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mmu_circRad50_341
Basic information of circular RNA
PanCircBase ID:
mmu_circRad50_341
mm39_Chr. Position ID:
chr11|53576976|53579104|-
Gene name:
Rad50
Transcript:
ENSMUST00000020649.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
11,10
Exon/intron offsets:
0,1945
Genomic length:
2128
Exon/intron sizes in nt:
1,58,183
Flanking exon/introns:
chr11:53575128-53576976|chr11:53579104-53582939
Splice length:
341
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GAACGTGAATTAAGCAAGGCCGAGAAAAATAGCAGCATAGAAACCCTAAAAGCAGAGGTAATGAGCCTCCAAAATGAGAAAGCTGACCTGGACAGGAGCTTGCGAAAGCTGGACCAGGAGATGGAGCAGTTAAACCATCATACAACAACCCGCACACAGATGGAGATGCTCACCAAAGACAAAACTGACAAAGATGAACAGATCAGAAAAATAAAGTCTAGGCACAGTGATGAACTAACTTCACTGTTGGGGTACTTTCCTAACAAAAAACAGCTTGAAGACTGGCTTCATTCTAAATCCAAAGAAATTAATCAGACCAGGGACAGACTTGCCAAACTGAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AACAGCTTGAAGACTGGCTT
57.64
CCTGTCCAGGTCAGCTTTCT
59.31
169
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAACAGCTTGAAGACTGGCT
57.64
CCTGTCCAGGTCAGCTTTCT
59.31
170
PCR template sequence:
CACTGTTGGGGTACTTTCCTAACAAAAAACAGCTTGAAGACTGGCTTCATTCTAAATCCAAAGAAATTAATCAGACCAGGGACAGACTTGCCAAACTGAAGAACGTGAATTAAGCAAGGCCGAGAAAAATAGCAGCATAGAAACCCTAAAAGCAGAGGTAATGAGCCTCCAAAATGAGAAAGCTGACCTGGACAGGAGCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-17-5p(1), mmu-miR-223-3p(1), mmu-miR-106b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTGCCAAACTGAAGAACGTGAATTAA
siRNA sets
TTAATTCACGTTCTTCAGT, ATTCACGTTCTTCAGTTTG, TTCACGTTCTTCAGTTTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAD50_341_ORF_1
1.1352
0.193680554
0.441640678
294
ORF sequence:
ATGAGCCTCCAAAATGAGAAAGCTGACCTGGACAGGAGCTTGCGAAAGCTGGACCAGGAGATGGAGCAGTTAAACCATCATACAACAACCCGCACACAGATGGAGATGCTCACCAAAGACAAAACTGACAAAGATGAACAGATCAGAAAAATAAAGTCTAGGCACAGTGATGAACTAACTTCACTGTTGGGGTACTTTCCTAACAAAAAACAGCTTGAAGACTGGCTTCATTCTAAATCCAAAGAAATTAATCAGACCAGGGACAGACTTGCCAAACTGAAGAACGTGAATTAA
Peptide sequence:
MSLQNEKADLDRSLRKLDQEMEQLNHHTTTRTQMEMLTKDKTDKDEQIRKIKSRHSDELTSLLGYFPNKKQLEDWLHSKSKEINQTRDRLAKLKNVN
IRESfinder result
IRESfinder score
0.603216076
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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