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mmu_circPtprt_616
Basic information of circular RNA
PanCircBase ID:
mmu_circPtprt_616
mm39_Chr. Position ID:
chr2|161574798|161654056|-
Gene name:
Ptprt
Transcript:
ENSMUST00000109443.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
13,12,11,10
Exon/intron offsets:
0,33345,77671,79056
Genomic length:
79258
Exon/intron sizes in nt:
37,27,41,03,202
Flanking exon/introns:
chr2:161540029-161574798|chr2:161654056-161743367
Splice length:
616
Other database IDs:
circAtlas: mmu-Ptprt_0034
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
ATTAACTACAAGGCTGTGGGCTCACTGGATCCAAGTGCTGACCTCTCCAGCCAGAGGGGAAAGGTGTTCAAACTCCGGAATGAAACCCACCACCTCTTTGTGGGTCTGTACCCTGGGACTACCTACTCTTTCACCATCAAGGCCAGCACAGCCAAGGGCTTTGGACCCCCAGTCACTACTCGGATTGCCACCAAGATTTCAGCTCCATCAATGCCTGAATATGACGCAGATACCCCACTCAATGAAACAGATACAACCATCACGGTGATGCTCAAACCCGCCCAGTCCAGGGGAGCCCCAGTCAGTGTTTACCAGCTGGTTGTCAAGGAGGAGCGACTCCAGAAGTCTCGGAGAGCAGCTGACATCATTGAGTGTTTCTCAGTACCTGTGAGCTACCGGAACGCCTCCAACCTCGATTCGCTACACTACTTTGCTGCTGAGCTGAAGCCCTCCAACCTGCCTGTCACCCAGCCATTTACAGTGGGAGACAACAAGACCTACAATGGCTACTGGAACCCTCCTCTCTCCCCATTGAAGAGCTACAGCATCTACTTCCAGGCCCTCAGCAAAGCAAATGGAGAGACAAAAATCAACTGTGTGCGTCTGGCTACAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCATCTACTTCCAGGCCCTC
59.89
TGGTGGGTTTCATTCCGGAG
59.96
164
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCATCTACTTCCAGGCCCTC
59.89
GGTGGGTTTCATTCCGGAGT
59.96
163
PCR template sequence:
CCTCCTCTCTCCCCATTGAAGAGCTACAGCATCTACTTCCAGGCCCTCAGCAAAGCAAATGGAGAGACAAAAATCAACTGTGTGCGTCTGGCTACAAAAGATTAACTACAAGGCTGTGGGCTCACTGGATCCAAGTGCTGACCTCTCCAGCCAGAGGGGAAAGGTGTTCAAACTCCGGAATGAAACCCACCACCTCTTTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-134-5p(1), mmu-miR-15a-5p(1), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-181a-5p(1), mmu-miR-30e-5p(1), mmu-miR-30a-5p(1), mmu-miR-196a-5p(1), mmu-miR-185-5p(1), mmu-miR-181b-5p(1), mmu-miR-30d-5p(1), mmu-miR-136-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGGCTACAAAAGATTAACTACAAGG
siRNA sets
TTGTAGTTAATCTTTTGTA, CTTGTAGTTAATCTTTTGT, GTAGTTAATCTTTTGTAGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTPRT_616_ORF_1
1.048
0.345010874
0.944208112
657
ORF sequence:
ATGGAGAGACAAAAATCAACTGTGTGCGTCTGGCTACAAAAGATTAACTACAAGGCTGTGGGCTCACTGGATCCAAGTGCTGACCTCTCCAGCCAGAGGGGAAAGGTGTTCAAACTCCGGAATGAAACCCACCACCTCTTTGTGGGTCTGTACCCTGGGACTACCTACTCTTTCACCATCAAGGCCAGCACAGCCAAGGGCTTTGGACCCCCAGTCACTACTCGGATTGCCACCAAGATTTCAGCTCCATCAATGCCTGAATATGACGCAGATACCCCACTCAATGAAACAGATACAACCATCACGGTGATGCTCAAACCCGCCCAGTCCAGGGGAGCCCCAGTCAGTGTTTACCAGCTGGTTGTCAAGGAGGAGCGACTCCAGAAGTCTCGGAGAGCAGCTGACATCATTGAGTGTTTCTCAGTACCTGTGAGCTACCGGAACGCCTCCAACCTCGATTCGCTACACTACTTTGCTGCTGAGCTGAAGCCCTCCAACCTGCCTGTCACCCAGCCATTTACAGTGGGAGACAACAAGACCTACAATGGCTACTGGAACCCTCCTCTCTCCCCATTGAAGAGCTACAGCATCTACTTCCAGGCCCTCAGCAAAGCAAATGGAGAGACAAAAATCAACTGTGTGCGTCTGGCTACAAAA
Peptide sequence:
MERQKSTVCVWLQKINYKAVGSLDPSADLSSQRGKVFKLRNETHHLFVGLYPGTTYSFTIKASTAKGFGPPVTTRIATKISAPSMPEYDADTPLNETDTTITVMLKPAQSRGAPVSVYQLVVKEERLQKSRRAADIIECFSVPVSYRNASNLDSLHYFAAELKPSNLPVTQPFTVGDNKTYNGYWNPPLSPLKSYSIYFQALSKANGETKINCVRLATK
IRESfinder result
IRESfinder score
0.547369682
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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