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mmu_circSdk2_583
Basic information of circular RNA
PanCircBase ID:
mmu_circSdk2_583
mm39_Chr. Position ID:
chr11|113757817|113760746|-
Gene name:
Sdk2
Transcript:
ENSMUST00000041627.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
12,11,10,9
Exon/intron offsets:
0,913,1858,2734
Genomic length:
2929
Exon/intron sizes in nt:
1,03,16,81,17,195
Flanking exon/introns:
chr11:113750816-113757817|chr11:113760746-113763656
Splice length:
583
Other database IDs:
circAtlas: mmu-Sdk2_0003
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_130004
Human Ortholog IDs:
Mature spliced Sequence:
GGGTACCGCCTCCCTCCATCACCTGGTACAAGGACGCTGCGTTGGTGGAGGTGGGGAAGCTAACCCGCTTCAAGCAGCGCAGCGATGGCGGCCTGCAGATCAGCGGCCTGCTGCCCGACGACACCGGCATGCTCCAGTGCTTTGCCCACAATGCAGCTGGCGAGGCCCAGACCTCCACCTACCTGGCTGTCACCAGCATTGCCCCTAATATCACCAGAGGCCCCCTTGACAGCACGGTGATTGACGGCATGTCGGTGGTACTAGCATGTGAGACCTCAGGGGCACCACGGCCTGCTATCACTTGGCAAAAAGGGGAGCGCATCTTGGCCAGTGGCTCTGTCCAGCTGCCTCGATTCACACTGCTGGAATCTGGCAGCCTGCTCATTAGCCCAACCCACATCTCGGACGCCGGCACCTACACTTGTTTGGCCACCAACTCTCGGGGAGTAGACGAGGCGTCAGCAGACCTGGTGGTGTGGGCCCGGACACGCATCACTAAGCCACCCCAGGACCAGAGTGTCATCAAGGGCACCCAGGCCTCCATGGTGTGTGGAGTGACCCACGATCCCAGAGTGACTGTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CATCACTAAGCCACCCCAGG
60.11
GTTAGCTTCCCCACCTCCAC
60.04
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATCACTAAGCCACCCCAGGA
60.25
GTTAGCTTCCCCACCTCCAC
60.04
156
PCR template sequence:
GGACACGCATCACTAAGCCACCCCAGGACCAGAGTGTCATCAAGGGCACCCAGGCCTCCATGGTGTGTGGAGTGACCCACGATCCCAGAGTGACTGTCAGGGGTACCGCCTCCCTCCATCACCTGGTACAAGGACGCTGCGTTGGTGGAGGTGGGGAAGCTAACCCGCTTCAAGCAGCGCAGCGATGGCGGCCTGCAGAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-33-5p(1), mmu-miR-125b-5p(1), mmu-miR-138-5p(1), mmu-miR-214-3p(1), mmu-miR-125b-1-3p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GAGTGACTGTCAGGGGTACCGCCTCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSDK2_583_ORF_1
0.7799
0.290393594
0.895823831
663
ORF sequence:
ATGCTCCAGTGCTTTGCCCACAATGCAGCTGGCGAGGCCCAGACCTCCACCTACCTGGCTGTCACCAGCATTGCCCCTAATATCACCAGAGGCCCCCTTGACAGCACGGTGATTGACGGCATGTCGGTGGTACTAGCATGTGAGACCTCAGGGGCACCACGGCCTGCTATCACTTGGCAAAAAGGGGAGCGCATCTTGGCCAGTGGCTCTGTCCAGCTGCCTCGATTCACACTGCTGGAATCTGGCAGCCTGCTCATTAGCCCAACCCACATCTCGGACGCCGGCACCTACACTTGTTTGGCCACCAACTCTCGGGGAGTAGACGAGGCGTCAGCAGACCTGGTGGTGTGGGCCCGGACACGCATCACTAAGCCACCCCAGGACCAGAGTGTCATCAAGGGCACCCAGGCCTCCATGGTGTGTGGAGTGACCCACGATCCCAGAGTGACTGTCAGGGGTACCGCCTCCCTCCATCACCTGGTACAAGGACGCTGCGTTGGTGGAGGTGGGGAAGCTAACCCGCTTCAAGCAGCGCAGCGATGGCGGCCTGCAGATCAGCGGCCTGCTGCCCGACGACACCGGCATGCTCCAGTGCTTTGCCCACAATGCAGCTGGCGAGGCCCAGACCTCCACCTACCTGGCTGTCACCAGCATTGCCCCTAA
Peptide sequence:
MLQCFAHNAAGEAQTSTYLAVTSIAPNITRGPLDSTVIDGMSVVLACETSGAPRPAITWQKGERILASGSVQLPRFTLLESGSLLISPTHISDAGTYTCLATNSRGVDEASADLVVWARTRITKPPQDQSVIKGTQASMVCGVTHDPRVTVRGTASLHHLVQGRCVGGGGEANPLQAAQRWRPADQRPAARRHRHAPVLCPQCSWRGPDLHLPGCHQHCP
IRESfinder result
IRESfinder score
0.333617228
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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