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mmu_circPdxdc1_431
Basic information of circular RNA
PanCircBase ID:
mmu_circPdxdc1_431
mm39_Chr. Position ID:
chr16|13658150|13665653|-
Gene name:
Pdxdc1
Transcript:
ENSMUST00000023361.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
17,16,15,14
Exon/intron offsets:
0,3484,5048,7439
Genomic length:
7503
Exon/intron sizes in nt:
172,106,89,64
Flanking exon/introns:
chr16:13657619-13658150|chr16:13665653-13672258
Splice length:
431
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGGAAGATGAGCTCAGTTCTCCAGTAGTGGTGTTCAGGTTTTTCCAGGAATTACCAGCCTCAGATTCAGCGTTTAAAGCTGTTCCTGTATCCAACATAGCACCTGCAGCAGTTGGCCGGGAAAGACACTCCTGTGATGCACTGAACCGCTGGTTGGGTGAACAGTTGAAACAGTTGGTGCCTCAGTGTGGCCTCACTGTCATAGACCTGGAGGTAGATGGCACATGTGTTCGGTTCAGCCCTCTGATGACAGCAGAAGGGTTAGGAACTCGAGGAGAGGATGTCGATCAGCTCATTACCTGCATCCAAAGCAAACTACCAGTCCTGACCTGCACACTACAGCTTCGGGAAGAATTCAAGCAGGAGGTAGAGGGGACAGCAGGGCTCCTGTATGTTGATGACCCCAACTGGCCTGGAATCGGGGTTGTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCACACTACAGCTTCGGGAA
60.32
AACGCTGAATCTGAGGCTGG
60.39
174
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAAGCAGGAGGTAGAGGGGA
60.33
AACGCTGAATCTGAGGCTGG
60.39
149
PCR template sequence:
GCACACTACAGCTTCGGGAAGAATTCAAGCAGGAGGTAGAGGGGACAGCAGGGCTCCTGTATGTTGATGACCCCAACTGGCCTGGAATCGGGGTTGTCAGGTGGAAGATGAGCTCAGTTCTCCAGTAGTGGTGTTCAGGTTTTTCCAGGAATTACCAGCCTCAGATTCAGCGTTTAAAGCTGTTCCTGTATCCAACATAG
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
TCGGGGTTGTCAGGTGGAAGATGAGC
siRNA sets
CTTCCACCTGACAACCCCG, ATCTTCCACCTGACAACCC, TCTTCCACCTGACAACCCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDXDC1_431_ORF_1
0.9074
0.179933257
0.213645813
213
ORF sequence:
ATGACAGCAGAAGGGTTAGGAACTCGAGGAGAGGATGTCGATCAGCTCATTACCTGCATCCAAAGCAAACTACCAGTCCTGACCTGCACACTACAGCTTCGGGAAGAATTCAAGCAGGAGGTAGAGGGGACAGCAGGGCTCCTGTATGTTGATGACCCCAACTGGCCTGGAATCGGGGTTGTCAGGTGGAAGATGAGCTCAGTTCTCCAGTAG
Peptide sequence:
MTAEGLGTRGEDVDQLITCIQSKLPVLTCTLQLREEFKQEVEGTAGLLYVDDPNWPGIGVVRWKMSSVLQ
IRESfinder result
IRESfinder score
0.42646637
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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