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mmu_circSdk1_405
Basic information of circular RNA
PanCircBase ID:
mmu_circSdk1_405
mm39_Chr. Position ID:
chr5|142080278|142085967|+
Gene name:
Sdk1
Transcript:
ENSMUST00000085774.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
26,27,28
Exon/intron offsets:
0,2210,5590
Genomic length:
5689
Exon/intron sizes in nt:
116,190,99
Flanking exon/introns:
chr5:142071580-142080278|chr5:142085967-142100145
Splice length:
405
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TTCCTTCAGCAGCTCCTGAAAATGTGTCTGCAGAGGCTGTCAGCTCCACCCAGATCCTACTGACTTGGGCTTCAGTTCCTGAGCAGGACCAGAATGGGCTCATCCTAGGCTACAAGGTTCTATACTGTGCCAAAGACCTGGACCCAGAGCCCAGAAGCCACGTGGTACGAGGGAACCACACGCAGTCTGCGCTGCTGGCTGGCCTGCGAAAGTTCGTGGTCTATGAGCTCCAAGTGCTGGCGTTCACACGGATCGGGAATGGGGTCCCCAGCTCACCTCTCATCCTGGAGCGCACCAAAGATGACACCCCAGGTCCCCCCGTGCGGCTGGTGTTCCCCGAAGTAAGACTTACTGCAGTGCGGATTGTGTGGCAGCCCCCAGAGGAGCCCAATGGTGTGATTCTGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TACTGCAGTGCGGATTGTGT
59.97
CCCATTCTGGTCCTGCTCAG
60.11
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGGTGTTCCCCGAAGTAA
59.96
CCCATTCTGGTCCTGCTCAG
60.11
178
PCR template sequence:
ACCCCAGGTCCCCCCGTGCGGCTGGTGTTCCCCGAAGTAAGACTTACTGCAGTGCGGATTGTGTGGCAGCCCCCAGAGGAGCCCAATGGTGTGATTCTGGTTCCTTCAGCAGCTCCTGAAAATGTGTCTGCAGAGGCTGTCAGCTCCACCCAGATCCTACTGACTTGGGCTTCAGTTCCTGAGCAGGACCAGAATGGGCT
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-326-3p(1), mmu-miR-503-5p(1), mmu-miR-96-5p(1), mmu-miR-542-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGTGTGATTCTGGTTCCTTCAGCAGC
siRNA sets
GAAGGAACCAGAATCACAC, AAGGAACCAGAATCACACC, CTGAAGGAACCAGAATCAC
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
0.419233864
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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