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mmu_circCdc42bpa_1293
Basic information of circular RNA
PanCircBase ID:
mmu_circCdc42bpa_1293
mm39_Chr. Position ID:
chr1|179864393|179912070|+
Gene name:
Cdc42bpa
Transcript:
ENSMUST00000097453.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
4,5,6,7,8,9,10,11,12
Exon/intron offsets:
0,3223,24961,28137,30322,32468,35516,37741,47543
Genomic length:
47677
Exon/intron sizes in nt:
9,61,49,94,20,12,49,80,00,00,00,000
Flanking exon/introns:
chr1:179859153-179864393|chr1:179912070-179921508
Splice length:
1293
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ACAGCGTGCTTTCGTGAAGAGAGGGATGTGTTGGTAAATGGAGACAGTAAGTGGATAACCACTCTGCACTATGCTTTCCAGGATGACAATAACTTATACCTGGTTATGGATTATTATGTTGGTGGGGATTTACTTACTCTGCTCAGCAAATTTGAAGATAGATTGCCTGAAGAGATGGCTCGGTTTTACTTGGCTGAGATGGTGATAGCCATTGACTCAGTTCACCAGCTCCACTATGTTCACAGAGACATCAAACCTGACAATATATTGATGGATATGAATGGACATATTCGTTTAGCAGATTTTGGTTCTTGTCTGAAGCTGATGGAAGATGGAACGGTCCAGTCCTCGGTGGCAGTTGGAACTCCAGATTATATTTCTCCGGAAATCCTTCAGGCTATGGAAGACGGAAAAGGCAGATATGGACCAGAGTGTGACTGGTGGTCCTTGGGGGTCTGTATGTATGAGATGCTTTACGGAGAAACACCATTCTATGCAGAGTCTCTGGTGGAGACATATGGAAAAATTATGAATCACAAAGAGCGGTTTCAGTTTCCAGCCCAAGTGACAGACGTGTCCGAAAATGCTAAAGATCTTATTCGAAGACTCATTTGTAGTAGAGAACATCGACTTGGCCAAAATGGAATAGAAGACTTTAAGAAGCATCCATTCTTCAGTGGAATTGATTGGGATAACATTCGGAATTGTGAAGCACCTTACATCCCAGAAGTTAGTAGCCCGACAGATACGTCAAATTTTGATGTGGATGACGACTGTTTAAAAAATTCTGAAACAATGCCCCCACCAACACATACTGCATTTTCTGGCCATCATCTACCATTTGTTGGTTTTACATATACTAGTAGCTGTGTTCTTTCTGATCGGAGCTGTTTAAGAGTCACAGCAGGCCCCACCTCATTGGACCTTGATGTCAGTGTCCAGAGGACTCTAGACAATAACTTAGCAACTGAGGCTTATGAAAGGAGAATTAAGCGGCTTGAGCAGGAAAAGCTTGAACTGACTAGAAAACTTCAAGAGTCAACACAGACTGTTCAAGCTCTGCAATATTCAACTGTTGATGGTCCACTAACGGCAAGCAAAGATTTAGAAATTAAAAGTCTGAAAGAAGAGATTGAAAAACTAAGGAAACAAGTAGCAGAAGTGAATCATTTGGAACAACAACTTGAAGAAGCTAATTCTGTGAGACGAGAACTAGATGATGCTTTCAGGCAAATCAAAGCTTCTGAAAAACAAATCAAAACTTTGCAGCAGGAAAGAGAAGAACTAAATAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTTTCAGGCAAATCAAAGCT
57.96
GTCATCCTGGAAAGCATAGTGC
59.38
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTTTCAGGCAAATCAAAGCT
57.96
TCATCCTGGAAAGCATAGTGC
58.08
158
PCR template sequence:
TAATTCTGTGAGACGAGAACTAGATGATGCTTTCAGGCAAATCAAAGCTTCTGAAAAACAAATCAAAACTTTGCAGCAGGAAAGAGAAGAACTAAATAAGACAGCGTGCTTTCGTGAAGAGAGGGATGTGTTGGTAAATGGAGACAGTAAGTGGATAACCACTCTGCACTATGCTTTCCAGGATGACAATAACTTATACC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-140-5p(1), mmu-miR-18a-5p(1), mmu-miR-132-3p(1), mmu-miR-138-5p(1), mmu-miR-212-3p(1), mmu-miR-382-5p(1), mmu-miR-383-5p(1), mmu-miR-466d-3p(1), mmu-miR-1198-5p(1), mmu-miR-539-5p(1), mmu-miR-466b-3p(1), mmu-miR-3061-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAACTAAATAAGACAGCGTGCTTTC
siRNA sets
AAAGCACGCTGTCTTATTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDC42BPA_1293_ORF_1
1.0671
0.090195582
0.999999679
2481
ORF sequence:
ATGGATTATTATGTTGGTGGGGATTTACTTACTCTGCTCAGCAAATTTGAAGATAGATTGCCTGAAGAGATGGCTCGGTTTTACTTGGCTGAGATGGTGATAGCCATTGACTCAGTTCACCAGCTCCACTATGTTCACAGAGACATCAAACCTGACAATATATTGATGGATATGAATGGACATATTCGTTTAGCAGATTTTGGTTCTTGTCTGAAGCTGATGGAAGATGGAACGGTCCAGTCCTCGGTGGCAGTTGGAACTCCAGATTATATTTCTCCGGAAATCCTTCAGGCTATGGAAGACGGAAAAGGCAGATATGGACCAGAGTGTGACTGGTGGTCCTTGGGGGTCTGTATGTATGAGATGCTTTACGGAGAAACACCATTCTATGCAGAGTCTCTGGTGGAGACATATGGAAAAATTATGAATCACAAAGAGCGGTTTCAGTTTCCAGCCCAAGTGACAGACGTGTCCGAAAATGCTAAAGATCTTATTCGAAGACTCATTTGTAGTAGAGAACATCGACTTGGCCAAAATGGAATAGAAGACTTTAAGAAGCATCCATTCTTCAGTGGAATTGATTGGGATAACATTCGGAATTGTGAAGCACCTTACATCCCAGAAGTTAGTAGCCCGACAGATACGTCAAATTTTGATGTGGATGACGACTGTTTAAAAAATTCTGAAACAATGCCCCCACCAACACATACTGCATTTTCTGGCCATCATCTACCATTTGTTGGTTTTACATATACTAGTAGCTGTGTTCTTTCTGATCGGAGCTGTTTAAGAGTCACAGCAGGCCCCACCTCATTGGACCTTGATGTCAGTGTCCAGAGGACTCTAGACAATAACTTAGCAACTGAGGCTTATGAAAGGAGAATTAAGCGGCTTGAGCAGGAAAAGCTTGAACTGACTAGAAAACTTCAAGAGTCAACACAGACTGTTCAAGCTCTGCAATATTCAACTGTTGATGGTCCACTAACGGCAAGCAAAGATTTAGAAATTAAAAGTCTGAAAGAAGAGATTGAAAAACTAAGGAAACAAGTAGCAGAAGTGAATCATTTGGAACAACAACTTGAAGAAGCTAATTCTGTGAGACGAGAACTAGATGATGCTTTCAGGCAAATCAAAGCTTCTGAAAAACAAATCAAAACTTTGCAGCAGGAAAGAGAAGAACTAAATAAGACAGCGTGCTTTCGTGAAGAGAGGGATGTGTTGGTAAATGGAGACAGTAAGTGGATAACCACTCTGCACTATGCTTTCCAGGATGACAATAACTTATACCTGGTTATGGATTATTATGTTGGTGGGGATTTACTTACTCTGCTCAGCAAATTTGAAGATAGATTGCCTGAAGAGATGGCTCGGTTTTACTTGGCTGAGATGGTGATAGCCATTGACTCAGTTCACCAGCTCCACTATGTTCACAGAGACATCAAACCTGACAATATATTGATGGATATGAATGGACATATTCGTTTAGCAGATTTTGGTTCTTGTCTGAAGCTGATGGAAGATGGAACGGTCCAGTCCTCGGTGGCAGTTGGAACTCCAGATTATATTTCTCCGGAAATCCTTCAGGCTATGGAAGACGGAAAAGGCAGATATGGACCAGAGTGTGACTGGTGGTCCTTGGGGGTCTGTATGTATGAGATGCTTTACGGAGAAACACCATTCTATGCAGAGTCTCTGGTGGAGACATATGGAAAAATTATGAATCACAAAGAGCGGTTTCAGTTTCCAGCCCAAGTGACAGACGTGTCCGAAAATGCTAAAGATCTTATTCGAAGACTCATTTGTAGTAGAGAACATCGACTTGGCCAAAATGGAATAGAAGACTTTAAGAAGCATCCATTCTTCAGTGGAATTGATTGGGATAACATTCGGAATTGTGAAGCACCTTACATCCCAGAAGTTAGTAGCCCGACAGATACGTCAAATTTTGATGTGGATGACGACTGTTTAAAAAATTCTGAAACAATGCCCCCACCAACACATACTGCATTTTCTGGCCATCATCTACCATTTGTTGGTTTTACATATACTAGTAGCTGTGTTCTTTCTGATCGGAGCTGTTTAAGAGTCACAGCAGGCCCCACCTCATTGGACCTTGATGTCAGTGTCCAGAGGACTCTAGACAATAACTTAGCAACTGAGGCTTATGAAAGGAGAATTAAGCGGCTTGAGCAGGAAAAGCTTGAACTGACTAGAAAACTTCAAGAGTCAACACAGACTGTTCAAGCTCTGCAATATTCAACTGTTGATGGTCCACTAACGGCAAGCAAAGATTTAGAAATTAAAAGTCTGAAAGAAGAGATTGAAAAACTAAGGAAACAAGTAGCAGAAGTGAATCATTTGGAACAACAACTTGAAGAAGCTAATTCTGTGAGACGAGAACTAGATGATGCTTTCAGGCAAATCAAAGCTTCTGAAAAACAAATCAAAACTTTGCAGCAGGAAAGAGAAGAACTAAATAAG
Peptide sequence:
MDYYVGGDLLTLLSKFEDRLPEEMARFYLAEMVIAIDSVHQLHYVHRDIKPDNILMDMNGHIRLADFGSCLKLMEDGTVQSSVAVGTPDYISPEILQAMEDGKGRYGPECDWWSLGVCMYEMLYGETPFYAESLVETYGKIMNHKERFQFPAQVTDVSENAKDLIRRLICSREHRLGQNGIEDFKKHPFFSGIDWDNIRNCEAPYIPEVSSPTDTSNFDVDDDCLKNSETMPPPTHTAFSGHHLPFVGFTYTSSCVLSDRSCLRVTAGPTSLDLDVSVQRTLDNNLATEAYERRIKRLEQEKLELTRKLQESTQTVQALQYSTVDGPLTASKDLEIKSLKEEIEKLRKQVAEVNHLEQQLEEANSVRRELDDAFRQIKASEKQIKTLQQEREELNKTACFREERDVLVNGDSKWITTLHYAFQDDNNLYLVMDYYVGGDLLTLLSKFEDRLPEEMARFYLAEMVIAIDSVHQLHYVHRDIKPDNILMDMNGHIRLADFGSCLKLMEDGTVQSSVAVGTPDYISPEILQAMEDGKGRYGPECDWWSLGVCMYEMLYGETPFYAESLVETYGKIMNHKERFQFPAQVTDVSENAKDLIRRLICSREHRLGQNGIEDFKKHPFFSGIDWDNIRNCEAPYIPEVSSPTDTSNFDVDDDCLKNSETMPPPTHTAFSGHHLPFVGFTYTSSCVLSDRSCLRVTAGPTSLDLDVSVQRTLDNNLATEAYERRIKRLEQEKLELTRKLQESTQTVQALQYSTVDGPLTASKDLEIKSLKEEIEKLRKQVAEVNHLEQQLEEANSVRRELDDAFRQIKASEKQIKTLQQEREELNK
IRESfinder result
IRESfinder score
0.632540038
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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