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mmu_circAtr_489
Basic information of circular RNA
PanCircBase ID:
mmu_circAtr_489
mm39_Chr. Position ID:
chr9|95781089|95789486|+
Gene name:
Atr
Transcript:
ENSMUST00000034980.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
23,24,25,26
Exon/intron offsets:
0,4626,6701,8259
Genomic length:
8397
Exon/intron sizes in nt:
1,14,11,61,21,138
Flanking exon/introns:
chr9:95779795-95781089|chr9:95789486-95790302
Splice length:
489
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ACTGGAGTAGAAGATTTAAGCTTTGCCTATGGATTGCTAATGGAGCTAACAAGAGCTTACCTTGCATATGCTGATAACAGCCGAGCACAAGATTCAGCTGCTTATGCTATTCAGGAGTTGCTTTCTATTTATGACTGTAGAGAGATGCAGAGCAATGGCCCAGGTTACCAGTTGTGGAAAAGATTCCCTGAGCATGTCCGGGAAATATTAGAGCCTCATCTCAATACTAGATATAAGAGTTCCCAGAAATCAACAGATTGGTCTGGAGTAACGAAGCCAATTTACTTAAGTAAACTAGGTAATAACTTTGCAGAATGGTCATCATCTTGGGCAGGTTATCTTATAACAAAGGTTCGGGATAATCTTGCCAGTAAGATCTTCACATGCTGTAGCATAATGATGAAGCATGATTTTAAAGTCACCATCTATCTTCTTCCACATATCCTAGTATATGTCTTGTTGGGTTGTAATCAAGAAGATCAGCAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTCACCATCTATCTTCTTCCACA
58.97
TGAATCTTGTGCTCGGCTGT
59.96
169
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTCACCATCTATCTTCTTCCACA
57.66
TGAATCTTGTGCTCGGCTGT
59.96
168
PCR template sequence:
TAGCATAATGATGAAGCATGATTTTAAAGTCACCATCTATCTTCTTCCACATATCCTAGTATATGTCTTGTTGGGTTGTAATCAAGAAGATCAGCAAGAGACTGGAGTAGAAGATTTAAGCTTTGCCTATGGATTGCTAATGGAGCTAACAAGAGCTTACCTTGCATATGCTGATAACAGCCGAGCACAAGATTCAGCTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-143-3p(1), mmu-miR-300-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGATCAGCAAGAGACTGGAGTAGAAG
siRNA sets
TTCTACTCCAGTCTCTTGC, TCTACTCCAGTCTCTTGCT, CTTCTACTCCAGTCTCTTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATR_489_ORF_1
0.6646
-0.020408713
0.934784248
939
ORF sequence:
ATGGAGCTAACAAGAGCTTACCTTGCATATGCTGATAACAGCCGAGCACAAGATTCAGCTGCTTATGCTATTCAGGAGTTGCTTTCTATTTATGACTGTAGAGAGATGCAGAGCAATGGCCCAGGTTACCAGTTGTGGAAAAGATTCCCTGAGCATGTCCGGGAAATATTAGAGCCTCATCTCAATACTAGATATAAGAGTTCCCAGAAATCAACAGATTGGTCTGGAGTAACGAAGCCAATTTACTTAAGTAAACTAGGTAATAACTTTGCAGAATGGTCATCATCTTGGGCAGGTTATCTTATAACAAAGGTTCGGGATAATCTTGCCAGTAAGATCTTCACATGCTGTAGCATAATGATGAAGCATGATTTTAAAGTCACCATCTATCTTCTTCCACATATCCTAGTATATGTCTTGTTGGGTTGTAATCAAGAAGATCAGCAAGAGACTGGAGTAGAAGATTTAAGCTTTGCCTATGGATTGCTAATGGAGCTAACAAGAGCTTACCTTGCATATGCTGATAACAGCCGAGCACAAGATTCAGCTGCTTATGCTATTCAGGAGTTGCTTTCTATTTATGACTGTAGAGAGATGCAGAGCAATGGCCCAGGTTACCAGTTGTGGAAAAGATTCCCTGAGCATGTCCGGGAAATATTAGAGCCTCATCTCAATACTAGATATAAGAGTTCCCAGAAATCAACAGATTGGTCTGGAGTAACGAAGCCAATTTACTTAAGTAAACTAGGTAATAACTTTGCAGAATGGTCATCATCTTGGGCAGGTTATCTTATAACAAAGGTTCGGGATAATCTTGCCAGTAAGATCTTCACATGCTGTAGCATAATGATGAAGCATGATTTTAAAGTCACCATCTATCTTCTTCCACATATCCTAGTATATGTCTTGTTGGGTTGTAATCAAGAAGATCAGCAAGAG
Peptide sequence:
MELTRAYLAYADNSRAQDSAAYAIQELLSIYDCREMQSNGPGYQLWKRFPEHVREILEPHLNTRYKSSQKSTDWSGVTKPIYLSKLGNNFAEWSSSWAGYLITKVRDNLASKIFTCCSIMMKHDFKVTIYLLPHILVYVLLGCNQEDQQETGVEDLSFAYGLLMELTRAYLAYADNSRAQDSAAYAIQELLSIYDCREMQSNGPGYQLWKRFPEHVREILEPHLNTRYKSSQKSTDWSGVTKPIYLSKLGNNFAEWSSSWAGYLITKVRDNLASKIFTCCSIMMKHDFKVTIYLLPHILVYVLLGCNQEDQQE
IRESfinder result
IRESfinder score
0.621948785
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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