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mmu_circPtpn13_657
Basic information of circular RNA
PanCircBase ID:
mmu_circPtpn13_657
mm39_Chr. Position ID:
chr5|103705744|103710239|+
Gene name:
Ptpn13
Transcript:
ENSMUST00000048957.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
26,27,28,29,30
Exon/intron offsets:
0,1258,1992,4053,4396
Genomic length:
4495
Exon/intron sizes in nt:
94,86,163,215,99
Flanking exon/introns:
chr5:103704085-103705744|chr5:103710239-103711876
Splice length:
657
Other database IDs:
CIRCpedia: MMU_CIRCpedia_980, circAtlas: mmu-Ptpn13_0007
Human Ortholog IDs:
Mature spliced Sequence:
GGAGGTGTGAATACCAGCGTCCGACATGGTGGTATTTATGTGAAAGCCATTATTCCCAAAGGAGCGGCAGAGTCAGATGGCAGAATTCACAAAGGTGATCGTGTGCTGGCTGTTAATGGAGTCAGTCTGGAAGGAGCTACCCACAAGCAAGCTGTGGAAACGTTAAGAAACACAGGGCAGGTGGTCCATCTGTTGTTAGAAAAGGGGCAGGTGCCAACATCTAGGGAACGGGATCCTGCAGGCCCACAGAGCCCCCCTCCAGACCAAGACGCCCAAAGACAAGCCCCGGAAAAGGTGGCGAAGCAAACACCCCATGTCAAAGACTACAGCTTTGTTACTGAAGATAATACATTTGAGGTCAAGCTGTTTAAAAATAGCTCAGGCCTTGGATTCAGTTTTTCTCGGGAAGATAATCTTATACCAGAACAAATAAATGGCAGCATAGTAAGGGTTAAAAAGCTCTTCCCTGGACAGCCGGCAGCAGAAAGTGGGAAAATCGATGTTGGAGATGTTATATTGAAAGTTAACGGAGCCCCCTTGAAGGGACTGTCTCAGCAGGACGTCATCTCTGCTCTCAGGGGAACAGCTCCAGAAGTGTCCTTGCTTCTCTGCAGACCGGCACCTGGTGTGCTACCAGAAATCGATACTACATTTTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTCCAGAAGTGTCCTTGCT
59.96
CTGCCGCTCCTTTGGGAATA
60.11
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCTCCAGAAGTGTCCTTGC
59.96
CTGCCGCTCCTTTGGGAATA
60.11
143
PCR template sequence:
GGACGTCATCTCTGCTCTCAGGGGAACAGCTCCAGAAGTGTCCTTGCTTCTCTGCAGACCGGCACCTGGTGTGCTACCAGAAATCGATACTACATTTTTGGGAGGTGTGAATACCAGCGTCCGACATGGTGGTATTTATGTGAAAGCCATTATTCCCAAAGGAGCGGCAGAGTCAGATGGCAGAATTCACAAAGGTGATC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(1), mmu-miR-143-3p(1), mmu-miR-96-5p(1), mmu-miR-370-3p(1), mmu-miR-802-5p(1), mmu-miR-344d-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
TACTACATTTTTGGGAGGTGTGAATA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.492073089
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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