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mmu_circCdc73_642
Basic information of circular RNA
PanCircBase ID:
mmu_circCdc73_642
mm39_Chr. Position ID:
chr1|143503239|143553593|-
Gene name:
Cdc73
Transcript:
ENSMUST00000018337.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
13,12,11,10,9,8,7
Exon/intron offsets:
0,344,7530,40123,42488,43828,50137
Genomic length:
50354
Exon/intron sizes in nt:
88,36,58,65,79,99,217
Flanking exon/introns:
chr1:143493178-143503239|chr1:143553593-143561660
Splice length:
642
Other database IDs:
CIRCpedia: MMU_CIRCpedia_216193, circAtlas: mmu-Cdc73_0019
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GTCTTTGTCTGAAGCCATGTCAGTGGAAAAAATTGCTGCAATCAAAGCCAAAATTATGGCTAAGAAAAGATCTACTATCAAGACTGATCTAGATGATGATATAACTGCCCTTAAACAGAGGAGTTTTGTGGATGCTGAGGTAGATGTGACCAGAGATATTGTCAGCAGAGAGAGAGTGTGGAGGACAAGAACAACTATTTTACAGAGCACAGGAAAGAATTTTTCAAAGAATATTTTTGCAATTCTTCAATCTGTAAAAGCCAGAGAAGAAGGTCGTGCCCCTGAACAACGGCCAGCTCCAAATGCAGCCCCCGTGGATCCTACATTGCGTACAAAACAGCCTATTCCAGCTGCTTACAACAGATATGACCAAGAAAGATTCAAAGGCAAAGAAGAAACGGAAGGCTTTAAGATCGATACTATGGGCACCTACCATGGCATGACACTGAAATCTGTAACGGAAGGTGCATCTGCTCGTAAGACTCAAACTCCTGCAGCCCAGCCTGTACCTAGACCAGTGTCTCAAGCCAGACCCCCCCCAAATCAGAAGAAAGGGTCACGGACACCCATTATTATTATTCCTGCAGCTACCACTTCTTTAATAACTATGCTTAATGCAAAAGACCTTCTACAGGATCTGAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGAAAGGGTCACGGACACC
59.89
TTTGGCTTTGATTGCAGCAA
57.38
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGAAAGGGTCACGGACACC
59.89
TTTTGGCTTTGATTGCAGCA
57.38
148
PCR template sequence:
ATCAGAAGAAAGGGTCACGGACACCCATTATTATTATTCCTGCAGCTACCACTTCTTTAATAACTATGCTTAATGCAAAAGACCTTCTACAGGATCTGAAGTCTTTGTCTGAAGCCATGTCAGTGGAAAAAATTGCTGCAATCAAAGCCAAAATTATGGCTAAGAAAAGATCTACTATCAAGACTGATCTAGATGATGAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-501-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TACAGGATCTGAAGTCTTTGTCTGAA
siRNA sets
AAAGACTTCAGATCCTGTA, CAAAGACTTCAGATCCTGT, ACAAAGACTTCAGATCCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDC73_642_ORF_1
1.0538
0.098542534
0.99802527
1266
ORF sequence:
ATGTCAGTGGAAAAAATTGCTGCAATCAAAGCCAAAATTATGGCTAAGAAAAGATCTACTATCAAGACTGATCTAGATGATGATATAACTGCCCTTAAACAGAGGAGTTTTGTGGATGCTGAGGTAGATGTGACCAGAGATATTGTCAGCAGAGAGAGAGTGTGGAGGACAAGAACAACTATTTTACAGAGCACAGGAAAGAATTTTTCAAAGAATATTTTTGCAATTCTTCAATCTGTAAAAGCCAGAGAAGAAGGTCGTGCCCCTGAACAACGGCCAGCTCCAAATGCAGCCCCCGTGGATCCTACATTGCGTACAAAACAGCCTATTCCAGCTGCTTACAACAGATATGACCAAGAAAGATTCAAAGGCAAAGAAGAAACGGAAGGCTTTAAGATCGATACTATGGGCACCTACCATGGCATGACACTGAAATCTGTAACGGAAGGTGCATCTGCTCGTAAGACTCAAACTCCTGCAGCCCAGCCTGTACCTAGACCAGTGTCTCAAGCCAGACCCCCCCCAAATCAGAAGAAAGGGTCACGGACACCCATTATTATTATTCCTGCAGCTACCACTTCTTTAATAACTATGCTTAATGCAAAAGACCTTCTACAGGATCTGAAGTCTTTGTCTGAAGCCATGTCAGTGGAAAAAATTGCTGCAATCAAAGCCAAAATTATGGCTAAGAAAAGATCTACTATCAAGACTGATCTAGATGATGATATAACTGCCCTTAAACAGAGGAGTTTTGTGGATGCTGAGGTAGATGTGACCAGAGATATTGTCAGCAGAGAGAGAGTGTGGAGGACAAGAACAACTATTTTACAGAGCACAGGAAAGAATTTTTCAAAGAATATTTTTGCAATTCTTCAATCTGTAAAAGCCAGAGAAGAAGGTCGTGCCCCTGAACAACGGCCAGCTCCAAATGCAGCCCCCGTGGATCCTACATTGCGTACAAAACAGCCTATTCCAGCTGCTTACAACAGATATGACCAAGAAAGATTCAAAGGCAAAGAAGAAACGGAAGGCTTTAAGATCGATACTATGGGCACCTACCATGGCATGACACTGAAATCTGTAACGGAAGGTGCATCTGCTCGTAAGACTCAAACTCCTGCAGCCCAGCCTGTACCTAGACCAGTGTCTCAAGCCAGACCCCCCCCAAATCAGAAGAAAGGGTCACGGACACCCATTATTATTATTCCTGCAGCTACCACTTCTTTAATAACTATGCTTAATGCAAAAGACCTTCTACAGGATCTG
Peptide sequence:
MSVEKIAAIKAKIMAKKRSTIKTDLDDDITALKQRSFVDAEVDVTRDIVSRERVWRTRTTILQSTGKNFSKNIFAILQSVKAREEGRAPEQRPAPNAAPVDPTLRTKQPIPAAYNRYDQERFKGKEETEGFKIDTMGTYHGMTLKSVTEGASARKTQTPAAQPVPRPVSQARPPPNQKKGSRTPIIIIPAATTSLITMLNAKDLLQDLKSLSEAMSVEKIAAIKAKIMAKKRSTIKTDLDDDITALKQRSFVDAEVDVTRDIVSRERVWRTRTTILQSTGKNFSKNIFAILQSVKAREEGRAPEQRPAPNAAPVDPTLRTKQPIPAAYNRYDQERFKGKEETEGFKIDTMGTYHGMTLKSVTEGASARKTQTPAAQPVPRPVSQARPPPNQKKGSRTPIIIIPAATTSLITMLNAKDLLQDL
IRESfinder result
IRESfinder score
0.534562328
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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