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mmu_circScyl1_406
Basic information of circular RNA
PanCircBase ID:
mmu_circScyl1_406
mm39_Chr. Position ID:
chr19|5816185|5819839|-
Gene name:
Scyl1
Transcript:
ENSMUST00000236978.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
6,5,4
Exon/intron offsets:
0,3311,3563
Genomic length:
3654
Exon/intron sizes in nt:
159,156,91
Flanking exon/introns:
chr19:5815445-5816185|chr19:5819839-5820230
Splice length:
406
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTCAGCAGACATGTGGCGCTTGGGCTGCCTCATCTGGGAAGTTTTCAATGGGTCTCTACCTCGGGCAGCTGCCCTGCGCAACCCTGGGAAGATCCCCAAATCCCTGGTGACCCATTACTGTGAACTGGTGGGAGCTAACCCAAAAGTACGTCCCAACCCGGCCCGCTTCCTGCAGAACTGCCGGGCACCCGGTGGCTTCATGAGCAACCGCTTTGTTGAGACCAACCTCTTCCTGGAGGAGATTCAGATCAAAGAGCCAGCTGAGAAGCAGAAGTTCTTCCAAGAGCTGAGCAAGAGTCTAGACTCATTTCCCGAAGATTTCTGTCGACACAAGGTGCTGCCCCAGCTACTGACTGCCTTTGAGTTTGGCAATGCTGGGGCCGTGGTCCTCACACCTCTCTTCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCAGCTACTGACTGCCTTT
59.67
GGATCTTCCCAGGGTTGCG
60.45
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCCGAAGATTTCTGTCGACA
59.11
AACTTCCCAGATGAGGCAGC
60.03
140
PCR template sequence:
ATTTCCCGAAGATTTCTGTCGACACAAGGTGCTGCCCCAGCTACTGACTGCCTTTGAGTTTGGCAATGCTGGGGCCGTGGTCCTCACACCTCTCTTCAAGGTCAGCAGACATGTGGCGCTTGGGCTGCCTCATCTGGGAAGTTTTCAATGGGTCTCTACCTCGGGCAGCTGCCCTGCGCAACCCTGGGAAGATCCCCAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-221-3p(1), mmu-let-7d-5p(1), mmu-miR-149-5p(1), mmu-miR-22-3p(1), mmu-miR-541-5p(1), mmu-miR-98-5p(1), mmu-miR-669d-5p(1), mmu-miR-1904(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACCTCTCTTCAAGGTCAGCAGACATG
siRNA sets
CTGCTGACCTTGAAGAGAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSCYL1_406_ORF_1
0.8546
0.279772032
0.771407456
519
ORF sequence:
ATGTGGCGCTTGGGCTGCCTCATCTGGGAAGTTTTCAATGGGTCTCTACCTCGGGCAGCTGCCCTGCGCAACCCTGGGAAGATCCCCAAATCCCTGGTGACCCATTACTGTGAACTGGTGGGAGCTAACCCAAAAGTACGTCCCAACCCGGCCCGCTTCCTGCAGAACTGCCGGGCACCCGGTGGCTTCATGAGCAACCGCTTTGTTGAGACCAACCTCTTCCTGGAGGAGATTCAGATCAAAGAGCCAGCTGAGAAGCAGAAGTTCTTCCAAGAGCTGAGCAAGAGTCTAGACTCATTTCCCGAAGATTTCTGTCGACACAAGGTGCTGCCCCAGCTACTGACTGCCTTTGAGTTTGGCAATGCTGGGGCCGTGGTCCTCACACCTCTCTTCAAGGTCAGCAGACATGTGGCGCTTGGGCTGCCTCATCTGGGAAGTTTTCAATGGGTCTCTACCTCGGGCAGCTGCCCTGCGCAACCCTGGGAAGATCCCCAAATCCCTGGTGACCCATTACTGTGA
Peptide sequence:
MWRLGCLIWEVFNGSLPRAAALRNPGKIPKSLVTHYCELVGANPKVRPNPARFLQNCRAPGGFMSNRFVETNLFLEEIQIKEPAEKQKFFQELSKSLDSFPEDFCRHKVLPQLLTAFEFGNAGAVVLTPLFKVSRHVALGLPHLGSFQWVSTSGSCPAQPWEDPQIPGDPLL
IRESfinder result
IRESfinder score
0.638931779
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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