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mmu_circPde10a_461
Basic information of circular RNA
PanCircBase ID:
mmu_circPde10a_461
mm39_Chr. Position ID:
chr17|8975793|9149391|+
Gene name:
Pde10a
Transcript:
ENSMUST00000115724.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
2,3,4,5,6
Exon/intron offsets:
0,141899,163542,172130,173548
Genomic length:
173598
Exon/intron sizes in nt:
132,129,29,121,50
Flanking exon/introns:
chr17:8745947-8975793|chr17:9149391-9159972
Splice length:
461
Other database IDs:
circAtlas: mmu-Pde10a_0029
Human Ortholog IDs:
Mature spliced Sequence:
GCTGCCTCCCATTCGCACTTAAAGGTGGGAGCAAGGGCCCCGCTCTATTGGCACTTCGAAACCGCACAGACTCTCGGGGGCAGATGAGCAATGACTCCACAGAAGGCACCGTGGGCTCCTGCAACGCAACAGGTTTGACGGATGAAAAGGTGAAGGCCTATCTTTCTCTCCATCCCCAGGTATTAGATGAATTTGTTTCTGAAAGTGTTAGTGCAGAGACTGTGGAAAAGTGGCTGAAGAGGAAAACCAACAAAGCAAAAGATGAACCATCTCCCAAGGAAGTCAGCAGGTACCAGGATACGAATATGCAGGGAGTCGTGTACGAGCTGAACAGCTACATAGAGCAGCGCCTGGACACGGGCGGGGACAACCACCTGCTCCTCTATGAGCTCAGCAGCATCATCAGGATAGCCACAAAAGCCGACGGATTTGCACTGTACTTCCTTGGAGAGTGCAATAAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAAAGCCGACGGATTTGCAC
60.04
AGTCATTGCTCATCTGCCCC
60.11
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACAAAAGCCGACGGATTTGC
60.04
AGTCATTGCTCATCTGCCCC
60.11
144
PCR template sequence:
CGGGGACAACCACCTGCTCCTCTATGAGCTCAGCAGCATCATCAGGATAGCCACAAAAGCCGACGGATTTGCACTGTACTTCCTTGGAGAGTGCAATAATGCTGCCTCCCATTCGCACTTAAAGGTGGGAGCAAGGGCCCCGCTCTATTGGCACTTCGAAACCGCACAGACTCTCGGGGGCAGATGAGCAATGACTCCAC
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-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-20a-5p(1), mmu-miR-32-5p(1), mmu-miR-19b-3p(1), mmu-miR-92a-3p(1), mmu-miR-19a-3p(1), mmu-miR-25-3p(1), mmu-miR-185-5p(1), mmu-miR-335-3p(1), mmu-miR-3065-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAGTGCAATAATGCTGCCTCCCATT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPDE10A_461_ORF_1
1.1306
0.295765784
0.802612086
465
ORF sequence:
ATGAGCAATGACTCCACAGAAGGCACCGTGGGCTCCTGCAACGCAACAGGTTTGACGGATGAAAAGGTGAAGGCCTATCTTTCTCTCCATCCCCAGGTATTAGATGAATTTGTTTCTGAAAGTGTTAGTGCAGAGACTGTGGAAAAGTGGCTGAAGAGGAAAACCAACAAAGCAAAAGATGAACCATCTCCCAAGGAAGTCAGCAGGTACCAGGATACGAATATGCAGGGAGTCGTGTACGAGCTGAACAGCTACATAGAGCAGCGCCTGGACACGGGCGGGGACAACCACCTGCTCCTCTATGAGCTCAGCAGCATCATCAGGATAGCCACAAAAGCCGACGGATTTGCACTGTACTTCCTTGGAGAGTGCAATAATGCTGCCTCCCATTCGCACTTAAAGGTGGGAGCAAGGGCCCCGCTCTATTGGCACTTCGAAACCGCACAGACTCTCGGGGGCAGATGA
Peptide sequence:
MSNDSTEGTVGSCNATGLTDEKVKAYLSLHPQVLDEFVSESVSAETVEKWLKRKTNKAKDEPSPKEVSRYQDTNMQGVVYELNSYIEQRLDTGGDNHLLLYELSSIIRIATKADGFALYFLGECNNAASHSHLKVGARAPLYWHFETAQTLGGR
IRESfinder result
IRESfinder score
0.37635641
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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