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mmu_circPdxdc1_751_1
Basic information of circular RNA
PanCircBase ID:
mmu_circPdxdc1_751_1
mm39_Chr. Position ID:
chr16|13661634|13687745|-
Gene name:
Pdxdc1
Transcript:
ENSMUST00000023361.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
16,15,14,13,12,11,10,9,8
Exon/intron offsets:
0,1564,3955,10624,13606,15086,15339,16183,26032
Genomic length:
26111
Exon/intron sizes in nt:
106,89,64,51,126,102,49,85,79
Flanking exon/introns:
chr16:13658322-13661634|chr16:13687745-13690318
Splice length:
751
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GACGTTGCCTTTCTCGAGAAACTGATCAAAGATGACGTAGAAAGAGGAAGACTGCCCTTGCTGCTTGTTGCAAATGCTGGAACTGCAGCAGTTGGACACACAGACAAGATTGGACGTTTGAAGGAACTCTGTGAGCAGTACGGCATTTGGCTTCATGTGGAAGGTGTGAATCTGGCAACATTGGCTCTAGGTTATGTCTCCTCATCTGTGCTGGCTGCAACCAAGTGCGATAGCATGACACTAACTCCTGGCCTATGGCTAGGTTTGCCAGCTGTTCCTGCAGTGACACTCTACAAACATGACGATCCTGCCTTGACACTAGTTGCTGGTCTTACATCAAATAAGCCTGCAGACAAACTCCGAGCCCTACCACTCTGGTTGTCTCTACAGTACTTGGGACTTGATGGCATTGTGGAGAGAATAAAGCATGCTTGTCATCTGAGTCAACGGTTGCAAGAAAGTTTGAAGAAAGTGGACCACATCAAAATCTTGGTGGAAGATGAGCTCAGTTCTCCAGTAGTGGTGTTCAGGTTTTTCCAGGAATTACCAGCCTCAGATTCAGCGTTTAAAGCTGTTCCTGTATCCAACATAGCACCTGCAGCAGTTGGCCGGGAAAGACACTCCTGTGATGCACTGAACCGCTGGTTGGGTGAACAGTTGAAACAGTTGGTGCCTCAGTGTGGCCTCACTGTCATAGACCTGGAGGTAGATGGCACATGTGTTCGGTTCAGCCCTCTGATGACAGCAGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AACAGTTGGTGCCTCAGTGT
59.74
GCAAGGGCAGTCTTCCTCTT
59.96
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACAGTTGGTGCCTCAGTGTG
60.46
GCAAGGGCAGTCTTCCTCTT
59.96
150
PCR template sequence:
GAACAGTTGAAACAGTTGGTGCCTCAGTGTGGCCTCACTGTCATAGACCTGGAGGTAGATGGCACATGTGTTCGGTTCAGCCCTCTGATGACAGCAGAAGGACGTTGCCTTTCTCGAGAAACTGATCAAAGATGACGTAGAAAGAGGAAGACTGCCCTTGCTGCTTGTTGCAAATGCTGGAACTGCAGCAGTTGGACACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-92a-3p(1), mmu-miR-322-5p(1), 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
ATGACAGCAGAAGGACGTTGCCTTTC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDXDC1_751_1_ORF_1
1.003
0.08299498
0.712949491
552
ORF sequence:
ATGACACTAACTCCTGGCCTATGGCTAGGTTTGCCAGCTGTTCCTGCAGTGACACTCTACAAACATGACGATCCTGCCTTGACACTAGTTGCTGGTCTTACATCAAATAAGCCTGCAGACAAACTCCGAGCCCTACCACTCTGGTTGTCTCTACAGTACTTGGGACTTGATGGCATTGTGGAGAGAATAAAGCATGCTTGTCATCTGAGTCAACGGTTGCAAGAAAGTTTGAAGAAAGTGGACCACATCAAAATCTTGGTGGAAGATGAGCTCAGTTCTCCAGTAGTGGTGTTCAGGTTTTTCCAGGAATTACCAGCCTCAGATTCAGCGTTTAAAGCTGTTCCTGTATCCAACATAGCACCTGCAGCAGTTGGCCGGGAAAGACACTCCTGTGATGCACTGAACCGCTGGTTGGGTGAACAGTTGAAACAGTTGGTGCCTCAGTGTGGCCTCACTGTCATAGACCTGGAGGTAGATGGCACATGTGTTCGGTTCAGCCCTCTGATGACAGCAGAAGGACGTTGCCTTTCTCGAGAAACTGATCAAAGATGA
Peptide sequence:
MTLTPGLWLGLPAVPAVTLYKHDDPALTLVAGLTSNKPADKLRALPLWLSLQYLGLDGIVERIKHACHLSQRLQESLKKVDHIKILVEDELSSPVVVFRFFQELPASDSAFKAVPVSNIAPAAVGRERHSCDALNRWLGEQLKQLVPQCGLTVIDLEVDGTCVRFSPLMTAEGRCLSRETDQR
IRESfinder result
IRESfinder score
0.425000623
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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