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mmu_circVdac1_437
Basic information of circular RNA
PanCircBase ID:
mmu_circVdac1_437
mm39_Chr. Position ID:
chr11|52274676|52278300|+
Gene name:
Vdac1
Transcript:
ENSMUST00000102758.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
6,7,8
Exon/intron offsets:
0,1733,3566
Genomic length:
3624
Exon/intron sizes in nt:
228,151,58
Flanking exon/introns:
chr11:52267527-52274676|chr11:52278300-52279258
Splice length:
437
Other database IDs:
circAtlas: mmu-Vdac1_0008
circBase: hsa_circ_0073924, CIRCpedia: HSA_CIRCpedia_173657
Human Ortholog IDs:
Mature spliced Sequence:
GAAAAAAAATGCTAAAATCAAGACAGGGTACAAGAGGGAGCACATCAACCTCGGCTGTGACGTGGACTTTGACATCGCTGGGCCCTCGATCCGGGGCGCTCTGGTGCTTGGCTATGAGGGTTGGCTGGCTGGCTACCAGATGAATTTTGAGACCTCGAAGTCCCGAGTGACCCAGAGCAACTTCGCAGTTGGCTATAAGACGGATGAATTCCAGCTTCATACTAATGTGAATGACGGGACAGAGTTTGGTGGCTCCATTTACCAGAAGGTGAACAAGAAGTTGGAGACTGCTGTCAATCTCGCCTGGACTGCAGGAAACAGTAACACTCGCTTCGGAATAGCAGCCAAGTATCAGGTCGACCCTGATGCCTGCTTTTCGGCCAAAGTGAACAACTCTAGCCTGATTGGCTTAGGGTACACTCAGACCCTAAAACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGCCAAGTATCAGGTCGA
59.82
AGCGATGTCAAAGTCCACGT
59.97
176
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCAGCCAAGTATCAGGTCG
59.82
AGCGATGTCAAAGTCCACGT
59.97
177
PCR template sequence:
ATAGCAGCCAAGTATCAGGTCGACCCTGATGCCTGCTTTTCGGCCAAAGTGAACAACTCTAGCCTGATTGGCTTAGGGTACACTCAGACCCTAAAACCAGGAAAAAAAATGCTAAAATCAAGACAGGGTACAAGAGGGAGCACATCAACCTCGGCTGTGACGTGGACTTTGACATCGCTGGGCCCTCGATCCGGGGCGCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-326-3p(1), mmu-miR-23a-3p(1), mmu-miR-673-5p(1), mmu-miR-339-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACCCTAAAACCAGGAAAAAAAATGCT
siRNA sets
TTTTTTTTCCTGGTTTTAG, ATTTTTTTTCCTGGTTTTA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVDAC1_437_ORF_1
0.7815
0.197754297
0.545046613
441
ORF sequence:
ATGAATTTTGAGACCTCGAAGTCCCGAGTGACCCAGAGCAACTTCGCAGTTGGCTATAAGACGGATGAATTCCAGCTTCATACTAATGTGAATGACGGGACAGAGTTTGGTGGCTCCATTTACCAGAAGGTGAACAAGAAGTTGGAGACTGCTGTCAATCTCGCCTGGACTGCAGGAAACAGTAACACTCGCTTCGGAATAGCAGCCAAGTATCAGGTCGACCCTGATGCCTGCTTTTCGGCCAAAGTGAACAACTCTAGCCTGATTGGCTTAGGGTACACTCAGACCCTAAAACCAGGAAAAAAAATGCTAAAATCAAGACAGGGTACAAGAGGGAGCACATCAACCTCGGCTGTGACGTGGACTTTGACATCGCTGGGCCCTCGATCCGGGGCGCTCTGGTGCTTGGCTATGAGGGTTGGCTGGCTGGCTACCAGATGA
Peptide sequence:
MNFETSKSRVTQSNFAVGYKTDEFQLHTNVNDGTEFGGSIYQKVNKKLETAVNLAWTAGNSNTRFGIAAKYQVDPDACFSAKVNNSSLIGLGYTQTLKPGKKMLKSRQGTRGSTSTSAVTWTLTSLGPRSGALWCLAMRVGWLATR
IRESfinder result
IRESfinder score
0.355037248
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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