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mmu_circVps4a_330
Basic information of circular RNA
PanCircBase ID:
mmu_circVps4a_330
mm39_Chr. Position ID:
chr8|107763474|107765841|+
Gene name:
Vps4a
Transcript:
ENSMUST00000034388.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
3,4,5
Exon/intron offsets:
0,2085,2247
Genomic length:
2367
Exon/intron sizes in nt:
1,48,62,120
Flanking exon/introns:
chr8:107763380-107763474|chr8:107765841-107767505
Splice length:
330
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATGAAGCACACAGTGACAAGGCCAAGGAGAGCATTCGAGCAAAGTGCATGCAGTACCTAGACAGAGCGGAGAAGCTGAAGGATTATTTACGAAACAAAGAGAAACATGGCAAGAAGCCAGTCAAAGAGAACCAGAGTGAAGGCAAGGGTAGTGACAGTGACAGTGAAGGGGATAATCCAGAGAAAAAGAAGTTACAAGAACAATTGATGGGTGCTGTTGTGATGGAGAAGCCGAACATACGGTGGAATGATGTAGCTGGACTGGAGGGGGCTAAAGAGGCTCTCAAAGAAGCTGTGATTTTGCCAATTAAATTCCCACACTTATTCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGACTGGAGGGGGCTAAAGA
60.62
TTCAGCTTCTCCGCTCTGTC
59.76
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGACTGGAGGGGGCTAAAGA
60.62
CTTCAGCTTCTCCGCTCTGT
59.75
153
PCR template sequence:
CCGAACATACGGTGGAATGATGTAGCTGGACTGGAGGGGGCTAAAGAGGCTCTCAAAGAAGCTGTGATTTTGCCAATTAAATTCCCACACTTATTCACAGATGAAGCACACAGTGACAAGGCCAAGGAGAGCATTCGAGCAAAGTGCATGCAGTACCTAGACAGAGCGGAGAAGCTGAAGGATTATTTACGAAACAAAGA
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-221-3p(1), mmu-miR-222-3p(1), mmu-miR-182-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
CACTTATTCACAGATGAAGCACACAG
siRNA sets
CTTCATCTGTGAATAAGTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVPS4A_330_ORF_1
1.145
0.332967329
0.933918591
612
ORF sequence:
ATGCAGTACCTAGACAGAGCGGAGAAGCTGAAGGATTATTTACGAAACAAAGAGAAACATGGCAAGAAGCCAGTCAAAGAGAACCAGAGTGAAGGCAAGGGTAGTGACAGTGACAGTGAAGGGGATAATCCAGAGAAAAAGAAGTTACAAGAACAATTGATGGGTGCTGTTGTGATGGAGAAGCCGAACATACGGTGGAATGATGTAGCTGGACTGGAGGGGGCTAAAGAGGCTCTCAAAGAAGCTGTGATTTTGCCAATTAAATTCCCACACTTATTCACAGATGAAGCACACAGTGACAAGGCCAAGGAGAGCATTCGAGCAAAGTGCATGCAGTACCTAGACAGAGCGGAGAAGCTGAAGGATTATTTACGAAACAAAGAGAAACATGGCAAGAAGCCAGTCAAAGAGAACCAGAGTGAAGGCAAGGGTAGTGACAGTGACAGTGAAGGGGATAATCCAGAGAAAAAGAAGTTACAAGAACAATTGATGGGTGCTGTTGTGATGGAGAAGCCGAACATACGGTGGAATGATGTAGCTGGACTGGAGGGGGCTAAAGAGGCTCTCAAAGAAGCTGTGATTTTGCCAATTAAATTCCCACACTTATTCACA
Peptide sequence:
MQYLDRAEKLKDYLRNKEKHGKKPVKENQSEGKGSDSDSEGDNPEKKKLQEQLMGAVVMEKPNIRWNDVAGLEGAKEALKEAVILPIKFPHLFTDEAHSDKAKESIRAKCMQYLDRAEKLKDYLRNKEKHGKKPVKENQSEGKGSDSDSEGDNPEKKKLQEQLMGAVVMEKPNIRWNDVAGLEGAKEALKEAVILPIKFPHLFT
IRESfinder result
IRESfinder score
0.324585627
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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