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mmu_circRad52_303
Basic information of circular RNA
PanCircBase ID:
mmu_circRad52_303
mm39_Chr. Position ID:
chr6|119897070|119897989|+
Gene name:
Rad52
Transcript:
ENSMUST00000162461.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
10,11
Exon/intron offsets:
0,697
Genomic length:
919
Exon/intron sizes in nt:
81,222
Flanking exon/introns:
chr6:119896038-119897070|chr6:119897989-119899432
Splice length:
303
Other database IDs:
circBase: mmu_circ_0001516, CIRCpedia: MMU_CIRCpedia_4990, circAtlas: mmu-Rad52_0005
Human Ortholog IDs:
Mature spliced Sequence:
CAGTACTTCCAGCCCCTCCAAAACACAGCACCCCTGTAACTGCAGCCTCAGAACTCCTCCAGGAGAAAGTCGTCTTTCCAGATAACCTTGAAGAGAACCTTGAAATGTGGGACCTTACTCCAGACTTAGAGGACATCATTAAGCCCTTGTGTAGAGCAGAACCAGCCCAAACTTCTGCCACTCGAACCTTCAACAACCAGGACAGCGTCCCACATATCCATTGCCATCAGAAACCACAAGAAAAGCCTGGACCTGGGCACCTGCAGACCTGCAACACCAACCAGCATGTTCTAGGTAGCAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCGTCCCACATATCCATTGC
59.41
GGAGTTCTGAGGCTGCAGTT
59.96
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCGTCCCACATATCCATTGC
59.41
GAGGAGTTCTGAGGCTGCAG
60.11
158
PCR template sequence:
AGCGTCCCACATATCCATTGCCATCAGAAACCACAAGAAAAGCCTGGACCTGGGCACCTGCAGACCTGCAACACCAACCAGCATGTTCTAGGTAGCAGAGCAGTACTTCCAGCCCCTCCAAAACACAGCACCCCTGTAACTGCAGCCTCAGAACTCCTCCAGGAGAAAGTCGTCTTTCCAGATAACCTTGAAGAGAACCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-298-5p(1), mmu-miR-342-5p(1), mmu-miR-27a-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-190b-5p(1), mmu-miR-188-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
CTAGGTAGCAGAGCAGTACTTCCAGC
siRNA sets
GAAGTACTGCTCTGCTACC, AAGTACTGCTCTGCTACCT, GCTGGAAGTACTGCTCTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAD52_303_ORF_1
0.9837
0.186333392
0.720966643
501
ORF sequence:
ATGTGGGACCTTACTCCAGACTTAGAGGACATCATTAAGCCCTTGTGTAGAGCAGAACCAGCCCAAACTTCTGCCACTCGAACCTTCAACAACCAGGACAGCGTCCCACATATCCATTGCCATCAGAAACCACAAGAAAAGCCTGGACCTGGGCACCTGCAGACCTGCAACACCAACCAGCATGTTCTAGGTAGCAGAGCAGTACTTCCAGCCCCTCCAAAACACAGCACCCCTGTAACTGCAGCCTCAGAACTCCTCCAGGAGAAAGTCGTCTTTCCAGATAACCTTGAAGAGAACCTTGAAATGTGGGACCTTACTCCAGACTTAGAGGACATCATTAAGCCCTTGTGTAGAGCAGAACCAGCCCAAACTTCTGCCACTCGAACCTTCAACAACCAGGACAGCGTCCCACATATCCATTGCCATCAGAAACCACAAGAAAAGCCTGGACCTGGGCACCTGCAGACCTGCAACACCAACCAGCATGTTCTAGGTAGCAGA
Peptide sequence:
MWDLTPDLEDIIKPLCRAEPAQTSATRTFNNQDSVPHIHCHQKPQEKPGPGHLQTCNTNQHVLGSRAVLPAPPKHSTPVTAASELLQEKVVFPDNLEENLEMWDLTPDLEDIIKPLCRAEPAQTSATRTFNNQDSVPHIHCHQKPQEKPGPGHLQTCNTNQHVLGSR
IRESfinder result
IRESfinder score
0.78759165
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
RPF, cORF, m6A
mmu_circRad52_001
Evidence
Peptide sequence:
MWDLTPDLEDIIKPLCRAEPAQTSATRTFNNQDSVPHIHCHQKPQEKPGPGHLQTCNTNQHVLGSRAVLPAPPKHSTPVTAASELLQEKVVFPDNLEENLEMWDLTPDLEDIIKPLCRAEPAQTSATRTFNNQDSVPHIHCHQKPQEKPGPGHLQTCNTNQHVLGSRAVLPAPPKHSTPVTAASELLQEKVVFPDNLEENLE
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