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mmu_circAppbp2_534
Basic information of circular RNA
PanCircBase ID:
mmu_circAppbp2_534
mm39_Chr. Position ID:
chr11|85100765|85107350|-
Gene name:
Appbp2
Transcript:
ENSMUST00000018625.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,4296,5170,6496
Genomic length:
6585
Exon/intron sizes in nt:
169,124,152,89
Flanking exon/introns:
chr11:85095149-85100765|chr11:85107350-85125497
Splice length:
534
Other database IDs:
circBase: mmu_circ_0000304, CIRCpedia: MMU_CIRCpedia_213660, circAtlas: mmu-Appbp2_0003
circAtlas: hsa-APPBP2_0006, CIRCpedia: HSA_CIRCpedia_21744
Human Ortholog IDs:
Mature spliced Sequence:
CTTTACCAACAGGGACGCTTGTGTCAGCTCGGCAGTGAATTCTGTGAATTGGAAGTTTTTGCTAAAGTTTTGAGAGCTTTGGATAAAAGACATTTGCTCCACCACTGTTTTCAGGCTCTGATGGACCATGGCGTTAAGGTAGCTTCCGTCTTGGCCTACTCCTTCAGTAGACGGTGCTCTTACATAGCAGAGTCCGACGCTGCAGTAAAGGAGAAGGCCATCCAGGTTGGCTTTGTCTTAGGTGGCTTTCTTTCTGATGCAGGCTGGTACAGTGATGCTGAAAAGGTTTTTCTGTCCTGCCTTCAGTTGTGTACGCTACATGATGAGATGCTCCACTGGTTCCGAGCAGTGGAGTGTTGTGTGAGGTTGCTTCATGTGCGAAATGGAAATTGTAAATATCATCTAGGTGAAGAAACATTTAAATTAGCTCAGACATACATGGATAAGCTGTCTAAACATGGCCAGCAAGCAAATAGAGCTGCTCTCTACGGAGAACTATGTGCACTCCTGTTTGCAAAAAGCCACTATGATGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGTCTAAACATGGCCAGC
59.55
TCCAATTCACAGAATTCACTGCC
59.49
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGATAAGCTGTCTAAACATGGCC
59.43
CACAGAATTCACTGCCGAGC
59.55
140
PCR template sequence:
ATACATGGATAAGCTGTCTAAACATGGCCAGCAAGCAAATAGAGCTGCTCTCTACGGAGAACTATGTGCACTCCTGTTTGCAAAAAGCCACTATGATGAGCTTTACCAACAGGGACGCTTGTGTCAGCTCGGCAGTGAATTCTGTGAATTGGAAGTTTTTGCTAAAGTTTTGAGAGCTTTGGATAAAAGACATTTGCTCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-342-3p(1), mmu-miR-377-3p(1), mmu-miR-129-5p(1), mmu-miR-335-3p(1), mmu-miR-490-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCACTATGATGAGCTTTACCAACAGG
siRNA sets
GTAAAGCTCATCATAGTGG, TTGGTAAAGCTCATCATAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAPPBP2_534_ORF_1
0.8032
0.052213529
0.963740989
948
ORF sequence:
ATGGACCATGGCGTTAAGGTAGCTTCCGTCTTGGCCTACTCCTTCAGTAGACGGTGCTCTTACATAGCAGAGTCCGACGCTGCAGTAAAGGAGAAGGCCATCCAGGTTGGCTTTGTCTTAGGTGGCTTTCTTTCTGATGCAGGCTGGTACAGTGATGCTGAAAAGGTTTTTCTGTCCTGCCTTCAGTTGTGTACGCTACATGATGAGATGCTCCACTGGTTCCGAGCAGTGGAGTGTTGTGTGAGGTTGCTTCATGTGCGAAATGGAAATTGTAAATATCATCTAGGTGAAGAAACATTTAAATTAGCTCAGACATACATGGATAAGCTGTCTAAACATGGCCAGCAAGCAAATAGAGCTGCTCTCTACGGAGAACTATGTGCACTCCTGTTTGCAAAAAGCCACTATGATGAGCTTTACCAACAGGGACGCTTGTGTCAGCTCGGCAGTGAATTCTGTGAATTGGAAGTTTTTGCTAAAGTTTTGAGAGCTTTGGATAAAAGACATTTGCTCCACCACTGTTTTCAGGCTCTGATGGACCATGGCGTTAAGGTAGCTTCCGTCTTGGCCTACTCCTTCAGTAGACGGTGCTCTTACATAGCAGAGTCCGACGCTGCAGTAAAGGAGAAGGCCATCCAGGTTGGCTTTGTCTTAGGTGGCTTTCTTTCTGATGCAGGCTGGTACAGTGATGCTGAAAAGGTTTTTCTGTCCTGCCTTCAGTTGTGTACGCTACATGATGAGATGCTCCACTGGTTCCGAGCAGTGGAGTGTTGTGTGAGGTTGCTTCATGTGCGAAATGGAAATTGTAAATATCATCTAGGTGAAGAAACATTTAAATTAGCTCAGACATACATGGATAAGCTGTCTAAACATGGCCAGCAAGCAAATAGAGCTGCTCTCTACGGAGAACTATGTGCACTCCTGTTTGCAAAAAGCCACTATGATGAG
Peptide sequence:
MDHGVKVASVLAYSFSRRCSYIAESDAAVKEKAIQVGFVLGGFLSDAGWYSDAEKVFLSCLQLCTLHDEMLHWFRAVECCVRLLHVRNGNCKYHLGEETFKLAQTYMDKLSKHGQQANRAALYGELCALLFAKSHYDELYQQGRLCQLGSEFCELEVFAKVLRALDKRHLLHHCFQALMDHGVKVASVLAYSFSRRCSYIAESDAAVKEKAIQVGFVLGGFLSDAGWYSDAEKVFLSCLQLCTLHDEMLHWFRAVECCVRLLHVRNGNCKYHLGEETFKLAQTYMDKLSKHGQQANRAALYGELCALLFAKSHYDE
IRESfinder result
IRESfinder score
0.504083621
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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