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mmu_circPdxdc1_751_2
Basic information of circular RNA
PanCircBase ID:
mmu_circPdxdc1_751_2
mm39_Chr. Position ID:
chr16|13672258|13694031|-
Gene name:
Pdxdc1
Transcript:
ENSMUST00000023361.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
13,12,11,10,9,8,7,6
Exon/intron offsets:
0,2982,4462,4715,5559,15408,18060,21583
Genomic length:
21773
Exon/intron sizes in nt:
51,12,61,02,49,85,79,60,000
Flanking exon/introns:
chr16:13665653-13672258|chr16:13694031-13697289
Splice length:
751
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTACGAAAATGGATGTGCATATTTCCACGAGGAAGAGAGGGAAGGACTTGCTAAGATCTGTAGGCTTGCCATTCATTCTCGCTATGAAGACTTTGTTGTAGATGGATTCAACGTGTTATATAACAAAAAGCCTGTCATATATCTTAGTGCTGCCGCTAGACCTGGCCTGGGCCAATACCTTTGTAATCAGCTTGGCTTACCCTTCCCCTGCCTGTGCCGTGTGCCCTGTAACACTATGTTTGGATCCCAGCATCAGATGGACGTTGCCTTTCTCGAGAAACTGATCAAAGATGACGTAGAAAGAGGAAGACTGCCCTTGCTGCTTGTTGCAAATGCTGGAACTGCAGCAGTTGGACACACAGACAAGATTGGACGTTTGAAGGAACTCTGTGAGCAGTACGGCATTTGGCTTCATGTGGAAGGTGTGAATCTGGCAACATTGGCTCTAGGTTATGTCTCCTCATCTGTGCTGGCTGCAACCAAGTGCGATAGCATGACACTAACTCCTGGCCTATGGCTAGGTTTGCCAGCTGTTCCTGCAGTGACACTCTACAAACATGACGATCCTGCCTTGACACTAGTTGCTGGTCTTACATCAAATAAGCCTGCAGACAAACTCCGAGCCCTACCACTCTGGTTGTCTCTACAGTACTTGGGACTTGATGGCATTGTGGAGAGAATAAAGCATGCTTGTCATCTGAGTCAACGGTTGCAAGAAAGTTTGAAGAAAGTGGACCACATCAAAATCTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGGACTTGATGGCATTGTGG
59.18
GCGAGAATGAATGGCAAGCC
60.25
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGACTTGATGGCATTGTGG
59.18
TTCCCTCTCTTCCTCGTGGA
59.59
140
PCR template sequence:
CTTGGGACTTGATGGCATTGTGGAGAGAATAAAGCATGCTTGTCATCTGAGTCAACGGTTGCAAGAAAGTTTGAAGAAAGTGGACCACATCAAAATCTTGGTACGAAAATGGATGTGCATATTTCCACGAGGAAGAGAGGGAAGGACTTGCTAAGATCTGTAGGCTTGCCATTCATTCTCGCTATGAAGACTTTGTTGTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-92a-3p(1), mmu-miR-322-5p(1), mmu-miR-410-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CATCAAAATCTTGGTACGAAAATGGA
siRNA sets
TTTTCGTACCAAGATTTTG, TTTCGTACCAAGATTTTGA, ATTTTCGTACCAAGATTTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDXDC1_751_2_ORF_1
0.964
0.057417977
0.703192086
570
ORF sequence:
ATGTTTGGATCCCAGCATCAGATGGACGTTGCCTTTCTCGAGAAACTGATCAAAGATGACGTAGAAAGAGGAAGACTGCCCTTGCTGCTTGTTGCAAATGCTGGAACTGCAGCAGTTGGACACACAGACAAGATTGGACGTTTGAAGGAACTCTGTGAGCAGTACGGCATTTGGCTTCATGTGGAAGGTGTGAATCTGGCAACATTGGCTCTAGGTTATGTCTCCTCATCTGTGCTGGCTGCAACCAAGTGCGATAGCATGACACTAACTCCTGGCCTATGGCTAGGTTTGCCAGCTGTTCCTGCAGTGACACTCTACAAACATGACGATCCTGCCTTGACACTAGTTGCTGGTCTTACATCAAATAAGCCTGCAGACAAACTCCGAGCCCTACCACTCTGGTTGTCTCTACAGTACTTGGGACTTGATGGCATTGTGGAGAGAATAAAGCATGCTTGTCATCTGAGTCAACGGTTGCAAGAAAGTTTGAAGAAAGTGGACCACATCAAAATCTTGGTACGAAAATGGATGTGCATATTTCCACGAGGAAGAGAGGGAAGGACTTGCTAA
Peptide sequence:
MFGSQHQMDVAFLEKLIKDDVERGRLPLLLVANAGTAAVGHTDKIGRLKELCEQYGIWLHVEGVNLATLALGYVSSSVLAATKCDSMTLTPGLWLGLPAVPAVTLYKHDDPALTLVAGLTSNKPADKLRALPLWLSLQYLGLDGIVERIKHACHLSQRLQESLKKVDHIKILVRKWMCIFPRGREGRTC
IRESfinder result
IRESfinder score
0.505774636
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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