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mmu_circDedd_549
Basic information of circular RNA
PanCircBase ID:
mmu_circDedd_549
mm39_Chr. Position ID:
chr1|171158801|171166498|+
Gene name:
Dedd
Transcript:
ENSMUST00000111299.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
2,3,4
Exon/intron offsets:
0,7018,7589
Genomic length:
7697
Exon/intron sizes in nt:
5,23,89,108
Flanking exon/introns:
chr1:171157094-171158801|chr1:171166498-171167760
Splice length:
549
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GCTTTGAAACTTGTGCTAGGAAGAGCCCTGGGGATTTAAGTTTCTTGCAAAGATCACTGGAGATTGCAGCTGCTGAGCAGAGATTCTGGAAAGCACTCTATTTCTGAGCCTCTAGCATGGCGGGCCTAAAGAGGCGGGCAAGCCAGGTGTGGCCCGAAGAGCGTGGGGAGCAAGAACATGGGCTCTACAGCCTCCACCGCATGTTCGACATCGTGGGCACCCACCTAACACACAGAGATGTCCGAGTGCTTTCCTTCCTTTTTGTTGATGTTATTGATGACCATGAACGTGGACTCATCCGAAATGGACGTGACTTCTTATTGGCACTGGAGCGCCAGGGCCGCTGTGACGAGAGTAACTTTCGCCAGGTGCTGCAGCTGCTGCGCATCATCACTCGCCATGACTTGCTGCCCTACGTTACTCTCAAGAAGAGACGAGCTGTGTGCCCTGATCTTGTAGACAAGTATCTGGAGGAAACATCAATTCGCTATGTGACCCCCAGAGCCCTCAGTGACCCAGAACCGAGGCCTCCCCAGCCCTCTAAAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATTCGCTATGTGACCCCCAG
59.53
TCAGCAGCTGCAATCTCCAG
60.39
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATTCGCTATGTGACCCCCAG
59.53
CTCAGCAGCTGCAATCTCCA
60.39
144
PCR template sequence:
GATCTTGTAGACAAGTATCTGGAGGAAACATCAATTCGCTATGTGACCCCCAGAGCCCTCAGTGACCCAGAACCGAGGCCTCCCCAGCCCTCTAAAACAGGCTTTGAAACTTGTGCTAGGAAGAGCCCTGGGGATTTAAGTTTCTTGCAAAGATCACTGGAGATTGCAGCTGCTGAGCAGAGATTCTGGAAAGCACTCTA
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-384-3p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCCTCTAAAACAGGCTTTGAAACTTG
siRNA sets
TTCAAAGCCTGTTTTAGAG, TTTCAAAGCCTGTTTTAGA, GTTTCAAAGCCTGTTTTAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDEDD_549_ORF_1
0.9716
0.28897314
0.834290283
540
ORF sequence:
ATGGCGGGCCTAAAGAGGCGGGCAAGCCAGGTGTGGCCCGAAGAGCGTGGGGAGCAAGAACATGGGCTCTACAGCCTCCACCGCATGTTCGACATCGTGGGCACCCACCTAACACACAGAGATGTCCGAGTGCTTTCCTTCCTTTTTGTTGATGTTATTGATGACCATGAACGTGGACTCATCCGAAATGGACGTGACTTCTTATTGGCACTGGAGCGCCAGGGCCGCTGTGACGAGAGTAACTTTCGCCAGGTGCTGCAGCTGCTGCGCATCATCACTCGCCATGACTTGCTGCCCTACGTTACTCTCAAGAAGAGACGAGCTGTGTGCCCTGATCTTGTAGACAAGTATCTGGAGGAAACATCAATTCGCTATGTGACCCCCAGAGCCCTCAGTGACCCAGAACCGAGGCCTCCCCAGCCCTCTAAAACAGGCTTTGAAACTTGTGCTAGGAAGAGCCCTGGGGATTTAAGTTTCTTGCAAAGATCACTGGAGATTGCAGCTGCTGAGCAGAGATTCTGGAAAGCACTCTATTTCTGA
Peptide sequence:
MAGLKRRASQVWPEERGEQEHGLYSLHRMFDIVGTHLTHRDVRVLSFLFVDVIDDHERGLIRNGRDFLLALERQGRCDESNFRQVLQLLRIITRHDLLPYVTLKKRRAVCPDLVDKYLEETSIRYVTPRALSDPEPRPPQPSKTGFETCARKSPGDLSFLQRSLEIAAAEQRFWKALYF
IRESfinder result
IRESfinder score
0.453624081
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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