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mmu_circPtpn12_470
Basic information of circular RNA
PanCircBase ID:
mmu_circPtpn12_470
mm39_Chr. Position ID:
chr5|21206269|21214582|-
Gene name:
Ptpn12
Transcript:
ENSMUST00000030556.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
12,11,10,9,8
Exon/intron offsets:
0,1151,1345,4077,8170
Genomic length:
8313
Exon/intron sizes in nt:
86,96,78,67,143
Flanking exon/introns:
chr5:21203754-21206269|chr5:21214582-21216682
Splice length:
470
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GAATCCCGTCGGCTCTATCAGTTTCATTACGTGAACTGGCCAGACCATGATGTTCCTTCGTCATTTGATTCTATTCTGGACATGATAAGCTTAATGAGGAAATACCAAGAACATGAAGATGTGCCTATTTGTATTCATTGCAGTGCAGGCTGTGGACGAACAGGTGCTATTTGTGCCATAGATTACACGTGGAACTTACTGAAAGCAGGGAAAATTCCAGAGGAATTTAATGTATTTAATTTAATACAAGAAATGAGAACACAGAGGCACTCGGCAGTACAAACAAAGGAGCAGTATGAACTTGTTCATAGGGCTATTGCTCAACTGTTTGAAAAACAGCTACAACTGTATGAAATTCATGGAGCACAGAAGATCGCTGATGGTAATGAAATTACCACTGGAACTATGGTCAGTTCCATTGATAGCGAGAAGCAAGACTCTCCTCCGCCAAAGCCACCGCGGACTCGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCACTGGAACTATGGTCAGT
58.38
TGACGAAGGAACATCATGGTCT
59.43
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCACTGGAACTATGGTCAGTT
59.02
TGACGAAGGAACATCATGGTCT
59.43
140
PCR template sequence:
AGATCGCTGATGGTAATGAAATTACCACTGGAACTATGGTCAGTTCCATTGATAGCGAGAAGCAAGACTCTCCTCCGCCAAAGCCACCGCGGACTCGAAGGAATCCCGTCGGCTCTATCAGTTTCATTACGTGAACTGGCCAGACCATGATGTTCCTTCGTCATTTGATTCTATTCTGGACATGATAAGCTTAATGAGGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-183-5p(1), mmu-miR-5101(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CGCGGACTCGAAGGAATCCCGTCGGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTPN12_470_ORF_1
0.8247
0.028708258
0.363185297
423
ORF sequence:
ATGATAAGCTTAATGAGGAAATACCAAGAACATGAAGATGTGCCTATTTGTATTCATTGCAGTGCAGGCTGTGGACGAACAGGTGCTATTTGTGCCATAGATTACACGTGGAACTTACTGAAAGCAGGGAAAATTCCAGAGGAATTTAATGTATTTAATTTAATACAAGAAATGAGAACACAGAGGCACTCGGCAGTACAAACAAAGGAGCAGTATGAACTTGTTCATAGGGCTATTGCTCAACTGTTTGAAAAACAGCTACAACTGTATGAAATTCATGGAGCACAGAAGATCGCTGATGGTAATGAAATTACCACTGGAACTATGGTCAGTTCCATTGATAGCGAGAAGCAAGACTCTCCTCCGCCAAAGCCACCGCGGACTCGAAGGAATCCCGTCGGCTCTATCAGTTTCATTACGTGA
Peptide sequence:
MISLMRKYQEHEDVPICIHCSAGCGRTGAICAIDYTWNLLKAGKIPEEFNVFNLIQEMRTQRHSAVQTKEQYELVHRAIAQLFEKQLQLYEIHGAQKIADGNEITTGTMVSSIDSEKQDSPPPKPPRTRRNPVGSISFIT
IRESfinder result
IRESfinder score
0.635345864
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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