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mmu_circPdcd4_1003
Basic information of circular RNA
PanCircBase ID:
mmu_circPdcd4_1003
mm39_Chr. Position ID:
chr19|53899358|53915764|+
Gene name:
Pdcd4
Transcript:
ENSMUST00000074371.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
4,5,6,7,8,9,10,11
Exon/intron offsets:
0,1884,8687,10290,11089,15278,15607,16266
Genomic length:
16406
Exon/intron sizes in nt:
9,51,14,22,29,81,15,10,00,00,000
Flanking exon/introns:
chr19:53897845-53899358|chr19:53915764-53917513
Splice length:
1003
Other database IDs:
circAtlas: mmu-Pdcd4_0012
Human Ortholog IDs:
Mature spliced Sequence:
GTGGTGCAGGCGGCAAGGGTGTCTGGGGCACACCTGGACAGGTGTATGATGTGGAAGAGGTGGATGTGAAAGATCCAAACTATGATGACGACCAGGAGAACTGTGTTTATGAAACTGTAGTTTTGCCCCTGGATGAGACCGCATTTGAGAAGACTCTAACACCAATTATACAGGAATACTTTGAGCATGGAGATACAAATGAAGTTGCGGAGATGTTAAGAGACTTAAACCTTGGGGAGATGAAGAGTGGCGTGCCGGTGTTGGCAGTGTCCTTAGCCTTGGAGGGGAAGGCCAGCCACCGGGAGATGACATCCAAGCTGCTTTCTGACCTTTGCGGGACGGTGATGAGCACAAATGACGTGGAAAAGTCATTTGACAAGTTGCTGAAGGATCTCCCTGAGCTAGCCTTGGACACTCCTAGGGCACCGCAGTTGGTGGGCCAGTTTATTGCTAGAGCTGTTGGAGATGGAATCTTATGTAATACCTATATCGATAGTTACAAAGGAACTGTAGATTGTGTACAGGCTCGAGCTGCTCTGGATAAGGCTACTGTGCTCCTGAGTATGTCCAAAGGCGGGAAGCGGAAAGACAGTGTGTGGGGATCTGGAGGCGGGCAACAGCCTGTCAATCACCTTGTTAAAGAGATTGATATGCTGCTTAAAGAGTATTTACTCTCTGGAGATATATCTGAAGCTGAACACTGCCTTAAGGAACTGGAAGTACCTCATTTTCACCACGAGCTTGTATATGAAGCCATTGTAATGGTTTTAGAGTCAACTGGAGAAAGTGCATTCAAGATGATCTTAGATTTATTAAAATCCTTGTGGAAGTCTTCTACTATTACCATAGACCAAATGAAAAGAGGCTATGAGAGAATTTACAATGAAATCCCAGACATTAATCTGGATGTCCCACACTCATACTCTGTTCTTGAGAGATTTGTGGAGGAATGTTTTCAGGCTGGAATAATTTCCAAACAACTCCGTGATCTTTGTCCATCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGATGTCCCACACTCATACTC
59.23
TCACATCCACCTCTTCCACA
58.27
169
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGATGTCCCACACTCATACT
58.17
TCACATCCACCTCTTCCACA
58.27
169
PCR template sequence:
TGGATGTCCCACACTCATACTCTGTTCTTGAGAGATTTGTGGAGGAATGTTTTCAGGCTGGAATAATTTCCAAACAACTCCGTGATCTTTGTCCATCAAGGTGGTGCAGGCGGCAAGGGTGTCTGGGGCACACCTGGACAGGTGTATGATGTGGAAGAGGTGGATGTGAAAGATCCAAACTATGATGACGACCAGGAGAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-690(2), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-135a-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-34b-5p(1), mmu-miR-193b-3p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTGTCCATCAAGGTGGTGCAGGCGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDCD4_1003_ORF_1
0.8732
0.069510585
0.935821432
840
ORF sequence:
ATGTTAAGAGACTTAAACCTTGGGGAGATGAAGAGTGGCGTGCCGGTGTTGGCAGTGTCCTTAGCCTTGGAGGGGAAGGCCAGCCACCGGGAGATGACATCCAAGCTGCTTTCTGACCTTTGCGGGACGGTGATGAGCACAAATGACGTGGAAAAGTCATTTGACAAGTTGCTGAAGGATCTCCCTGAGCTAGCCTTGGACACTCCTAGGGCACCGCAGTTGGTGGGCCAGTTTATTGCTAGAGCTGTTGGAGATGGAATCTTATGTAATACCTATATCGATAGTTACAAAGGAACTGTAGATTGTGTACAGGCTCGAGCTGCTCTGGATAAGGCTACTGTGCTCCTGAGTATGTCCAAAGGCGGGAAGCGGAAAGACAGTGTGTGGGGATCTGGAGGCGGGCAACAGCCTGTCAATCACCTTGTTAAAGAGATTGATATGCTGCTTAAAGAGTATTTACTCTCTGGAGATATATCTGAAGCTGAACACTGCCTTAAGGAACTGGAAGTACCTCATTTTCACCACGAGCTTGTATATGAAGCCATTGTAATGGTTTTAGAGTCAACTGGAGAAAGTGCATTCAAGATGATCTTAGATTTATTAAAATCCTTGTGGAAGTCTTCTACTATTACCATAGACCAAATGAAAAGAGGCTATGAGAGAATTTACAATGAAATCCCAGACATTAATCTGGATGTCCCACACTCATACTCTGTTCTTGAGAGATTTGTGGAGGAATGTTTTCAGGCTGGAATAATTTCCAAACAACTCCGTGATCTTTGTCCATCAAGGTGGTGCAGGCGGCAAGGGTGTCTGGGGCACACCTGGACAGGTGTATGA
Peptide sequence:
MLRDLNLGEMKSGVPVLAVSLALEGKASHREMTSKLLSDLCGTVMSTNDVEKSFDKLLKDLPELALDTPRAPQLVGQFIARAVGDGILCNTYIDSYKGTVDCVQARAALDKATVLLSMSKGGKRKDSVWGSGGGQQPVNHLVKEIDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIVMVLESTGESAFKMILDLLKSLWKSSTITIDQMKRGYERIYNEIPDINLDVPHSYSVLERFVEECFQAGIISKQLRDLCPSRWCRRQGCLGHTWTGV
IRESfinder result
IRESfinder score
0.523528678
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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