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mmu_ciVdac1_874
Basic information of circular RNA
PanCircBase ID:
mmu_ciVdac1_874
mm39_Chr. Position ID:
chr11|52278300|52279174|+
Gene name:
Vdac1
Transcript:
ENSMUST00000102758.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
8
Exon/intron offsets:
0
Genomic length:
874
Exon/intron sizes in nt:
874
Flanking exon/introns:
chr11:52278300-52279258
Splice length:
874
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTATGTGTTGTTGCCCATGTGCAAAGCTCGTTCTCGGTTGCATTTTGCTGATGTCTGCTATTGCTGAGGGACATTATAAACGAGTATATATAAGCTTTTATAATTAAATGTTTATAAAGGAAGTTGTGAAGTCATTGTAAAAAGAAAAAGAGAGTCTGAGAAATAGAAAGCAGAAGGAACCTGTCTGGGCTAACTCACATCACAGCTCTAGTTATTTTCTCCTTTCCTTTCCCCAGTATGTGATATGTGATAGCTGCTTCCAGACTGTAGTCAAAACTAGCCTGTCAGTCATCCTCACGATGGAAAGACTAGGGTATAGGGATGTAGTGGGTCTTCTATGCATAGTTATTCCATCCTCTCACTGGTGTGTGAGGGCTGCAGAAATCCCACTCAAGGCTGACTATGTAATATGAAAATCAAGTTCTTCCAGGGAAAACCATCCCGTTTGATCTAAAATTACAAGTAAGCCCCAGGAAAAGAAGTTTATTGTTTTTTTTTTTGTGTGTGTGTGTGTGTGTGTGTGTGTATGCTCACGTGTTATGAAAGTGAATGTAAGACTCAGGCTGTTACAAGATAGGGTTTCCCTCCAAGGCAATACTGCTCAAGCAACTTACTGAGTTGGGGCAGCAGCGGATGGCACACTCATTGTAATGGGACTGCAGGAGGCTGGAAGGGAGGGGGATTCGGAAGTACGTTCCAGCAGGGTCTCTGCTCTGTGTGCCAGTGATGGCCGTTGCATGTGTTGATTCGAGGATAGCAGCAGGTCAGGTTGTATTACAGAGCACACCTTGAAGGGTCGCCTCGCTTGGCCACTGCTGACTGCACCTGGAACAGATTCTGACCTTGATTCTGACCTTGATGCTAACCTCTCTTC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGAGCACACCTTGAAGGGT
59.89
ATGCAACCGAGAACGAGCTT
60.32
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGAGCACACCTTGAAGGGT
59.89
AATGCAACCGAGAACGAGCT
60.32
141
PCR template sequence:
TTACAGAGCACACCTTGAAGGGTCGCCTCGCTTGGCCACTGCTGACTGCACCTGGAACAGATTCTGACCTTGATTCTGACCTTGATGCTAACCTCTCTTCGTATGTGTTGTTGCCCATGTGCAAAGCTCGTTCTCGGTTGCATTTTGCTGATGTCTGCTATTGCTGAGGGACATTATAAACGAGTATATATAAGCTTTTA
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-181b-5p(1), mmu-miR-382-3p(1), mmu-miR-370-3p(1), mmu-miR-466d-3p(1), mmu-miR-27a-5p(1), mmu-miR-335-3p(1), mmu-miR-452-3p(1), mmu-miR-466b-3p(1), mmu-miR-540-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTAACCTCTCTTCGTATGTGTTGTTG
siRNA sets
AACAACACATACGAAGAGA, CAACACATACGAAGAGAGG, AACACATACGAAGAGAGGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIVDAC1_874_ORF_1
0.5466
-0.404867041
0.006462779
123
ORF sequence:
ATGCTAACCTCTCTTCGTATGTGTTGTTGCCCATGTGCAAAGCTCGTTCTCGGTTGCATTTTGCTGATGTCTGCTATTGCTGAGGGACATTATAAACGAGTATATATAAGCTTTTATAATTAA
Peptide sequence:
MLTSLRMCCCPCAKLVLGCILLMSAIAEGHYKRVYISFYN
IRESfinder result
IRESfinder score
0.630692953
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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