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mmu_circSec22c_299
Basic information of circular RNA
PanCircBase ID:
mmu_circSec22c_299
mm39_Chr. Position ID:
chr9|121517264|121519481|-
Gene name:
Sec22c
Transcript:
ENSMUST00000078547.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
6,5
Exon/intron offsets:
0,2037
Genomic length:
2217
Exon/intron sizes in nt:
1,19,180
Flanking exon/introns:
chr9:121514654-121517264|chr9:121519481-121521975
Splice length:
299
Other database IDs:
CIRCpedia: MMU_CIRCpedia_5578, circAtlas: mmu-Sec22c_0004
Human Ortholog IDs:
Mature spliced Sequence:
ACAGTGTCATTCAGAAAACAAAGTGGCATTTTAACCACATGAGCTCCTCCCAGATGAAGAGTGGCTTAGAAAAGATCCAAGAGGAGCTCGAGTTCCAGCCTCCAGCAGTCCTGTCCCTAGAGGACACAGATGTGGCAAATGGCATGCTGAACGGCCACACCCCAGTGCACTCTGAGCCTGCTCCGAACCTCCGGATGAAGCCGGTGACAGCCCTGGGTGTCCTCTCCCTTGTTCTCAACATCATGTGCGCGGCCCTGAACCTCATCCGTGGAGTTCACCTCGCAGAGCATTCTTTACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTGAACCTCATCCGTGGAG
59.82
GGAACTCGAGCTCCTCTTGG
59.83
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGTGTCCTCTCCCTTGTTC
59.67
GCCACTCTTCATCTGGGAGG
59.82
150
PCR template sequence:
GCCGGTGACAGCCCTGGGTGTCCTCTCCCTTGTTCTCAACATCATGTGCGCGGCCCTGAACCTCATCCGTGGAGTTCACCTCGCAGAGCATTCTTTACAGACAGTGTCATTCAGAAAACAAAGTGGCATTTTAACCACATGAGCTCCTCCCAGATGAAGAGTGGCTTAGAAAAGATCCAAGAGGAGCTCGAGTTCCAGCC
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-222-3p(1), mmu-miR-370-3p(1), mmu-miR-484(1)
siRNAs for circular RNA silencing
Junction sequence
GCATTCTTTACAGACAGTGTCATTCA
siRNA sets
ATGACACTGTCTGTAAAGA, AATGACACTGTCTGTAAAG, CACTGTCTGTAAAGAATGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSEC22C_299_ORF_1
1.0642
0.273685724
0.506865659
303
ORF sequence:
ATGAGCTCCTCCCAGATGAAGAGTGGCTTAGAAAAGATCCAAGAGGAGCTCGAGTTCCAGCCTCCAGCAGTCCTGTCCCTAGAGGACACAGATGTGGCAAATGGCATGCTGAACGGCCACACCCCAGTGCACTCTGAGCCTGCTCCGAACCTCCGGATGAAGCCGGTGACAGCCCTGGGTGTCCTCTCCCTTGTTCTCAACATCATGTGCGCGGCCCTGAACCTCATCCGTGGAGTTCACCTCGCAGAGCATTCTTTACAGACAGTGTCATTCAGAAAACAAAGTGGCATTTTAACCACATGA
Peptide sequence:
MSSSQMKSGLEKIQEELEFQPPAVLSLEDTDVANGMLNGHTPVHSEPAPNLRMKPVTALGVLSLVLNIMCAALNLIRGVHLAEHSLQTVSFRKQSGILTT
IRESfinder result
IRESfinder score
0.608679482
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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