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mmu_circPsd3_547
Basic information of circular RNA
PanCircBase ID:
mmu_circPsd3_547
mm39_Chr. Position ID:
chr8|68335632|68361538|-
Gene name:
Psd3
Transcript:
ENSMUST00000212505.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
9,8,7,6,5
Exon/intron offsets:
0,21136,23278,25505,25702
Genomic length:
25906
Exon/intron sizes in nt:
90,59,113,81,204
Flanking exon/introns:
chr8:68243593-68335632|chr8:68361538-68413038
Splice length:
547
Other database IDs:
circBase: mmu_circ_0001681, circAtlas: mmu-Psd3_0029
Human Ortholog IDs:
Mature spliced Sequence:
GGACCGTTGCTTTGCTGAGGGGAAAACAACAGGAGTAGATGCTGGTTCTGAAATGGGGAGCACTGACATTCTGGAAAAGGAGACCACAGAAAGTCTCAGCAATGGGACCAACAGCAATGTGGAAGCAGCTAAAAGATTGGCCAAACGCTTGTATCATCTAGACAGATTCAAGAGATCGGACGTTGCAAAACATCTAGGCAAAAACAATGAATTTAGCAAGCTAGTTGCAGAGGAGTATCTGAAGTTTTTTGATTTCACGGGGATGACGCTGGATCAGTCTCTCAGGTATTTTTTAAAAGCATTTTCTCTTGTGGGAGAAACCCAGGAGCGTGAGAGAGTATTAATACATTTTTCCAATAGATATTTTTCTTGTAATCCAGACACTATCACCTCAAAAGATGGAGTTCATTGCCTCACCTGTGCTATGATGCTGCTCAACACAGATCTGCATGGCCATAATATTGGAAAGAAGATGACTTGCCAGGAGTTCATTACAAATCTCCAAGGAGTAAATGAAGGTGGGGATTTCTCCAAGGATCTTCTGAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGATGACTTGCCAGGAGTTCA
59.02
CAGAATGTCAGTGCTCCCCA
59.67
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGATGACTTGCCAGGAGTTCA
59.02
CCAGAATGTCAGTGCTCCCC
60.39
151
PCR template sequence:
GCATGGCCATAATATTGGAAAGAAGATGACTTGCCAGGAGTTCATTACAAATCTCCAAGGAGTAAATGAAGGTGGGGATTTCTCCAAGGATCTTCTGAAAGGACCGTTGCTTTGCTGAGGGGAAAACAACAGGAGTAGATGCTGGTTCTGAAATGGGGAGCACTGACATTCTGGAAAAGGAGACCACAGAAAGTCTCAGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-15a-5p(1), mmu-miR-103-3p(1), mmu-miR-205-5p(1), mmu-miR-15b-5p(1), mmu-miR-136-5p(1), mmu-miR-362-5p(1), mmu-miR-107-3p(1), mmu-miR-539-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGATCTTCTGAAAGGACCGTTGCTTT
siRNA sets
AAAGCAACGGTCCTTTCAG, AAGCAACGGTCCTTTCAGA, CAACGGTCCTTTCAGAAGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPSD3_547_ORF_1
0.916
0.040919834
0.575426616
513
ORF sequence:
ATGGGGAGCACTGACATTCTGGAAAAGGAGACCACAGAAAGTCTCAGCAATGGGACCAACAGCAATGTGGAAGCAGCTAAAAGATTGGCCAAACGCTTGTATCATCTAGACAGATTCAAGAGATCGGACGTTGCAAAACATCTAGGCAAAAACAATGAATTTAGCAAGCTAGTTGCAGAGGAGTATCTGAAGTTTTTTGATTTCACGGGGATGACGCTGGATCAGTCTCTCAGGTATTTTTTAAAAGCATTTTCTCTTGTGGGAGAAACCCAGGAGCGTGAGAGAGTATTAATACATTTTTCCAATAGATATTTTTCTTGTAATCCAGACACTATCACCTCAAAAGATGGAGTTCATTGCCTCACCTGTGCTATGATGCTGCTCAACACAGATCTGCATGGCCATAATATTGGAAAGAAGATGACTTGCCAGGAGTTCATTACAAATCTCCAAGGAGTAAATGAAGGTGGGGATTTCTCCAAGGATCTTCTGAAAGGACCGTTGCTTTGCTGA
Peptide sequence:
MGSTDILEKETTESLSNGTNSNVEAAKRLAKRLYHLDRFKRSDVAKHLGKNNEFSKLVAEEYLKFFDFTGMTLDQSLRYFLKAFSLVGETQERERVLIHFSNRYFSCNPDTITSKDGVHCLTCAMMLLNTDLHGHNIGKKMTCQEFITNLQGVNEGGDFSKDLLKGPLLC
IRESfinder result
IRESfinder score
0.594271574
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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