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mmu_circTfdp2_307
Basic information of circular RNA
PanCircBase ID:
mmu_circTfdp2_307
mm39_Chr. Position ID:
chr9|96177017|96179823|+
Gene name:
Tfdp2
Transcript:
ENSMUST00000165120.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
4,5
Exon/intron offsets:
0,2662
Genomic length:
2806
Exon/intron sizes in nt:
1,63,144
Flanking exon/introns:
chr9:96105251-96177017|chr9:96179823-96182424
Splice length:
307
Other database IDs:
CIRCpedia: MMU_CIRCpedia_35344, circAtlas: mmu-Tfdp2_0009
circBase: hsa_circ_0122210, circAtlas: hsa-TFDP2_0009, CIRCpedia: HSA_CIRCpedia_124614
Human Ortholog IDs:
Mature spliced Sequence:
TAAACGAAGCAAAAAAGGAGATAAAAATGGGAAAGGCTTGAGACATTTTTCAATGAAGGTGTGTGAGAAAGTTCAGCGGAAAGGCACAACGTCATACAATGAGGTAGCTGATGAGCTGGTATCTGAGTTTACCAACTCAAATAACCATCTGGCAGCTGATTCGGCTTATGATCAGAAGAACATTAGACGAAGAGTTTATGATGCTTTAAATGTACTAATGGCGATGAACATAATTTCAAAGGAAAAAAAAGAAATCAAGTGGATTGGCCTGCCTACCAATTCTGCTCAGGAATGCCAGAACCTGGAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGTGGATTGGCCTGCCTAC
60.03
GTTGTGCCTTTCCGCTGAAC
60.32
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAAGTGGATTGGCCTGCCTA
60.03
GTTGTGCCTTTCCGCTGAAC
60.32
142
PCR template sequence:
AAATGTACTAATGGCGATGAACATAATTTCAAAGGAAAAAAAAGAAATCAAGTGGATTGGCCTGCCTACCAATTCTGCTCAGGAATGCCAGAACCTGGAATAAACGAAGCAAAAAAGGAGATAAAAATGGGAAAGGCTTGAGACATTTTTCAATGAAGGTGTGTGAGAAAGTTCAGCGGAAAGGCACAACGTCATACAAT
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-22-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCAGAACCTGGAATAAACGAAGCAAA
siRNA sets
TTTGCTTCGTTTATTCCAG,TTCGTTTATTCCAGGTTCT,TGCTTCGTTTATTCCAGGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTFDP2_307_ORF_1
1.0381
0.204449184
0.34767888
258
ORF sequence:
ATGAAGGTGTGTGAGAAAGTTCAGCGGAAAGGCACAACGTCATACAATGAGGTAGCTGATGAGCTGGTATCTGAGTTTACCAACTCAAATAACCATCTGGCAGCTGATTCGGCTTATGATCAGAAGAACATTAGACGAAGAGTTTATGATGCTTTAAATGTACTAATGGCGATGAACATAATTTCAAAGGAAAAAAAAGAAATCAAGTGGATTGGCCTGCCTACCAATTCTGCTCAGGAATGCCAGAACCTGGAATAA
Peptide sequence:
MKVCEKVQRKGTTSYNEVADELVSEFTNSNNHLAADSAYDQKNIRRRVYDALNVLMAMNIISKEKKEIKWIGLPTNSAQECQNLE
IRESfinder result
IRESfinder score
0.419756719
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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