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mmu_circPank3_431
Basic information of circular RNA
PanCircBase ID:
mmu_circPank3_431
mm39_Chr. Position ID:
chr11|35668393|35669579|+
Gene name:
Pank3
Transcript:
ENSMUST00000018990.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,4
Exon/intron offsets:
0,1009
Genomic length:
1186
Exon/intron sizes in nt:
2,54,177
Flanking exon/introns:
chr11:35667265-35668393|chr11:35669579-35672410
Splice length:
431
Other database IDs:
circAtlas: mmu-Pank3_0004
CIRCpedia: HSA_CIRCpedia_102234
Human Ortholog IDs:
Mature spliced Sequence:
ATTGGAAACCTCCACCTGCACAAACTGGATGAACTTGACTGCCTTGTAAAGGGCTTGCTGTACATAGATTCCGTCAGTTTCAATGGACAAGCAGAATGCTATTATTTTGCTAATGCCTCAGAACCCGAGCGATGCCAAAAGATGCCTTTTAACCTGGATGATCCTTACCCACTGCTGGTAGTGAATATTGGCTCAGGAGTCAGTATTTTAGCAGTCCATTCCAAAGACAACTATAAAAGAGTGACTGGGACAAGCCTTGGAGGGGGCACCTTTCTTGGTTTATGCAGTTTGTTGACTGGCTGTGAAAGTTTTGAAGAGGCTCTGGAAATGGCATCCAAAGGTGACAGCACCCAAGCTGATAGGTTGGTCCGAGATATTTATGGAGGAGATTATGAAAGATTTGGTCTGCCAGGTTGGGCGGTGGCATCTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCACCCAAGCTGATAGGTT
59
TGCTTGTCCATTGAAACTGACG
59.71
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCACCCAAGCTGATAGGTT
59
GCTTGTCCATTGAAACTGACGG
60.35
178
PCR template sequence:
CATCCAAAGGTGACAGCACCCAAGCTGATAGGTTGGTCCGAGATATTTATGGAGGAGATTATGAAAGATTTGGTCTGCCAGGTTGGGCGGTGGCATCTAGATTGGAAACCTCCACCTGCACAAACTGGATGAACTTGACTGCCTTGTAAAGGGCTTGCTGTACATAGATTCCGTCAGTTTCAATGGACAAGCAGAATGCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-181b-5p(1), mmu-miR-680(1), mmu-miR-490-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
CGGTGGCATCTAGATTGGAAACCTCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPANK3_431_ORF_1
0.7352
0.018261724
0.201801659
339
ORF sequence:
ATGCCTTTTAACCTGGATGATCCTTACCCACTGCTGGTAGTGAATATTGGCTCAGGAGTCAGTATTTTAGCAGTCCATTCCAAAGACAACTATAAAAGAGTGACTGGGACAAGCCTTGGAGGGGGCACCTTTCTTGGTTTATGCAGTTTGTTGACTGGCTGTGAAAGTTTTGAAGAGGCTCTGGAAATGGCATCCAAAGGTGACAGCACCCAAGCTGATAGGTTGGTCCGAGATATTTATGGAGGAGATTATGAAAGATTTGGTCTGCCAGGTTGGGCGGTGGCATCTAGATTGGAAACCTCCACCTGCACAAACTGGATGAACTTGACTGCCTTGTAA
Peptide sequence:
MPFNLDDPYPLLVVNIGSGVSILAVHSKDNYKRVTGTSLGGGTFLGLCSLLTGCESFEEALEMASKGDSTQADRLVRDIYGGDYERFGLPGWAVASRLETSTCTNWMNLTAL
IRESfinder result
IRESfinder score
0.521279435
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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