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mmu_circPtprd_288
Basic information of circular RNA
PanCircBase ID:
mmu_circPtprd_288
mm39_Chr. Position ID:
chr4|76161881|76165135|-
Gene name:
Ptprd
Transcript:
ENSMUST00000107289.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
4,3
Exon/intron offsets:
0,3108
Genomic length:
3254
Exon/intron sizes in nt:
142,146
Flanking exon/introns:
chr4:76058939-76161881|chr4:76165135-76243416
Splice length:
288
Other database IDs:
circBase: mmu_circ_0011781, CIRCpedia: MMU_CIRCpedia_29287, circAtlas: mmu-Ptprd_0015
circBase: hsa_circ_0139121, circAtlas: hsa-PTPRD_0015, CIRCpedia: HSA_CIRCpedia_64538
Human Ortholog IDs:
Mature spliced Sequence:
CACCCCCCAGGTTTACACGAACTCCGGTTGATCAGACAGGGGTCTCTGGAGGAGTTGCATCATTCATTTGTCAAGCTACAGGAGACCCAAGACCTAAAATTGTCTGGAACAAAAAAGGAAAGAAAGTCAGCAACCAGAGATTTGAGGTAATAGAATTTGACGATGGATCTGGATCAGTACTCAGAATACAGCCCTTAAGGACTCCACGGGATGAGGCCATTTATGAATGTGTGGCCTCGAATAATGTGGGAGAAATCAGTGTGTCCACAAGACTCACAGTTTTACGTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCCCTTAAGGACTCCACG
60.11
GACCCCTGTCTGATCAACCG
60.11
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCCCTTAAGGACTCCACG
60.11
CCCTGTCTGATCAACCGGAG
59.82
141
PCR template sequence:
CAGCCCTTAAGGACTCCACGGGATGAGGCCATTTATGAATGTGTGGCCTCGAATAATGTGGGAGAAATCAGTGTGTCCACAAGACTCACAGTTTTACGTGCACCCCCCAGGTTTACACGAACTCCGGTTGATCAGACAGGGGTCTCTGGAGGAGTTGCATCATTCATTTGTCAAGCTACAGGAGACCCAAGACCTAAAAT
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-339-5p(1), mmu-miR-181b-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACAGTTTTACGTGCACCCCCCAGGTT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTPRD_288_ORF_1
1.0187
-0.054183544
0.125828032
228
ORF sequence:
ATGAGGCCATTTATGAATGTGTGGCCTCGAATAATGTGGGAGAAATCAGTGTGTCCACAAGACTCACAGTTTTACGTGCACCCCCCAGGTTTACACGAACTCCGGTTGATCAGACAGGGGTCTCTGGAGGAGTTGCATCATTCATTTGTCAAGCTACAGGAGACCCAAGACCTAAAATTGTCTGGAACAAAAAAGGAAAGAAAGTCAGCAACCAGAGATTTGAGGTAA
Peptide sequence:
MRPFMNVWPRIMWEKSVCPQDSQFYVHPPGLHELRLIRQGSLEELHHSFVKLQETQDLKLSGTKKERKSATRDLR
IRESfinder result
IRESfinder score
0.657099433
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
RPF, cORF, MS, m6A
mmu_circPtprd_003
Evidence
Peptide sequence:
MRPFMNVWPRIMWEKSVCPQDSQFYVHPPGLHELRLIRQGSLEELHHSFVKLQETQDLKLSGTKKERKSATRDLR*
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