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mmu_circPpil3_356
Basic information of circular RNA
PanCircBase ID:
mmu_circPpil3_356
mm39_Chr. Position ID:
chr1|58473489|58481758|-
Gene name:
Ppil3
Transcript:
ENSMUST00000117069.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,5,4,3
Exon/intron offsets:
0,4013,6512,8194
Genomic length:
8269
Exon/intron sizes in nt:
119,68,94,75
Flanking exon/introns:
chr1:58470489-58473489|chr1:58481758-58483747
Splice length:
356
Other database IDs:
CIRCpedia: MMU_CIRCpedia_223146, circAtlas: mmu-Ppil3_0001
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_135235
Human Ortholog IDs:
Mature spliced Sequence:
TCTGTGACACTGCATACAGATGTGGGAGATATCAAGATAGAAGTCTTCTGTGAGAGAACACCCAAAACATGTGAGAATTTCTTGGCTCTTTGTGCCAGTAATTACTACAACGGCTGTGTGTTTCATAGAAATATCAAGGGCTTCATGGTTCAAACAGGAGATCCAACAGGTACTGGAAGAGGAGGTAGCAGCATCTGGGCCAAAAAGTTTGAGGATGAATACAGTGAATATCTGAAGCACAATGTTCGAGGTGTTGTATCTATGGCTAATAATGGCCCAAATACCAATGGATCTCAGTTCTTCATCACCTATGGCAAGCAGCCACACTTGGACATGAAATATACAGTGTTTGGAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CATCACCTATGGCAAGCAGC
59.33
GCACAAAGAGCCAAGAAATTCTC
58.77
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CATCACCTATGGCAAGCAGC
59.33
GCACAAAGAGCCAAGAAATTCT
57.75
149
PCR template sequence:
TATCTATGGCTAATAATGGCCCAAATACCAATGGATCTCAGTTCTTCATCACCTATGGCAAGCAGCCACACTTGGACATGAAATATACAGTGTTTGGAAATCTGTGACACTGCATACAGATGTGGGAGATATCAAGATAGAAGTCTTCTGTGAGAGAACACCCAAAACATGTGAGAATTTCTTGGCTCTTTGTGCCAGTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-7b-5p(1), mmu-miR-146a-5p(1), mmu-miR-434-3p(1), mmu-miR-218-5p(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CAGTGTTTGGAAATCTGTGACACTGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPPIL3_356_ORF_1
0.9336
0.194755043
0.241044602
219
ORF sequence:
ATGGTTCAAACAGGAGATCCAACAGGTACTGGAAGAGGAGGTAGCAGCATCTGGGCCAAAAAGTTTGAGGATGAATACAGTGAATATCTGAAGCACAATGTTCGAGGTGTTGTATCTATGGCTAATAATGGCCCAAATACCAATGGATCTCAGTTCTTCATCACCTATGGCAAGCAGCCACACTTGGACATGAAATATACAGTGTTTGGAAATCTGTGA
Peptide sequence:
MVQTGDPTGTGRGGSSIWAKKFEDEYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGKQPHLDMKYTVFGNL
IRESfinder result
IRESfinder score
0.617277093
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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