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mmu_circVps54_235
Basic information of circular RNA
PanCircBase ID:
mmu_circVps54_235
mm39_Chr. Position ID:
chr11|21241032|21242131|+
Gene name:
Vps54
Transcript:
ENSMUST00000109578.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
8,9
Exon/intron offsets:
0,991
Genomic length:
1099
Exon/intron sizes in nt:
1,27,108
Flanking exon/introns:
chr11:21228060-21241032|chr11:21242131-21245340
Splice length:
235
Other database IDs:
circAtlas: mmu-Vps54_0018
Human Ortholog IDs:
Mature spliced Sequence:
GCATTTGGGATCACAGCTTTGTGAATTAGAAAAGCTGATTGATAAAATGATGATTGCAGAATTTTCTACTTATTCTCATAGTGACTTAAATAGACCACTGGAAGGTGAATGCCAAGTTTTAGAAGAGGAAAGATTAGTATCTCTTGTATTTGGGCTTTTGAAACAAAGAAAACTTAATTTTTTAGAAATCTATGGTGAAGAAATGATTATTACAGCAAAGAACATCATTAAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGGCTTTTGAAACAAAGAAAACT
58.44
TGCAATCATCATTTTATCAATCAGCT
58.28
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGGCTTTTGAAACAAAGAAAACT
58.44
TCTGCAATCATCATTTTATCAATCAGC
59.13
145
PCR template sequence:
AGTATCTCTTGTATTTGGGCTTTTGAAACAAAGAAAACTTAATTTTTTAGAAATCTATGGTGAAGAAATGATTATTACAGCAAAGAACATCATTAAAGAGGCATTTGGGATCACAGCTTTGTGAATTAGAAAAGCTGATTGATAAAATGATGATTGCAGAATTTTCTACTTATTCTCATAGTGACTTAAATAGACCACTG
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-320-3p(1), mmu-miR-381-3p(1), mmu-miR-224-5p(1), mmu-miR-350-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CATCATTAAAGAGGCATTTGGGATCA
siRNA sets
AAATGCCTCTTTAATGATG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVPS54_235_ORF_1
0.8866
-0.156123589
0.062586029
213
ORF sequence:
ATGATGATTGCAGAATTTTCTACTTATTCTCATAGTGACTTAAATAGACCACTGGAAGGTGAATGCCAAGTTTTAGAAGAGGAAAGATTAGTATCTCTTGTATTTGGGCTTTTGAAACAAAGAAAACTTAATTTTTTAGAAATCTATGGTGAAGAAATGATTATTACAGCAAAGAACATCATTAAAGAGGCATTTGGGATCACAGCTTTGTGA
Peptide sequence:
MMIAEFSTYSHSDLNRPLEGECQVLEEERLVSLVFGLLKQRKLNFLEIYGEEMIITAKNIIKEAFGITAL
IRESfinder result
IRESfinder score
0.827180795
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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