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mmu_circAfdn_503
Basic information of circular RNA
PanCircBase ID:
mmu_circAfdn_503
mm39_Chr. Position ID:
chr17|14116349|14122876|+
Gene name:
Afdn
Transcript:
ENSMUST00000170827.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
30,31,32
Exon/intron offsets:
0,2857,6442
Genomic length:
6527
Exon/intron sizes in nt:
135,283,85
Flanking exon/introns:
chr17:14109239-14116349|chr17:14122876-14124115
Splice length:
503
Other database IDs:
CIRCpedia: MMU_CIRCpedia_219423, circAtlas: mmu-Mllt4_0068
Human Ortholog IDs:
Mature spliced Sequence:
ATGCAGGATGAGGAGCGCAGGCGCCAGCAACAGTTGGAAGAGATGCGGAAACGAGAAGCAGAAGATCGAGTAAGACAAGAGGAAGATGGACGCCATCAGGAGGAGGAGCGAGTAAAGAGAGATGCTGAAGAAAAGAGGCGACAGGAGGAAGGGTATTACAGCCGCCTAGAAGCTGAGAGGCGCCGACAGCACGAAGAGGCAGCACGCAGGCTGCTGGAGCCTGAAGAGCCCGGGCTGAGCCGACCTCCACTTCCACGGGACTATGAGCCCCCGTCCTTGTCCTCAGCACCCTGTGCCCCTCCTCCCCCACCTCAGCGAAACGCATCCTACCTCAAAACACAGGTCCTCTCCCCAGACTCGCTGTTCACTGCCAAGTTTGTTGCGTATGATGAGGAGGAGGAGGACTACGGCCCAGCAGGACCAAACTCTTACTCGGGATCTGCAGGCACAGCTGTGGGAGCCTATGATGCCCCTCGGGAAGCGAGAGAGAAACTGACTAGGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCAGCAGGACCAAACTCTT
59.89
TGCTTCTCGTTTCCGCATCT
60.04
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCCAGCAGGACCAAACTCTT
59.89
TCTGCTTCTCGTTTCCGCAT
60.04
155
PCR template sequence:
ACTACGGCCCAGCAGGACCAAACTCTTACTCGGGATCTGCAGGCACAGCTGTGGGAGCCTATGATGCCCCTCGGGAAGCGAGAGAGAAACTGACTAGGAGATGCAGGATGAGGAGCGCAGGCGCCAGCAACAGTTGGAAGAGATGCGGAAACGAGAAGCAGAAGATCGAGTAAGACAAGAGGAAGATGGACGCCATCAGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-let-7a-5p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-34c-5p(1), mmu-miR-223-3p(1), mmu-miR-34a-5p(1), mmu-let-7c-5p(1), mmu-miR-495-3p(1), mmu-miR-370-3p(1), mmu-miR-34b-5p(1), mmu-miR-98-5p(1), mmu-miR-484(1), mmu-miR-188-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
AACTGACTAGGAGATGCAGGATGAGG
siRNA sets
ATCCTGCATCTCCTAGTCA, CATCCTGCATCTCCTAGTC, TCATCCTGCATCTCCTAGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAFDN_503_ORF_1
0.8124
0.440123715
0.900266782
576
ORF sequence:
ATGCAGGATGAGGAGCGCAGGCGCCAGCAACAGTTGGAAGAGATGCGGAAACGAGAAGCAGAAGATCGAGTAAGACAAGAGGAAGATGGACGCCATCAGGAGGAGGAGCGAGTAAAGAGAGATGCTGAAGAAAAGAGGCGACAGGAGGAAGGGTATTACAGCCGCCTAGAAGCTGAGAGGCGCCGACAGCACGAAGAGGCAGCACGCAGGCTGCTGGAGCCTGAAGAGCCCGGGCTGAGCCGACCTCCACTTCCACGGGACTATGAGCCCCCGTCCTTGTCCTCAGCACCCTGTGCCCCTCCTCCCCCACCTCAGCGAAACGCATCCTACCTCAAAACACAGGTCCTCTCCCCAGACTCGCTGTTCACTGCCAAGTTTGTTGCGTATGATGAGGAGGAGGAGGACTACGGCCCAGCAGGACCAAACTCTTACTCGGGATCTGCAGGCACAGCTGTGGGAGCCTATGATGCCCCTCGGGAAGCGAGAGAGAAACTGACTAGGAGATGCAGGATGAGGAGCGCAGGCGCCAGCAACAGTTGGAAGAGATGCGGAAACGAGAAGCAGAAGATCGAGTAA
Peptide sequence:
MQDEERRRQQQLEEMRKREAEDRVRQEEDGRHQEEERVKRDAEEKRRQEEGYYSRLEAERRRQHEEAARRLLEPEEPGLSRPPLPRDYEPPSLSSAPCAPPPPPQRNASYLKTQVLSPDSLFTAKFVAYDEEEEDYGPAGPNSYSGSAGTAVGAYDAPREAREKLTRRCRMRSAGASNSWKRCGNEKQKIE
IRESfinder result
IRESfinder score
0.175050125
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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