top of page
mmu_circXpo1_396
Basic information of circular RNA
PanCircBase ID:
mmu_circXpo1_396
mm39_Chr. Position ID:
chr11|23227035|23228925|+
Gene name:
Xpo1
Transcript:
ENSMUST00000020538.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
7,8,9,10
Exon/intron offsets:
0,1107,1640,1770
Genomic length:
1890
Exon/intron sizes in nt:
4,51,82,49,120
Flanking exon/introns:
chr11:23226488-23227035|chr11:23228925-23230373
Splice length:
396
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AAAGAAAAGGTGTATATTGGGAAATTGAATATGATTCTTGTTCAGATACTTAAGCAAGAGTGGCCTAAGCATTGGCCAACTTTTATCAGTGACATTGTTGGAGCGAGTAGGACCAGTGAAAGTCTATGTCAAAATAATATGGTGATTCTTAAACTCTTGAGTGAAGAAGTGTTTGATTTCTCTAGTGGACAGATAACCCAAGTTAAAGCAAAGCATTTAAAAGACAGCATGTGCAATGAGTTTTCACAAATATTTCAGCTTTGTCAGTTTGTGATGGAAAATTCCCAAAATGCTCCCCTTGTTCATGCTACATTAGAAACACTGCTGAGATTTCTGAACTGGATTCCACTGGGATACATCTTTGAGACCAAGTTAATCAGCACATTAATTTACAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGAACTGGATTCCACTGGG
59.37
GCCAATGCTTAGGCCACTCT
60.39
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTGAACTGGATTCCACTGGG
59.96
GCCAATGCTTAGGCCACTCT
60.39
141
PCR template sequence:
CCTTGTTCATGCTACATTAGAAACACTGCTGAGATTTCTGAACTGGATTCCACTGGGATACATCTTTGAGACCAAGTTAATCAGCACATTAATTTACAAGAAAGAAAAGGTGTATATTGGGAAATTGAATATGATTCTTGTTCAGATACTTAAGCAAGAGTGGCCTAAGCATTGGCCAACTTTTATCAGTGACATTGTTG
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-32-5p(1), mmu-miR-216a-5p(1), mmu-miR-203-3p(1), mmu-miR-320-3p(1), mmu-miR-25-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTAATTTACAAGAAAGAAAAGGTGT
siRNA sets
TTTCTTTCTTGTAAATTAA, TTTTCTTTCTTGTAAATTA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCXPO1_396_ORF_1
0.9644
-0.083826911
0.843952025
762
ORF sequence:
ATGATTCTTGTTCAGATACTTAAGCAAGAGTGGCCTAAGCATTGGCCAACTTTTATCAGTGACATTGTTGGAGCGAGTAGGACCAGTGAAAGTCTATGTCAAAATAATATGGTGATTCTTAAACTCTTGAGTGAAGAAGTGTTTGATTTCTCTAGTGGACAGATAACCCAAGTTAAAGCAAAGCATTTAAAAGACAGCATGTGCAATGAGTTTTCACAAATATTTCAGCTTTGTCAGTTTGTGATGGAAAATTCCCAAAATGCTCCCCTTGTTCATGCTACATTAGAAACACTGCTGAGATTTCTGAACTGGATTCCACTGGGATACATCTTTGAGACCAAGTTAATCAGCACATTAATTTACAAGAAAGAAAAGGTGTATATTGGGAAATTGAATATGATTCTTGTTCAGATACTTAAGCAAGAGTGGCCTAAGCATTGGCCAACTTTTATCAGTGACATTGTTGGAGCGAGTAGGACCAGTGAAAGTCTATGTCAAAATAATATGGTGATTCTTAAACTCTTGAGTGAAGAAGTGTTTGATTTCTCTAGTGGACAGATAACCCAAGTTAAAGCAAAGCATTTAAAAGACAGCATGTGCAATGAGTTTTCACAAATATTTCAGCTTTGTCAGTTTGTGATGGAAAATTCCCAAAATGCTCCCCTTGTTCATGCTACATTAGAAACACTGCTGAGATTTCTGAACTGGATTCCACTGGGATACATCTTTGAGACCAAGTTAATCAGCACATTAATTTACAAG
Peptide sequence:
MILVQILKQEWPKHWPTFISDIVGASRTSESLCQNNMVILKLLSEEVFDFSSGQITQVKAKHLKDSMCNEFSQIFQLCQFVMENSQNAPLVHATLETLLRFLNWIPLGYIFETKLISTLIYKKEKVYIGKLNMILVQILKQEWPKHWPTFISDIVGASRTSESLCQNNMVILKLLSEEVFDFSSGQITQVKAKHLKDSMCNEFSQIFQLCQFVMENSQNAPLVHATLETLLRFLNWIPLGYIFETKLISTLIYK
IRESfinder result
IRESfinder score
0.866343002
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page