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mmu_circVps36_140
Basic information of circular RNA
PanCircBase ID:
mmu_circVps36_140
mm39_Chr. Position ID:
chr8|22688913|22692360|+
Gene name:
Vps36
Transcript:
ENSMUST00000033866.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
2,3
Exon/intron offsets:
0,3376
Genomic length:
3447
Exon/intron sizes in nt:
69,71
Flanking exon/introns:
chr8:22682982-22688913|chr8:22692360-22695682
Splice length:
140
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATAAAATTTGATGCCGGGACTCTTCTTCTTAGTACACACCGGCTGATTTGGAGAGACCAGAAGAATAATGAGTGCTGCATGGCCATTCCCCTGTCTCAGATTGTGTTCATCGAGGAGCAGGCAGCTGGAATCGGGAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CATGGCCATTCCCCTGTCTC
60.47
TGGTCTCTCCAAATCAGCCG
59.75
122
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CATGGCCATTCCCCTGTCTC
60.47
GTCTCTCCAAATCAGCCGGT
59.75
120
PCR template sequence:
AGTGCTGCATGGCCATTCCCCTGTCTCAGATTGTGTTCATCGAGGAGCAGGCAGCTGGAATCGGGAAGAGATAAAATTTGATGCCGGGACTCTTCTTCTTAGTACACACCGGCTGATTTGGAGAGACCAGAAGAATAATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-22-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAATCGGGAAGAGATAAAATTTGATG
siRNA sets
CAAATTTTATCTCTTCCCG,TCAAATTTTATCTCTTCCC,TTTTATCTCTTCCCGATTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVPS36_140_ORF_1
0.8705
-0.405931517
0.009154309
84
ORF sequence:
ATGAGTGCTGCATGGCCATTCCCCTGTCTCAGATTGTGTTCATCGAGGAGCAGGCAGCTGGAATCGGGAAGAGATAAAATTTGA
Peptide sequence:
MSAAWPFPCLRLCSSRSRQLESGRDKI
IRESfinder result
IRESfinder score
0.400049287
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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