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mmu_circPum3_694
Basic information of circular RNA
PanCircBase ID:
mmu_circPum3_694
mm39_Chr. Position ID:
chr19|27394134|27400981|-
Gene name:
Pum3
Transcript:
ENSMUST00000076219.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
11,10,9,8,7,6,5
Exon/intron offsets:
0,2060,3283,4562,5620,5919,6771
Genomic length:
6847
Exon/intron sizes in nt:
99,79,104,175,67,94,76
Flanking exon/introns:
chr19:27393339-27394134|chr19:27400981-27401608
Splice length:
694
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AAAAGATTGTGACAAGGAAAAACGGGTGAAGCTCATGAGTGATTTGCAGAAGTTGATTCAAGGGAAAATTAAAACTATCGCCTTTGCACATGACTCGACGCGCGTGATCCAGTGCTTCATTCAGTATGGGAACGAGGAGCAGAGGAAGCAGGCTTTCCAAGAGTTGCAAGGCGACTTGGTTGAATTAAGTAAAGCCAAATATTCCAGGAATATCGTTAAGAAATTTCTCATGTATGGAAGTAAGCCACAAGTTGCGGAGATAATCAGAAGTTTTAAAGGTCATGTGAGGAAGATGCTGCGGCATTCGGAGGCATCGGCCATTGTGGAGTACGCATACAACGACAAAGCCATTTTGGAACAGAGGAACATGCTGACAGAGGAGCTCTATGGGAACACGTTTCAGCTTTACAAGTCAGCAGATCACCCAACGCTGGACAAGGTGCTGGAGCTGCAGCCAGCAAAGCTAGAGCTTATCATGGACGAGATGAAGCAGATTCTGACACCGATGGCCCAAAAGGAAGCTGTGATTAAGCACTCACTCGTTCATAAAGTATTCTTGGACTTTTTTACCTACGCACCCCCAAAACCTCGATCAGAACTAATTGAAGCCATCCGGGAAGCAGTGGTGTACCTGGCCCACACACACGATGGCGCCAGAGTGGCCATGCACTGCCTGTGGCACGGCACACCCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGAAGCAGTGGTGTACCTGG
60.32
GTCGAGTCATGTGCAAAGGC
59.83
178
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGAAGCAGTGGTGTACCTG
60.32
GTCGAGTCATGTGCAAAGGC
59.83
179
PCR template sequence:
AGAACTAATTGAAGCCATCCGGGAAGCAGTGGTGTACCTGGCCCACACACACGATGGCGCCAGAGTGGCCATGCACTGCCTGTGGCACGGCACACCCAAGAAAAGATTGTGACAAGGAAAAACGGGTGAAGCTCATGAGTGATTTGCAGAAGTTGATTCAAGGGAAAATTAAAACTATCGCCTTTGCACATGACTCGACG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(2), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-152-3p(1), mmu-miR-34b-5p(1), mmu-miR-673-5p(1), mmu-miR-539-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CGGCACACCCAAGAAAAGATTGTGAC
siRNA sets
AATCTTTTCTTGGGTGTGC, GTCACAATCTTTTCTTGGG, TCTTTTCTTGGGTGTGCCG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPUM3_694_ORF_1
1.1677
0.319039693
0.972014159
741
ORF sequence:
ATGGCGCCAGAGTGGCCATGCACTGCCTGTGGCACGGCACACCCAAGAAAAGATTGTGACAAGGAAAAACGGGTGAAGCTCATGAGTGATTTGCAGAAGTTGATTCAAGGGAAAATTAAAACTATCGCCTTTGCACATGACTCGACGCGCGTGATCCAGTGCTTCATTCAGTATGGGAACGAGGAGCAGAGGAAGCAGGCTTTCCAAGAGTTGCAAGGCGACTTGGTTGAATTAAGTAAAGCCAAATATTCCAGGAATATCGTTAAGAAATTTCTCATGTATGGAAGTAAGCCACAAGTTGCGGAGATAATCAGAAGTTTTAAAGGTCATGTGAGGAAGATGCTGCGGCATTCGGAGGCATCGGCCATTGTGGAGTACGCATACAACGACAAAGCCATTTTGGAACAGAGGAACATGCTGACAGAGGAGCTCTATGGGAACACGTTTCAGCTTTACAAGTCAGCAGATCACCCAACGCTGGACAAGGTGCTGGAGCTGCAGCCAGCAAAGCTAGAGCTTATCATGGACGAGATGAAGCAGATTCTGACACCGATGGCCCAAAAGGAAGCTGTGATTAAGCACTCACTCGTTCATAAAGTATTCTTGGACTTTTTTACCTACGCACCCCCAAAACCTCGATCAGAACTAATTGAAGCCATCCGGGAAGCAGTGGTGTACCTGGCCCACACACACGATGGCGCCAGAGTGGCCATGCACTGCCTGTGGCACGGCACACCCAAG
Peptide sequence:
MAPEWPCTACGTAHPRKDCDKEKRVKLMSDLQKLIQGKIKTIAFAHDSTRVIQCFIQYGNEEQRKQAFQELQGDLVELSKAKYSRNIVKKFLMYGSKPQVAEIIRSFKGHVRKMLRHSEASAIVEYAYNDKAILEQRNMLTEELYGNTFQLYKSADHPTLDKVLELQPAKLELIMDEMKQILTPMAQKEAVIKHSLVHKVFLDFFTYAPPKPRSELIEAIREAVVYLAHTHDGARVAMHCLWHGTPK
IRESfinder result
IRESfinder score
0.358349651
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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