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mmu_circAlg13_479
Basic information of circular RNA
PanCircBase ID:
mmu_circAlg13_479
mm39_Chr. Position ID:
chrX|143127256|143132415|+
Gene name:
Alg13
Transcript:
ENSMUST00000238864.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
11,12,13,14,15
Exon/intron offsets:
0,1351,2421,3699,5031
Genomic length:
5159
Exon/intron sizes in nt:
76,109,65,101,128
Flanking exon/introns:
chrX:143125805-143127256|chrX:143132415-143133278
Splice length:
479
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AACTGAAGAGGCTGCCGCCTGTTCCAGTGCTGCAAGTACACCAGAAGGCAATAAGCAAGGGACAGAAAGACAAAAGGTTCCAGAAAGTCCGTCAAAGATGCTGTTTCCCTATAAGGTGCTGAAAGCTCTGGATCCAGAAATCTATCGAAATGTGGAATTTGATGCTTGGTTGGACAGTAGAAAAGAACTTCAAAAATCAGAGTGTGTGGAGTATGGTGGAAGATATTACTTTTTAGGAGACAAATGTCAGGTTTGCATGGAATCAGGTGGAAAATATTATAATGCTCACATTCAGGAAATTGATAATGATAAAAGTTCAGTAGTAGTTTTCATTGAGGAATTTGCAGAAAGGCATTCAATTCCGCTGGCCCATGTAAGACCAGTCAACCAAGTGGCACTTCTTCCTTCCTGGAATGCCATACCAATTCGTAATGGAAGAGGTTATCCAACTATAACTGGAGGCTATTTCCCTGAAATAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGTCAACCAAGTGGCACT
60.47
GGTGTACTTGCAGCACTGGA
60.25
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGTCAACCAAGTGGCACT
60.47
TGCCTTCTGGTGTACTTGCA
59.53
150
PCR template sequence:
CCAGTCAACCAAGTGGCACTTCTTCCTTCCTGGAATGCCATACCAATTCGTAATGGAAGAGGTTATCCAACTATAACTGGAGGCTATTTCCCTGAAATAGAACTGAAGAGGCTGCCGCCTGTTCCAGTGCTGCAAGTACACCAGAAGGCAATAAGCAAGGGACAGAAAGACAAAAGGTTCCAGAAAGTCCGTCAAAGATG
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-23a-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTCCCTGAAATAGAACTGAAGAGGCT
siRNA sets
CTTCAGTTCTATTTCAGGG, TCTTCAGTTCTATTTCAGG, TTCAGTTCTATTTCAGGGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCALG13_479_ORF_1
0.8769
0.004808748
0.505475123
504
ORF sequence:
ATGCTGTTTCCCTATAAGGTGCTGAAAGCTCTGGATCCAGAAATCTATCGAAATGTGGAATTTGATGCTTGGTTGGACAGTAGAAAAGAACTTCAAAAATCAGAGTGTGTGGAGTATGGTGGAAGATATTACTTTTTAGGAGACAAATGTCAGGTTTGCATGGAATCAGGTGGAAAATATTATAATGCTCACATTCAGGAAATTGATAATGATAAAAGTTCAGTAGTAGTTTTCATTGAGGAATTTGCAGAAAGGCATTCAATTCCGCTGGCCCATGTAAGACCAGTCAACCAAGTGGCACTTCTTCCTTCCTGGAATGCCATACCAATTCGTAATGGAAGAGGTTATCCAACTATAACTGGAGGCTATTTCCCTGAAATAGAACTGAAGAGGCTGCCGCCTGTTCCAGTGCTGCAAGTACACCAGAAGGCAATAAGCAAGGGACAGAAAGACAAAAGGTTCCAGAAAGTCCGTCAAAGATGCTGTTTCCCTATAAGGTGCTGA
Peptide sequence:
MLFPYKVLKALDPEIYRNVEFDAWLDSRKELQKSECVEYGGRYYFLGDKCQVCMESGGKYYNAHIQEIDNDKSSVVVFIEEFAERHSIPLAHVRPVNQVALLPSWNAIPIRNGRGYPTITGGYFPEIELKRLPPVPVLQVHQKAISKGQKDKRFQKVRQRCCFPIRC
IRESfinder result
IRESfinder score
0.613174254
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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