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mmu_circSdk2_266
Basic information of circular RNA
PanCircBase ID:
mmu_circSdk2_266
mm39_Chr. Position ID:
chr11|113682200|113684264|-
Gene name:
Sdk2
Transcript:
ENSMUST00000041627.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
44,43
Exon/intron offsets:
0,1925
Genomic length:
2064
Exon/intron sizes in nt:
1,27,139
Flanking exon/introns:
chr11:113671969-113682200|chr11:113684264-113684548
Splice length:
266
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GAGGGAATACCAAGTCAGGAGCGCTCGGCCACGGGGAGATGCTAAGCTTGGATGAAAGCAGTTTCCCTGCTCTGGAGCTCAACAACCGTCGGCTGTCCGTAAAGAACTCCTTCTGCAGGAAGAACGGCTTGTACACCAGGTCCCCTCCCAGGCCCAGTCCAGGTAGCCTACATTACTCTGATGAAGACGTCACCAAGTACAACGACCTCATCCCAGCTGAGAGCAGCAGCCTGACTGAGAAGCCCTCGGAGATCTCTGACTCCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTCATCCCAGCTGAGAGCAG
59.89
GACGGTTGTTGAGCTCCAGA
59.97
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTCATCCCAGCTGAGAGCAG
59.89
ACGGTTGTTGAGCTCCAGAG
59.97
149
PCR template sequence:
CCTACATTACTCTGATGAAGACGTCACCAAGTACAACGACCTCATCCCAGCTGAGAGCAGCAGCCTGACTGAGAAGCCCTCGGAGATCTCTGACTCCCAGGAGGGAATACCAAGTCAGGAGCGCTCGGCCACGGGGAGATGCTAAGCTTGGATGAAAGCAGTTTCCCTGCTCTGGAGCTCAACAACCGTCGGCTGTCCGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
NA
Interacting miRNAs (#binding sites)
NA
siRNAs for circular RNA silencing
Junction sequence
CTCTGACTCCCAGGAGGGAATACCAA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSDK2_266_ORF_1
0.7469
0.342369923
0.378302179
273
ORF sequence:
ATGCTAAGCTTGGATGAAAGCAGTTTCCCTGCTCTGGAGCTCAACAACCGTCGGCTGTCCGTAAAGAACTCCTTCTGCAGGAAGAACGGCTTGTACACCAGGTCCCCTCCCAGGCCCAGTCCAGGTAGCCTACATTACTCTGATGAAGACGTCACCAAGTACAACGACCTCATCCCAGCTGAGAGCAGCAGCCTGACTGAGAAGCCCTCGGAGATCTCTGACTCCCAGGAGGGAATACCAAGTCAGGAGCGCTCGGCCACGGGGAGATGCTAA
Peptide sequence:
MLSLDESSFPALELNNRRLSVKNSFCRKNGLYTRSPPRPSPGSLHYSDEDVTKYNDLIPAESSSLTEKPSEISDSQEGIPSQERSATGRC
IRESfinder result
IRESfinder score
0.370917482
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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