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mmu_circAk9_287
Basic information of circular RNA
PanCircBase ID:
mmu_circAk9_287
mm39_Chr. Position ID:
chr10|41243113|41246201|+
Gene name:
Ak9
Transcript:
ENSMUST00000173494.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
19,20
Exon/intron offsets:
0,2926
Genomic length:
3088
Exon/intron sizes in nt:
1,25,162
Flanking exon/introns:
chr10:41234646-41243113|chr10:41246201-41258797
Splice length:
287
Other database IDs:
circAtlas: mmu-Ak9_0002
Human Ortholog IDs:
Mature spliced Sequence:
AAAAGTCAAAGAAGAGGAACTGAGACTGGAAGAAGAAAAACAAAGGCTGATGGAACTTGCAACTAAGAAATCAAAAGGCAGGCACAGACTAACAACACTGGTAGCACATCACTTAGCCTTGCCTTATCCTGACTATCCTGATAATGAAGCCGAGGAGGAGGTTGAGGATTCTGAAATTCATGAAGAGTCTGAGGCACAAGAAATACCTGAGTACACCCGAGGGTCATCATTGCCTGAGGCGTCTGAAACATCTGAGACCCCAGAAGGAGACCATGAACCTGAAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TACCTGAGTACACCCGAGGG
60.03
AGTCTGTGCCTGCCTTTTGA
59.82
174
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGAGGGTCATCATTGCCTGA
59.82
AGTCTGTGCCTGCCTTTTGA
59.82
160
PCR template sequence:
TCTGAGGCACAAGAAATACCTGAGTACACCCGAGGGTCATCATTGCCTGAGGCGTCTGAAACATCTGAGACCCCAGAAGGAGACCATGAACCTGAAGCAGAAAAGTCAAAGAAGAGGAACTGAGACTGGAAGAAGAAAAACAAAGGCTGATGGAACTTGCAACTAAGAAATCAAAAGGCAGGCACAGACTAACAACACTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-199a-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GAACCTGAAGCAGAAAAGTCAAAGAA
siRNA sets
TTGACTTTTCTGCTTCAGG,TTTGACTTTTCTGCTTCAG,CTTTGACTTTTCTGCTTCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAK9_287_ORF_1
1.276
0.190531039
0.44493723
261
ORF sequence:
ATGGAACTTGCAACTAAGAAATCAAAAGGCAGGCACAGACTAACAACACTGGTAGCACATCACTTAGCCTTGCCTTATCCTGACTATCCTGATAATGAAGCCGAGGAGGAGGTTGAGGATTCTGAAATTCATGAAGAGTCTGAGGCACAAGAAATACCTGAGTACACCCGAGGGTCATCATTGCCTGAGGCGTCTGAAACATCTGAGACCCCAGAAGGAGACCATGAACCTGAAGCAGAAAAGTCAAAGAAGAGGAACTGA
Peptide sequence:
MELATKKSKGRHRLTTLVAHHLALPYPDYPDNEAEEEVEDSEIHEESEAQEIPEYTRGSSLPEASETSETPEGDHEPEAEKSKKRN
IRESfinder result
IRESfinder score
0.55597876
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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