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mmu_circCdc73_776
Basic information of circular RNA
PanCircBase ID:
mmu_circCdc73_776
mm39_Chr. Position ID:
chr1|143545727|143575060|-
Gene name:
Cdc73
Transcript:
ENSMUST00000018337.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
9,8,7,6,5,4,3,2
Exon/intron offsets:
0,1340,7649,15933,21285,21424,25403,29227
Genomic length:
29333
Exon/intron sizes in nt:
7,99,92,17,89,53,63,70,000
Flanking exon/introns:
chr1:143543427-143545727|chr1:143575060-143578231
Splice length:
776
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GACCGGAAAGGAAGGCCAACCCAGAGAGTACTACACATTGGATTCTATCTTATTTCTCCTTAATAATGTGCACCTTTCGCATCCTGTTTATGTCCGGCGTGCAGCTACTGAAAATATTCCTGTGGTTAGAAGACCCGACCGAAAAGATCTACTTGGATATCTCAATGGGGAAGCATCAACATCAGCAAGCATAGACAGGAGTGCCCCCTTGGAAATAGGTCTTCAGCGGTCTACTCAAGTCAAAAGAGCTGCAGATGAAGTTTTAGCAGAAGCAAAGAAACCACGGATTGAGGATGAAGAGTGTGTGCGCCTTGATAAAGAGAGATTGGCAGCTCGTTTGGAAGGCCATAAAGAAGGGATCGTGCAGACTGAGCAGATTAGGTCTTTGTCTGAAGCCATGTCAGTGGAAAAAATTGCTGCAATCAAAGCCAAAATTATGGCTAAGAAAAGATCTACTATCAAGACTGATCTAGATGATGATATAACTGCCCTTAAACAGAGGAGTTTTGTGGATGCTGAGGTAGATGTGACCAGAGATATTGTCAGCAGAGAGAGAGTGTGGAGGACAAGAACAACTATTTTACAGAGCACAGGAAAGAATTTTTCAAAGAATATTTTTGCAATTCTTCAATCTGTAAAAGCCAGAGAAGAAGGTCGTGCCCCTGAACAACGGCCAGCTCCAAATGCAGCCCCCGTGGATCCTACATTGCGTACAAAACAGCCTATTCCAGCTGCTTACAACAGATATGACCAAGAAAGATTCAAAGGCAAAGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCCCGTGGATCCTACATTG
59.89
AGGATGCGAAAGGTGCACAT
60.32
172
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCGTGGATCCTACATTGCGT
60.18
AGGATGCGAAAGGTGCACAT
60.32
169
PCR template sequence:
GCTCCAAATGCAGCCCCCGTGGATCCTACATTGCGTACAAAACAGCCTATTCCAGCTGCTTACAACAGATATGACCAAGAAAGATTCAAAGGCAAAGAAGGACCGGAAAGGAAGGCCAACCCAGAGAGTACTACACATTGGATTCTATCTTATTTCTCCTTAATAATGTGCACCTTTCGCATCCTGTTTATGTCCGGCGT
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-18a-5p(1), mmu-miR-326-3p(1), mmu-miR-22-3p(1), mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAAGGCAAAGAAGGACCGGAAAGGAA
siRNA sets
TTTCCGGTCCTTCTTTGCC, CTTTCCGGTCCTTCTTTGC, TTCCGGTCCTTCTTTGCCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDC73_776_ORF_1
0.9616
0.068725843
0.716018038
573
ORF sequence:
ATGTCAGTGGAAAAAATTGCTGCAATCAAAGCCAAAATTATGGCTAAGAAAAGATCTACTATCAAGACTGATCTAGATGATGATATAACTGCCCTTAAACAGAGGAGTTTTGTGGATGCTGAGGTAGATGTGACCAGAGATATTGTCAGCAGAGAGAGAGTGTGGAGGACAAGAACAACTATTTTACAGAGCACAGGAAAGAATTTTTCAAAGAATATTTTTGCAATTCTTCAATCTGTAAAAGCCAGAGAAGAAGGTCGTGCCCCTGAACAACGGCCAGCTCCAAATGCAGCCCCCGTGGATCCTACATTGCGTACAAAACAGCCTATTCCAGCTGCTTACAACAGATATGACCAAGAAAGATTCAAAGGCAAAGAAGGACCGGAAAGGAAGGCCAACCCAGAGAGTACTACACATTGGATTCTATCTTATTTCTCCTTAATAATGTGCACCTTTCGCATCCTGTTTATGTCCGGCGTGCAGCTACTGAAAATATTCCTGTGGTTAGAAGACCCGACCGAAAAGATCTACTTGGATATCTCAATGGGGAAGCATCAACATCAGCAAGCATAG
Peptide sequence:
MSVEKIAAIKAKIMAKKRSTIKTDLDDDITALKQRSFVDAEVDVTRDIVSRERVWRTRTTILQSTGKNFSKNIFAILQSVKAREEGRAPEQRPAPNAAPVDPTLRTKQPIPAAYNRYDQERFKGKEGPERKANPESTTHWILSYFSLIMCTFRILFMSGVQLLKIFLWLEDPTEKIYLDISMGKHQHQQA
IRESfinder result
IRESfinder score
0.503880139
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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