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mmu_circXpo1_282
Basic information of circular RNA
PanCircBase ID:
mmu_circXpo1_282
mm39_Chr. Position ID:
chr11|23217661|23227080|+
Gene name:
Xpo1
Transcript:
ENSMUST00000020538.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
4,5,6,7
Exon/intron offsets:
0,3471,8765,9374
Genomic length:
9419
Exon/intron sizes in nt:
102,73,62,45
Flanking exon/introns:
chr11:23211966-23217661|chr11:23227080-23228142
Splice length:
282
Other database IDs:
circAtlas: mmu-Xpo1_0005
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_168786
Human Ortholog IDs:
Mature spliced Sequence:
CAAAGAATGGCTCAAGAAGTACTGACACATTTAAAGGAGCATCCTGATGCTTGGACACGGGTCGACACAATATTGGAGTTTTCGCAGAACATGAACACGAAATACTATGGACTACAGATTTTGGAAAATGTGATCAAAACAAGGTGGAAGATCCTTCCAAGGAACCAGTGTGAAGGAATAAAAAAATATGTTGTTGGTCTCATTATCAAGACATCCTCTGACCCAACTTGTGTAGAGAAAGAAAAGGTGTATATTGGGAAATTGAATATGATTCTTGTTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTCTGACCCAACTTGTGT
58.49
TATTGTGTCGACCCGTGTCC
59.76
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GACATCCTCTGACCCAACTTGT
59.96
TATTGTGTCGACCCGTGTCC
59.76
145
PCR template sequence:
AAAATATGTTGTTGGTCTCATTATCAAGACATCCTCTGACCCAACTTGTGTAGAGAAAGAAAAGGTGTATATTGGGAAATTGAATATGATTCTTGTTCAGCAAAGAATGGCTCAAGAAGTACTGACACATTTAAAGGAGCATCCTGATGCTTGGACACGGGTCGACACAATATTGGAGTTTTCGCAGAACATGAACACGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-miR-23a-3p(1), mmu-miR-540-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GATTCTTGTTCAGCAAAGAATGGCTC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCXPO1_282_ORF_1
1.024
0.035695515
0.694371443
558
ORF sequence:
ATGGCTCAAGAAGTACTGACACATTTAAAGGAGCATCCTGATGCTTGGACACGGGTCGACACAATATTGGAGTTTTCGCAGAACATGAACACGAAATACTATGGACTACAGATTTTGGAAAATGTGATCAAAACAAGGTGGAAGATCCTTCCAAGGAACCAGTGTGAAGGAATAAAAAAATATGTTGTTGGTCTCATTATCAAGACATCCTCTGACCCAACTTGTGTAGAGAAAGAAAAGGTGTATATTGGGAAATTGAATATGATTCTTGTTCAGCAAAGAATGGCTCAAGAAGTACTGACACATTTAAAGGAGCATCCTGATGCTTGGACACGGGTCGACACAATATTGGAGTTTTCGCAGAACATGAACACGAAATACTATGGACTACAGATTTTGGAAAATGTGATCAAAACAAGGTGGAAGATCCTTCCAAGGAACCAGTGTGAAGGAATAAAAAAATATGTTGTTGGTCTCATTATCAAGACATCCTCTGACCCAACTTGTGTAGAGAAAGAAAAGGTGTATATTGGGAAATTGAATATGATTCTTGTTCAG
Peptide sequence:
MAQEVLTHLKEHPDAWTRVDTILEFSQNMNTKYYGLQILENVIKTRWKILPRNQCEGIKKYVVGLIIKTSSDPTCVEKEKVYIGKLNMILVQQRMAQEVLTHLKEHPDAWTRVDTILEFSQNMNTKYYGLQILENVIKTRWKILPRNQCEGIKKYVVGLIIKTSSDPTCVEKEKVYIGKLNMILVQ
IRESfinder result
IRESfinder score
0.616952163
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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