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mmu_circAtat1_431
Basic information of circular RNA
PanCircBase ID:
mmu_circAtat1_431
mm39_Chr. Position ID:
chr17|36212259|36215227|-
Gene name:
Atat1
Transcript:
ENSMUST00000061052.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
10,9,8,7
Exon/intron offsets:
0,615,2740,2922
Genomic length:
2968
Exon/intron sizes in nt:
244,72,69,46
Flanking exon/introns:
chr17:36209359-36212259|chr17:36215227-36219454
Splice length:
431
Other database IDs:
circBase: mmu_circ_0006743, CIRCpedia: MMU_CIRCpedia_17940, circAtlas: mmu-Atat1_0002
Human Ortholog IDs:
Mature spliced Sequence:
GTGAACAACTTTGTCATCTTTGAAGGCTTCTTTGCCCATCAGCACCGGCCCCCCACTTCCTCTCTGAGAGCAACTCGACACTCTCGTGCTGCTGTGGCCGATCCCATACCTGCTGCTCCAGCACGGAAGCTGCCACCAAAAAGAGCAGAGGGAGACATTAAGCCATACTCTTCCAGTGACAGAGAATTCCTGAAGGTAGCTGTGGAGCCTCCTTGGCCCCTGAACAGGGCCCCTCGGCGTGCCACACCTCCAGCCCACCCACCTCCACGTTCTAGCAGCCTGGGCAACTCACCGGATCGGGGTCCCCTTCGGCCCTTTGTTCCAGAGCAGGAGCTGCTTCGCTCCCTGCGTCTCTGTCCCCCACACCCTACTGCACGCCTTCTGCTGGCCACTGACCCTGGAGGCAGCCCAGCCCAGCGCAGACGCACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTCTGTCCCCCACACCCTA
59.92
TCTCAGAGAGGAAGTGGGGG
59.96
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGTCCCCCACACCCTAC
60.23
TCTCAGAGAGGAAGTGGGGG
59.96
148
PCR template sequence:
AGCTGCTTCGCTCCCTGCGTCTCTGTCCCCCACACCCTACTGCACGCCTTCTGCTGGCCACTGACCCTGGAGGCAGCCCAGCCCAGCGCAGACGCACCAGGTGAACAACTTTGTCATCTTTGAAGGCTTCTTTGCCCATCAGCACCGGCCCCCCACTTCCTCTCTGAGAGCAACTCGACACTCTCGTGCTGCTGTGGCCG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(2), mmu-miR-15a-5p(2), mmu-miR-135a-5p(1), mmu-miR-15b-5p(1), mmu-miR-382-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCAGACGCACCAGGTGAACAACTTTG
siRNA sets
AAGTTGTTCACCTGGTGCG, AAAGTTGTTCACCTGGTGC, GTTGTTCACCTGGTGCGTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.617086008
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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