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mmu_circUsp20_227
Basic information of circular RNA
PanCircBase ID:
mmu_circUsp20_227
mm39_Chr. Position ID:
chr2|30906504|30907321|+
Gene name:
Usp20
Transcript:
ENSMUST00000102849.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
17,18
Exon/intron offsets:
0,636
Genomic length:
817
Exon/intron sizes in nt:
46,181
Flanking exon/introns:
chr2:30906333-30906504|chr2:30907321-30907396
Splice length:
227
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GCTTCGGAATGGCGTGAAGTACTGTAAAGTCCTATGTCTGCCTGAGATTCTGTGCGTCCACCTGAAGCGCTTCCGGCATGAGGTGATGTACTCCTTCAAGGTCAGCAGCCATGTCTCTTTCCCCCTCGAGGGACTGGACCTACGCCCTTTTCTGGCCAAGGAGTGCACGTCCCAGGTCACCACCTATGACCTCCTCTCTGTCATCTGTCACCATGGCACAGCAGGCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTTTCTGGCCAAGGAGTGCA
60.11
CAGGTGGACGCACAGAATCT
60.04
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTTTCTGGCCAAGGAGTGCA
60.11
GGTGGACGCACAGAATCTCA
60.04
142
PCR template sequence:
GAGGGACTGGACCTACGCCCTTTTCTGGCCAAGGAGTGCACGTCCCAGGTCACCACCTATGACCTCCTCTCTGTCATCTGTCACCATGGCACAGCAGGCAGCTTCGGAATGGCGTGAAGTACTGTAAAGTCCTATGTCTGCCTGAGATTCTGTGCGTCCACCTGAAGCGCTTCCGGCATGAGGTGATGTACTCCTTCAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-216a-5p(1), mmu-miR-101b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGCACAGCAGGCAGCTTCGGAATGGC
siRNA sets
CATTCCGAAGCTGCCTGCT, CCATTCCGAAGCTGCCTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUSP20_227_ORF_1
1.1165
0.253254466
0.270006009
159
ORF sequence:
ATGTACTCCTTCAAGGTCAGCAGCCATGTCTCTTTCCCCCTCGAGGGACTGGACCTACGCCCTTTTCTGGCCAAGGAGTGCACGTCCCAGGTCACCACCTATGACCTCCTCTCTGTCATCTGTCACCATGGCACAGCAGGCAGCTTCGGAATGGCGTGA
Peptide sequence:
MYSFKVSSHVSFPLEGLDLRPFLAKECTSQVTTYDLLSVICHHGTAGSFGMA
IRESfinder result
IRESfinder score
0.230934327
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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