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mmu_circVps8_455
Basic information of circular RNA
PanCircBase ID:
mmu_circVps8_455
mm39_Chr. Position ID:
chr16|21314629|21330311|+
Gene name:
Vps8
Transcript:
ENSMUST00000096191.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
21,22,23,24,25
Exon/intron offsets:
0,4308,8518,10890,15639
Genomic length:
15682
Exon/intron sizes in nt:
47,223,90,52,43
Flanking exon/introns:
chr16:21297233-21314629|chr16:21330311-21336032
Splice length:
455
Other database IDs:
circAtlas: mmu-Vps8_0050
Human Ortholog IDs:
Mature spliced Sequence:
GATACGGTGCCAGTCATAGTGGACTACTGCCTTCTGCTCCAGCGAAAGGATCTTCTATTTGGTCAAATGTACGACAAATTAAGTGAAAATTCCGTCGCAAAAGGCGTGTTTTTGGAGTGCCTTGAGCCATATATCTTAAGTGATAAACTGGTGGGGATTACTCCCCAGGTCATGAAGGACTTAATTGTTCATTTCCAAGATAAAAAACTGCTGGAGAATGTGGAAGCCCTCATTGTCCACATGGACATCACCAGCCTCGACATTCAGCAGGTGGTCCTCATGTGTTGGGAGAATCGTCTGTATGACGCCATGGTCTATGTCTACAACCGAGGCATGAATGAGTTTATCAGTCCGATGGAGAAGCTTTTCAAAGTCATCGCCCCACCTCTGAATGCAGGGAAGACTCTTACAGATGAGCAAGTTGTTATGGGCAACAAGCTTCTGGTGTACATCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTCAAAGTCATCGCCCCACC
60.61
GATCCTTTCGCTGGAGCAGA
59.82
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCAAAGTCATCGCCCCACC
60.61
AGATCCTTTCGCTGGAGCAG
59.82
142
PCR template sequence:
TGGAGAAGCTTTTCAAAGTCATCGCCCCACCTCTGAATGCAGGGAAGACTCTTACAGATGAGCAAGTTGTTATGGGCAACAAGCTTCTGGTGTACATCAGGATACGGTGCCAGTCATAGTGGACTACTGCCTTCTGCTCCAGCGAAAGGATCTTCTATTTGGTCAAATGTACGACAAATTAAGTGAAAATTCCGTCGCAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-124-3p(1), mmu-miR-150-5p(1), mmu-miR-205-5p(1), mmu-miR-138-5p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-370-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGGTGTACATCAGGATACGGTGCCAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVPS8_455_ORF_1
1.2873
0.306708805
0.790478318
408
ORF sequence:
ATGTACGACAAATTAAGTGAAAATTCCGTCGCAAAAGGCGTGTTTTTGGAGTGCCTTGAGCCATATATCTTAAGTGATAAACTGGTGGGGATTACTCCCCAGGTCATGAAGGACTTAATTGTTCATTTCCAAGATAAAAAACTGCTGGAGAATGTGGAAGCCCTCATTGTCCACATGGACATCACCAGCCTCGACATTCAGCAGGTGGTCCTCATGTGTTGGGAGAATCGTCTGTATGACGCCATGGTCTATGTCTACAACCGAGGCATGAATGAGTTTATCAGTCCGATGGAGAAGCTTTTCAAAGTCATCGCCCCACCTCTGAATGCAGGGAAGACTCTTACAGATGAGCAAGTTGTTATGGGCAACAAGCTTCTGGTGTACATCAGGATACGGTGCCAGTCATAG
Peptide sequence:
MYDKLSENSVAKGVFLECLEPYILSDKLVGITPQVMKDLIVHFQDKKLLENVEALIVHMDITSLDIQQVVLMCWENRLYDAMVYVYNRGMNEFISPMEKLFKVIAPPLNAGKTLTDEQVVMGNKLLVYIRIRCQS
IRESfinder result
IRESfinder score
0.514099297
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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