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mmu_circBest3_389
Basic information of circular RNA
PanCircBase ID:
mmu_circBest3_389
mm39_Chr. Position ID:
chr10|116828968|116838579|+
Gene name:
Best3
Transcript:
ENSMUST00000020378.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
4,5
Exon/intron offsets:
0,9456
Genomic length:
9611
Exon/intron sizes in nt:
234,155
Flanking exon/introns:
chr10:116828507-116828968|chr10:116838579-116839789
Splice length:
389
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GGTTTTACGTCACTCTGGTAGTGAACCGATGGTGGAACCAGTTTGTGAATCTGCCTTGGCCAGACAGGCTGATGCTCCTCATTTCCAGCAGTGTCCACGGGAGCGACCAGCATGGGCGCCTGCTCAGAAGGACGCTGATGCGCTACGTCAACCTGACGTCCCTGCTCATCTTCCGCTCGGTGAGCACCGCGGTGTACAAGAGGTTTCCCACCATGGACCACGTGGTCGAAGCAGGTTTTATGACGGCAGATGAGAGGAAATTATTCGACCACCTCAAATCGCCTCATCTGAAGTACTGGGTTCCCTTCATTTGGTTTGGAAATCTTGCAACCAAAGCCCGGAATGAAGGCAGAATCAGAGACAGCGTTGATCTACAATCACTGATGACT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AATCTTGCAACCAAAGCCCG
59.68
GAGGAGCATCAGCCTGTCTG
60.18
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCAGAATCAGAGACAGCGT
60.11
CGTGGACACTGCTGGAAATG
59.48
141
PCR template sequence:
GAAGTACTGGGTTCCCTTCATTTGGTTTGGAAATCTTGCAACCAAAGCCCGGAATGAAGGCAGAATCAGAGACAGCGTTGATCTACAATCACTGATGACTGGTTTTACGTCACTCTGGTAGTGAACCGATGGTGGAACCAGTTTGTGAATCTGCCTTGGCCAGACAGGCTGATGCTCCTCATTTCCAGCAGTGTCCACGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-205-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATCACTGATGACTGGTTTTACGTCAC
siRNA sets
TAAAACCAGTCATCAGTGA, GTAAAACCAGTCATCAGTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCBEST3_389_ORF_1
1.165
0.241907107
0.584331541
339
ORF sequence:
ATGCTCCTCATTTCCAGCAGTGTCCACGGGAGCGACCAGCATGGGCGCCTGCTCAGAAGGACGCTGATGCGCTACGTCAACCTGACGTCCCTGCTCATCTTCCGCTCGGTGAGCACCGCGGTGTACAAGAGGTTTCCCACCATGGACCACGTGGTCGAAGCAGGTTTTATGACGGCAGATGAGAGGAAATTATTCGACCACCTCAAATCGCCTCATCTGAAGTACTGGGTTCCCTTCATTTGGTTTGGAAATCTTGCAACCAAAGCCCGGAATGAAGGCAGAATCAGAGACAGCGTTGATCTACAATCACTGATGACTGGTTTTACGTCACTCTGGTAG
Peptide sequence:
MLLISSSVHGSDQHGRLLRRTLMRYVNLTSLLIFRSVSTAVYKRFPTMDHVVEAGFMTADERKLFDHLKSPHLKYWVPFIWFGNLATKARNEGRIRDSVDLQSLMTGFTSLW
IRESfinder result
IRESfinder score
0.31744102
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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