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mmu_ciVps54_838
Basic information of circular RNA
PanCircBase ID:
mmu_ciVps54_838
mm39_Chr. Position ID:
chr11|21248850|21249688|+
Gene name:
Vps54
Transcript:
ENSMUST00000109578.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
11
Exon/intron offsets:
0
Genomic length:
838
Exon/intron sizes in nt:
838
Flanking exon/introns:
chr11:21248850-21249977
Splice length:
838
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGCTTACATATCAGTTGCCTGGAATATCTGAAATTCAGTCAGCTTTCTGGACAGTGCTCAGAACTGAAATATATTTGGGTGAGGGTAAGTTTTTATGTACATAATGATATCTTTGGGCCTTGGTTTTAGTTGCTTGCATTCCCTCCAGTCTGCCTTTGATGTGTGTCTGTGCTGATTGGACTTACTCAGCCTCCACTGACTCAGAAAATTTGAACTTGGAATCTGCTTCCTTAGAATCATGTCCATCCCTAAAAGAAACCAAATGTTTCAGAGAGGAAGCAATGCATTTGAGATTTGCAGCTATGACTATCAAAATCCTTTATTTCTTAATAGTTCTTAAAAATAGTAGTTTATGTAAGCTATTTTTCGTTTACCTAGCTTTCAGTGTTTAAGTGTTTCCTCTGTATCAAGTACCATTAAGATAAGTGTAATGAGGTGGAGCTAACAGTGTAGAAGAAAGAGACCAAGATGAATAGAGAGATAATTTTAGATGACAATAAATGTTCTTAAACAAACAAAGCAAAACCACAGTAGAGCAGCCACAACTGCATTTGTGGGAGAGTCACTGAAGGAAGGTCTCTTTGAGGAAACCGCCATGTTTTGCTAGGACCCAAGTGATGAGAAGGACAGTGTACAAAGGTTACAGGGAAGAGCTGTCTGTTCAGAGGAGGCAGCAGAAGTGTTGAGTGAGAACAGGCTCGGAGTGATCAGACAACAGAATGAGACATCCCCATGTGACAGTATAATGCTAAGGAATATAAGCTATTGTTCTTTTAAGCAGGTGGATGTACTAATAAGTTTCTCTGAGAGGTATTTGGCACAGCATGATTAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTTCTTTTAAGCAGGTGGATGT
58.53
TTCAGTTCTGAGCACTGTCCA
59.24
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGTTCTTTTAAGCAGGTGGATGT
59.11
TCAGTTCTGAGCACTGTCCAG
59.66
140
PCR template sequence:
TGACAGTATAATGCTAAGGAATATAAGCTATTGTTCTTTTAAGCAGGTGGATGTACTAATAAGTTTCTCTGAGAGGTATTTGGCACAGCATGATTAAGAGGTAAGCTTACATATCAGTTGCCTGGAATATCTGAAATTCAGTCAGCTTTCTGGACAGTGCTCAGAACTGAAATATATTTGGGTGAGGGTAAGTTTTTATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-25-3p(1), mmu-miR-5101(1), mmu-miR-188-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
GCATGATTAAGAGGTAAGCTTACATA
siRNA sets
TAAGCTTACCTCTTAATCA, AAGCTTACCTCTTAATCAT, TATGTAAGCTTACCTCTTA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.802721173
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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