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mmu_circPtpn4_242
Basic information of circular RNA
PanCircBase ID:
mmu_circPtpn4_242
mm39_Chr. Position ID:
chr1|119643676|119649766|-
Gene name:
Ptpn4
Transcript:
ENSMUST00000064091.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
13,12
Exon/intron offsets:
0,5917
Genomic length:
6090
Exon/intron sizes in nt:
69,173
Flanking exon/introns:
chr1:119635631-119643676|chr1:119649766-119653762
Splice length:
242
Other database IDs:
circBase: hsa_circ_0056244, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_37669
Human Ortholog IDs:
Mature spliced Sequence:
CATGAATCTAGAGAAACATTACTGGGATTTAATATGGTGAATTATAGAGCATGTAAAACTTTGTGGAAAGCGTGTGTAGAACATCATACATTCTTCCGCCTGGATAGACCACTTCCACCTCAAAAAAATTTTTTTGCACATTATTTTACATTGGGTTCCAAATTCCGGTACTGTGGGAGAACTGAAGTCCAGTCAGTTCAATATGGCAAAGAAAAGGCAAATAAAGACAGGGTATTTGCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCGGTACTGTGGGAGAACT
59.89
ACACACGCTTTCCACAAAGT
58.54
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCGGTACTGTGGGAGAACTG
59.75
ACACACGCTTTCCACAAAGT
58.54
155
PCR template sequence:
ATTTTACATTGGGTTCCAAATTCCGGTACTGTGGGAGAACTGAAGTCCAGTCAGTTCAATATGGCAAAGAAAAGGCAAATAAAGACAGGGTATTTGCAAGCATGAATCTAGAGAAACATTACTGGGATTTAATATGGTGAATTATAGAGCATGTAAAACTTTGTGGAAAGCGTGTGTAGAACATCATACATTCTTCCGCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-101a-3p(1), mmu-miR-188-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGGTATTTGCAAGCATGAATCTAGAG
siRNA sets
TTCATGCTTGCAAATACCC, CTCTAGATTCATGCTTGCA, ATTCATGCTTGCAAATACC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTPN4_242_ORF_1
0.3974
-0.21286986
0.026885586
249
ORF sequence:
ATGGTGAATTATAGAGCATGTAAAACTTTGTGGAAAGCGTGTGTAGAACATCATACATTCTTCCGCCTGGATAGACCACTTCCACCTCAAAAAAATTTTTTTGCACATTATTTTACATTGGGTTCCAAATTCCGGTACTGTGGGAGAACTGAAGTCCAGTCAGTTCAATATGGCAAAGAAAAGGCAAATAAAGACAGGGTATTTGCAAGCATGAATCTAGAGAAACATTACTGGGATTTAATATGGTGA
Peptide sequence:
MVNYRACKTLWKACVEHHTFFRLDRPLPPQKNFFAHYFTLGSKFRYCGRTEVQSVQYGKEKANKDRVFASMNLEKHYWDLIW
IRESfinder result
IRESfinder score
0.701933203
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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