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mmu_circAppbp2_259
Basic information of circular RNA
PanCircBase ID:
mmu_circAppbp2_259
mm39_Chr. Position ID:
chr11|85095059|85100934|-
Gene name:
Appbp2
Transcript:
ENSMUST00000018625.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
6,5
Exon/intron offsets:
0,5706
Genomic length:
5875
Exon/intron sizes in nt:
90,169
Flanking exon/introns:
chr11:85092496-85095059|chr11:85100934-85105061
Splice length:
259
Other database IDs:
circAtlas: hsa-APPBP2_0005, CIRCpedia: HSA_CIRCpedia_368842
Human Ortholog IDs:
Mature spliced Sequence:
GTTGCTTCATGTGCGAAATGGAAATTGTAAATATCATCTAGGTGAAGAAACATTTAAATTAGCTCAGACATACATGGATAAGCTGTCTAAACATGGCCAGCAAGCAAATAGAGCTGCTCTCTACGGAGAACTATGTGCACTCCTGTTTGCAAAAAGCCACTATGATGAGGCATACAAGTGGTGCGTTGAGGCAATGAAGGAAATTACAGCAGGCTTACCAGTCAAAGTTGTGGTGGATGTTTTAAGACAAGCTTCTAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGCGTTGAGGCAATGAAGG
60.11
CTGGCCATGTTTAGACAGCT
57.88
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGTGCGTTGAGGCAATGAAG
60.11
CTGGCCATGTTTAGACAGCT
57.88
180
PCR template sequence:
CTATGATGAGGCATACAAGTGGTGCGTTGAGGCAATGAAGGAAATTACAGCAGGCTTACCAGTCAAAGTTGTGGTGGATGTTTTAAGACAAGCTTCTAAGGTTGCTTCATGTGCGAAATGGAAATTGTAAATATCATCTAGGTGAAGAAACATTTAAATTAGCTCAGACATACATGGATAAGCTGTCTAAACATGGCCAG
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-205-5p(1), mmu-miR-129-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACAAGCTTCTAAGGTTGCTTCATGTG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAPPBP2_259_ORF_1
0.8516
-0.003606685
0.106445021
216
ORF sequence:
ATGGATAAGCTGTCTAAACATGGCCAGCAAGCAAATAGAGCTGCTCTCTACGGAGAACTATGTGCACTCCTGTTTGCAAAAAGCCACTATGATGAGGCATACAAGTGGTGCGTTGAGGCAATGAAGGAAATTACAGCAGGCTTACCAGTCAAAGTTGTGGTGGATGTTTTAAGACAAGCTTCTAAGGTTGCTTCATGTGCGAAATGGAAATTGTAA
Peptide sequence:
MDKLSKHGQQANRAALYGELCALLFAKSHYDEAYKWCVEAMKEITAGLPVKVVVDVLRQASKVASCAKWKL
IRESfinder result
IRESfinder score
0.369273278
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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