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mmu_circCdc16_869
Basic information of circular RNA
PanCircBase ID:
mmu_circCdc16_869
mm39_Chr. Position ID:
chr8|13812850|13821450|+
Gene name:
Cdc16
Transcript:
ENSMUST00000043962.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
6,7,8,9,10,11,12,13
Exon/intron offsets:
0,969,1718,3567,4687,5710,6526,8447
Genomic length:
8600
Exon/intron sizes in nt:
1,60,92,13,48,05,07,41,00,000
Flanking exon/introns:
chr8:13811117-13812850|chr8:13821450-13823340
Splice length:
869
Other database IDs:
CIRCpedia: MMU_CIRCpedia_216634, circAtlas: mmu-Cdc16_0009
circBase: hsa_circ_0099950, circAtlas: hsa-CDC16_0017, CIRCpedia: HSA_CIRCpedia_10230
Human Ortholog IDs:
Mature spliced Sequence:
ATAAAGAGCTCGATTTGTCTCCTGAGAGGGAAGATCTATGATGCTTTAGATAATCGCACCCTGGCTACCTACAGTTACAAAGAGGCTCTGAAACTGGATGTCTACTGCTTTGAAGCCTTTGACCTTTTGACATCACACCACATGCTGACAGCACAGGAAGAAAAAGAACTTCTGGACTCCCTGCCTCTTAACAAGCTCTGTGCTGAAGAACAAGAGTTGCTGCGATTTGTATTTGAGAACAAATTAAAGAAGTATAATAAGCCCAGTGAAACGGTCATTCCCGAGTCAGTGGACGGCTTGCAGGAGAATCTGGACGTGGTAGTGTCTTTAGCTGAGAGACACTATTACAACTGTGATTTTAAGATGTGCTACAAGCTTACTTCTACAGTGATGGAGAAAGATCCTTTCCATGCAAACTGTTTACCTGTGCACATAGGAACTCTTGTGGAGCTGAATAAAGCGAATGAACTTTTCTATCTTTCTCACAAACTGGTGGATTTATATCCGAGTAATCCTGTGTCTTGGTTTGCGGTGGGATGTTACTATCTCATGGTTGGTCATAAAAATGAGCATGCCAGAAGATATCTCAGCAAAGCTACCACGTTGGAGAAGACCTACGGTCCTGCCTGGATAGCCTACGGGCATTCCTTCGCTGTGGAGAGTGAGCACGACCAAGCAATGGCTGCTTACTTCACAGCAGCACAGCTGATGAAGGGGTGTCACTTGCCAATGCTATATATTGGATTAGAATATGGTCTGACCAATAACTCGAAACTGGCTGAGCGGTTCTTTGGCCAAGCTCTGAGCATCGCCCCAGAAGACCCATTTGTCATCCATGAGGTTGGAGTGGTTGCCTTTCAGAATGGAGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AACTGGCTGAGCGGTTCTTT
60.18
GGTAGCCAGGGTGCGATTAT
59.6
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAACTGGCTGAGCGGTTCTT
60.18
GGTAGCCAGGGTGCGATTAT
59.6
167
PCR template sequence:
CGAAACTGGCTGAGCGGTTCTTTGGCCAAGCTCTGAGCATCGCCCCAGAAGACCCATTTGTCATCCATGAGGTTGGAGTGGTTGCCTTTCAGAATGGAGAATAAAGAGCTCGATTTGTCTCCTGAGAGGGAAGATCTATGATGCTTTAGATAATCGCACCCTGGCTACCTACAGTTACAAAGAGGCTCTGAAACTGGATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(1), mmu-miR-30e-5p(1), mmu-miR-322-5p(1), mmu-miR-709(1), mmu-miR-182-5p(1), mmu-miR-544-5p(1), mmu-miR-542-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTCAGAATGGAGAATAAAGAGCTCGA
siRNA sets
CTCTTTATTCTCCATTCTG, TCGAGCTCTTTATTCTCCA, TCTTTATTCTCCATTCTGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDC16_869_ORF_1
1.0168
0.186146365
0.934046582
732
ORF sequence:
ATGCTGACAGCACAGGAAGAAAAAGAACTTCTGGACTCCCTGCCTCTTAACAAGCTCTGTGCTGAAGAACAAGAGTTGCTGCGATTTGTATTTGAGAACAAATTAAAGAAGTATAATAAGCCCAGTGAAACGGTCATTCCCGAGTCAGTGGACGGCTTGCAGGAGAATCTGGACGTGGTAGTGTCTTTAGCTGAGAGACACTATTACAACTGTGATTTTAAGATGTGCTACAAGCTTACTTCTACAGTGATGGAGAAAGATCCTTTCCATGCAAACTGTTTACCTGTGCACATAGGAACTCTTGTGGAGCTGAATAAAGCGAATGAACTTTTCTATCTTTCTCACAAACTGGTGGATTTATATCCGAGTAATCCTGTGTCTTGGTTTGCGGTGGGATGTTACTATCTCATGGTTGGTCATAAAAATGAGCATGCCAGAAGATATCTCAGCAAAGCTACCACGTTGGAGAAGACCTACGGTCCTGCCTGGATAGCCTACGGGCATTCCTTCGCTGTGGAGAGTGAGCACGACCAAGCAATGGCTGCTTACTTCACAGCAGCACAGCTGATGAAGGGGTGTCACTTGCCAATGCTATATATTGGATTAGAATATGGTCTGACCAATAACTCGAAACTGGCTGAGCGGTTCTTTGGCCAAGCTCTGAGCATCGCCCCAGAAGACCCATTTGTCATCCATGAGGTTGGAGTGGTTGCCTTTCAGAATGGAGAATAA
Peptide sequence:
MLTAQEEKELLDSLPLNKLCAEEQELLRFVFENKLKKYNKPSETVIPESVDGLQENLDVVVSLAERHYYNCDFKMCYKLTSTVMEKDPFHANCLPVHIGTLVELNKANELFYLSHKLVDLYPSNPVSWFAVGCYYLMVGHKNEHARRYLSKATTLEKTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMKGCHLPMLYIGLEYGLTNNSKLAERFFGQALSIAPEDPFVIHEVGVVAFQNGE
IRESfinder result
IRESfinder score
0.602372662
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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