGGTCCACTAACGGCAAGCAAAGATTTAGAAATTAAAAGTCTGAAAGAAGAGATTGAAAAACTAAGGAAACAAGTAGCAGAAGTGAATCATTTGGAACAACAACTTGAAGAAGCTAATTCTGTGAGACGAGAACTAGATGATGCTTTCAGGCAAATCAAAGCTTCTGAAAAACAAATCAAAACTTTGCAGCAGGAAAGAGAAGAACTAAATAAG
Peptide sequence:
MPPPTHTAFSGHHLPFVGFTYTSSCVLSDRSCLRVTAGPTSLDLDVSVQRTLDNNLATEAYERRIKRLEQEKLELTRKLQESTQTVQALQYSTVDGPLTASKDLEIKSLKEEIEKLRKQVAEVNHLEQQLEEANSVRRELDDAFRQIKASEKQIKTLQQEREELNKETMPPPTHTAFSGHHLPFVGFTYTSSCVLSDRSCLRVTAGPTSLDLDVSVQRTLDNNLATEAYERRIKRLEQEKLELTRKLQESTQTVQALQYSTVDGPLTASKDLEIKSLKEEIEKLRKQVAEVNHLEQQLEEANSVRRELDDAFRQIKASEKQIKTLQQEREELNK
IRESfinder result
IRESfinder score
0.663104893
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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