top of page
mmu_circAtp13a3_600
Basic information of circular RNA
PanCircBase ID:
mmu_circAtp13a3_600
mm39_Chr. Position ID:
chr16|30141689|30155080|-
Gene name:
Atp13a3
Transcript:
ENSMUST00000061350.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
32,31,30,29,28
Exon/intron offsets:
0,6084,9327,10887,13318
Genomic length:
13391
Exon/intron sizes in nt:
81,89,188,169,73
Flanking exon/introns:
chr16:30134719-30141689|chr16:30155080-30156319
Splice length:
600
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATCTTGAGTAACCTGGGAGACTTTCAGTTTCTCTTCATTGATCTGGCAATCATTTTGGTAGTAGTATTTACAATGAGTTTAAATCCTGCCTGGAAAGAGCTTGTGGCACAGAGACCACCTTCAGGCCTTATATCTGGGGCGCTCCTCTTCTCCGTCTTGTCTCAGATTGTGATCTCCGTTGGATTTCAGTCGCTGGGTTTTTTCTGGGTCAAGCAGTATAAAGTGTGCGATCCAAATTCAGATGTTTGTAATACAACAAGAAGCGCATGTTGGAACTCGTCACACTTATACAATGGGACTGAACTCGATTCGTGTAAAATACAAAATTATGAAAATACCACAGTATTTTTTATCTCCAGTTTCCAGTACCTCACAGTGGCGGTTGCCTTTTCAAAAGGAAAACCATTCAGGCAGCCTTGCTACAAGAATTATTTTTTTGTTATATCTGTGATTATTTTGTATGTTTTCATATTATTCATCATGTTGCATCCAGTTGCCTCTGTTGACCAGGTTCTTGAGATTATGTGTGTACCATACCAGTGGCGCATATATATGCTTATCATTGTTCTTATCAATGCCTTCGTGTCTATCACGGTGGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTACCATACCAGTGGCGCAT
60.18
TCCAGGCAGGATTTAAACTCA
56.91
166
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGTACCATACCAGTGGCG
59.75
TCCAGGCAGGATTTAAACTCA
56.91
169
PCR template sequence:
TGTTGACCAGGTTCTTGAGATTATGTGTGTACCATACCAGTGGCGCATATATATGCTTATCATTGTTCTTATCAATGCCTTCGTGTCTATCACGGTGGAGATCTTGAGTAACCTGGGAGACTTTCAGTTTCTCTTCATTGATCTGGCAATCATTTTGGTAGTAGTATTTACAATGAGTTTAAATCCTGCCTGGAAAGAGC
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-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-216a-5p(1), mmu-miR-483-5p(1), mmu-miR-410-3p(1), mmu-miR-335-3p(1), mmu-miR-339-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TATCACGGTGGAGATCTTGAGTAACC
siRNA sets
TTACTCAAGATCTCCACCG, TACTCAAGATCTCCACCGT, GTTACTCAAGATCTCCACC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATP13A3_600_ORF_1
0.8062
-0.081964345
0.982587169
1128
ORF sequence:
ATGAGTTTAAATCCTGCCTGGAAAGAGCTTGTGGCACAGAGACCACCTTCAGGCCTTATATCTGGGGCGCTCCTCTTCTCCGTCTTGTCTCAGATTGTGATCTCCGTTGGATTTCAGTCGCTGGGTTTTTTCTGGGTCAAGCAGTATAAAGTGTGCGATCCAAATTCAGATGTTTGTAATACAACAAGAAGCGCATGTTGGAACTCGTCACACTTATACAATGGGACTGAACTCGATTCGTGTAAAATACAAAATTATGAAAATACCACAGTATTTTTTATCTCCAGTTTCCAGTACCTCACAGTGGCGGTTGCCTTTTCAAAAGGAAAACCATTCAGGCAGCCTTGCTACAAGAATTATTTTTTTGTTATATCTGTGATTATTTTGTATGTTTTCATATTATTCATCATGTTGCATCCAGTTGCCTCTGTTGACCAGGTTCTTGAGATTATGTGTGTACCATACCAGTGGCGCATATATATGCTTATCATTGTTCTTATCAATGCCTTCGTGTCTATCACGGTGGAGATCTTGAGTAACCTGGGAGACTTTCAGTTTCTCTTCATTGATCTGGCAATCATTTTGGTAGTAGTATTTACAATGAGTTTAAATCCTGCCTGGAAAGAGCTTGTGGCACAGAGACCACCTTCAGGCCTTATATCTGGGGCGCTCCTCTTCTCCGTCTTGTCTCAGATTGTGATCTCCGTTGGATTTCAGTCGCTGGGTTTTTTCTGGGTCAAGCAGTATAAAGTGTGCGATCCAAATTCAGATGTTTGTAATACAACAAGAAGCGCATGTTGGAACTCGTCACACTTATACAATGGGACTGAACTCGATTCGTGTAAAATACAAAATTATGAAAATACCACAGTATTTTTTATCTCCAGTTTCCAGTACCTCACAGTGGCGGTTGCCTTTTCAAAAGGAAAACCATTCAGGCAGCCTTGCTACAAGAATTATTTTTTTGTTATATCTGTGATTATTTTGTATGTTTTCATATTATTCATCATGTTGCATCCAGTTGCCTCTGTTGACCAGGTTCTTGAGATTATGTGTGTACCATACCAGTGGCGCATATATATGCTTATCATTGTTCTTATCAATGCCTTCGTGTCTATCACGGTGGAG
Peptide sequence:
MSLNPAWKELVAQRPPSGLISGALLFSVLSQIVISVGFQSLGFFWVKQYKVCDPNSDVCNTTRSACWNSSHLYNGTELDSCKIQNYENTTVFFISSFQYLTVAVAFSKGKPFRQPCYKNYFFVISVIILYVFILFIMLHPVASVDQVLEIMCVPYQWRIYMLIIVLINAFVSITVEILSNLGDFQFLFIDLAIILVVVFTMSLNPAWKELVAQRPPSGLISGALLFSVLSQIVISVGFQSLGFFWVKQYKVCDPNSDVCNTTRSACWNSSHLYNGTELDSCKIQNYENTTVFFISSFQYLTVAVAFSKGKPFRQPCYKNYFFVISVIILYVFILFIMLHPVASVDQVLEIMCVPYQWRIYMLIIVLINAFVSITVE
IRESfinder result
IRESfinder score
0.878218217
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page