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mmu_circCdc42bpa_965
Basic information of circular RNA
PanCircBase ID:
mmu_circCdc42bpa_965
mm39_Chr. Position ID:
chr1|179826926|179894964|+
Gene name:
Cdc42bpa
Transcript:
ENSMUST00000097453.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
2,3,4,5,6,7,8
Exon/intron offsets:
0,32143,37467,40690,62428,65604,67789
Genomic length:
68038
Exon/intron sizes in nt:
92,84,96,14,99,42,01,200
Flanking exon/introns:
chr1:179788852-179826926|chr1:179894964-179896861
Splice length:
965
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CTAAACCATTTACTTCTAAAGTGAAGCAAATGCGATTACATAGAGAAGACTTTGAAATATTAAAGGTGATTGGTCGAGGAGCTTTTGGGGAGGTTGCTGTAGTTAAACTAAAAAATGCAGATAAAGTATTCGCCATGAAAATTCTGAACAAGTGGGAAATGCTGAAAAGAGCTGAGACAGCGTGCTTTCGTGAAGAGAGGGATGTGTTGGTAAATGGAGACAGTAAGTGGATAACCACTCTGCACTATGCTTTCCAGGATGACAATAACTTATACCTGGTTATGGATTATTATGTTGGTGGGGATTTACTTACTCTGCTCAGCAAATTTGAAGATAGATTGCCTGAAGAGATGGCTCGGTTTTACTTGGCTGAGATGGTGATAGCCATTGACTCAGTTCACCAGCTCCACTATGTTCACAGAGACATCAAACCTGACAATATATTGATGGATATGAATGGACATATTCGTTTAGCAGATTTTGGTTCTTGTCTGAAGCTGATGGAAGATGGAACGGTCCAGTCCTCGGTGGCAGTTGGAACTCCAGATTATATTTCTCCGGAAATCCTTCAGGCTATGGAAGACGGAAAAGGCAGATATGGACCAGAGTGTGACTGGTGGTCCTTGGGGGTCTGTATGTATGAGATGCTTTACGGAGAAACACCATTCTATGCAGAGTCTCTGGTGGAGACATATGGAAAAATTATGAATCACAAAGAGCGGTTTCAGTTTCCAGCCCAAGTGACAGACGTGTCCGAAAATGCTAAAGATCTTATTCGAAGACTCATTTGTAGTAGAGAACATCGACTTGGCCAAAATGGAATAGAAGACTTTAAGAAGCATCCATTCTTCAGTGGAATTGATTGGGATAACATTCGGAATTGTGAAGCACCTTACATCCCAGAAGTTAGTAGCCCGACAGATACGTCAAATTTTGATGTGGATGACGACTGTTTAAAAAATTCT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCCCGACAGATACGTCAAA
59.11
CAACCTCCCCAAAAGCTCCT
59.89
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCCAGAAGTTAGTAGCCCGA
59.99
CAACCTCCCCAAAAGCTCCT
59.89
164
PCR template sequence:
GGATAACATTCGGAATTGTGAAGCACCTTACATCCCAGAAGTTAGTAGCCCGACAGATACGTCAAATTTTGATGTGGATGACGACTGTTTAAAAAATTCTCTAAACCATTTACTTCTAAAGTGAAGCAAATGCGATTACATAGAGAAGACTTTGAAATATTAAAGGTGATTGGTCGAGGAGCTTTTGGGGAGGTTGCTGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
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-466d-3p(1), mmu-miR-539-5p(1), mmu-miR-466b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTAAAAAATTCTCTAAACCATTTAC
siRNA sets
AAATGGTTTAGAGAATTTT, TAAATGGTTTAGAGAATTT, AATGGTTTAGAGAATTTTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDC42BPA_965_ORF_1
0.9351
0.125344091
0.979981642
960
ORF sequence:
ATGCGATTACATAGAGAAGACTTTGAAATATTAAAGGTGATTGGTCGAGGAGCTTTTGGGGAGGTTGCTGTAGTTAAACTAAAAAATGCAGATAAAGTATTCGCCATGAAAATTCTGAACAAGTGGGAAATGCTGAAAAGAGCTGAGACAGCGTGCTTTCGTGAAGAGAGGGATGTGTTGGTAAATGGAGACAGTAAGTGGATAACCACTCTGCACTATGCTTTCCAGGATGACAATAACTTATACCTGGTTATGGATTATTATGTTGGTGGGGATTTACTTACTCTGCTCAGCAAATTTGAAGATAGATTGCCTGAAGAGATGGCTCGGTTTTACTTGGCTGAGATGGTGATAGCCATTGACTCAGTTCACCAGCTCCACTATGTTCACAGAGACATCAAACCTGACAATATATTGATGGATATGAATGGACATATTCGTTTAGCAGATTTTGGTTCTTGTCTGAAGCTGATGGAAGATGGAACGGTCCAGTCCTCGGTGGCAGTTGGAACTCCAGATTATATTTCTCCGGAAATCCTTCAGGCTATGGAAGACGGAAAAGGCAGATATGGACCAGAGTGTGACTGGTGGTCCTTGGGGGTCTGTATGTATGAGATGCTTTACGGAGAAACACCATTCTATGCAGAGTCTCTGGTGGAGACATATGGAAAAATTATGAATCACAAAGAGCGGTTTCAGTTTCCAGCCCAAGTGACAGACGTGTCCGAAAATGCTAAAGATCTTATTCGAAGACTCATTTGTAGTAGAGAACATCGACTTGGCCAAAATGGAATAGAAGACTTTAAGAAGCATCCATTCTTCAGTGGAATTGATTGGGATAACATTCGGAATTGTGAAGCACCTTACATCCCAGAAGTTAGTAGCCCGACAGATACGTCAAATTTTGATGTGGATGACGACTGTTTAAAAAATTCTCTAAACCATTTACTTCTAAAGTGA
Peptide sequence:
MRLHREDFEILKVIGRGAFGEVAVVKLKNADKVFAMKILNKWEMLKRAETACFREERDVLVNGDSKWITTLHYAFQDDNNLYLVMDYYVGGDLLTLLSKFEDRLPEEMARFYLAEMVIAIDSVHQLHYVHRDIKPDNILMDMNGHIRLADFGSCLKLMEDGTVQSSVAVGTPDYISPEILQAMEDGKGRYGPECDWWSLGVCMYEMLYGETPFYAESLVETYGKIMNHKERFQFPAQVTDVSENAKDLIRRLICSREHRLGQNGIEDFKKHPFFSGIDWDNIRNCEAPYIPEVSSPTDTSNFDVDDDCLKNSLNHLLLK
IRESfinder result
IRESfinder score
0.605057936
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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