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mmu_circCops3_566
Basic information of circular RNA
PanCircBase ID:
mmu_circCops3_566
mm39_Chr. Position ID:
chr11|59718671|59727846|-
Gene name:
Cops3
Transcript:
ENSMUST00000019517.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,2301,5038,5186,9045
Genomic length:
9175
Exon/intron sizes in nt:
18,09,35,01,13,130
Flanking exon/introns:
chr11:59717256-59718671|chr11:59727846-59730495
Splice length:
566
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GGCAAATGACTCAGCTTTGTGAACTCATCAACAAGAGTGGAGAACTCCTTGCGAAGAACTTGTCCCATCTGGACACTGTGCTTGGGGCTTTAGATGTTCAAGAACACTCTTTGGGTGTCCTTGCTGTTCTGTTTGTGAAGTTCTCAATGCCCAGTGTTCCTGACTTCGAAACACTATTCTCACAGGTTCAGCTTTTCATCAGTACATGTAATGGCGAGCACATTCGATATGCAACAGATACGTTTGCTGGGCTTTGCCATCAGCTAACAAATGCACTTGTGGAAAGAAAACAGCCCCTTCGAGGAATTGGCATCCTTAAGCAAGCCATAGACAAGATGCAGATGAATACCAACCAACTGACCTCAGTACATGCCGATCTCTGCCAGCTTTGTTTACTAGCGAAGTGCTTTAAACCTGCCCTTCCATATCTTGATGTGGATATGATGGATATCTGTAAAGAGAATGGAGCCTATGATGCAAAACACTTTCTGTGCTACTACTATTATGGAGGAATGATCTATACGGGGCTGAAGAACTTTGAAAGAGCGCTGTACTTTTATGAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGAGGAATGATCTATACGGGGC
59.83
AAGCACAGTGTCCAGATGGG
59.96
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAGGAATGATCTATACGGGGC
59.83
CCCAAGCACAGTGTCCAGAT
59.96
146
PCR template sequence:
AGCCTATGATGCAAAACACTTTCTGTGCTACTACTATTATGGAGGAATGATCTATACGGGGCTGAAGAACTTTGAAAGAGCGCTGTACTTTTATGAGCAGGGCAAATGACTCAGCTTTGTGAACTCATCAACAAGAGTGGAGAACTCCTTGCGAAGAACTTGTCCCATCTGGACACTGTGCTTGGGGCTTTAGATGTTCA
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-320-3p(3), mmu-miR-136-5p(2), mmu-miR-350-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTTTTATGAGCAGGGCAAATGACTCA
siRNA sets
TTTGCCCTGCTCATAAAAG, ATTTGCCCTGCTCATAAAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCOPS3_566_ORF_1
0.964
0.129712464
0.762560061
570
ORF sequence:
ATGACTCAGCTTTGTGAACTCATCAACAAGAGTGGAGAACTCCTTGCGAAGAACTTGTCCCATCTGGACACTGTGCTTGGGGCTTTAGATGTTCAAGAACACTCTTTGGGTGTCCTTGCTGTTCTGTTTGTGAAGTTCTCAATGCCCAGTGTTCCTGACTTCGAAACACTATTCTCACAGGTTCAGCTTTTCATCAGTACATGTAATGGCGAGCACATTCGATATGCAACAGATACGTTTGCTGGGCTTTGCCATCAGCTAACAAATGCACTTGTGGAAAGAAAACAGCCCCTTCGAGGAATTGGCATCCTTAAGCAAGCCATAGACAAGATGCAGATGAATACCAACCAACTGACCTCAGTACATGCCGATCTCTGCCAGCTTTGTTTACTAGCGAAGTGCTTTAAACCTGCCCTTCCATATCTTGATGTGGATATGATGGATATCTGTAAAGAGAATGGAGCCTATGATGCAAAACACTTTCTGTGCTACTACTATTATGGAGGAATGATCTATACGGGGCTGAAGAACTTTGAAAGAGCGCTGTACTTTTATGAGCAGGGCAAATGA
Peptide sequence:
MTQLCELINKSGELLAKNLSHLDTVLGALDVQEHSLGVLAVLFVKFSMPSVPDFETLFSQVQLFISTCNGEHIRYATDTFAGLCHQLTNALVERKQPLRGIGILKQAIDKMQMNTNQLTSVHADLCQLCLLAKCFKPALPYLDVDMMDICKENGAYDAKHFLCYYYYGGMIYTGLKNFERALYFYEQGK
IRESfinder result
IRESfinder score
0.604463268
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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