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mmu_circAppbp2_558
Basic information of circular RNA
PanCircBase ID:
mmu_circAppbp2_558
mm39_Chr. Position ID:
chr11|85091119|85100934|-
Gene name:
Appbp2
Transcript:
ENSMUST00000018625.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
9,8,7,6,5
Exon/intron offsets:
0,1122,1309,3940,9646
Genomic length:
9815
Exon/intron sizes in nt:
12,51,06,68,90,169
Flanking exon/introns:
chr11:85088977-85091119|chr11:85100934-85105061
Splice length:
558
Other database IDs:
circAtlas: mmu-Appbp2_0008
circBase: hsa_circ_0044964, circAtlas: hsa-APPBP2_0014, CIRCpedia: HSA_CIRCpedia_21740
Human Ortholog IDs:
Mature spliced Sequence:
GTTGCTTCATGTGCGAAATGGAAATTGTAAATATCATCTAGGTGAAGAAACATTTAAATTAGCTCAGACATACATGGATAAGCTGTCTAAACATGGCCAGCAAGCAAATAGAGCTGCTCTCTACGGAGAACTATGTGCACTCCTGTTTGCAAAAAGCCACTATGATGAGGCATACAAGTGGTGCGTTGAGGCAATGAAGGAAATTACAGCAGGCTTACCAGTCAAAGTTGTGGTGGATGTTTTAAGACAAGCTTCTAAGGCTTGTGTAGTCAAACGTGAATTTAAGAAGGCAGAACAGTTAATTAAACATGCAGTGTATTTGGCACGAGATCATTTCGGATCCAAACACCCAAAATACTCTGACACACTGCTAGATTATGGGTTCTACTTACTCAATGTAGACAATATCTGTCAGTCTGTTGCAATTTACCAGGCAGCCCTCGACATTCGACAGTCAGTGTTTGGTGGCAAAAATATTCATGTAGCAACAGCTCATGAAGACCTGGCCTACTCTTCCTACGTTCACCAGTACAGCTCTGGAAAATTCGACAATGCACT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACAGCTCATGAAGACCTGGC
60.04
CTGGCCATGTTTAGACAGCT
57.88
171
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACAGCTCATGAAGACCTGGC
60.04
CTGGCCATGTTTAGACAGCTT
58.56
171
PCR template sequence:
TGTTTGGTGGCAAAAATATTCATGTAGCAACAGCTCATGAAGACCTGGCCTACTCTTCCTACGTTCACCAGTACAGCTCTGGAAAATTCGACAATGCACTGTTGCTTCATGTGCGAAATGGAAATTGTAAATATCATCTAGGTGAAGAAACATTTAAATTAGCTCAGACATACATGGATAAGCTGTCTAAACATGGCCAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-205-5p(1), mmu-miR-217-5p(1), mmu-miR-129-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCGACAATGCACTGTTGCTTCATGTG
siRNA sets
CACATGAAGCAACAGTGCA,ATGAAGCAACAGTGCATTG,TGAAGCAACAGTGCATTGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAPPBP2_558_ORF_1
0.9206
0.127102949
0.988734164
1041
ORF sequence:
ATGGATAAGCTGTCTAAACATGGCCAGCAAGCAAATAGAGCTGCTCTCTACGGAGAACTATGTGCACTCCTGTTTGCAAAAAGCCACTATGATGAGGCATACAAGTGGTGCGTTGAGGCAATGAAGGAAATTACAGCAGGCTTACCAGTCAAAGTTGTGGTGGATGTTTTAAGACAAGCTTCTAAGGCTTGTGTAGTCAAACGTGAATTTAAGAAGGCAGAACAGTTAATTAAACATGCAGTGTATTTGGCACGAGATCATTTCGGATCCAAACACCCAAAATACTCTGACACACTGCTAGATTATGGGTTCTACTTACTCAATGTAGACAATATCTGTCAGTCTGTTGCAATTTACCAGGCAGCCCTCGACATTCGACAGTCAGTGTTTGGTGGCAAAAATATTCATGTAGCAACAGCTCATGAAGACCTGGCCTACTCTTCCTACGTTCACCAGTACAGCTCTGGAAAATTCGACAATGCACTGTTGCTTCATGTGCGAAATGGAAATTGTAAATATCATCTAGGTGAAGAAACATTTAAATTAGCTCAGACATACATGGATAAGCTGTCTAAACATGGCCAGCAAGCAAATAGAGCTGCTCTCTACGGAGAACTATGTGCACTCCTGTTTGCAAAAAGCCACTATGATGAGGCATACAAGTGGTGCGTTGAGGCAATGAAGGAAATTACAGCAGGCTTACCAGTCAAAGTTGTGGTGGATGTTTTAAGACAAGCTTCTAAGGCTTGTGTAGTCAAACGTGAATTTAAGAAGGCAGAACAGTTAATTAAACATGCAGTGTATTTGGCACGAGATCATTTCGGATCCAAACACCCAAAATACTCTGACACACTGCTAGATTATGGGTTCTACTTACTCAATGTAGACAATATCTGTCAGTCTGTTGCAATTTACCAGGCAGCCCTCGACATTCGACAGTCAGTGTTTGGTGGCAAAAATATTCATGTAGCAACAGCTCATGAAGACCTGGCCTACTCTTCCTACGTTCACCAGTACAGCTCTGGAAAATTCGACAATGCA
Peptide sequence:
MDKLSKHGQQANRAALYGELCALLFAKSHYDEAYKWCVEAMKEITAGLPVKVVVDVLRQASKACVVKREFKKAEQLIKHAVYLARDHFGSKHPKYSDTLLDYGFYLLNVDNICQSVAIYQAALDIRQSVFGGKNIHVATAHEDLAYSSYVHQYSSGKFDNALLLHVRNGNCKYHLGEETFKLAQTYMDKLSKHGQQANRAALYGELCALLFAKSHYDEAYKWCVEAMKEITAGLPVKVVVDVLRQASKACVVKREFKKAEQLIKHAVYLARDHFGSKHPKYSDTLLDYGFYLLNVDNICQSVAIYQAALDIRQSVFGGKNIHVATAHEDLAYSSYVHQYSSGKFDNA
IRESfinder result
IRESfinder score
0.590243667
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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