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mmu_circPde5a_243
Basic information of circular RNA
PanCircBase ID:
mmu_circPde5a_243
mm39_Chr. Position ID:
chr3|122633190|122636757|+
Gene name:
Pde5a
Transcript:
ENSMUST00000066728.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
16,17,18
Exon/intron offsets:
0,1429,3503
Genomic length:
3567
Exon/intron sizes in nt:
101,78,64
Flanking exon/introns:
chr3:122629289-122633190|chr3:122636757-122645298
Splice length:
243
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GGCAACCAGATTCTCAGTGGCCTCTCCATTGACGAATATAAGACCACACTGAAAATAATCAAGCAAGCAATTTTAGCCACAGACCTAGCACTGTACATTAAGAGACGAGGAGAATTTTTTGAACTTATACGAAAAAATCAATTCAGTTTTGAAGATCCTCTTCAAAAGGAGTTGTTTCTAGCAATGCTGATGACAGCCTGCGACCTCTCTGCGATTACTAAACCCTGGCCTATTCAACAACGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCGACCTCTCTGCGATTAC
59.9
TACAGTGCTAGGTCTGTGGC
59.1
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGCGACCTCTCTGCGATTA
59.62
ACAGTGCTAGGTCTGTGGCT
60.83
140
PCR template sequence:
CAGTTTTGAAGATCCTCTTCAAAAGGAGTTGTTTCTAGCAATGCTGATGACAGCCTGCGACCTCTCTGCGATTACTAAACCCTGGCCTATTCAACAACGGGGCAACCAGATTCTCAGTGGCCTCTCCATTGACGAATATAAGACCACACTGAAAATAATCAAGCAAGCAATTTTAGCCACAGACCTAGCACTGTACATTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
NA
Interacting miRNAs (#binding sites)
NA
siRNAs for circular RNA silencing
Junction sequence
TATTCAACAACGGGGCAACCAGATTC
siRNA sets
GAATCTGGTTGCCCCGTTG, AATCTGGTTGCCCCGTTGT, ATCTGGTTGCCCCGTTGTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDE5A_243_ORF_1
0.8435
0.083015574
0.238682058
303
ORF sequence:
ATGCTGATGACAGCCTGCGACCTCTCTGCGATTACTAAACCCTGGCCTATTCAACAACGGGGCAACCAGATTCTCAGTGGCCTCTCCATTGACGAATATAAGACCACACTGAAAATAATCAAGCAAGCAATTTTAGCCACAGACCTAGCACTGTACATTAAGAGACGAGGAGAATTTTTTGAACTTATACGAAAAAATCAATTCAGTTTTGAAGATCCTCTTCAAAAGGAGTTGTTTCTAGCAATGCTGATGACAGCCTGCGACCTCTCTGCGATTACTAAACCCTGGCCTATTCAACAACGG
Peptide sequence:
MLMTACDLSAITKPWPIQQRGNQILSGLSIDEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFSFEDPLQKELFLAMLMTACDLSAITKPWPIQQR
IRESfinder result
IRESfinder score
0.673821486
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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