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mmu_circVapa_174
Basic information of circular RNA
PanCircBase ID:
mmu_circVapa_174
mm39_Chr. Position ID:
chr17|65889574|65889748|-
Gene name:
Vapa
Transcript:
ENSMUST00000024897.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
1
Exon/intron indexes:
5
Exon/intron offsets:
0
Genomic length:
174
Exon/intron sizes in nt:
174
Flanking exon/introns:
chr17:65887842-65889574|chr17:65889748-65899285
Splice length:
174
Other database IDs:
CIRCpedia: HSA_CIRCpedia_368209
Human Ortholog IDs:
Mature spliced Sequence:
AATGATATGGAACCTAGCAAAGCTGTTCCACTGAATGCATCCAAACAAGACGGACCCCTGCCAAAACCACACAGTGTTTCACTCAATGATACGGAAACAAGGAAACTGATGGAAGAGTGCAAGCGACTCCAGGGAGAAATGATGAAGCTCTCAGAAGAAAACCGACACCTGAGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAAGAGTGCAAGCGACTCCA
60.32
GGGGTCCGTCTTGTTTGGAT
59.96
121
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAAGAGTGCAAGCGACTC
60.32
GGGGTCCGTCTTGTTTGGAT
59.96
123
PCR template sequence:
GATACGGAAACAAGGAAACTGATGGAAGAGTGCAAGCGACTCCAGGGAGAAATGATGAAGCTCTCAGAAGAAAACCGACACCTGAGAAATGATATGGAACCTAGCAAAGCTGTTCCACTGAATGCATCCAAACAAGACGGACCCCTGCCAAAACCACACAGTGTTTCACTCAAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-429-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCGACACCTGAGAAATGATATGGAAC
siRNA sets
TATCATTTCTCAGGTGTCG, ATCATTTCTCAGGTGTCGG, TTCCATATCATTTCTCAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVAPA_174_ORF_1
0.9238
0.25825369
0.497635481
342
ORF sequence:
ATGGAACCTAGCAAAGCTGTTCCACTGAATGCATCCAAACAAGACGGACCCCTGCCAAAACCACACAGTGTTTCACTCAATGATACGGAAACAAGGAAACTGATGGAAGAGTGCAAGCGACTCCAGGGAGAAATGATGAAGCTCTCAGAAGAAAACCGACACCTGAGAAATGATATGGAACCTAGCAAAGCTGTTCCACTGAATGCATCCAAACAAGACGGACCCCTGCCAAAACCACACAGTGTTTCACTCAATGATACGGAAACAAGGAAACTGATGGAAGAGTGCAAGCGACTCCAGGGAGAAATGATGAAGCTCTCAGAAGAAAACCGACACCTGAGA
Peptide sequence:
MEPSKAVPLNASKQDGPLPKPHSVSLNDTETRKLMEECKRLQGEMMKLSEENRHLRNDMEPSKAVPLNASKQDGPLPKPHSVSLNDTETRKLMEECKRLQGEMMKLSEENRHLR
IRESfinder result
IRESfinder score
0.309382688
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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