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mmu_circScn9a_297
Basic information of circular RNA
PanCircBase ID:
mmu_circScn9a_297
mm39_Chr. Position ID:
chr2|66331956|66335366|-
Gene name:
Scn9a
Transcript:
ENSMUST00000100063.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
22,21
Exon/intron offsets:
0,3236
Genomic length:
3410
Exon/intron sizes in nt:
1,23,174
Flanking exon/introns:
chr2:66325234-66331956|chr2:66335366-66338863
Splice length:
297
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GCTTTTGAGGATATATATATTGAAAAGAAAAAGACCATTAAGATTATCCTGGAGTATGCTGACAAGATATTCACCTACATCTTCATTCTGGAAATGCTTCTAAAATGGGTGGCATACGGGTATAAAACATATTTCACTAATGCCTGGTGTTGGCTGGACTTCTTAATTGTTGATGTGTCTCTAGTTACTTTAGTAGCCAACACTCTTGGCTACTCAGACCTTGGCCCCATTAAATCTCTACGGACACTGAGGGCCCTAAGACCCCTAAGAGCTTTGTCTAGATTTGAAGGAATGAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TACTCAGACCTTGGCCCCAT
60.25
TCTTGTCAGCATACTCCAGGA
58.18
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGGCTACTCAGACCTTGGC
59.68
TCTTGTCAGCATACTCCAGGA
58.18
159
PCR template sequence:
CAACACTCTTGGCTACTCAGACCTTGGCCCCATTAAATCTCTACGGACACTGAGGGCCCTAAGACCCCTAAGAGCTTTGTCTAGATTTGAAGGAATGAGGGCTTTTGAGGATATATATATTGAAAAGAAAAAGACCATTAAGATTATCCTGGAGTATGCTGACAAGATATTCACCTACATCTTCATTCTGGAAATGCTTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-190b-5p(1), mmu-miR-99a-5p(1), mmu-miR-344-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGAAGGAATGAGGGCTTTTGAGGATA
siRNA sets
TATCCTCAAAAGCCCTCAT, CAAAAGCCCTCATTCCTTC, CTCAAAAGCCCTCATTCCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSCN9A_297_ORF_1
0.6867
-0.030751756
0.379810267
501
ORF sequence:
ATGCTTCTAAAATGGGTGGCATACGGGTATAAAACATATTTCACTAATGCCTGGTGTTGGCTGGACTTCTTAATTGTTGATGTGTCTCTAGTTACTTTAGTAGCCAACACTCTTGGCTACTCAGACCTTGGCCCCATTAAATCTCTACGGACACTGAGGGCCCTAAGACCCCTAAGAGCTTTGTCTAGATTTGAAGGAATGAGGGCTTTTGAGGATATATATATTGAAAAGAAAAAGACCATTAAGATTATCCTGGAGTATGCTGACAAGATATTCACCTACATCTTCATTCTGGAAATGCTTCTAAAATGGGTGGCATACGGGTATAAAACATATTTCACTAATGCCTGGTGTTGGCTGGACTTCTTAATTGTTGATGTGTCTCTAGTTACTTTAGTAGCCAACACTCTTGGCTACTCAGACCTTGGCCCCATTAAATCTCTACGGACACTGAGGGCCCTAAGACCCCTAAGAGCTTTGTCTAGATTTGAAGGAATGAGG
Peptide sequence:
MLLKWVAYGYKTYFTNAWCWLDFLIVDVSLVTLVANTLGYSDLGPIKSLRTLRALRPLRALSRFEGMRAFEDIYIEKKKTIKIILEYADKIFTYIFILEMLLKWVAYGYKTYFTNAWCWLDFLIVDVSLVTLVANTLGYSDLGPIKSLRTLRALRPLRALSRFEGMR
IRESfinder result
IRESfinder score
0.788393856
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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