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mmu_circVps35l_585
Basic information of circular RNA
PanCircBase ID:
mmu_circVps35l_585
mm39_Chr. Position ID:
chr7|118359383|118379522|+
Gene name:
Vps35l
Transcript:
ENSMUST00000059390.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
8,9,10,11,12,13,14
Exon/intron offsets:
0,6204,12860,13839,15131,19527,20016
Genomic length:
20139
Exon/intron sizes in nt:
85,60,97,48,94,78,123
Flanking exon/introns:
chr7:118353157-118359383|chr7:118379522-118389232
Splice length:
585
Other database IDs:
circAtlas: mmu-9030624J02Rik_0008
circBase: hsa_circ_0105134, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_16813
Human Ortholog IDs:
Mature spliced Sequence:
TGTTCAAAGCTGCTGTCAGACACGAGTGTTATTCAGTTCTACCCAAGCAAGTTTGTCCTCATCACCGACATCCTTGATACGTTTGGAAAGCTGGTCTATGAGCGCATCTCCTCGATGTGTGTGGACAGCCGCAGTGCCTTGCCAGATCATTTCTCCCCAGAGAACGTGAACGACACAGCCAAGGAGACATGCCTGAATTGGTTTTTCAAGATCGCTTCCATCCGGGAACTCATTCCAAGATTTTATGTGGAAGCATCCATCCTGAAGTGTAACAAGTTCCTCTCCAAAACGGGGATTTCAGAGTGCCTGCCCCGACTAACCTGCATGATCAGAGGGATCGGAGACCCACTCGTGTCCGTGTACGCCCGGGCCTACCTGTGTCGGGTGGGGATCGAAGTGGCCCCGCACCTCAAGGAGAGCCTCAATAAGAACTTCTTTGACTTCCTGCTGACATTTAAACAGATTCATGGGGACACTGTCCAGAACCAGCTGGTGGCCCAGGGTGTGGAGCTGCTGTCCTATCTCCCTCTGTACTCGCCTGCCATGGGCTGGATCTTCCAGTGTGTCTCCTACCACGCTCCAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCTGCTGTCCTATCTCCCT
59.74
GGATGTCGGTGATGAGGACA
59.18
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTGTGGAGCTGCTGTCCTAT
59.46
GGATGTCGGTGATGAGGACA
59.18
156
PCR template sequence:
CCAGCTGGTGGCCCAGGGTGTGGAGCTGCTGTCCTATCTCCCTCTGTACTCGCCTGCCATGGGCTGGATCTTCCAGTGTGTCTCCTACCACGCTCCAGAGTGTTCAAAGCTGCTGTCAGACACGAGTGTTATTCAGTTCTACCCAAGCAAGTTTGTCCTCATCACCGACATCCTTGATACGTTTGGAAAGCTGGTCTATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-124-3p(1), mmu-miR-214-3p(1), mmu-miR-325-3p(1), mmu-miR-539-5p(1), mmu-miR-3470b(1), mmu-miR-544-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCACGCTCCAGAGTGTTCAAAGCTGC
siRNA sets
TGAACACTCTGGAGCGTGG, TTGAACACTCTGGAGCGTG, CAGCTTTGAACACTCTGGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVPS35L_585_ORF_1
1.321
0.403938458
0.998434707
1056
ORF sequence:
ATGTGTGTGGACAGCCGCAGTGCCTTGCCAGATCATTTCTCCCCAGAGAACGTGAACGACACAGCCAAGGAGACATGCCTGAATTGGTTTTTCAAGATCGCTTCCATCCGGGAACTCATTCCAAGATTTTATGTGGAAGCATCCATCCTGAAGTGTAACAAGTTCCTCTCCAAAACGGGGATTTCAGAGTGCCTGCCCCGACTAACCTGCATGATCAGAGGGATCGGAGACCCACTCGTGTCCGTGTACGCCCGGGCCTACCTGTGTCGGGTGGGGATCGAAGTGGCCCCGCACCTCAAGGAGAGCCTCAATAAGAACTTCTTTGACTTCCTGCTGACATTTAAACAGATTCATGGGGACACTGTCCAGAACCAGCTGGTGGCCCAGGGTGTGGAGCTGCTGTCCTATCTCCCTCTGTACTCGCCTGCCATGGGCTGGATCTTCCAGTGTGTCTCCTACCACGCTCCAGAGTGTTCAAAGCTGCTGTCAGACACGAGTGTTATTCAGTTCTACCCAAGCAAGTTTGTCCTCATCACCGACATCCTTGATACGTTTGGAAAGCTGGTCTATGAGCGCATCTCCTCGATGTGTGTGGACAGCCGCAGTGCCTTGCCAGATCATTTCTCCCCAGAGAACGTGAACGACACAGCCAAGGAGACATGCCTGAATTGGTTTTTCAAGATCGCTTCCATCCGGGAACTCATTCCAAGATTTTATGTGGAAGCATCCATCCTGAAGTGTAACAAGTTCCTCTCCAAAACGGGGATTTCAGAGTGCCTGCCCCGACTAACCTGCATGATCAGAGGGATCGGAGACCCACTCGTGTCCGTGTACGCCCGGGCCTACCTGTGTCGGGTGGGGATCGAAGTGGCCCCGCACCTCAAGGAGAGCCTCAATAAGAACTTCTTTGACTTCCTGCTGACATTTAAACAGATTCATGGGGACACTGTCCAGAACCAGCTGGTGGCCCAGGGTGTGGAGCTGCTGTCCTATCTCCCTCTGTACTCGCCTGCCATGGGCTGGATCTTCCAGTGTGTCTCCTACCACGCTCCAGAG
Peptide sequence:
MCVDSRSALPDHFSPENVNDTAKETCLNWFFKIASIRELIPRFYVEASILKCNKFLSKTGISECLPRLTCMIRGIGDPLVSVYARAYLCRVGIEVAPHLKESLNKNFFDFLLTFKQIHGDTVQNQLVAQGVELLSYLPLYSPAMGWIFQCVSYHAPECSKLLSDTSVIQFYPSKFVLITDILDTFGKLVYERISSMCVDSRSALPDHFSPENVNDTAKETCLNWFFKIASIRELIPRFYVEASILKCNKFLSKTGISECLPRLTCMIRGIGDPLVSVYARAYLCRVGIEVAPHLKESLNKNFFDFLLTFKQIHGDTVQNQLVAQGVELLSYLPLYSPAMGWIFQCVSYHAPE
IRESfinder result
IRESfinder score
0.692252981
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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