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mmu_circCdc73_905
Basic information of circular RNA
PanCircBase ID:
mmu_circCdc73_905
mm39_Chr. Position ID:
chr1|143491040|143553593|-
Gene name:
Cdc73
Transcript:
ENSMUST00000018337.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
15,14,13,12,11,10,9,8,7
Exon/intron offsets:
0,1976,12199,12543,19729,52322,54687,56027,62336
Genomic length:
62553
Exon/intron sizes in nt:
10,11,62,88,36,58,65,70,00,000
Flanking exon/introns:
chr1:143485249-143491040|chr1:143553593-143561660
Splice length:
905
Other database IDs:
CIRCpedia: MMU_CIRCpedia_9369, circAtlas: mmu-Cdc73_0020
Human Ortholog IDs:
Mature spliced Sequence:
GTCTTTGTCTGAAGCCATGTCAGTGGAAAAAATTGCTGCAATCAAAGCCAAAATTATGGCTAAGAAAAGATCTACTATCAAGACTGATCTAGATGATGATATAACTGCCCTTAAACAGAGGAGTTTTGTGGATGCTGAGGTAGATGTGACCAGAGATATTGTCAGCAGAGAGAGAGTGTGGAGGACAAGAACAACTATTTTACAGAGCACAGGAAAGAATTTTTCAAAGAATATTTTTGCAATTCTTCAATCTGTAAAAGCCAGAGAAGAAGGTCGTGCCCCTGAACAACGGCCAGCTCCAAATGCAGCCCCCGTGGATCCTACATTGCGTACAAAACAGCCTATTCCAGCTGCTTACAACAGATATGACCAAGAAAGATTCAAAGGCAAAGAAGAAACGGAAGGCTTTAAGATCGATACTATGGGCACCTACCATGGCATGACACTGAAATCTGTAACGGAAGGTGCATCTGCTCGTAAGACTCAAACTCCTGCAGCCCAGCCTGTACCTAGACCAGTGTCTCAAGCCAGACCCCCCCCAAATCAGAAGAAAGGGTCACGGACACCCATTATTATTATTCCTGCAGCTACCACTTCTTTAATAACTATGCTTAATGCAAAAGACCTTCTACAGGATCTGAAATTTGTCCCATCAGATGAGAAGAAGAAACAGGGTTGTCAACGAGAAAATGAAACACTAATACAGAGAAGAAAAGACCAGATGCAACCAGGGGGCACAGCAATTAGTGTCACAGTACCTTACAGAGTAGTAGACCAGCCCCTGAAACTTATGCCTCAAGACTGGGATCGAGTTGTGGCTGTTTTTGTACAAGGTCCTGCTTGGCAATTCAAAGGTTGGCCATGGCTTCTCCCTGATGGATCACCAGTTGACATATTTGCGAAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCGAGTTGTGGCTGTTTTTGT
58.91
TTTGGCTTTGATTGCAGCAA
57.38
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCGAGTTGTGGCTGTTTTTGT
58.91
TTTTGGCTTTGATTGCAGCA
57.38
151
PCR template sequence:
GATCGAGTTGTGGCTGTTTTTGTACAAGGTCCTGCTTGGCAATTCAAAGGTTGGCCATGGCTTCTCCCTGATGGATCACCAGTTGACATATTTGCGAAAAGTCTTTGTCTGAAGCCATGTCAGTGGAAAAAATTGCTGCAATCAAAGCCAAAATTATGGCTAAGAAAAGATCTACTATCAAGACTGATCTAGATGATGAT
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
ATATTTGCGAAAAGTCTTTGTCTGAA
siRNA sets
TTCAGACAAAGACTTTTCG, TCAGACAAAGACTTTTCGC, CAGACAAAGACTTTTCGCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDC73_905_ORF_1
0.9678
0.013185398
0.974605055
981
ORF sequence:
ATGTCAGTGGAAAAAATTGCTGCAATCAAAGCCAAAATTATGGCTAAGAAAAGATCTACTATCAAGACTGATCTAGATGATGATATAACTGCCCTTAAACAGAGGAGTTTTGTGGATGCTGAGGTAGATGTGACCAGAGATATTGTCAGCAGAGAGAGAGTGTGGAGGACAAGAACAACTATTTTACAGAGCACAGGAAAGAATTTTTCAAAGAATATTTTTGCAATTCTTCAATCTGTAAAAGCCAGAGAAGAAGGTCGTGCCCCTGAACAACGGCCAGCTCCAAATGCAGCCCCCGTGGATCCTACATTGCGTACAAAACAGCCTATTCCAGCTGCTTACAACAGATATGACCAAGAAAGATTCAAAGGCAAAGAAGAAACGGAAGGCTTTAAGATCGATACTATGGGCACCTACCATGGCATGACACTGAAATCTGTAACGGAAGGTGCATCTGCTCGTAAGACTCAAACTCCTGCAGCCCAGCCTGTACCTAGACCAGTGTCTCAAGCCAGACCCCCCCCAAATCAGAAGAAAGGGTCACGGACACCCATTATTATTATTCCTGCAGCTACCACTTCTTTAATAACTATGCTTAATGCAAAAGACCTTCTACAGGATCTGAAATTTGTCCCATCAGATGAGAAGAAGAAACAGGGTTGTCAACGAGAAAATGAAACACTAATACAGAGAAGAAAAGACCAGATGCAACCAGGGGGCACAGCAATTAGTGTCACAGTACCTTACAGAGTAGTAGACCAGCCCCTGAAACTTATGCCTCAAGACTGGGATCGAGTTGTGGCTGTTTTTGTACAAGGTCCTGCTTGGCAATTCAAAGGTTGGCCATGGCTTCTCCCTGATGGATCACCAGTTGACATATTTGCGAAAAGTCTTTGTCTGAAGCCATGTCAGTGGAAAAAATTGCTGCAATCAAAGCCAAAATTATGGCTAAGAAAAGATCTACTATCAAGACTGATCTAG
Peptide sequence:
MSVEKIAAIKAKIMAKKRSTIKTDLDDDITALKQRSFVDAEVDVTRDIVSRERVWRTRTTILQSTGKNFSKNIFAILQSVKAREEGRAPEQRPAPNAAPVDPTLRTKQPIPAAYNRYDQERFKGKEETEGFKIDTMGTYHGMTLKSVTEGASARKTQTPAAQPVPRPVSQARPPPNQKKGSRTPIIIIPAATTSLITMLNAKDLLQDLKFVPSDEKKKQGCQRENETLIQRRKDQMQPGGTAISVTVPYRVVDQPLKLMPQDWDRVVAVFVQGPAWQFKGWPWLLPDGSPVDIFAKSLCLKPCQWKKLLQSKPKLWLRKDLLSRLI
IRESfinder result
IRESfinder score
0.518717833
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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