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mmu_circBrox_409
Basic information of circular RNA
PanCircBase ID:
mmu_circBrox_409
mm39_Chr. Position ID:
chr1|183062363|183065786|-
Gene name:
Brox
Transcript:
ENSMUST00000057062.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
12,11,10,9
Exon/intron offsets:
0,415,1686,3333
Genomic length:
3423
Exon/intron sizes in nt:
151,82,86,90
Flanking exon/introns:
chr1:183061193-183062363|chr1:183065786-183066600
Splice length:
409
Other database IDs:
CIRCpedia: MMU_CIRCpedia_12481
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_148877
Human Ortholog IDs:
Mature spliced Sequence:
TGACAATCGCCCGAGCCATTGAGCTGAAGCACGCTCCGGGACTGATCGCTGCACTCGCCTATGACACAGCCAGCTTCTACCAGAAAGCAGATCATACTTTGTCCAGTTTGGAGCCTGCACACTCTGCTAAATGGAGAAAGTACCTTCACTTGAAGATGTGCTTCTACACAGCGTATGCGTATTGCTACCATGGCCAGACTCTGTTGGCGAGCGATAAGTGTGGAGAAGCCATCCGATCTCTCCAAGAAGCAGAAAAATTGTACGCAGAGGCAGAAGCCCTATGCAAAGAGTACGGGGAAACCAAAGGACCAGGGCCGACGGCCAAGCCGTCAGGACACTTGTTCTTCCGGAAGCTTGGGAGCCTTGTGAAGAACACCCTGGACAAATGTCAGAGAGAAAATGGCTTCAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCCGTCAGGACACTTGTT
59.82
TGTGTCATAGGCGAGTGCAG
60.11
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCCGTCAGGACACTTGTT
59.82
CTGTGTCATAGGCGAGTGCA
60.11
155
PCR template sequence:
CAGGGCCGACGGCCAAGCCGTCAGGACACTTGTTCTTCCGGAAGCTTGGGAGCCTTGTGAAGAACACCCTGGACAAATGTCAGAGAGAAAATGGCTTCATTGACAATCGCCCGAGCCATTGAGCTGAAGCACGCTCCGGGACTGATCGCTGCACTCGCCTATGACACAGCCAGCTTCTACCAGAAAGCAGATCATACTTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-135a-5p(1), mmu-miR-207(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
AAAATGGCTTCATTGACAATCGCCCG
siRNA sets
ATTGTCAATGAAGCCATTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCBROX_409_ORF_1
0.8227
0.292201044
0.615752991
417
ORF sequence:
ATGGCTTCATTGACAATCGCCCGAGCCATTGAGCTGAAGCACGCTCCGGGACTGATCGCTGCACTCGCCTATGACACAGCCAGCTTCTACCAGAAAGCAGATCATACTTTGTCCAGTTTGGAGCCTGCACACTCTGCTAAATGGAGAAAGTACCTTCACTTGAAGATGTGCTTCTACACAGCGTATGCGTATTGCTACCATGGCCAGACTCTGTTGGCGAGCGATAAGTGTGGAGAAGCCATCCGATCTCTCCAAGAAGCAGAAAAATTGTACGCAGAGGCAGAAGCCCTATGCAAAGAGTACGGGGAAACCAAAGGACCAGGGCCGACGGCCAAGCCGTCAGGACACTTGTTCTTCCGGAAGCTTGGGAGCCTTGTGAAGAACACCCTGGACAAATGTCAGAGAGAAAATGGCTTC
Peptide sequence:
MASLTIARAIELKHAPGLIAALAYDTASFYQKADHTLSSLEPAHSAKWRKYLHLKMCFYTAYAYCYHGQTLLASDKCGEAIRSLQEAEKLYAEAEALCKEYGETKGPGPTAKPSGHLFFRKLGSLVKNTLDKCQRENGF
IRESfinder result
IRESfinder score
0.263328554
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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