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mmu_circAtm_1562
Basic information of circular RNA
PanCircBase ID:
mmu_circAtm_1562
mm39_Chr. Position ID:
chr9|53390880|53402340|-
Gene name:
Atm
Transcript:
ENSMUST00000118282.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
36,35,34,33,32,31,30,29,28,27
Exon/intron offsets:
0,993,2721,4492,6428,7233,8325,8969,10530,11333
Genomic length:
11460
Exon/intron sizes in nt:
17,81,77,14,21,72,96,10,00,00,00,00,00,000
Flanking exon/introns:
chr9:53385003-53390880|chr9:53402340-53403540
Splice length:
1562
Other database IDs:
circAtlas: mmu-Atm_0015
Human Ortholog IDs:
Mature spliced Sequence:
GGATTTGGATCCTGCCCCCAACCCGCCATATTTCCCCTCACATGTCATTCAGGCAACGTTTGCTTACATCAGCAACTGTCATAAAACCAAGTTTAAAAGCATTCTAGAAATTCTTTCTAAAATCCCCGATTCCTATCAGAAAATACTTCTGGCCATTTGTGAACAAGCAGCTGAGACAAATAATGTCTTTAAAAAGCACAGAATTCTTAAAATATATCACCTGTTTGTTAGTTTATTACTGAAAGATATACAGAGTGGCCTGGGAGGGGCTTGGGCCTTTGTCCTTCGCGATGTTATTTATACTCTGATTCACTACATCAACAAAAGGTCTTCTCATTTCACAGATGTGTCGTTGCGTAGCTTTTCCCTTTGCTGTGACCTATTAAGTCGAGTTTGTCATACAGCTGTAACTCAATGTAAGGATGCTCTAGAAAGCCATCTTCACGTTATCGTTGGCACACTTATTCCCCTTGTGGATTATCAGGAAGTTCAAGAACAGGTATTGGACCTGTTGAAGTACTTAGTGATAGATAACAAAGACAATAAAAACCTCTCTGTCACAATTAAGCTTTTGGATCCCTTTCCTGACCATGTTATTTTTAAGGACTTGCGTCTTACTCAACAGAAAATCAAATATAGTGGAGGACCTTTTTCACTCTTAGAGGAAATAAACCATTTTCTCTCAGTAAGTGCTTACAATCCACTTCCGCTGACCAGGCTTGAAGGACTGAAGGATCTTCGAAGACAACTGGAGCAACATAAAGATCAGATGCTAGATCTTCTGAGAGCGTCTCAAGATAACCCACAAGATGGCATTGTGGTGAAGCTAGTTGTCAGCTTGTTGCAGTTATCCAAGATGGCAGTGAACCAGACTGGTGAAAGAGAAGTTTTAGAGGCTGTCGGAAGGTGTTTGGGAGAAATAGGTCCTCTGGATTTCTCCACCATAGCTGTCCAGCATAACAAAGATGTGTCCTATACCAAAGCCTACGGGTTACCTGAAGACAGAGAACTTCAGTGGACCTTGATAATGCTGACTGCCCTCAACAATACCCTGGTAGAGGACAGTGTCAAAATTCGATCTGCTGCTGCTACCTGTTTGAAAAACATTTTGGCTACAAAGATTGGACATATTTTCTGGGAGAATTATAAGACATCAGCGGATCCAATGCTGACCTATCTACAACCTTTTAGAACATCGAGGAAAAAGTTTTTAGAAGTGCCCCGATCTGTTAAAGAAGATGTTTTAGAAGGCCTGGATGCTGTGAATCTGTGGGTTCCTCAAAGTGAAAGTCATGACATTTGGATAAAGACACTGACGTGTGCCTTTCTGGACAGTGGAGGCATAAACAGTGAAATTCTCCAGTTATTAAAGCCAATGTGTGAAGTGAAAACCGACTTCTGTCAGATGTTGCTGCCATACTTGATCCATGATGTTTTACTGCAAGATACACATGAATCGTGGAGAACTCTGCTGTCTGCGCACGTCCGAGGATTTTTCACTAGTTGTTTTAAGCATTCCTCCCAAGCAAGCCGCTCAGCAACTCCTGCAAATTCGGATTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGAACTCTGCTGTCTGCGC
60.37
TGTGAGGGGAAATATGGCGG
59.82
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGCACGTCCGAGGATTTTTC
59.91
ACGTTGCCTGAATGACATGTG
59.46
143
PCR template sequence:
AGAACTCTGCTGTCTGCGCACGTCCGAGGATTTTTCACTAGTTGTTTTAAGCATTCCTCCCAAGCAAGCCGCTCAGCAACTCCTGCAAATTCGGATTCAGGGATTTGGATCCTGCCCCCAACCCGCCATATTTCCCCTCACATGTCATTCAGGCAACGTTTGCTTACATCAGCAACTGTCATAAAACCAAGTTTAAAAGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-124-3p(1), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-150-5p(1), mmu-miR-135a-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-203-3p(1), mmu-miR-495-3p(1), mmu-miR-434-5p(1), mmu-miR-673-5p(1), mmu-miR-3470b(1), mmu-miR-350-3p(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AATTCGGATTCAGGGATTTGGATCCT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATM_1562_ORF_1
0.7208
0.027673571
0.932901571
900
ORF sequence:
ATGCTAGATCTTCTGAGAGCGTCTCAAGATAACCCACAAGATGGCATTGTGGTGAAGCTAGTTGTCAGCTTGTTGCAGTTATCCAAGATGGCAGTGAACCAGACTGGTGAAAGAGAAGTTTTAGAGGCTGTCGGAAGGTGTTTGGGAGAAATAGGTCCTCTGGATTTCTCCACCATAGCTGTCCAGCATAACAAAGATGTGTCCTATACCAAAGCCTACGGGTTACCTGAAGACAGAGAACTTCAGTGGACCTTGATAATGCTGACTGCCCTCAACAATACCCTGGTAGAGGACAGTGTCAAAATTCGATCTGCTGCTGCTACCTGTTTGAAAAACATTTTGGCTACAAAGATTGGACATATTTTCTGGGAGAATTATAAGACATCAGCGGATCCAATGCTGACCTATCTACAACCTTTTAGAACATCGAGGAAAAAGTTTTTAGAAGTGCCCCGATCTGTTAAAGAAGATGTTTTAGAAGGCCTGGATGCTGTGAATCTGTGGGTTCCTCAAAGTGAAAGTCATGACATTTGGATAAAGACACTGACGTGTGCCTTTCTGGACAGTGGAGGCATAAACAGTGAAATTCTCCAGTTATTAAAGCCAATGTGTGAAGTGAAAACCGACTTCTGTCAGATGTTGCTGCCATACTTGATCCATGATGTTTTACTGCAAGATACACATGAATCGTGGAGAACTCTGCTGTCTGCGCACGTCCGAGGATTTTTCACTAGTTGTTTTAAGCATTCCTCCCAAGCAAGCCGCTCAGCAACTCCTGCAAATTCGGATTCAGGGATTTGGATCCTGCCCCCAACCCGCCATATTTCCCCTCACATGTCATTCAGGCAACGTTTGCTTACATCAGCAACTGTCATAAAACCAAGTTTAAAAGCATTCTAG
Peptide sequence:
MLDLLRASQDNPQDGIVVKLVVSLLQLSKMAVNQTGEREVLEAVGRCLGEIGPLDFSTIAVQHNKDVSYTKAYGLPEDRELQWTLIMLTALNNTLVEDSVKIRSAAATCLKNILATKIGHIFWENYKTSADPMLTYLQPFRTSRKKFLEVPRSVKEDVLEGLDAVNLWVPQSESHDIWIKTLTCAFLDSGGINSEILQLLKPMCEVKTDFCQMLLPYLIHDVLLQDTHESWRTLLSAHVRGFFTSCFKHSSQASRSATPANSDSGIWILPPTRHISPHMSFRQRLLTSATVIKPSLKAF
IRESfinder result
IRESfinder score
0.741672934
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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