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mmu_circPdcd4_939
Basic information of circular RNA
PanCircBase ID:
mmu_circPdcd4_939
mm39_Chr. Position ID:
chr19|53895879|53909746|+
Gene name:
Pdcd4
Transcript:
ENSMUST00000074371.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
2,3,4,5,6,7
Exon/intron offsets:
0,1663,3479,5363,12166,13769
Genomic length:
13867
Exon/intron sizes in nt:
107,303,95,114,222,98
Flanking exon/introns:
chr19:53880887-53895879|chr19:53909746-53910447
Splice length:
939
Other database IDs:
CIRCpedia: MMU_CIRCpedia_217694
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
ATCCTCAAGGAAGACTTGCATTTAGTAAGTTGTGTATAATCAGTGCAAGCGAAATTAAGGAAAAATGGATATAGAAAATGAGCAGACACTGAATGTGAACCCCACTGACCCTGACAATTTAAGCGACTCTCTCTTTTCTGGAGATGAAGAAAATGCTGGCACTGAAGAAATAAAGAATGAAATAAATGGAAATTGGATTTCCGCATCTACTATTAATGAAGCTAGAATCAATGCAAAAGCCAAAAGACGACTGCGGAAAAATTCATCCCGGGACTCTGGCCGAGGAGACTCAGTCAGTGACAATGGAAGTGAAGCGGTTAGAAGTGGAGTTGCTGTGCCCACCAGTCCAAAAGGAAGGTTGCTAGATAGGCGGTCCAGATCTGGGAAAGGAAGGGGGCTGCCAAAGAAAGGTGGTGCAGGCGGCAAGGGTGTCTGGGGCACACCTGGACAGGTGTATGATGTGGAAGAGGTGGATGTGAAAGATCCAAACTATGATGACGACCAGGAGAACTGTGTTTATGAAACTGTAGTTTTGCCCCTGGATGAGACCGCATTTGAGAAGACTCTAACACCAATTATACAGGAATACTTTGAGCATGGAGATACAAATGAAGTTGCGGAGATGTTAAGAGACTTAAACCTTGGGGAGATGAAGAGTGGCGTGCCGGTGTTGGCAGTGTCCTTAGCCTTGGAGGGGAAGGCCAGCCACCGGGAGATGACATCCAAGCTGCTTTCTGACCTTTGCGGGACGGTGATGAGCACAAATGACGTGGAAAAGTCATTTGACAAGTTGCTGAAGGATCTCCCTGAGCTAGCCTTGGACACTCCTAGGGCACCGCAGTTGGTGGGCCAGTTTATTGCTAGAGCTGTTGGAGATGGAATCTTATGTAATACCTATATCGATAGTTACAAAGGAACTGTAGATTGTGTACAGGCTCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGTGGGCCAGTTTATTGCT
59.89
TCCTTAATTTCGCTTGCACTGA
58.59
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGTGGGCCAGTTTATTGCT
59.89
TTCCTTAATTTCGCTTGCACTGA
59.18
159
PCR template sequence:
AGTTGGTGGGCCAGTTTATTGCTAGAGCTGTTGGAGATGGAATCTTATGTAATACCTATATCGATAGTTACAAAGGAACTGTAGATTGTGTACAGGCTCGATCCTCAAGGAAGACTTGCATTTAGTAAGTTGTGTATAATCAGTGCAAGCGAAATTAAGGAAAAATGGATATAGAAAATGAGCAGACACTGAATGTGAAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-690(2), mmu-miR-33-5p(1), mmu-miR-181b-5p(1), mmu-miR-193b-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GTGTACAGGCTCGATCCTCAAGGAAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDCD4_939_ORF_1
1.0781
0.186538644
0.981571484
900
ORF sequence:
ATGGATATAGAAAATGAGCAGACACTGAATGTGAACCCCACTGACCCTGACAATTTAAGCGACTCTCTCTTTTCTGGAGATGAAGAAAATGCTGGCACTGAAGAAATAAAGAATGAAATAAATGGAAATTGGATTTCCGCATCTACTATTAATGAAGCTAGAATCAATGCAAAAGCCAAAAGACGACTGCGGAAAAATTCATCCCGGGACTCTGGCCGAGGAGACTCAGTCAGTGACAATGGAAGTGAAGCGGTTAGAAGTGGAGTTGCTGTGCCCACCAGTCCAAAAGGAAGGTTGCTAGATAGGCGGTCCAGATCTGGGAAAGGAAGGGGGCTGCCAAAGAAAGGTGGTGCAGGCGGCAAGGGTGTCTGGGGCACACCTGGACAGGTGTATGATGTGGAAGAGGTGGATGTGAAAGATCCAAACTATGATGACGACCAGGAGAACTGTGTTTATGAAACTGTAGTTTTGCCCCTGGATGAGACCGCATTTGAGAAGACTCTAACACCAATTATACAGGAATACTTTGAGCATGGAGATACAAATGAAGTTGCGGAGATGTTAAGAGACTTAAACCTTGGGGAGATGAAGAGTGGCGTGCCGGTGTTGGCAGTGTCCTTAGCCTTGGAGGGGAAGGCCAGCCACCGGGAGATGACATCCAAGCTGCTTTCTGACCTTTGCGGGACGGTGATGAGCACAAATGACGTGGAAAAGTCATTTGACAAGTTGCTGAAGGATCTCCCTGAGCTAGCCTTGGACACTCCTAGGGCACCGCAGTTGGTGGGCCAGTTTATTGCTAGAGCTGTTGGAGATGGAATCTTATGTAATACCTATATCGATAGTTACAAAGGAACTGTAGATTGTGTACAGGCTCGATCCTCAAGGAAGACTTGCATTTAG
Peptide sequence:
MDIENEQTLNVNPTDPDNLSDSLFSGDEENAGTEEIKNEINGNWISASTINEARINAKAKRRLRKNSSRDSGRGDSVSDNGSEAVRSGVAVPTSPKGRLLDRRSRSGKGRGLPKKGGAGGKGVWGTPGQVYDVEEVDVKDPNYDDDQENCVYETVVLPLDETAFEKTLTPIIQEYFEHGDTNEVAEMLRDLNLGEMKSGVPVLAVSLALEGKASHREMTSKLLSDLCGTVMSTNDVEKSFDKLLKDLPELALDTPRAPQLVGQFIARAVGDGILCNTYIDSYKGTVDCVQARSSRKTCI
IRESfinder result
IRESfinder score
0.359753188
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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