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mmu_circRps6ka2_303
Basic information of circular RNA
PanCircBase ID:
mmu_circRps6ka2_303
mm39_Chr. Position ID:
chr17|7523229|7529615|+
Gene name:
Rps6ka2
Transcript:
ENSMUST00000024575.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
8,9,10
Exon/intron offsets:
0,5173,6297
Genomic length:
6386
Exon/intron sizes in nt:
143,71,89
Flanking exon/introns:
chr17:7521848-7523229|chr17:7529615-7538990
Splice length:
303
Other database IDs:
CIRCpedia: HSA_CIRCpedia_54322
Human Ortholog IDs:
Mature spliced Sequence:
ATTTTGGCTTGAGCAAGGAGGCCACCGACCATGACAAGAGAGCCTATTCATTCTGTGGGACTATTGAATACATGGCGCCCGAGGTGGTGAACCGGCGTGGACACACACAGAGTGCCGACTGGTGGTCCTTCGGTGTGCTCATGTTCGAGATGCTCACAGGGTCCCTGCCATTCCAGGGGAAGGACAGGAAGGAAACAATGGCCCTCATCCTCAAAGCCAAGCTGGGTATGCCTCAGTTCCTCAGTGCGGAGGCTCAGAGCCTGCTCAGGGCCCTTTTCAAGCGGAACCCCTGCAACAGGCTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGCCTCAGTTCCTCAGTGC
60.04
TCGGGCGCCATGTATTCAAT
60.18
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTCAGTTCCTCAGTGCGGAG
60.11
TCGGGCGCCATGTATTCAAT
60.18
154
PCR template sequence:
CTCATCCTCAAAGCCAAGCTGGGTATGCCTCAGTTCCTCAGTGCGGAGGCTCAGAGCCTGCTCAGGGCCCTTTTCAAGCGGAACCCCTGCAACAGGCTAGATTTTGGCTTGAGCAAGGAGGCCACCGACCATGACAAGAGAGCCTATTCATTCTGTGGGACTATTGAATACATGGCGCCCGAGGTGGTGAACCGGCGTGG
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-10b-5p(1), mmu-miR-10a-5p(1), mmu-miR-351-5p(1), mmu-miR-125a-5p(1), mmu-miR-484(1), mmu-miR-3470b(1)
siRNAs for circular RNA silencing
Junction sequence
TGCAACAGGCTAGATTTTGGCTTGAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRPS6KA2_303_ORF_1
1.2375
0.374491344
0.91898879
534
ORF sequence:
ATGGCGCCCGAGGTGGTGAACCGGCGTGGACACACACAGAGTGCCGACTGGTGGTCCTTCGGTGTGCTCATGTTCGAGATGCTCACAGGGTCCCTGCCATTCCAGGGGAAGGACAGGAAGGAAACAATGGCCCTCATCCTCAAAGCCAAGCTGGGTATGCCTCAGTTCCTCAGTGCGGAGGCTCAGAGCCTGCTCAGGGCCCTTTTCAAGCGGAACCCCTGCAACAGGCTAGATTTTGGCTTGAGCAAGGAGGCCACCGACCATGACAAGAGAGCCTATTCATTCTGTGGGACTATTGAATACATGGCGCCCGAGGTGGTGAACCGGCGTGGACACACACAGAGTGCCGACTGGTGGTCCTTCGGTGTGCTCATGTTCGAGATGCTCACAGGGTCCCTGCCATTCCAGGGGAAGGACAGGAAGGAAACAATGGCCCTCATCCTCAAAGCCAAGCTGGGTATGCCTCAGTTCCTCAGTGCGGAGGCTCAGAGCCTGCTCAGGGCCCTTTTCAAGCGGAACCCCTGCAACAGGCTA
Peptide sequence:
MAPEVVNRRGHTQSADWWSFGVLMFEMLTGSLPFQGKDRKETMALILKAKLGMPQFLSAEAQSLLRALFKRNPCNRLDFGLSKEATDHDKRAYSFCGTIEYMAPEVVNRRGHTQSADWWSFGVLMFEMLTGSLPFQGKDRKETMALILKAKLGMPQFLSAEAQSLLRALFKRNPCNRL
IRESfinder result
IRESfinder score
0.189539802
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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