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mmu_circPtpn4_237
Basic information of circular RNA
PanCircBase ID:
mmu_circPtpn4_237
mm39_Chr. Position ID:
chr1|119649593|119653826|-
Gene name:
Ptpn4
Transcript:
ENSMUST00000064091.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
12,11
Exon/intron offsets:
0,4169
Genomic length:
4233
Exon/intron sizes in nt:
173,64
Flanking exon/introns:
chr1:119643745-119649593|chr1:119653826-119669084
Splice length:
237
Other database IDs:
CIRCpedia: MMU_CIRCpedia_4880, circAtlas: mmu-Ptpn4_0068
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GTTGAAGATTGTAAAAATTTCTTTTAAATGCAAACAGTTTTTTATTCAACTTAGAAAAGAGTTGCATGAATCTAGAGAAACATTACTGGGATTTAATATGGTGAATTATAGAGCATGTAAAACTTTGTGGAAAGCGTGTGTAGAACATCATACATTCTTCCGCCTGGATAGACCACTTCCACCTCAAAAAAATTTTTTTGCACATTATTTTACATTGGGTTCCAAATTCCGGTACTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTTCCGCCTGGATAGACCA
60.03
TGTTTCTCTAGATTCATGCAACTCT
58.29
164
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGCCTGGATAGACCACTTCC
59.89
TGTTTCTCTAGATTCATGCAACTCT
58.29
159
PCR template sequence:
GTGTAGAACATCATACATTCTTCCGCCTGGATAGACCACTTCCACCTCAAAAAAATTTTTTTGCACATTATTTTACATTGGGTTCCAAATTCCGGTACTGGTTGAAGATTGTAAAAATTTCTTTTAAATGCAAACAGTTTTTTATTCAACTTAGAAAAGAGTTGCATGAATCTAGAGAAACATTACTGGGATTTAATATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
NA
Interacting miRNAs (#binding sites)
NA
siRNAs for circular RNA silencing
Junction sequence
AATTCCGGTACTGGTTGAAGATTGTA
siRNA sets
AATCTTCAACCAGTACCGG, ATCTTCAACCAGTACCGGA, ACAATCTTCAACCAGTACC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTPN4_237_ORF_1
0.4519
-0.276964631
0.055194455
375
ORF sequence:
ATGGTGAATTATAGAGCATGTAAAACTTTGTGGAAAGCGTGTGTAGAACATCATACATTCTTCCGCCTGGATAGACCACTTCCACCTCAAAAAAATTTTTTTGCACATTATTTTACATTGGGTTCCAAATTCCGGTACTGGTTGAAGATTGTAAAAATTTCTTTTAAATGCAAACAGTTTTTTATTCAACTTAGAAAAGAGTTGCATGAATCTAGAGAAACATTACTGGGATTTAATATGGTGAATTATAGAGCATGTAAAACTTTGTGGAAAGCGTGTGTAGAACATCATACATTCTTCCGCCTGGATAGACCACTTCCACCTCAAAAAAATTTTTTTGCACATTATTTTACATTGGGTTCCAAATTCCGGTAC
Peptide sequence:
MVNYRACKTLWKACVEHHTFFRLDRPLPPQKNFFAHYFTLGSKFRYWLKIVKISFKCKQFFIQLRKELHESRETLLGFNMVNYRACKTLWKACVEHHTFFRLDRPLPPQKNFFAHYFTLGSKFRY
IRESfinder result
IRESfinder score
0.89339849
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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