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mmu_circPtprt_579
Basic information of circular RNA
PanCircBase ID:
mmu_circPtprt_579
mm39_Chr. Position ID:
chr2|161608143|161654056|-
Gene name:
Ptprt
Transcript:
ENSMUST00000109443.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
12,11,10
Exon/intron offsets:
0,44326,45711
Genomic length:
45913
Exon/intron sizes in nt:
27,41,03,202
Flanking exon/introns:
chr2:161574835-161608143|chr2:161654056-161743367
Splice length:
579
Other database IDs:
CIRCpedia: MMU_CIRCpedia_11223, circAtlas: mmu-Ptprt_0011
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_145557
Human Ortholog IDs:
Mature spliced Sequence:
ATTAACTACAAGGCTGTGGGCTCACTGGATCCAAGTGCTGACCTCTCCAGCCAGAGGGGAAAGGTGTTCAAACTCCGGAATGAAACCCACCACCTCTTTGTGGGTCTGTACCCTGGGACTACCTACTCTTTCACCATCAAGGCCAGCACAGCCAAGGGCTTTGGACCCCCAGTCACTACTCGGATTGCCACCAAGATTTCAGCTCCATCAATGCCTGAATATGACGCAGATACCCCACTCAATGAAACAGATACAACCATCACGGTGATGCTCAAACCCGCCCAGTCCAGGGGAGCCCCAGTCAGTGTTTACCAGCTGGTTGTCAAGGAGGAGCGACTCCAGAAGTCTCGGAGAGCAGCTGACATCATTGAGTGTTTCTCAGTACCTGTGAGCTACCGGAACGCCTCCAACCTCGATTCGCTACACTACTTTGCTGCTGAGCTGAAGCCCTCCAACCTGCCTGTCACCCAGCCATTTACAGTGGGAGACAACAAGACCTACAATGGCTACTGGAACCCTCCTCTCTCCCCATTGAAGAGCTACAGCATCTACTTCCAGGCCCTCAGCAAAGCAAATGGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAACCCTCCTCTCTCCCCAT
60.03
TGGTGGGTTTCATTCCGGAG
59.96
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCCTCCTCTCTCCCCATTGA
60.03
TGGTGGGTTTCATTCCGGAG
59.96
156
PCR template sequence:
AGTGGGAGACAACAAGACCTACAATGGCTACTGGAACCCTCCTCTCTCCCCATTGAAGAGCTACAGCATCTACTTCCAGGCCCTCAGCAAAGCAAATGGAATTAACTACAAGGCTGTGGGCTCACTGGATCCAAGTGCTGACCTCTCCAGCCAGAGGGGAAAGGTGTTCAAACTCCGGAATGAAACCCACCACCTCTTTG
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
CAAAGCAAATGGAATTAACTACAAGG
siRNA sets
TTGTAGTTAATTCCATTTG, TGTAGTTAATTCCATTTGC, GTAGTTAATTCCATTTGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTPRT_579_ORF_1
1.1245
0.40470924
0.995115278
948
ORF sequence:
ATGCCTGAATATGACGCAGATACCCCACTCAATGAAACAGATACAACCATCACGGTGATGCTCAAACCCGCCCAGTCCAGGGGAGCCCCAGTCAGTGTTTACCAGCTGGTTGTCAAGGAGGAGCGACTCCAGAAGTCTCGGAGAGCAGCTGACATCATTGAGTGTTTCTCAGTACCTGTGAGCTACCGGAACGCCTCCAACCTCGATTCGCTACACTACTTTGCTGCTGAGCTGAAGCCCTCCAACCTGCCTGTCACCCAGCCATTTACAGTGGGAGACAACAAGACCTACAATGGCTACTGGAACCCTCCTCTCTCCCCATTGAAGAGCTACAGCATCTACTTCCAGGCCCTCAGCAAAGCAAATGGAATTAACTACAAGGCTGTGGGCTCACTGGATCCAAGTGCTGACCTCTCCAGCCAGAGGGGAAAGGTGTTCAAACTCCGGAATGAAACCCACCACCTCTTTGTGGGTCTGTACCCTGGGACTACCTACTCTTTCACCATCAAGGCCAGCACAGCCAAGGGCTTTGGACCCCCAGTCACTACTCGGATTGCCACCAAGATTTCAGCTCCATCAATGCCTGAATATGACGCAGATACCCCACTCAATGAAACAGATACAACCATCACGGTGATGCTCAAACCCGCCCAGTCCAGGGGAGCCCCAGTCAGTGTTTACCAGCTGGTTGTCAAGGAGGAGCGACTCCAGAAGTCTCGGAGAGCAGCTGACATCATTGAGTGTTTCTCAGTACCTGTGAGCTACCGGAACGCCTCCAACCTCGATTCGCTACACTACTTTGCTGCTGAGCTGAAGCCCTCCAACCTGCCTGTCACCCAGCCATTTACAGTGGGAGACAACAAGACCTACAATGGCTACTGGAACCCTCCTCTCTCCCCATTGAAGAGCTACAGCATCTACTTCCAGGCCCTCAGCAAAGCAAATGGA
Peptide sequence:
MPEYDADTPLNETDTTITVMLKPAQSRGAPVSVYQLVVKEERLQKSRRAADIIECFSVPVSYRNASNLDSLHYFAAELKPSNLPVTQPFTVGDNKTYNGYWNPPLSPLKSYSIYFQALSKANGINYKAVGSLDPSADLSSQRGKVFKLRNETHHLFVGLYPGTTYSFTIKASTAKGFGPPVTTRIATKISAPSMPEYDADTPLNETDTTITVMLKPAQSRGAPVSVYQLVVKEERLQKSRRAADIIECFSVPVSYRNASNLDSLHYFAAELKPSNLPVTQPFTVGDNKTYNGYWNPPLSPLKSYSIYFQALSKANG
IRESfinder result
IRESfinder score
0.550185534
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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