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mmu_circScn9a_447
Basic information of circular RNA
PanCircBase ID:
mmu_circScn9a_447
mm39_Chr. Position ID:
chr2|66335192|66345776|-
Gene name:
Scn9a
Transcript:
ENSMUST00000100063.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
21,20,19
Exon/intron offsets:
0,3671,10466
Genomic length:
10584
Exon/intron sizes in nt:
17,41,55,118
Flanking exon/introns:
chr2:66332079-66335192|chr2:66345776-66356951
Splice length:
447
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AGACGGAACCGATCAAGTTCTTCAGAGTGCAGCACAGTTGATAACCCTCTGCCAGGAGAAGAGGAGGCAGAAGCTGAGCCTATCAATGCAGATGAGCCCGAAGCCTGTTTTACAGATGGCTGTGTGAGGAGATTTCCATGCTGCCAAGTTAACATAGACTCCGGGAAAGGGAAAGTTTGGTGGACCATCCGGAAGACCTGCTACAGGATAGTGGAGCACAGCTGGTTTGAAAGCTTCATTGTTCTCATGATCCTGCTCAGCAGTGGAGCTCTGGCTTTTGAGGATATATATATTGAAAAGAAAAAGACCATTAAGATTATCCTGGAGTATGCTGACAAGATATTCACCTACATCTTCATTCTGGAAATGCTTCTAAAATGGGTGGCATACGGGTATAAAACATATTTCACTAATGCCTGGTGTTGGCTGGACTTCTTAATTGTTGAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAAATGGGTGGCATACGGGT
59.96
GCTTCTGCCTCCTCTTCTCC
59.82
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAAATGGGTGGCATACGGGT
59.96
CCTCCTCTTCTCCTGGCAGA
60.33
140
PCR template sequence:
CTACATCTTCATTCTGGAAATGCTTCTAAAATGGGTGGCATACGGGTATAAAACATATTTCACTAATGCCTGGTGTTGGCTGGACTTCTTAATTGTTGATAGACGGAACCGATCAAGTTCTTCAGAGTGCAGCACAGTTGATAACCCTCTGCCAGGAGAAGAGGAGGCAGAAGCTGAGCCTATCAATGCAGATGAGCCCG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-204-5p(1), mmu-miR-33-5p(1), mmu-miR-24-3p(1), mmu-miR-127-5p(1), mmu-miR-27a-5p(1), mmu-miR-342-3p(1), mmu-miR-190b-5p(1), mmu-miR-207(1), mmu-miR-3470b(1), mmu-miR-99a-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTTAATTGTTGATAGACGGAACCGAT
siRNA sets
ATCGGTTCCGTCTATCAAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSCN9A_447_ORF_1
0.944
0.170287455
0.865750615
648
ORF sequence:
ATGATCCTGCTCAGCAGTGGAGCTCTGGCTTTTGAGGATATATATATTGAAAAGAAAAAGACCATTAAGATTATCCTGGAGTATGCTGACAAGATATTCACCTACATCTTCATTCTGGAAATGCTTCTAAAATGGGTGGCATACGGGTATAAAACATATTTCACTAATGCCTGGTGTTGGCTGGACTTCTTAATTGTTGATAGACGGAACCGATCAAGTTCTTCAGAGTGCAGCACAGTTGATAACCCTCTGCCAGGAGAAGAGGAGGCAGAAGCTGAGCCTATCAATGCAGATGAGCCCGAAGCCTGTTTTACAGATGGCTGTGTGAGGAGATTTCCATGCTGCCAAGTTAACATAGACTCCGGGAAAGGGAAAGTTTGGTGGACCATCCGGAAGACCTGCTACAGGATAGTGGAGCACAGCTGGTTTGAAAGCTTCATTGTTCTCATGATCCTGCTCAGCAGTGGAGCTCTGGCTTTTGAGGATATATATATTGAAAAGAAAAAGACCATTAAGATTATCCTGGAGTATGCTGACAAGATATTCACCTACATCTTCATTCTGGAAATGCTTCTAAAATGGGTGGCATACGGGTATAAAACATATTTCACTAATGCCTGGTGTTGGCTGGACTTCTTAATTGTTGAT
Peptide sequence:
MILLSSGALAFEDIYIEKKKTIKIILEYADKIFTYIFILEMLLKWVAYGYKTYFTNAWCWLDFLIVDRRNRSSSSECSTVDNPLPGEEEAEAEPINADEPEACFTDGCVRRFPCCQVNIDSGKGKVWWTIRKTCYRIVEHSWFESFIVLMILLSSGALAFEDIYIEKKKTIKIILEYADKIFTYIFILEMLLKWVAYGYKTYFTNAWCWLDFLIVD
IRESfinder result
IRESfinder score
0.618747594
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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