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mmu_ciSptan1_499
Basic information of circular RNA
PanCircBase ID:
mmu_ciSptan1_499
mm39_Chr. Position ID:
chr2|29917143|29917642|+
Gene name:
Sptan1
Transcript:
ENSMUST00000113719.9
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
49
Exon/intron offsets:
0
Genomic length:
499
Exon/intron sizes in nt:
499
Flanking exon/introns:
chr2:29917143-29917642
Splice length:
499
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGCTTGCCCTCTAGAGCTAGCCAGGGACTGTGGTGCTCCTGGCAGCTGGATGCCAAGCCTCCAGCTCTGGGACACAGGGAGCTTGTTTGAAACCTGGTCCCTAGCCAGGCATCTGGCTACAGTTTGGCATCTGTAATTCCACAATCCAGGAGGATGGCTGTGAACTAGAGTCCAACTTGGTTCATATTTATTTGTGCCATTTGAGGCCATAGCAAAACCCTGTTTCCTCAGAAAAAATGGGGTGGTGGGGAGGACTGCTTAGACTAAGACTATCATAGTCTGATTGGTTTCCAGAGCAATAGCAATAGCGGGCTCTGCATGGTTCATTGCCCCAAAGACGATGTTGGCAACTGTCCCAAGGGAGGTAGACCAGTCACACCTGGCACACAGGCTCGGGCAGAAGAGTGCTAATGTTCTGTATTTTCTTCTTTCTACATCATCCTGATTGCTGCTGTATGTGGATACTACCACGGCTCCTGGACACTTGGATCTCCATAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTGATTGCTGCTGTATGTGG
59.33
AAACAAGCTCCCTGTGTCCC
60.18
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGATACTACCACGGCTCCT
59.74
GACCAGGTTTCAAACAAGCTCC
59.97
140
PCR template sequence:
AGAAGAGTGCTAATGTTCTGTATTTTCTTCTTTCTACATCATCCTGATTGCTGCTGTATGTGGATACTACCACGGCTCCTGGACACTTGGATCTCCATAGGTGCTTGCCCTCTAGAGCTAGCCAGGGACTGTGGTGCTCCTGGCAGCTGGATGCCAAGCCTCCAGCTCTGGGACACAGGGAGCTTGTTTGAAACCTGGTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-137-3p(1), mmu-miR-134-5p(1), mmu-miR-15a-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-136-5p(1), mmu-miR-22-3p(1), mmu-miR-183-5p(1), mmu-miR-680(1), mmu-miR-673-5p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGGATCTCCATAGGTGCTTGCCCTCT
siRNA sets
AAGCACCTATGGAGATCCA, CAAGCACCTATGGAGATCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CISPTAN1_499_ORF_1
0.52
-0.225055472
0.026702557
225
ORF sequence:
ATGTTCTGTATTTTCTTCTTTCTACATCATCCTGATTGCTGCTGTATGTGGATACTACCACGGCTCCTGGACACTTGGATCTCCATAGGTGCTTGCCCTCTAGAGCTAGCCAGGGACTGTGGTGCTCCTGGCAGCTGGATGCCAAGCCTCCAGCTCTGGGACACAGGGAGCTTGTTTGAAACCTGGTCCCTAGCCAGGCATCTGGCTACAGTTTGGCATCTGTAA
Peptide sequence:
MFCIFFFLHHPDCCCMWILPRLLDTWISIGACPLELARDCGAPGSWMPSLQLWDTGSLFETWSLARHLATVWHL
IRESfinder result
IRESfinder score
0.69049658
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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