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mmu_circArmh3_425
Basic information of circular RNA
PanCircBase ID:
mmu_circArmh3_425
mm39_Chr. Position ID:
chr19|45961261|45967151|-
Gene name:
Armh3
Transcript:
ENSMUST00000045396.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,2144,2396,5777
Genomic length:
5890
Exon/intron sizes in nt:
108,147,57,113
Flanking exon/introns:
chr19:45954773-45961261|chr19:45967151-45986854
Splice length:
425
Other database IDs:
CIRCpedia: MMU_CIRCpedia_217134, circAtlas: mmu-9130011E15Rik_0006
circBase: hsa_circ_0092470, circAtlas: hsa-C10orf76_0007, CIRCpedia: HSA_CIRCpedia_189
Human Ortholog IDs:
Mature spliced Sequence:
GTTCTCTAGCCATGGCACAAGTAGAGAAACGGGGAGGCTTGCTCCGGAAATCTTCAGCCTCAAAAAAGCCTCTAAAGGAAAAAGTGGTGCTGATGTATGATGAGATTTTCATGACGGAGGACCCCAGTAAGTGTAGTCCACGGTTTTGGGAGGAACTCTTCCTCATGAAGGTGAATTTGGAGTATCTGGAAGGCAAGCTAGAGTCCCTGGATGGGGAGGAGCTGATGAAGATCAAGGACAACATTAACTGCTTATTTCAACACTGCATCCAGGCTCTGGGGGAGGAGCATCCAATCCGAGTTGTCAACGCCTTGCAGACCTTGTGTGCACTTATTCGAGGAGTCCACCAGAAGAATAAATCTACGTCTGGATTTGACATCATTAATATGCTGATGGGCTTTGACAAGGCAGAGCTGTGCATGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCGAGGAGTCCACCAGAAGA
59.6
AGATTTCCGGAGCAAGCCTC
60.11
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCGAGGAGTCCACCAGAAGA
59.6
AGGCTGAAGATTTCCGGAGC
60.11
151
PCR template sequence:
TGCACTTATTCGAGGAGTCCACCAGAAGAATAAATCTACGTCTGGATTTGACATCATTAATATGCTGATGGGCTTTGACAAGGCAGAGCTGTGCATGAAGGTTCTCTAGCCATGGCACAAGTAGAGAAACGGGGAGGCTTGCTCCGGAAATCTTCAGCCTCAAAAAAGCCTCTAAAGGAAAAAGTGGTGCTGATGTATGA
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-150-5p(1), mmu-miR-29b-3p(1), mmu-miR-29c-3p(1), mmu-miR-216a-5p(1), mmu-miR-467b-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCTGTGCATGAAGGTTCTCTAGCCAT
siRNA sets
GAGAACCTTCATGCACAGC, TAGAGAACCTTCATGCACA, AGAGAACCTTCATGCACAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARMH3_425_ORF_1
1.3036
0.336596141
0.830611342
423
ORF sequence:
ATGGCACAAGTAGAGAAACGGGGAGGCTTGCTCCGGAAATCTTCAGCCTCAAAAAAGCCTCTAAAGGAAAAAGTGGTGCTGATGTATGATGAGATTTTCATGACGGAGGACCCCAGTAAGTGTAGTCCACGGTTTTGGGAGGAACTCTTCCTCATGAAGGTGAATTTGGAGTATCTGGAAGGCAAGCTAGAGTCCCTGGATGGGGAGGAGCTGATGAAGATCAAGGACAACATTAACTGCTTATTTCAACACTGCATCCAGGCTCTGGGGGAGGAGCATCCAATCCGAGTTGTCAACGCCTTGCAGACCTTGTGTGCACTTATTCGAGGAGTCCACCAGAAGAATAAATCTACGTCTGGATTTGACATCATTAATATGCTGATGGGCTTTGACAAGGCAGAGCTGTGCATGAAGGTTCTCTAG
Peptide sequence:
MAQVEKRGGLLRKSSASKKPLKEKVVLMYDEIFMTEDPSKCSPRFWEELFLMKVNLEYLEGKLESLDGEELMKIKDNINCLFQHCIQALGEEHPIRVVNALQTLCALIRGVHQKNKSTSGFDIINMLMGFDKAELCMKVL
IRESfinder result
IRESfinder score
0.389819114
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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