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mmu_circAtl3_417
Basic information of circular RNA
PanCircBase ID:
mmu_circAtl3_417
mm39_Chr. Position ID:
chr19|7498151|7506434|+
Gene name:
Atl3
Transcript:
ENSMUST00000170373.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,7,8,9
Exon/intron offsets:
0,323,1282,8155
Genomic length:
8283
Exon/intron sizes in nt:
5,79,31,39,128
Flanking exon/introns:
chr19:7495961-7498151|chr19:7506434-7506972
Splice length:
417
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CTCTTCACAGAATATGGCCGCCTGGCAATGGATGAAATTTTCCAAAAACCTTTTCAGACACTGATGTTTTTGATTCGAGATTGGAGTTTCCCTTATGAATATAACTATGGACTGCAAGGAGGAATGGCATTTTTGGATAAGCGTTTACATGTGAAGGAACATCAACATGAAGAAATTCAGAATGTGAGAAATCATATTCACTCATGTTTCTCCGATGTCACCTGTTTTCTCTTACCACATCCAGGGCTCCAGGTGGCCACAAGCCCCAACTTTGATGGGAAATTGAAAGATATTGCTAGTGAATTCAAAGAGCAGTTACAGGCTCTAATACCATATGTACTAAATCCATCTAAATTAATGGAGAAGGAGATCAATGGTTCAAAAGTCACCTGCCGGGGATTGTTGGAATATTTTAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGTTCAAAAGTCACCTGCCG
59.69
TCATAAGGGAAACTCCAATCTCGA
59.29
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGTTCAAAAGTCACCTGCCG
59.69
TCATAAGGGAAACTCCAATCTCG
57.98
140
PCR template sequence:
ACAGGCTCTAATACCATATGTACTAAATCCATCTAAATTAATGGAGAAGGAGATCAATGGTTCAAAAGTCACCTGCCGGGGATTGTTGGAATATTTTAAGCTCTTCACAGAATATGGCCGCCTGGCAATGGATGAAATTTTCCAAAAACCTTTTCAGACACTGATGTTTTTGATTCGAGATTGGAGTTTCCCTTATGAAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-136-5p(1), mmu-miR-434-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGAATATTTTAAGCTCTTCACAGAAT
siRNA sets
ATTCTGTGAAGAGCTTAAA, GAAGAGCTTAAAATATTCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATL3_417_ORF_1
0.8138
0.058203473
0.909890813
807
ORF sequence:
ATGGATGAAATTTTCCAAAAACCTTTTCAGACACTGATGTTTTTGATTCGAGATTGGAGTTTCCCTTATGAATATAACTATGGACTGCAAGGAGGAATGGCATTTTTGGATAAGCGTTTACATGTGAAGGAACATCAACATGAAGAAATTCAGAATGTGAGAAATCATATTCACTCATGTTTCTCCGATGTCACCTGTTTTCTCTTACCACATCCAGGGCTCCAGGTGGCCACAAGCCCCAACTTTGATGGGAAATTGAAAGATATTGCTAGTGAATTCAAAGAGCAGTTACAGGCTCTAATACCATATGTACTAAATCCATCTAAATTAATGGAGAAGGAGATCAATGGTTCAAAAGTCACCTGCCGGGGATTGTTGGAATATTTTAAGCTCTTCACAGAATATGGCCGCCTGGCAATGGATGAAATTTTCCAAAAACCTTTTCAGACACTGATGTTTTTGATTCGAGATTGGAGTTTCCCTTATGAATATAACTATGGACTGCAAGGAGGAATGGCATTTTTGGATAAGCGTTTACATGTGAAGGAACATCAACATGAAGAAATTCAGAATGTGAGAAATCATATTCACTCATGTTTCTCCGATGTCACCTGTTTTCTCTTACCACATCCAGGGCTCCAGGTGGCCACAAGCCCCAACTTTGATGGGAAATTGAAAGATATTGCTAGTGAATTCAAAGAGCAGTTACAGGCTCTAATACCATATGTACTAAATCCATCTAAATTAATGGAGAAGGAGATCAATGGTTCAAAAGTCACCTGCCGGGGATTGTTGGAATATTTTAAG
Peptide sequence:
MDEIFQKPFQTLMFLIRDWSFPYEYNYGLQGGMAFLDKRLHVKEHQHEEIQNVRNHIHSCFSDVTCFLLPHPGLQVATSPNFDGKLKDIASEFKEQLQALIPYVLNPSKLMEKEINGSKVTCRGLLEYFKLFTEYGRLAMDEIFQKPFQTLMFLIRDWSFPYEYNYGLQGGMAFLDKRLHVKEHQHEEIQNVRNHIHSCFSDVTCFLLPHPGLQVATSPNFDGKLKDIASEFKEQLQALIPYVLNPSKLMEKEINGSKVTCRGLLEYFK
IRESfinder result
IRESfinder score
0.721331646
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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