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mmu_circVps13a_654
Basic information of circular RNA
PanCircBase ID:
mmu_circVps13a_654
mm39_Chr. Position ID:
chr19|16726889|16743904|-
Gene name:
Vps13a
Transcript:
ENSMUST00000068156.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,321,596,2593,4726,10061,10415,12623,16971
Genomic length:
17015
Exon/intron sizes in nt:
58,81,60,60,110,102,96,43,44
Flanking exon/introns:
chr19:16723442-16726889|chr19:16743904-16758033
Splice length:
654
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_352168
Human Ortholog IDs:
Mature spliced Sequence:
GAGCTGTGGCCCTCAAGAACCTTGTAATTAAAGAAAATGCATTGCATGAATTGGATGTACCATTCAAAGTTAAAGTTGGTCATATAGGTAGTCTTAAACTTAAAATTCCATGGAAAAACCTTTATACTCAACCAGTTGAAGCTGTTTTGGAAGAAATTTTTTTACTCATAGTGCCTTCTTCTAGAATACAGTATGATCCTATCAAAGAAGAAAAGCAACTCATGGAAACAAAGCAACAGGAACTAAAAAGAATAGAAAAAGCAAAACAGAAAGTATTTGATAAAGAAAAGCCTCGGGAGGAGAAACAGGACACGTTTACAGAAAAGTTAGTTACTCAGATCATACAGAACCTTCAAGTGCAAATCTCCAGCATCCATATTCGTTATGAAGACGATATCACAAATGGAGACAAACCACTCTCTTTTGGTATTTCCCTTCAAAATATCAGCCTTCAGACAACTGATCAATACTGGATCCCATGTTTACATGATAATACTGAAAAGCTAGTCCGGAAGCTAATCCGATTAGATAATCTCTTTGCTTACTGGAATGTGAACTCTGAGATGTTTTATCTGAATGATTACGATGAATCGCTGAAAGCCTTGAAAAATGGTATTGTGAATGAAAATATTGTTCCAGAAGGTTATGATTTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATCTGAATGATTACGATGAATCGCTG
59.91
ACATCCAATTCATGCAATGCA
57.1
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATCTGAATGATTACGATGAATCGCT
58.84
ACATCCAATTCATGCAATGCA
57.1
142
PCR template sequence:
AACTCTGAGATGTTTTATCTGAATGATTACGATGAATCGCTGAAAGCCTTGAAAAATGGTATTGTGAATGAAAATATTGTTCCAGAAGGTTATGATTTTGGAGCTGTGGCCCTCAAGAACCTTGTAATTAAAGAAAATGCATTGCATGAATTGGATGTACCATTCAAAGTTAAAGTTGGTCATATAGGTAGTCTTAAACT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-miR-140-5p(1), mmu-miR-23a-3p(1), mmu-miR-136-5p(1), mmu-miR-382-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGTTATGATTTTGGAGCTGTGGCCCT
siRNA sets
CAGCTCCAAAATCATAACC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVPS13A_654_ORF_1
1.0634
0.111185945
0.99327645
1086
ORF sequence:
ATGGAAACAAAGCAACAGGAACTAAAAAGAATAGAAAAAGCAAAACAGAAAGTATTTGATAAAGAAAAGCCTCGGGAGGAGAAACAGGACACGTTTACAGAAAAGTTAGTTACTCAGATCATACAGAACCTTCAAGTGCAAATCTCCAGCATCCATATTCGTTATGAAGACGATATCACAAATGGAGACAAACCACTCTCTTTTGGTATTTCCCTTCAAAATATCAGCCTTCAGACAACTGATCAATACTGGATCCCATGTTTACATGATAATACTGAAAAGCTAGTCCGGAAGCTAATCCGATTAGATAATCTCTTTGCTTACTGGAATGTGAACTCTGAGATGTTTTATCTGAATGATTACGATGAATCGCTGAAAGCCTTGAAAAATGGTATTGTGAATGAAAATATTGTTCCAGAAGGTTATGATTTTGGAGCTGTGGCCCTCAAGAACCTTGTAATTAAAGAAAATGCATTGCATGAATTGGATGTACCATTCAAAGTTAAAGTTGGTCATATAGGTAGTCTTAAACTTAAAATTCCATGGAAAAACCTTTATACTCAACCAGTTGAAGCTGTTTTGGAAGAAATTTTTTTACTCATAGTGCCTTCTTCTAGAATACAGTATGATCCTATCAAAGAAGAAAAGCAACTCATGGAAACAAAGCAACAGGAACTAAAAAGAATAGAAAAAGCAAAACAGAAAGTATTTGATAAAGAAAAGCCTCGGGAGGAGAAACAGGACACGTTTACAGAAAAGTTAGTTACTCAGATCATACAGAACCTTCAAGTGCAAATCTCCAGCATCCATATTCGTTATGAAGACGATATCACAAATGGAGACAAACCACTCTCTTTTGGTATTTCCCTTCAAAATATCAGCCTTCAGACAACTGATCAATACTGGATCCCATGTTTACATGATAATACTGAAAAGCTAGTCCGGAAGCTAATCCGATTAGATAATCTCTTTGCTTACTGGAATGTGAACTCTGAGATGTTTTATCTGAATGATTACGATGAATCGCTGAAAGCCTTGAAAAATGGTATTGTGAATGAAAATATTGTTCCAGAAGGTTATGATTTT
Peptide sequence:
METKQQELKRIEKAKQKVFDKEKPREEKQDTFTEKLVTQIIQNLQVQISSIHIRYEDDITNGDKPLSFGISLQNISLQTTDQYWIPCLHDNTEKLVRKLIRLDNLFAYWNVNSEMFYLNDYDESLKALKNGIVNENIVPEGYDFGAVALKNLVIKENALHELDVPFKVKVGHIGSLKLKIPWKNLYTQPVEAVLEEIFLLIVPSSRIQYDPIKEEKQLMETKQQELKRIEKAKQKVFDKEKPREEKQDTFTEKLVTQIIQNLQVQISSIHIRYEDDITNGDKPLSFGISLQNISLQTTDQYWIPCLHDNTEKLVRKLIRLDNLFAYWNVNSEMFYLNDYDESLKALKNGIVNENIVPEGYDF
IRESfinder result
IRESfinder score
0.769455716
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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