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mmu_circRps6ka2_425
Basic information of circular RNA
PanCircBase ID:
mmu_circRps6ka2_425
mm39_Chr. Position ID:
chr17|7538990|7550268|+
Gene name:
Rps6ka2
Transcript:
ENSMUST00000024575.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
11,12,13,14
Exon/intron offsets:
0,5871,10177,11152
Genomic length:
11278
Exon/intron sizes in nt:
65,10,31,31,126
Flanking exon/introns:
chr17:7529615-7538990|chr17:7550268-7556313
Splice length:
425
Other database IDs:
circAtlas: mmu-Rps6ka2_0001
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GTGCTGGTGTTGATGGAGTGGAGGAAATTAAACGTCACCCGTTCTTTGTCACCATAGACTGGAATAAGCTGTACCGCAAGGAGATCAAGCCACCCTTCAAGCCAGCAGTGGGCAGGCCTGAGGACACCTTCCACTTTGACCCCGAGTTTACTGCAAGGACCCCCACAGATTCTCCTGGTGTCCCCCCAAGTGCAAACGCCCACCACCTCTTCAGAGGATTCAGCTTTGTGGCCTCCAGCCTGGTCCAGGAGCCCTCACAGCAAGACGTGCCCAAGGCCCCCATTCACCCAATTGTGCAGCAGCTACATGGGAACAACATCCACTTCACTGACGGCTATGAGATCAAGGAGGACATCGGGGTGGGCTCCTACTCAGTGTGCAAGCGGTGTGTACACAAAGCCACGGATGCTGAGTATGCTGTGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTACTCAGTGTGCAAGCG
60.04
TGATCTCCTTGCGGTACAGC
59.82
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTACTCAGTGTGCAAGCG
60.04
GGCTTGATCTCCTTGCGGTA
59.82
151
PCR template sequence:
CACTGACGGCTATGAGATCAAGGAGGACATCGGGGTGGGCTCCTACTCAGTGTGCAAGCGGTGTGTACACAAAGCCACGGATGCTGAGTATGCTGTGAAGGTGCTGGTGTTGATGGAGTGGAGGAAATTAAACGTCACCCGTTCTTTGTCACCATAGACTGGAATAAGCTGTACCGCAAGGAGATCAAGCCACCCTTCAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-320-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-673-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTATGCTGTGAAGGTGCTGGTGTTGA
siRNA sets
AACACCAGCACCTTCACAG, TCAACACCAGCACCTTCAC, ACACCAGCACCTTCACAGC
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
0.451747629
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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