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mmu_circPdxdc1_310
Basic information of circular RNA
PanCircBase ID:
mmu_circPdxdc1_310
mm39_Chr. Position ID:
chr16|13661634|13672309|-
Gene name:
Pdxdc1
Transcript:
ENSMUST00000023361.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
16,15,14,13
Exon/intron offsets:
0,1564,3955,10624
Genomic length:
10675
Exon/intron sizes in nt:
106,89,64,51
Flanking exon/introns:
chr16:13658322-13661634|chr16:13672309-13675240
Splice length:
310
Other database IDs:
circAtlas: mmu-Pdxdc1_0006
circBase: hsa_circ_0009005, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_80951
Human Ortholog IDs:
Mature spliced Sequence:
AGTCAACGGTTGCAAGAAAGTTTGAAGAAAGTGGACCACATCAAAATCTTGGTGGAAGATGAGCTCAGTTCTCCAGTAGTGGTGTTCAGGTTTTTCCAGGAATTACCAGCCTCAGATTCAGCGTTTAAAGCTGTTCCTGTATCCAACATAGCACCTGCAGCAGTTGGCCGGGAAAGACACTCCTGTGATGCACTGAACCGCTGGTTGGGTGAACAGTTGAAACAGTTGGTGCCTCAGTGTGGCCTCACTGTCATAGACCTGGAGGTAGATGGCACATGTGTTCGGTTCAGCCCTCTGATGACAGCAGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AACAGTTGGTGCCTCAGTGT
59.74
ACTGAGCTCATCTTCCACCA
58.35
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACAGTTGGTGCCTCAGTGTG
60.46
ACTGAGCTCATCTTCCACCA
58.35
158
PCR template sequence:
GAACAGTTGAAACAGTTGGTGCCTCAGTGTGGCCTCACTGTCATAGACCTGGAGGTAGATGGCACATGTGTTCGGTTCAGCCCTCTGATGACAGCAGAAGAGTCAACGGTTGCAAGAAAGTTTGAAGAAAGTGGACCACATCAAAATCTTGGTGGAAGATGAGCTCAGTTCTCCAGTAGTGGTGTTCAGGTTTTTCCAGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-146a-5p(1), mmu-miR-152-3p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-1904(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATGACAGCAGAAGAGTCAACGGTTGC
siRNA sets
CAACCGTTGACTCTTCTGC, AACCGTTGACTCTTCTGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.444143199
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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