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mmu_circSdk2_314
Basic information of circular RNA
PanCircBase ID:
mmu_circSdk2_314
mm39_Chr. Position ID:
chr11|113748521|113750816|-
Gene name:
Sdk2
Transcript:
ENSMUST00000041627.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
14,13
Exon/intron offsets:
0,2118
Genomic length:
2295
Exon/intron sizes in nt:
137,177
Flanking exon/introns:
chr11:113747599-113748521|chr11:113750816-113757817
Splice length:
314
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTACGTGTGGGAGAAGGATGGGGCCACCCTGGCCGTGGAGACTAATCCTCGGATCCGCCTGGACAGAAATGGCTCCCTACACATCTCGCAGACGTGGTCAGGGGACATTGGCACGTATACCTGCCGGGTGCTCTCGGCTGGTGGCAATGACTCTCGCAACGCCCACCTGCGAGTCAGGCAGCTCCCCCATGCCCCTGAGCACCCTGTGGCAACCCTCAGCACCGTGGAGAGACGCGCCATCAACCTGACCTGGGCCAAACCCTTCGACGGCAACAGCCCTCTGATGCGCTACGTCTTGGAGATGTCAGAAAACA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTCAGCACCGTGGAGAGAC
59.79
CGAGGATTAGTCTCCACGGC
59.97
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AACCTGACCTGGGCCAAAC
60.15
CCATTTCTGTCCAGGCGGAT
60.11
145
PCR template sequence:
CTCAGCACCGTGGAGAGACGCGCCATCAACCTGACCTGGGCCAAACCCTTCGACGGCAACAGCCCTCTGATGCGCTACGTCTTGGAGATGTCAGAAAACAGTACGTGTGGGAGAAGGATGGGGCCACCCTGGCCGTGGAGACTAATCCTCGGATCCGCCTGGACAGAAATGGCTCCCTACACATCTCGCAGACGTGGTCA
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
ATGTCAGAAAACAGTACGTGTGGGAG
siRNA sets
ACACGTACTGTTTTCTGAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSDK2_314_ORF_1
1.0522
0.034646322
0.241209434
279
ORF sequence:
ATGCGCTACGTCTTGGAGATGTCAGAAAACAGTACGTGTGGGAGAAGGATGGGGCCACCCTGGCCGTGGAGACTAATCCTCGGATCCGCCTGGACAGAAATGGCTCCCTACACATCTCGCAGACGTGGTCAGGGGACATTGGCACGTATACCTGCCGGGTGCTCTCGGCTGGTGGCAATGACTCTCGCAACGCCCACCTGCGAGTCAGGCAGCTCCCCCATGCCCCTGAGCACCCTGTGGCAACCCTCAGCACCGTGGAGAGACGCGCCATCAACCTGA
Peptide sequence:
MRYVLEMSENSTCGRRMGPPWPWRLILGSAWTEMAPYTSRRRGQGTLARIPAGCSRLVAMTLATPTCESGSSPMPLSTLWQPSAPWRDAPST
IRESfinder result
IRESfinder score
0.162041209
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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