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mmu_circAp3b1_332
Basic information of circular RNA
PanCircBase ID:
mmu_circAp3b1_332
mm39_Chr. Position ID:
chr13|94531226|94540615|+
Gene name:
Ap3b1
Transcript:
ENSMUST00000022196.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
3,4,5
Exon/intron offsets:
0,8619,9228
Genomic length:
9389
Exon/intron sizes in nt:
75,96,161
Flanking exon/introns:
chr13:94527375-94531226|chr13:94540615-94545284
Splice length:
332
Other database IDs:
CIRCpedia: MMU_CIRCpedia_34801, circAtlas: mmu-Ap3b1_0046
Human Ortholog IDs:
Mature spliced Sequence:
ATGATTGCGAAGGGGAAAAATGCCTCGGAACTCTTCCCTGCTGTTGTGAAGAATGTGGCCAGTAAAAACATCGAGATCAAGAAGTTGGTGTACGTTTACCTTGTCCGATATGCTGAAGAACAGCAGGACCTGGCTCTTCTGTCCATAAGCACTTTCCAGCGAGCTTTGAAGGACCCGAATCAACTAATCCGTGCAAGTGCCTTGAGAGTTTTGTCAAGTATTAGAGTGCCAATTATCGTGCCTGTCATGATGCTGGCTATTAAGGAGGCTTCAGCTGACCTGTCGCCATATGTTAGGAAGAATGCAGCCCATGCTATTCAGAAGCTGTACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCCTGTCATGATGCTGGCTA
60.18
TCACAACAGCAGGGAAGAGT
58.87
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATCGTGCCTGTCATGATGCT
59.82
TCACAACAGCAGGGAAGAGT
58.87
147
PCR template sequence:
TTATCGTGCCTGTCATGATGCTGGCTATTAAGGAGGCTTCAGCTGACCTGTCGCCATATGTTAGGAAGAATGCAGCCCATGCTATTCAGAAGCTGTACAGATGATTGCGAAGGGGAAAAATGCCTCGGAACTCTTCCCTGCTGTTGTGAAGAATGTGGCCAGTAAAAACATCGAGATCAAGAAGTTGGTGTACGTTTACC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-106b-5p(1), mmu-miR-96-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAAGCTGTACAGATGATTGCGAAGG
siRNA sets
TTCGCAATCATCTGTACAG, TCGCAATCATCTGTACAGC, CTTCGCAATCATCTGTACA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAP3B1_332_ORF_1
1.1566
0.276580291
0.610100583
336
ORF sequence:
ATGATTGCGAAGGGGAAAAATGCCTCGGAACTCTTCCCTGCTGTTGTGAAGAATGTGGCCAGTAAAAACATCGAGATCAAGAAGTTGGTGTACGTTTACCTTGTCCGATATGCTGAAGAACAGCAGGACCTGGCTCTTCTGTCCATAAGCACTTTCCAGCGAGCTTTGAAGGACCCGAATCAACTAATCCGTGCAAGTGCCTTGAGAGTTTTGTCAAGTATTAGAGTGCCAATTATCGTGCCTGTCATGATGCTGGCTATTAAGGAGGCTTCAGCTGACCTGTCGCCATATGTTAGGAAGAATGCAGCCCATGCTATTCAGAAGCTGTACAGATGA
Peptide sequence:
MIAKGKNASELFPAVVKNVASKNIEIKKLVYVYLVRYAEEQQDLALLSISTFQRALKDPNQLIRASALRVLSSIRVPIIVPVMMLAIKEASADLSPYVRKNAAHAIQKLYR
IRESfinder result
IRESfinder score
0.4697753
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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