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mmu_circVps50_486
Basic information of circular RNA
PanCircBase ID:
mmu_circVps50_486
mm39_Chr. Position ID:
chr6|3588005|3594901|+
Gene name:
Vps50
Transcript:
ENSMUST00000001412.17
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
22,23,24,25
Exon/intron offsets:
0,4421,6012,6737
Genomic length:
6896
Exon/intron sizes in nt:
81,149,97,159
Flanking exon/introns:
chr6:3578915-3588005|chr6:3594901-3598471
Splice length:
486
Other database IDs:
CIRCpedia: MMU_CIRCpedia_227272, circAtlas: mmu-Ccdc132_0031
circBase: hsa_circ_0081049, circAtlas: hsa-VPS50_0041, CIRCpedia: HSA_CIRCpedia_157159
Human Ortholog IDs:
Mature spliced Sequence:
TTGGAATCAACAGGACTTGGCCTTAGTAGTAGCAGACTAAAAACAACTCTAAACAGAATTCAAGAAAGCCTTATTGACCTGGAGGGCTCAGCTGATCCAACTGCCACTCTCACAGCAGCCGAGGAAAGAAAGGAGAAGGTACCCAGCCCACACCTCAATCAGCTAGTGATTTTGACATCTGGGGATACATTGTATGGGTTGGCAGAGAGAGTGGTAGCCACAGAATCCTTAGTGTTCTTGGCTGAGCAGTTTGAGTTCCTTCAGCCACATTTGGATGCTGTGATGCCTGCAGTCAAAAAGCCCTTCCTGCAGCAGTTTTACTCCCAGACAGTCTCAACTGCCAGTGAACTGCGCAAGCCCATTTACTGGATTGTGGCTGGTAAAGCTATTGATTATGAACAGATGCTTCTCCTAATGATGAATGTGAAGTGGGATGTCAAAGAGATCATGTCACAGCACAACATCTATGTAGATGCATTGCTGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGAAGTGGGATGTCAAAGAGA
59.61
GCCCTCCAGGTCAATAAGGC
60.47
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGAAGTGGGATGTCAAAGAG
58.26
GCCCTCCAGGTCAATAAGGC
60.47
151
PCR template sequence:
TATTGATTATGAACAGATGCTTCTCCTAATGATGAATGTGAAGTGGGATGTCAAAGAGATCATGTCACAGCACAACATCTATGTAGATGCATTGCTGAAGTTGGAATCAACAGGACTTGGCCTTAGTAGTAGCAGACTAAAAACAACTCTAAACAGAATTCAAGAAAGCCTTATTGACCTGGAGGGCTCAGCTGATCCAA
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-181a-5p(1), mmu-miR-181b-5p(1), mmu-miR-541-5p(1), mmu-miR-224-5p(1), mmu-miR-207(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGCATTGCTGAAGTTGGAATCAACAG
siRNA sets
TTCCAACTTCAGCAATGCA, ATTCCAACTTCAGCAATGC, GATTCCAACTTCAGCAATG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCVPS50_486_ORF_1
1.0561
0.243416623
0.935391949
690
ORF sequence:
ATGCCTGCAGTCAAAAAGCCCTTCCTGCAGCAGTTTTACTCCCAGACAGTCTCAACTGCCAGTGAACTGCGCAAGCCCATTTACTGGATTGTGGCTGGTAAAGCTATTGATTATGAACAGATGCTTCTCCTAATGATGAATGTGAAGTGGGATGTCAAAGAGATCATGTCACAGCACAACATCTATGTAGATGCATTGCTGAAGTTGGAATCAACAGGACTTGGCCTTAGTAGTAGCAGACTAAAAACAACTCTAAACAGAATTCAAGAAAGCCTTATTGACCTGGAGGGCTCAGCTGATCCAACTGCCACTCTCACAGCAGCCGAGGAAAGAAAGGAGAAGGTACCCAGCCCACACCTCAATCAGCTAGTGATTTTGACATCTGGGGATACATTGTATGGGTTGGCAGAGAGAGTGGTAGCCACAGAATCCTTAGTGTTCTTGGCTGAGCAGTTTGAGTTCCTTCAGCCACATTTGGATGCTGTGATGCCTGCAGTCAAAAAGCCCTTCCTGCAGCAGTTTTACTCCCAGACAGTCTCAACTGCCAGTGAACTGCGCAAGCCCATTTACTGGATTGTGGCTGGTAAAGCTATTGATTATGAACAGATGCTTCTCCTAATGATGAATGTGAAGTGGGATGTCAAAGAGATCATGTCACAGCACAACATCTATGTAGATGCATTGCTGAAG
Peptide sequence:
MPAVKKPFLQQFYSQTVSTASELRKPIYWIVAGKAIDYEQMLLLMMNVKWDVKEIMSQHNIYVDALLKLESTGLGLSSSRLKTTLNRIQESLIDLEGSADPTATLTAAEERKEKVPSPHLNQLVILTSGDTLYGLAERVVATESLVFLAEQFEFLQPHLDAVMPAVKKPFLQQFYSQTVSTASELRKPIYWIVAGKAIDYEQMLLLMMNVKWDVKEIMSQHNIYVDALLK
IRESfinder result
IRESfinder score
0.608831206
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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