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mmu_circAtm_741_2
Basic information of circular RNA
PanCircBase ID:
mmu_circAtm_741_2
mm39_Chr. Position ID:
chr9|53407151|53412302|-
Gene name:
Atm
Transcript:
ENSMUST00000118282.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
23,22,21,20,19,18
Exon/intron offsets:
0,1281,3005,3270,4820,5068
Genomic length:
5151
Exon/intron sizes in nt:
174,121,131,76,156,83
Flanking exon/introns:
chr9:53406081-53407151|chr9:53412302-53414244
Splice length:
741
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TACTTAGTGCTCCTGAAGGATCTCCCTGGAAACGAGCACTCATTGCCAATGGAAGATGTTGTTGAACTTCTGCAACCATTATCCCTTGTGTGTTCTCTGCACCGACGTGACCAAGATGTCTGTAAAACGATTCTAAGCAATGTCCTTCATATAGTGACAAACCTAGGCCAGGGCAGTGTGGACATGGAGAGCACACGGATTGCTCAAGGACACTTCCTGACAGTGATGGGAGCATTTTGGCATTTGACAAAGGAAAAGAAATGTGTATTCTCTGTAAGAATGGCATTAGTAAAGTGTCTTCAAACATTGCTTGAGGCTGATCCATATTCCGAATGGGCAATTCTTAATGTAAAAGGACAAGACTTTCCTGTAAATGAAGCTTTTTCACAATTTCTTGCTGACGATCATCATCAAGTTCGGATGTTGGCTGCAGGGTCAGTCAACAGATTATTTCAGGATATGAGACAAGGCGATTTCTCCAGAAGCTTGAAAGCACTCCCTCTGAAGTTTCAGCAGACATCTTTTAACAATGCATACACGACAGCAGAGGCGGGGATCAGAGGACTGTTATGTGATTCTCAGAACCCTGATCTGCTGGATGAGATCTATAACAGAAAATCTGTACTACTGATGATGATAGCTGTGGTCTTGCACTGTAGCCCAGTCTGTGAAAAGCAGGCTTTGTTTGCTTTATGCAAGTCTGTGAAGGAAAACAGACTAGAACCTCATCTTGTGAAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGGTCTTGCACTGTAGCC
60.25
ATGAGTGCTCGTTTCCAGGG
60.04
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGGTCTTGCACTGTAGCC
60.25
GAGTGCTCGTTTCCAGGGAG
60.39
141
PCR template sequence:
TGTGGTCTTGCACTGTAGCCCAGTCTGTGAAAAGCAGGCTTTGTTTGCTTTATGCAAGTCTGTGAAGGAAAACAGACTAGAACCTCATCTTGTGAAAAAGTACTTAGTGCTCCTGAAGGATCTCCCTGGAAACGAGCACTCATTGCCAATGGAAGATGTTGTTGAACTTCTGCAACCATTATCCCTTGTGTGTTCTCTGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-155-5p(1), mmu-miR-152-3p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-10b-5p(1), mmu-miR-139-5p(1), mmu-miR-10a-5p(1), mmu-miR-127-5p(1), mmu-miR-212-3p(1), mmu-miR-199b-3p(1), mmu-miR-182-5p(1), mmu-miR-130b-3p(1), mmu-miR-199a-3p(1), mmu-miR-301a-3p(1), mmu-miR-539-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCTTGTGAAAAAGTACTTAGTGCTCC
siRNA sets
TAAGTACTTTTTCACAAGA, CTAAGTACTTTTTCACAAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATM_741_2_ORF_1
0.9449
0.001724736
0.998925365
1434
ORF sequence:
ATGGAAGATGTTGTTGAACTTCTGCAACCATTATCCCTTGTGTGTTCTCTGCACCGACGTGACCAAGATGTCTGTAAAACGATTCTAAGCAATGTCCTTCATATAGTGACAAACCTAGGCCAGGGCAGTGTGGACATGGAGAGCACACGGATTGCTCAAGGACACTTCCTGACAGTGATGGGAGCATTTTGGCATTTGACAAAGGAAAAGAAATGTGTATTCTCTGTAAGAATGGCATTAGTAAAGTGTCTTCAAACATTGCTTGAGGCTGATCCATATTCCGAATGGGCAATTCTTAATGTAAAAGGACAAGACTTTCCTGTAAATGAAGCTTTTTCACAATTTCTTGCTGACGATCATCATCAAGTTCGGATGTTGGCTGCAGGGTCAGTCAACAGATTATTTCAGGATATGAGACAAGGCGATTTCTCCAGAAGCTTGAAAGCACTCCCTCTGAAGTTTCAGCAGACATCTTTTAACAATGCATACACGACAGCAGAGGCGGGGATCAGAGGACTGTTATGTGATTCTCAGAACCCTGATCTGCTGGATGAGATCTATAACAGAAAATCTGTACTACTGATGATGATAGCTGTGGTCTTGCACTGTAGCCCAGTCTGTGAAAAGCAGGCTTTGTTTGCTTTATGCAAGTCTGTGAAGGAAAACAGACTAGAACCTCATCTTGTGAAAAAGTACTTAGTGCTCCTGAAGGATCTCCCTGGAAACGAGCACTCATTGCCAATGGAAGATGTTGTTGAACTTCTGCAACCATTATCCCTTGTGTGTTCTCTGCACCGACGTGACCAAGATGTCTGTAAAACGATTCTAAGCAATGTCCTTCATATAGTGACAAACCTAGGCCAGGGCAGTGTGGACATGGAGAGCACACGGATTGCTCAAGGACACTTCCTGACAGTGATGGGAGCATTTTGGCATTTGACAAAGGAAAAGAAATGTGTATTCTCTGTAAGAATGGCATTAGTAAAGTGTCTTCAAACATTGCTTGAGGCTGATCCATATTCCGAATGGGCAATTCTTAATGTAAAAGGACAAGACTTTCCTGTAAATGAAGCTTTTTCACAATTTCTTGCTGACGATCATCATCAAGTTCGGATGTTGGCTGCAGGGTCAGTCAACAGATTATTTCAGGATATGAGACAAGGCGATTTCTCCAGAAGCTTGAAAGCACTCCCTCTGAAGTTTCAGCAGACATCTTTTAACAATGCATACACGACAGCAGAGGCGGGGATCAGAGGACTGTTATGTGATTCTCAGAACCCTGATCTGCTGGATGAGATCTATAACAGAAAATCTGTACTACTGATGATGATAGCTGTGGTCTTGCACTGTAGCCCAGTCTGTGAAAAGCAGGCTTTGTTTGCTTTATGCAAGTCTGTGAAGGAAAACAGACTAGAACCTCATCTTGTGAAAAAG
Peptide sequence:
MEDVVELLQPLSLVCSLHRRDQDVCKTILSNVLHIVTNLGQGSVDMESTRIAQGHFLTVMGAFWHLTKEKKCVFSVRMALVKCLQTLLEADPYSEWAILNVKGQDFPVNEAFSQFLADDHHQVRMLAAGSVNRLFQDMRQGDFSRSLKALPLKFQQTSFNNAYTTAEAGIRGLLCDSQNPDLLDEIYNRKSVLLMMIAVVLHCSPVCEKQALFALCKSVKENRLEPHLVKKYLVLLKDLPGNEHSLPMEDVVELLQPLSLVCSLHRRDQDVCKTILSNVLHIVTNLGQGSVDMESTRIAQGHFLTVMGAFWHLTKEKKCVFSVRMALVKCLQTLLEADPYSEWAILNVKGQDFPVNEAFSQFLADDHHQVRMLAAGSVNRLFQDMRQGDFSRSLKALPLKFQQTSFNNAYTTAEAGIRGLLCDSQNPDLLDEIYNRKSVLLMMIAVVLHCSPVCEKQALFALCKSVKENRLEPHLVKK
IRESfinder result
IRESfinder score
0.66436913
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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