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mmu_circVps8_469
Basic information of circular RNA
PanCircBase ID:
mmu_circVps8_469
mm39_Chr. Position ID:
chr16|21351032|21372972|+
Gene name:
Vps8
Transcript:
ENSMUST00000096191.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
32,33,34,35,36
Exon/intron offsets:
0,780,7736,10985,21792
Genomic length:
21940
Exon/intron sizes in nt:
85,99,90,47,148
Flanking exon/introns:
chr16:21350112-21351032|chr16:21372972-21378083
Splice length:
469
Other database IDs:
CIRCpedia: MMU_CIRCpedia_216965, circAtlas: mmu-Vps8_0017
circAtlas: hsa-VPS8_0066
Human Ortholog IDs:
Mature spliced Sequence:
CTATCAAATCTGTGAATTTATGTATGAGCGGGAACACCAGTATGACAAGATCATTGACTGCTACCTGCACGACCCATTGAGAGAGGAAGAAGTCTTCAATTATATCCACAACATCTTATCTATTCCTGGTCACAGTGCTGAGGAGAAGCAGTCTGTGTGGCAGAAAGCAATGAATCATATGGAGGAACTTGTGTCCCTGAAGCCCTGCAAAGCCGCAGAGCTGGTGGCTACTCACTTTTCTGAGCAGATCGAAGTGGTCATTGGACAGCTTCAGAACCAGCTTTTGCTTTTCAAATTTTTGAGGAGTCTTCTTGATCCAAGGGAAGGTGTTCATGTCAATCAGGAGTTGCTGCAGATCCCGCCTCACATTACAGAGCAGTTCATTGAGCTGCTGTGCCAGTTCAGTCCTGACCAAGTCATACAGACACTGCAGGTCCTTGAGTGCTACCGTCTGGAGGAAACGATTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGCCAGTTCAGTCCTGAC
59.89
TCTCTCAATGGGTCGTGCAG
59.75
161
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGCCAGTTCAGTCCTGAC
59.89
CTCTCTCAATGGGTCGTGCA
59.75
162
PCR template sequence:
TACAGAGCAGTTCATTGAGCTGCTGTGCCAGTTCAGTCCTGACCAAGTCATACAGACACTGCAGGTCCTTGAGTGCTACCGTCTGGAGGAAACGATTCAGCTATCAAATCTGTGAATTTATGTATGAGCGGGAACACCAGTATGACAAGATCATTGACTGCTACCTGCACGACCCATTGAGAGAGGAAGAAGTCTTCAAT
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-322-5p(1), mmu-miR-320-3p(1), mmu-miR-466d-3p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
GGAAACGATTCAGCTATCAAATCTGT
siRNA sets
TGATAGCTGAATCGTTTCC, ATTTGATAGCTGAATCGTT, TTTGATAGCTGAATCGTTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVPS8_469_ORF_1
1.0725
0.206460884
0.87508144
606
ORF sequence:
ATGTCAATCAGGAGTTGCTGCAGATCCCGCCTCACATTACAGAGCAGTTCATTGAGCTGCTGTGCCAGTTCAGTCCTGACCAAGTCATACAGACACTGCAGGTCCTTGAGTGCTACCGTCTGGAGGAAACGATTCAGCTATCAAATCTGTGAATTTATGTATGAGCGGGAACACCAGTATGACAAGATCATTGACTGCTACCTGCACGACCCATTGAGAGAGGAAGAAGTCTTCAATTATATCCACAACATCTTATCTATTCCTGGTCACAGTGCTGAGGAGAAGCAGTCTGTGTGGCAGAAAGCAATGAATCATATGGAGGAACTTGTGTCCCTGAAGCCCTGCAAAGCCGCAGAGCTGGTGGCTACTCACTTTTCTGAGCAGATCGAAGTGGTCATTGGACAGCTTCAGAACCAGCTTTTGCTTTTCAAATTTTTGAGGAGTCTTCTTGATCCAAGGGAAGGTGTTCATGTCAATCAGGAGTTGCTGCAGATCCCGCCTCACATTACAGAGCAGTTCATTGAGCTGCTGTGCCAGTTCAGTCCTGACCAAGTCATACAGACACTGCAGGTCCTTGAGTGCTACCGTCTGGAGGAAACGATTCAG
Peptide sequence:
MSIRSCCRSRLTLQSSSLSCCASSVLTKSYRHCRSLSATVWRKRFSYQICEFMYEREHQYDKIIDCYLHDPLREEEVFNYIHNILSIPGHSAEEKQSVWQKAMNHMEELVSLKPCKAAELVATHFSEQIEVVIGQLQNQLLLFKFLRSLLDPREGVHVNQELLQIPPHITEQFIELLCQFSPDQVIQTLQVLECYRLEETIQ
IRESfinder result
IRESfinder score
0.747609284
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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