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mmu_circCkap5_401
Basic information of circular RNA
PanCircBase ID:
mmu_circCkap5_401
mm39_Chr. Position ID:
chr2|91379118|91381103|+
Gene name:
Ckap5
Transcript:
ENSMUST00000111338.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,4
Exon/intron offsets:
0,1778
Genomic length:
1985
Exon/intron sizes in nt:
194,207
Flanking exon/introns:
chr2:91376760-91379118|chr2:91381103-91385611
Splice length:
401
Other database IDs:
CIRCpedia: MMU_CIRCpedia_34120, circAtlas: mmu-Ckap5_0007
circAtlas: hsa-CKAP5_0016, CIRCpedia: HSA_CIRCpedia_365453
Human Ortholog IDs:
Mature spliced Sequence:
CTATGGAAAGCAAGATTAAGTGGGTATGAAGAAGCCTTGAAGATCTTCCAGAAAATAAAGGATGAAAAGAGTCCAGAATGGTCCAAATACTTAGGATTAATCAAAAAATTTGTCACTGATTCCAATGCAGTGGTTCAATTGAAAGGACTAGAAGCTGCACTTGTCTATGTTGAAAATGCTCATGTTGCAGGAAAAACAACGGGAGAGGTTGTATCAGGTGTTGTAAGTAAAGTCTTCAACCAACCTAAAGCCAAAGCCAAGGAACTGGGCATAGAGATTTGCCTCATGTATGTTGAGATTGAAAAAGGAGAGTCTGTACAAGAAGAGCTTCTGAAGGGCCTGGATAACAAGAACCCCAAGATCATAGTGGCCTGTATAGAAACACTGAGGAAAGCCTTAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGAGCTTCTGAAGGGCCTG
59.67
TGGACCATTCTGGACTCTTTTCA
59.61
164
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAAGAGCTTCTGAAGGGCCT
59.38
TGGACCATTCTGGACTCTTTTCA
59.61
165
PCR template sequence:
AAAAAGGAGAGTCTGTACAAGAAGAGCTTCTGAAGGGCCTGGATAACAAGAACCCCAAGATCATAGTGGCCTGTATAGAAACACTGAGGAAAGCCTTAAGCTATGGAAAGCAAGATTAAGTGGGTATGAAGAAGCCTTGAAGATCTTCCAGAAAATAAAGGATGAAAAGAGTCCAGAATGGTCCAAATACTTAGGATTAA
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-33-5p(1), mmu-miR-216a-5p(1), mmu-miR-217-5p(1), mmu-miR-434-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGAAAGCCTTAAGCTATGGAAAGCAA
siRNA sets
TTTCCATAGCTTAAGGCTT, CCATAGCTTAAGGCTTTCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCKAP5_401_ORF_1
1.0781
0.183894553
0.177860964
135
ORF sequence:
ATGTATGTTGAGATTGAAAAAGGAGAGTCTGTACAAGAAGAGCTTCTGAAGGGCCTGGATAACAAGAACCCCAAGATCATAGTGGCCTGTATAGAAACACTGAGGAAAGCCTTAAGCTATGGAAAGCAAGATTAA
Peptide sequence:
MYVEIEKGESVQEELLKGLDNKNPKIIVACIETLRKALSYGKQD
IRESfinder result
IRESfinder score
0.623736407
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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