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mmu_circPdia3_373
Basic information of circular RNA
PanCircBase ID:
mmu_circPdia3_373
mm39_Chr. Position ID:
chr2|121259934|121262880|+
Gene name:
Pdia3
Transcript:
ENSMUST00000028683.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
5,6,7
Exon/intron offsets:
0,2198,2820
Genomic length:
2946
Exon/intron sizes in nt:
130,117,126
Flanking exon/introns:
chr2:121257183-121259934|chr2:121262880-121263997
Splice length:
373
Other database IDs:
circAtlas: mmu-Pdia3_0005
circAtlas: hsa-PDIA3_0013
Human Ortholog IDs:
Mature spliced Sequence:
GTTTTTTCAGGGATTTATTCAGTGATGGGCACTCTGAATTCCTAAAAGCAGCCAGCAACTTGAGAGATAACTACCGATTTGCACACACCAACATTGAGTCTCTGGTGAAGGAGTACGATGATAATGGAGAGGGGATCACTATATTCCGTCCATTACATCTTGCTAACAAGTTTGAAGACAAAACTGTGGCATATACTGAAAAGAAAATGACCAGTGGCAAGATCAAGAAATTTATTCAGGATAGCATTTTTGGTCTCTGTCCTCATATGACGGAAGATAATAAAGATTTGATACAAGGCAAGGACTTACTCACCGCTTACTATGATGTGGACTATGAAAAGAATGCTAAAGGTTCTAACTACTGGAGAAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAAGGACTTACTCACCGCT
60.04
TCTCAAGTTGCTGGCTGCTT
60.18
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAAGGACTTACTCACCGCT
60.04
TGTTGGTGTGTGCAAATCGG
59.62
169
PCR template sequence:
AAGATAATAAAGATTTGATACAAGGCAAGGACTTACTCACCGCTTACTATGATGTGGACTATGAAAAGAATGCTAAAGGTTCTAACTACTGGAGAAACAGGTTTTTTCAGGGATTTATTCAGTGATGGGCACTCTGAATTCCTAAAAGCAGCCAGCAACTTGAGAGATAACTACCGATTTGCACACACCAACATTGAGTC
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-19b-3p(1), mmu-miR-19a-3p(1), mmu-miR-184-3p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-541-5p(1), mmu-miR-544-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTGGAGAAACAGGTTTTTTCAGGGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDIA3_373_ORF_1
1.0143
0.169887358
0.592131701
423
ORF sequence:
ATGATGTGGACTATGAAAAGAATGCTAAAGGTTCTAACTACTGGAGAAACAGGTTTTTTCAGGGATTTATTCAGTGATGGGCACTCTGAATTCCTAAAAGCAGCCAGCAACTTGAGAGATAACTACCGATTTGCACACACCAACATTGAGTCTCTGGTGAAGGAGTACGATGATAATGGAGAGGGGATCACTATATTCCGTCCATTACATCTTGCTAACAAGTTTGAAGACAAAACTGTGGCATATACTGAAAAGAAAATGACCAGTGGCAAGATCAAGAAATTTATTCAGGATAGCATTTTTGGTCTCTGTCCTCATATGACGGAAGATAATAAAGATTTGATACAAGGCAAGGACTTACTCACCGCTTACTATGATGTGGACTATGAAAAGAATGCTAAAGGTTCTAACTACTGGAGAAAC
Peptide sequence:
MMWTMKRMLKVLTTGETGFFRDLFSDGHSEFLKAASNLRDNYRFAHTNIESLVKEYDDNGEGITIFRPLHLANKFEDKTVAYTEKKMTSGKIKKFIQDSIFGLCPHMTEDNKDLIQGKDLLTAYYDVDYEKNAKGSNYWRN
IRESfinder result
IRESfinder score
0.636395247
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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