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mmu_circCdc73_381
Basic information of circular RNA
PanCircBase ID:
mmu_circCdc73_381
mm39_Chr. Position ID:
chr1|143561660|143575060|-
Gene name:
Cdc73
Transcript:
ENSMUST00000018337.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,5352,5491,9470,13294
Genomic length:
13400
Exon/intron sizes in nt:
89,53,63,70,106
Flanking exon/introns:
chr1:143553593-143561660|chr1:143575060-143578231
Splice length:
381
Other database IDs:
circAtlas: mmu-Cdc73_0016
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_29235
Human Ortholog IDs:
Mature spliced Sequence:
GACCGGAAAGGAAGGCCAACCCAGAGAGTACTACACATTGGATTCTATCTTATTTCTCCTTAATAATGTGCACCTTTCGCATCCTGTTTATGTCCGGCGTGCAGCTACTGAAAATATTCCTGTGGTTAGAAGACCCGACCGAAAAGATCTACTTGGATATCTCAATGGGGAAGCATCAACATCAGCAAGCATAGACAGGAGTGCCCCCTTGGAAATAGGTCTTCAGCGGTCTACTCAAGTCAAAAGAGCTGCAGATGAAGTTTTAGCAGAAGCAAAGAAACCACGGATTGAGGATGAAGAGTGTGTGCGCCTTGATAAAGAGAGATTGGCAGCTCGTTTGGAAGGCCATAAAGAAGGGATCGTGCAGACTGAGCAGATTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGATTGGCAGCTCGTTTGGA
59.96
AGGATGCGAAAGGTGCACAT
60.32
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGATTGGCAGCTCGTTTGGA
59.96
GGATGCGAAAGGTGCACATT
59.47
143
PCR template sequence:
CACGGATTGAGGATGAAGAGTGTGTGCGCCTTGATAAAGAGAGATTGGCAGCTCGTTTGGAAGGCCATAAAGAAGGGATCGTGCAGACTGAGCAGATTAGGACCGGAAAGGAAGGCCAACCCAGAGAGTACTACACATTGGATTCTATCTTATTTCTCCTTAATAATGTGCACCTTTCGCATCCTGTTTATGTCCGGCGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-18a-5p(1), mmu-miR-326-3p(1), mmu-miR-22-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGAGCAGATTAGGACCGGAAAGGAA
siRNA sets
TTTCCGGTCCTAATCTGCT, TTCCGGTCCTAATCTGCTC, TTCCTTTCCGGTCCTAATC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDC73_381_ORF_1
1.0281
-0.01307176
0.203030932
282
ORF sequence:
ATGAAGAGTGTGTGCGCCTTGATAAAGAGAGATTGGCAGCTCGTTTGGAAGGCCATAAAGAAGGGATCGTGCAGACTGAGCAGATTAGGACCGGAAAGGAAGGCCAACCCAGAGAGTACTACACATTGGATTCTATCTTATTTCTCCTTAATAATGTGCACCTTTCGCATCCTGTTTATGTCCGGCGTGCAGCTACTGAAAATATTCCTGTGGTTAGAAGACCCGACCGAAAAGATCTACTTGGATATCTCAATGGGGAAGCATCAACATCAGCAAGCATAG
Peptide sequence:
MKSVCALIKRDWQLVWKAIKKGSCRLSRLGPERKANPESTTHWILSYFSLIMCTFRILFMSGVQLLKIFLWLEDPTEKIYLDISMGKHQHQQA
IRESfinder result
IRESfinder score
0.517371848
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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