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mmu_circDmxl1_406
Basic information of circular RNA
PanCircBase ID:
mmu_circDmxl1_406
mm39_Chr. Position ID:
chr18|50052954|50055782|+
Gene name:
Dmxl1
Transcript:
ENSMUST00000180611.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
31,32,33
Exon/intron offsets:
0,942,2710
Genomic length:
2828
Exon/intron sizes in nt:
8,62,02,118
Flanking exon/introns:
chr18:50050788-50052954|chr18:50055782-50064977
Splice length:
406
Other database IDs:
circAtlas: mmu-Dmxl1_0006
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_158750
Human Ortholog IDs:
Mature spliced Sequence:
TTGGTCTTTGATGAGATTGGCTATGGTCCAGTTGGTGCTCAACAATTTGAAGACTTTCTATCCCTTTGCAGGTCATGATCTTGCAGAACTACCAGTTAGTTCACCTCTTTGTCATGCAGTTCTAAAAACTCTTCAATGCTGGGAACAAGTTCTTCTCCGGCGACTTGAAATCCATGGTGGACCACCTCAAAACTATATCTCAAGTCACACTTCTGAGGAGAATGTGTCTGCAGGCCCTGCAATACTCCGTCACAAAGCTTTACTAGAACCTACAAACACTCCTTTCAAATCCAAAAATCATCTCGCACTATCTGTGAAGAGGCTTTGGCAGTACTTGGTGAAACAGGAAGAAATTCAAGAAACTTTTATCAGAAATATATTCACAAAGAAACGATGTCTAAATGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGCTTTGGCAGTACTTGGT
59.52
TCTGCAAGATCATGACCTGCA
59.72
174
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCTTTGGCAGTACTTGGTG
59.4
TCTGCAAGATCATGACCTGCA
59.72
173
PCR template sequence:
ACTATCTGTGAAGAGGCTTTGGCAGTACTTGGTGAAACAGGAAGAAATTCAAGAAACTTTTATCAGAAATATATTCACAAAGAAACGATGTCTAAATGAGTTGGTCTTTGATGAGATTGGCTATGGTCCAGTTGGTGCTCAACAATTTGAAGACTTTCTATCCCTTTGCAGGTCATGATCTTGCAGAACTACCAGTTAGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-217-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATGTCTAAATGAGTTGGTCTTTGATG
siRNA sets
AAAGACCAACTCATTTAGA, AAGACCAACTCATTTAGAC, CAAAGACCAACTCATTTAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDMXL1_406_ORF_1
0.8731
-0.07600039
0.370835719
474
ORF sequence:
ATGAGATTGGCTATGGTCCAGTTGGTGCTCAACAATTTGAAGACTTTCTATCCCTTTGCAGGTCATGATCTTGCAGAACTACCAGTTAGTTCACCTCTTTGTCATGCAGTTCTAAAAACTCTTCAATGCTGGGAACAAGTTCTTCTCCGGCGACTTGAAATCCATGGTGGACCACCTCAAAACTATATCTCAAGTCACACTTCTGAGGAGAATGTGTCTGCAGGCCCTGCAATACTCCGTCACAAAGCTTTACTAGAACCTACAAACACTCCTTTCAAATCCAAAAATCATCTCGCACTATCTGTGAAGAGGCTTTGGCAGTACTTGGTGAAACAGGAAGAAATTCAAGAAACTTTTATCAGAAATATATTCACAAAGAAACGATGTCTAAATGAGTTGGTCTTTGATGAGATTGGCTATGGTCCAGTTGGTGCTCAACAATTTGAAGACTTTCTATCCCTTTGCAGGTCATGA
Peptide sequence:
MRLAMVQLVLNNLKTFYPFAGHDLAELPVSSPLCHAVLKTLQCWEQVLLRRLEIHGGPPQNYISSHTSEENVSAGPAILRHKALLEPTNTPFKSKNHLALSVKRLWQYLVKQEEIQETFIRNIFTKKRCLNELVFDEIGYGPVGAQQFEDFLSLCRS
IRESfinder result
IRESfinder score
0.75455357
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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