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mmu_circRps6ka2_528
Basic information of circular RNA
PanCircBase ID:
mmu_circRps6ka2_528
mm39_Chr. Position ID:
chr17|7516690|7529615|+
Gene name:
Rps6ka2
Transcript:
ENSMUST00000024575.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
5,6,7,8,9,10
Exon/intron offsets:
0,2248,5120,6539,11712,12836
Genomic length:
12925
Exon/intron sizes in nt:
80,107,38,143,71,89
Flanking exon/introns:
chr17:7514181-7516690|chr17:7529615-7538990
Splice length:
528
Other database IDs:
circBase: mmu_circ_0006985, circAtlas: mmu-Rps6ka2_0020
Human Ortholog IDs:
Mature spliced Sequence:
CCTTTCAGACCGAAGGCAAGCTCTACCTGATCCTGGACTTCCTGCGGGGAGGTGACCTCTTCACCAGGCTTTCCAAAGAGGTGATGTTCACGGAGGAGGATGTCAAGTTCTACCTGGCTGAGCTGGCCTTGGCTCTAGACCACCTCCATGGCCTGGGGATCATCTACAGGGATCTGAAGCCAGAGAATATCCTCCTGGATGAAGAGGGACACATTAAGATCACAGATTTTGGCTTGAGCAAGGAGGCCACCGACCATGACAAGAGAGCCTATTCATTCTGTGGGACTATTGAATACATGGCGCCCGAGGTGGTGAACCGGCGTGGACACACACAGAGTGCCGACTGGTGGTCCTTCGGTGTGCTCATGTTCGAGATGCTCACAGGGTCCCTGCCATTCCAGGGGAAGGACAGGAAGGAAACAATGGCCCTCATCCTCAAAGCCAAGCTGGGTATGCCTCAGTTCCTCAGTGCGGAGGCTCAGAGCCTGCTCAGGGCCCTTTTCAAGCGGAACCCCTGCAACAGGCTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGCCTCAGTTCCTCAGTGC
60.04
CCTCCTCCGTGAACATCACC
60.11
175
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTCAGTTCCTCAGTGCGGAG
60.11
CCTCCTCCGTGAACATCACC
60.11
171
PCR template sequence:
CTCATCCTCAAAGCCAAGCTGGGTATGCCTCAGTTCCTCAGTGCGGAGGCTCAGAGCCTGCTCAGGGCCCTTTTCAAGCGGAACCCCTGCAACAGGCTAGCCTTTCAGACCGAAGGCAAGCTCTACCTGATCCTGGACTTCCTGCGGGGAGGTGACCTCTTCACCAGGCTTTCCAAAGAGGTGATGTTCACGGAGGAGGA
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-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), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
TGCAACAGGCTAGCCTTTCAGACCGA
siRNA sets
GAAAGGCTAGCCTGTTGCA, TGAAAGGCTAGCCTGTTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRPS6KA2_528_ORF_1
1.3048
0.451052019
0.997569208
972
ORF sequence:
ATGTTCACGGAGGAGGATGTCAAGTTCTACCTGGCTGAGCTGGCCTTGGCTCTAGACCACCTCCATGGCCTGGGGATCATCTACAGGGATCTGAAGCCAGAGAATATCCTCCTGGATGAAGAGGGACACATTAAGATCACAGATTTTGGCTTGAGCAAGGAGGCCACCGACCATGACAAGAGAGCCTATTCATTCTGTGGGACTATTGAATACATGGCGCCCGAGGTGGTGAACCGGCGTGGACACACACAGAGTGCCGACTGGTGGTCCTTCGGTGTGCTCATGTTCGAGATGCTCACAGGGTCCCTGCCATTCCAGGGGAAGGACAGGAAGGAAACAATGGCCCTCATCCTCAAAGCCAAGCTGGGTATGCCTCAGTTCCTCAGTGCGGAGGCTCAGAGCCTGCTCAGGGCCCTTTTCAAGCGGAACCCCTGCAACAGGCTAGCCTTTCAGACCGAAGGCAAGCTCTACCTGATCCTGGACTTCCTGCGGGGAGGTGACCTCTTCACCAGGCTTTCCAAAGAGGTGATGTTCACGGAGGAGGATGTCAAGTTCTACCTGGCTGAGCTGGCCTTGGCTCTAGACCACCTCCATGGCCTGGGGATCATCTACAGGGATCTGAAGCCAGAGAATATCCTCCTGGATGAAGAGGGACACATTAAGATCACAGATTTTGGCTTGAGCAAGGAGGCCACCGACCATGACAAGAGAGCCTATTCATTCTGTGGGACTATTGAATACATGGCGCCCGAGGTGGTGAACCGGCGTGGACACACACAGAGTGCCGACTGGTGGTCCTTCGGTGTGCTCATGTTCGAGATGCTCACAGGGTCCCTGCCATTCCAGGGGAAGGACAGGAAGGAAACAATGGCCCTCATCCTCAAAGCCAAGCTGGGTATGCCTCAGTTCCTCAGTGCGGAGGCTCAGAGCCTGCTCAGGGCCCTTTTCAAGCGGAACCCCTGCAACAGGCTA
Peptide sequence:
MFTEEDVKFYLAELALALDHLHGLGIIYRDLKPENILLDEEGHIKITDFGLSKEATDHDKRAYSFCGTIEYMAPEVVNRRGHTQSADWWSFGVLMFEMLTGSLPFQGKDRKETMALILKAKLGMPQFLSAEAQSLLRALFKRNPCNRLAFQTEGKLYLILDFLRGGDLFTRLSKEVMFTEEDVKFYLAELALALDHLHGLGIIYRDLKPENILLDEEGHIKITDFGLSKEATDHDKRAYSFCGTIEYMAPEVVNRRGHTQSADWWSFGVLMFEMLTGSLPFQGKDRKETMALILKAKLGMPQFLSAEAQSLLRALFKRNPCNRL
IRESfinder result
IRESfinder score
0.259671684
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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