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mmu_ciFocad_517
Basic information of circular RNA
PanCircBase ID:
mmu_ciFocad_517
mm39_Chr. Position ID:
chr4|88148171|88148688|+
Gene name:
Focad
Transcript:
ENSMUST00000097992.10
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
13
Exon/intron offsets:
0
Genomic length:
517
Exon/intron sizes in nt:
517
Flanking exon/introns:
chr4:88148171-88148688
Splice length:
517
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGCTTAGCTATCCAGTTGTTGCATATTAAATGTGCTCTTTTCTCAGAAGAAAATATGGTTGTGTGGCAGAGCTGCTCAGATTTGGTAAGAGCAGTGGGTACCAGCAATGACTACCTTGGCAAATTTTGATTTATTGTGGTGTATTTGATCTGTAAATACAGTCACTTGTGTATGACTCAGAAATTGAGAACATAGAATAATCTTATTGCACTACTTCTGACATTTATCTCTCCGTTTGTATGGGAAAGTAATAGAAATAAGGTTGTGATTAGAGGCTTTGTAGAAAGGGTGAGATCTGGCCACTTGTTTTTCTGGGATGAACAATGCACAGGTCTGCAAGGAAAGCCTCTATAATCACAACAGCATTATTCTCTGCTGATTAGCAGAGATACGTTATAATTTCCAAATGCAAATGCAAGATTTGGAGGTGAAAATGTTGCATAAAGGATAATGATTATTCAGCTCGAGTTAGCAAATTACCTATTTTTGTGTGTGTGTGAAATGATTTTATTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGGAGGTGAAAATGTTGCA
56.05
AGCTCTGCCACACAACCATA
59.31
169
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGGAGGTGAAAATGTTGCA
56.05
CAGCTCTGCCACACAACCAT
60.89
170
PCR template sequence:
GCAAGATTTGGAGGTGAAAATGTTGCATAAAGGATAATGATTATTCAGCTCGAGTTAGCAAATTACCTATTTTTGTGTGTGTGTGAAATGATTTTATTAGGTAAGCTTAGCTATCCAGTTGTTGCATATTAAATGTGCTCTTTTCTCAGAAGAAAATATGGTTGTGTGGCAGAGCTGCTCAGATTTGGTAAGAGCAGTGG
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-155-5p(1), mmu-miR-134-5p(1), mmu-miR-196a-5p(1), mmu-miR-130b-3p(1), mmu-miR-301b-3p(1), mmu-miR-301a-3p(1), mmu-miR-377-3p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATGATTTTATTAGGTAAGCTTAGCTA
siRNA sets
TAAGCTTACCTAATAAAAT, AAGCTTACCTAATAAAATC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIFOCAD_517_ORF_1
0.7012
-0.458092643
0.005803526
96
ORF sequence:
ATGATTATTCAGCTCGAGTTAGCAAATTACCTATTTTTGTGTGTGTGTGAAATGATTTTATTAGGTAAGCTTAGCTATCCAGTTGTTGCATATTAA
Peptide sequence:
MIIQLELANYLFLCVCEMILLGKLSYPVVAY
IRESfinder result
IRESfinder score
0.764655494
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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