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mmu_circAtm_1080
Basic information of circular RNA
PanCircBase ID:
mmu_circAtm_1080
mm39_Chr. Position ID:
chr9|53393601|53401610|-
Gene name:
Atm
Transcript:
ENSMUST00000118282.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
34,33,32,31,30,29,28
Exon/intron offsets:
0,1771,3707,4512,5604,6248,7809
Genomic length:
8009
Exon/intron sizes in nt:
1,42,17,29,61,33,16,51,00,000
Flanking exon/introns:
chr9:53392050-53393601|chr9:53401610-53402213
Splice length:
1080
Other database IDs:
circAtlas: mmu-Atm_0061
Human Ortholog IDs:
Mature spliced Sequence:
GATTCCTATCAGAAAATACTTCTGGCCATTTGTGAACAAGCAGCTGAGACAAATAATGTCTTTAAAAAGCACAGAATTCTTAAAATATATCACCTGTTTGTTAGTTTATTACTGAAAGATATACAGAGTGGCCTGGGAGGGGCTTGGGCCTTTGTCCTTCGCGATGTTATTTATACTCTGATTCACTACATCAACAAAAGGTCTTCTCATTTCACAGATGTGTCGTTGCGTAGCTTTTCCCTTTGCTGTGACCTATTAAGTCGAGTTTGTCATACAGCTGTAACTCAATGTAAGGATGCTCTAGAAAGCCATCTTCACGTTATCGTTGGCACACTTATTCCCCTTGTGGATTATCAGGAAGTTCAAGAACAGGTATTGGACCTGTTGAAGTACTTAGTGATAGATAACAAAGACAATAAAAACCTCTCTGTCACAATTAAGCTTTTGGATCCCTTTCCTGACCATGTTATTTTTAAGGACTTGCGTCTTACTCAACAGAAAATCAAATATAGTGGAGGACCTTTTTCACTCTTAGAGGAAATAAACCATTTTCTCTCAGTAAGTGCTTACAATCCACTTCCGCTGACCAGGCTTGAAGGACTGAAGGATCTTCGAAGACAACTGGAGCAACATAAAGATCAGATGCTAGATCTTCTGAGAGCGTCTCAAGATAACCCACAAGATGGCATTGTGGTGAAGCTAGTTGTCAGCTTGTTGCAGTTATCCAAGATGGCAGTGAACCAGACTGGTGAAAGAGAAGTTTTAGAGGCTGTCGGAAGGTGTTTGGGAGAAATAGGTCCTCTGGATTTCTCCACCATAGCTGTCCAGCATAACAAAGATGTGTCCTATACCAAAGCCTACGGGTTACCTGAAGACAGAGAACTTCAGTGGACCTTGATAATGCTGACTGCCCTCAACAATACCCTGGTAGAGGACAGTGTCAAAATTCGATCTGCTGCTGCTACCTGTTTGAAAAACATTTTGGCTACAAAGATTGGACATATTTTCTGGGAGAATTATAAGACATCAGCGGATCCAATGCTGACCTATCTACAACCTTTTAGAACATCGAGGAAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTTGGCTACAAAGATTGGACA
55.69
TGCTTGTTCACAAATGGCCAG
59.93
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTTGGCTACAAAGATTGGACA
55.69
CTGCTTGTTCACAAATGGCCA
59.93
143
PCR template sequence:
TTTGGCTACAAAGATTGGACATATTTTCTGGGAGAATTATAAGACATCAGCGGATCCAATGCTGACCTATCTACAACCTTTTAGAACATCGAGGAAAAAGGATTCCTATCAGAAAATACTTCTGGCCATTTGTGAACAAGCAGCTGAGACAAATAATGTCTTTAAAAAGCACAGAATTCTTAAAATATATCACCTGTTTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
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-3470b(1), mmu-miR-350-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATCGAGGAAAAAGGATTCCTATCAGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATM_1080_ORF_1
0.9404
0.046915226
0.999500509
1518
ORF sequence:
ATGCTAGATCTTCTGAGAGCGTCTCAAGATAACCCACAAGATGGCATTGTGGTGAAGCTAGTTGTCAGCTTGTTGCAGTTATCCAAGATGGCAGTGAACCAGACTGGTGAAAGAGAAGTTTTAGAGGCTGTCGGAAGGTGTTTGGGAGAAATAGGTCCTCTGGATTTCTCCACCATAGCTGTCCAGCATAACAAAGATGTGTCCTATACCAAAGCCTACGGGTTACCTGAAGACAGAGAACTTCAGTGGACCTTGATAATGCTGACTGCCCTCAACAATACCCTGGTAGAGGACAGTGTCAAAATTCGATCTGCTGCTGCTACCTGTTTGAAAAACATTTTGGCTACAAAGATTGGACATATTTTCTGGGAGAATTATAAGACATCAGCGGATCCAATGCTGACCTATCTACAACCTTTTAGAACATCGAGGAAAAAGGATTCCTATCAGAAAATACTTCTGGCCATTTGTGAACAAGCAGCTGAGACAAATAATGTCTTTAAAAAGCACAGAATTCTTAAAATATATCACCTGTTTGTTAGTTTATTACTGAAAGATATACAGAGTGGCCTGGGAGGGGCTTGGGCCTTTGTCCTTCGCGATGTTATTTATACTCTGATTCACTACATCAACAAAAGGTCTTCTCATTTCACAGATGTGTCGTTGCGTAGCTTTTCCCTTTGCTGTGACCTATTAAGTCGAGTTTGTCATACAGCTGTAACTCAATGTAAGGATGCTCTAGAAAGCCATCTTCACGTTATCGTTGGCACACTTATTCCCCTTGTGGATTATCAGGAAGTTCAAGAACAGGTATTGGACCTGTTGAAGTACTTAGTGATAGATAACAAAGACAATAAAAACCTCTCTGTCACAATTAAGCTTTTGGATCCCTTTCCTGACCATGTTATTTTTAAGGACTTGCGTCTTACTCAACAGAAAATCAAATATAGTGGAGGACCTTTTTCACTCTTAGAGGAAATAAACCATTTTCTCTCAGTAAGTGCTTACAATCCACTTCCGCTGACCAGGCTTGAAGGACTGAAGGATCTTCGAAGACAACTGGAGCAACATAAAGATCAGATGCTAGATCTTCTGAGAGCGTCTCAAGATAACCCACAAGATGGCATTGTGGTGAAGCTAGTTGTCAGCTTGTTGCAGTTATCCAAGATGGCAGTGAACCAGACTGGTGAAAGAGAAGTTTTAGAGGCTGTCGGAAGGTGTTTGGGAGAAATAGGTCCTCTGGATTTCTCCACCATAGCTGTCCAGCATAACAAAGATGTGTCCTATACCAAAGCCTACGGGTTACCTGAAGACAGAGAACTTCAGTGGACCTTGATAATGCTGACTGCCCTCAACAATACCCTGGTAGAGGACAGTGTCAAAATTCGATCTGCTGCTGCTACCTGTTTGAAAAACATTTTGGCTACAAAGATTGGACATATTTTCTGGGAGAATTATAAGACATCAGCGGATCCAATGCTGACCTATCTACAACCTTTTAGAACATCGAGGAAAAAG
Peptide sequence:
MLDLLRASQDNPQDGIVVKLVVSLLQLSKMAVNQTGEREVLEAVGRCLGEIGPLDFSTIAVQHNKDVSYTKAYGLPEDRELQWTLIMLTALNNTLVEDSVKIRSAAATCLKNILATKIGHIFWENYKTSADPMLTYLQPFRTSRKKDSYQKILLAICEQAAETNNVFKKHRILKIYHLFVSLLLKDIQSGLGGAWAFVLRDVIYTLIHYINKRSSHFTDVSLRSFSLCCDLLSRVCHTAVTQCKDALESHLHVIVGTLIPLVDYQEVQEQVLDLLKYLVIDNKDNKNLSVTIKLLDPFPDHVIFKDLRLTQQKIKYSGGPFSLLEEINHFLSVSAYNPLPLTRLEGLKDLRRQLEQHKDQMLDLLRASQDNPQDGIVVKLVVSLLQLSKMAVNQTGEREVLEAVGRCLGEIGPLDFSTIAVQHNKDVSYTKAYGLPEDRELQWTLIMLTALNNTLVEDSVKIRSAAATCLKNILATKIGHIFWENYKTSADPMLTYLQPFRTSRKK
IRESfinder result
IRESfinder score
0.752490082
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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