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mmu_circPtcd3_343
Basic information of circular RNA
PanCircBase ID:
mmu_circPtcd3_343
mm39_Chr. Position ID:
chr6|71869452|71871865|-
Gene name:
Ptcd3
Transcript:
ENSMUST00000082094.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
14,13,12,11
Exon/intron offsets:
0,913,1818,2352
Genomic length:
2413
Exon/intron sizes in nt:
51,145,86,61
Flanking exon/introns:
chr6:71866670-71869452|chr6:71871865-71872888
Splice length:
343
Other database IDs:
circAtlas: hsa-PTCD3_0038
Human Ortholog IDs:
Mature spliced Sequence:
CACCGAGCTTATGCACAGGCACTGAACGTGTACACAGAGTTATTAAATAACAGACTTAGTGCTGATGTATATACCTTTAATGCATTGATTGAAGCAAAAACATTCATACTCAATGAGAAATTTGAGGAAAAATGGAATGATATACTGGATCTACTGAAACATATGGTTGCACAGAAAGTGAAACCAAATCTGCAGACTTTTAATACAATATTGAAAGGTCTCCGGAAGTGTTACTCACTTGGAAGGATACCAGCCTTACAGATACTACGTGAAATGAAACATATTGGAATAGAACCCTCACTTGCAACATACCATCATATTATTCACCTCTTTTATCCAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCCTCACTTGCAACATACCA
59.58
TGCTTCAATCAATGCATTAAAGGT
57.96
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCCTCACTTGCAACATACCA
59.58
TTGCTTCAATCAATGCATTAAAGGT
58.53
147
PCR template sequence:
AGGATACCAGCCTTACAGATACTACGTGAAATGAAACATATTGGAATAGAACCCTCACTTGCAACATACCATCATATTATTCACCTCTTTTATCCAAGAGCACCGAGCTTATGCACAGGCACTGAACGTGTACACAGAGTTATTAAATAACAGACTTAGTGCTGATGTATATACCTTTAATGCATTGATTGAAGCAAAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-29b-2-5p(1), mmu-miR-190b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTTATCCAAGAGCACCGAGCTTATG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTCD3_343_ORF_1
0.789
-0.237331634
0.043302968
231
ORF sequence:
ATGGTTGCACAGAAAGTGAAACCAAATCTGCAGACTTTTAATACAATATTGAAAGGTCTCCGGAAGTGTTACTCACTTGGAAGGATACCAGCCTTACAGATACTACGTGAAATGAAACATATTGGAATAGAACCCTCACTTGCAACATACCATCATATTATTCACCTCTTTTATCCAAGAGCACCGAGCTTATGCACAGGCACTGAACGTGTACACAGAGTTATTAAATAA
Peptide sequence:
MVAQKVKPNLQTFNTILKGLRKCYSLGRIPALQILREMKHIGIEPSLATYHHIIHLFYPRAPSLCTGTERVHRVIK
IRESfinder result
IRESfinder score
0.797719122
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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