top of page
mmu_circPtpn12_342
Basic information of circular RNA
PanCircBase ID:
mmu_circPtpn12_342
mm39_Chr. Position ID:
chr5|21210346|21219763|-
Gene name:
Ptpn12
Transcript:
ENSMUST00000030556.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
9,8,7,6
Exon/intron offsets:
0,4093,6336,9345
Genomic length:
9417
Exon/intron sizes in nt:
67,143,60,72
Flanking exon/introns:
chr5:21207692-21210346|chr5:21219763-21220708
Splice length:
342
Other database IDs:
circAtlas: mmu-Ptpn12_0017
circBase: hsa_circ_0134693, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_132671
Human Ortholog IDs:
Mature spliced Sequence:
AAAAAGTGTGAGCGCTACTGGCCTTTGTATGGAGAAGATCCTATAACATTTGCACCATTTAAAATTTCTTGTGAAAATGAACAAGCAAGAACCGACTACTTCATCCGAACACTTTTACTTGAATTTCAAAATGAATCCCGTCGGCTCTATCAGTTTCATTACGTGAACTGGCCAGACCATGATGTTCCTTCGTCATTTGATTCTATTCTGGACATGATAAGCTTAATGAGGAAATACCAAGAACATGAAGATGTGCCTATTTGTATTCATTGCAGTGCAGGCTGTGGACGAACAGGTGCTATTTGTGCCATAGATTACACGTGGAACTTACTGAAAGCAGGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGTGGACGAACAGGTGCTA
59.68
AGTCGGTTCTTGCTTGTTCA
57.67
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATTCATTGCAGTGCAGGCTG
59.47
AGTCGGTTCTTGCTTGTTCA
57.67
175
PCR template sequence:
ACATGAAGATGTGCCTATTTGTATTCATTGCAGTGCAGGCTGTGGACGAACAGGTGCTATTTGTGCCATAGATTACACGTGGAACTTACTGAAAGCAGGGAAAAAGTGTGAGCGCTACTGGCCTTTGTATGGAGAAGATCCTATAACATTTGCACCATTTAAAATTTCTTGTGAAAATGAACAAGCAAGAACCGACTACT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-183-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTGAAAGCAGGGAAAAAGTGTGAGC
siRNA sets
CTTTTTCCCTGCTTTCAGT, ACTTTTTCCCTGCTTTCAG, CTCACACTTTTTCCCTGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTPN12_342_ORF_1
0.6546
0.016707719
0.360174861
471
ORF sequence:
ATGATAAGCTTAATGAGGAAATACCAAGAACATGAAGATGTGCCTATTTGTATTCATTGCAGTGCAGGCTGTGGACGAACAGGTGCTATTTGTGCCATAGATTACACGTGGAACTTACTGAAAGCAGGGAAAAAGTGTGAGCGCTACTGGCCTTTGTATGGAGAAGATCCTATAACATTTGCACCATTTAAAATTTCTTGTGAAAATGAACAAGCAAGAACCGACTACTTCATCCGAACACTTTTACTTGAATTTCAAAATGAATCCCGTCGGCTCTATCAGTTTCATTACGTGAACTGGCCAGACCATGATGTTCCTTCGTCATTTGATTCTATTCTGGACATGATAAGCTTAATGAGGAAATACCAAGAACATGAAGATGTGCCTATTTGTATTCATTGCAGTGCAGGCTGTGGACGAACAGGTGCTATTTGTGCCATAGATTACACGTGGAACTTACTGAAAGCAGGG
Peptide sequence:
MISLMRKYQEHEDVPICIHCSAGCGRTGAICAIDYTWNLLKAGKKCERYWPLYGEDPITFAPFKISCENEQARTDYFIRTLLLEFQNESRRLYQFHYVNWPDHDVPSSFDSILDMISLMRKYQEHEDVPICIHCSAGCGRTGAICAIDYTWNLLKAG
IRESfinder result
IRESfinder score
0.73726017
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page