top of page
mmu_circAtg3_680
Basic information of circular RNA
PanCircBase ID:
mmu_circAtg3_680
mm39_Chr. Position ID:
chr16|44987342|45004172|+
Gene name:
Atg3
Transcript:
ENSMUST00000023343.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
3,4,5,6,7,8,9,10
Exon/intron offsets:
0,2886,4666,8269,11250,15676,15841,16702
Genomic length:
16830
Exon/intron sizes in nt:
50,71,108,50,82,35,156,128
Flanking exon/introns:
chr16:44982810-44987342|chr16:45004172-45006528
Splice length:
680
Other database IDs:
circAtlas: mmu-Atg3_0002
circAtlas: hsa-ATG3_0003
Human Ortholog IDs:
Mature spliced Sequence:
TTTGTGGCAGCTGGAGATCACTTAGTCCACCACTGTCCAACATGGCAATGGGCTACAGGGGAAGAATTGAAAGTGAAGGCATATCTTCCGACAGACAAACAATTTTTGGTAACCAAAAATGTTCCATGCTACAAGCGGTGTAAACAGATGGAGTATTCGGATGAATTGGAAGCTATCATTGAAGAAGATGATGGTGATGGGGGATGGGTAGATACATATCACAACACAGGTATTACAGGAATTACTGAAGCAGTTAAGGAGATTACACTGGAAAGCAAGGACAGTATAAAACTCCAAGATTGCTCAGCACTGTGTGATGAAGAAGACGAGGAAGATGAAGGGGAAGCTGCAGACATGGAAGAATATGAAGAGAGTGGATTGTTGGAAACAGATGAGGCTACCCTAGACACAAGGAAAATAGTGGAAGCCTGCAAAGCTAAGGCTGACGCTGGAGGTGAAGATGCTATTTTACAAACAAGAACATACGACCTGTACATCACTTACGACAAATATTACCAGACACCACGGCTATGGTTGTTTGGCTATGATGAGCAACGGCAGCCTTTAACAGTTGAGCACATGTATGAAGACATCAGTCAAGATCATGTGAAGAAAACAGTGACCATTGAAAACCATCCTCATCTCCCACCACCTCCTATGTGTTCAGTTCACCCATGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCATCCTCATCTCCCACCA
59.96
TGTCTGTCGGAAGATATGCCT
58.61
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTCATCTCCCACCACCTC
60.33
TGTCTGTCGGAAGATATGCCT
58.61
142
PCR template sequence:
TGTATGAAGACATCAGTCAAGATCATGTGAAGAAAACAGTGACCATTGAAAACCATCCTCATCTCCCACCACCTCCTATGTGTTCAGTTCACCCATGCAGTTTGTGGCAGCTGGAGATCACTTAGTCCACCACTGTCCAACATGGCAATGGGCTACAGGGGAAGAATTGAAAGTGAAGGCATATCTTCCGACAGACAAAC
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-705(1), mmu-miR-5101(1), mmu-miR-669d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTCACCCATGCAGTTTGTGGCAGCTG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATG3_680_ORF_1
1.0659
0.189922651
0.918323086
684
ORF sequence:
ATGCAGTTTGTGGCAGCTGGAGATCACTTAGTCCACCACTGTCCAACATGGCAATGGGCTACAGGGGAAGAATTGAAAGTGAAGGCATATCTTCCGACAGACAAACAATTTTTGGTAACCAAAAATGTTCCATGCTACAAGCGGTGTAAACAGATGGAGTATTCGGATGAATTGGAAGCTATCATTGAAGAAGATGATGGTGATGGGGGATGGGTAGATACATATCACAACACAGGTATTACAGGAATTACTGAAGCAGTTAAGGAGATTACACTGGAAAGCAAGGACAGTATAAAACTCCAAGATTGCTCAGCACTGTGTGATGAAGAAGACGAGGAAGATGAAGGGGAAGCTGCAGACATGGAAGAATATGAAGAGAGTGGATTGTTGGAAACAGATGAGGCTACCCTAGACACAAGGAAAATAGTGGAAGCCTGCAAAGCTAAGGCTGACGCTGGAGGTGAAGATGCTATTTTACAAACAAGAACATACGACCTGTACATCACTTACGACAAATATTACCAGACACCACGGCTATGGTTGTTTGGCTATGATGAGCAACGGCAGCCTTTAACAGTTGAGCACATGTATGAAGACATCAGTCAAGATCATGTGAAGAAAACAGTGACCATTGAAAACCATCCTCATCTCCCACCACCTCCTATGTGTTCAGTTCACCCATGC
Peptide sequence:
MQFVAAGDHLVHHCPTWQWATGEELKVKAYLPTDKQFLVTKNVPCYKRCKQMEYSDELEAIIEEDDGDGGWVDTYHNTGITGITEAVKEITLESKDSIKLQDCSALCDEEDEEDEGEAADMEEYEESGLLETDEATLDTRKIVEACKAKADAGGEDAILQTRTYDLYITYDKYYQTPRLWLFGYDEQRQPLTVEHMYEDISQDHVKKTVTIENHPHLPPPPMCSVHPC
IRESfinder result
IRESfinder score
0.416321485
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page