top of page
mmu_circXpo1_633
Basic information of circular RNA
PanCircBase ID:
mmu_circXpo1_633
mm39_Chr. Position ID:
chr11|23217661|23228925|+
Gene name:
Xpo1
Transcript:
ENSMUST00000020538.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
4,5,6,7,8,9,10
Exon/intron offsets:
0,3471,8765,9374,10481,11014,11144
Genomic length:
11264
Exon/intron sizes in nt:
10,27,36,24,51,82,49,100
Flanking exon/introns:
chr11:23211966-23217661|chr11:23228925-23230373
Splice length:
633
Other database IDs:
CIRCpedia: MMU_CIRCpedia_13731, circAtlas: mmu-Xpo1_0007
circBase: hsa_circ_0054893, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_41951
Human Ortholog IDs:
Mature spliced Sequence:
CAAAGAATGGCTCAAGAAGTACTGACACATTTAAAGGAGCATCCTGATGCTTGGACACGGGTCGACACAATATTGGAGTTTTCGCAGAACATGAACACGAAATACTATGGACTACAGATTTTGGAAAATGTGATCAAAACAAGGTGGAAGATCCTTCCAAGGAACCAGTGTGAAGGAATAAAAAAATATGTTGTTGGTCTCATTATCAAGACATCCTCTGACCCAACTTGTGTAGAGAAAGAAAAGGTGTATATTGGGAAATTGAATATGATTCTTGTTCAGATACTTAAGCAAGAGTGGCCTAAGCATTGGCCAACTTTTATCAGTGACATTGTTGGAGCGAGTAGGACCAGTGAAAGTCTATGTCAAAATAATATGGTGATTCTTAAACTCTTGAGTGAAGAAGTGTTTGATTTCTCTAGTGGACAGATAACCCAAGTTAAAGCAAAGCATTTAAAAGACAGCATGTGCAATGAGTTTTCACAAATATTTCAGCTTTGTCAGTTTGTGATGGAAAATTCCCAAAATGCTCCCCTTGTTCATGCTACATTAGAAACACTGCTGAGATTTCTGAACTGGATTCCACTGGGATACATCTTTGAGACCAAGTTAATCAGCACATTAATTTACAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGAACTGGATTCCACTGGGA
59.37
TCCAATATTGTGTCGACCCGT
59.45
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGAACTGGATTCCACTGGG
59.37
TCCAATATTGTGTCGACCCGT
59.45
141
PCR template sequence:
CCTTGTTCATGCTACATTAGAAACACTGCTGAGATTTCTGAACTGGATTCCACTGGGATACATCTTTGAGACCAAGTTAATCAGCACATTAATTTACAAGCAAAGAATGGCTCAAGAAGTACTGACACATTTAAAGGAGCATCCTGATGCTTGGACACGGGTCGACACAATATTGGAGTTTTCGCAGAACATGAACACGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-miR-32-5p(1), mmu-miR-216a-5p(1), mmu-miR-203-3p(1), mmu-miR-320-3p(1), mmu-miR-23a-3p(1), mmu-miR-25-3p(1), mmu-miR-540-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTAATTTACAAGCAAAGAATGGCTC
siRNA sets
ATTCTTTGCTTGTAAATTA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCXPO1_633_ORF_1
0.9336
-0.03424362
0.99557492
1260
ORF sequence:
ATGGCTCAAGAAGTACTGACACATTTAAAGGAGCATCCTGATGCTTGGACACGGGTCGACACAATATTGGAGTTTTCGCAGAACATGAACACGAAATACTATGGACTACAGATTTTGGAAAATGTGATCAAAACAAGGTGGAAGATCCTTCCAAGGAACCAGTGTGAAGGAATAAAAAAATATGTTGTTGGTCTCATTATCAAGACATCCTCTGACCCAACTTGTGTAGAGAAAGAAAAGGTGTATATTGGGAAATTGAATATGATTCTTGTTCAGATACTTAAGCAAGAGTGGCCTAAGCATTGGCCAACTTTTATCAGTGACATTGTTGGAGCGAGTAGGACCAGTGAAAGTCTATGTCAAAATAATATGGTGATTCTTAAACTCTTGAGTGAAGAAGTGTTTGATTTCTCTAGTGGACAGATAACCCAAGTTAAAGCAAAGCATTTAAAAGACAGCATGTGCAATGAGTTTTCACAAATATTTCAGCTTTGTCAGTTTGTGATGGAAAATTCCCAAAATGCTCCCCTTGTTCATGCTACATTAGAAACACTGCTGAGATTTCTGAACTGGATTCCACTGGGATACATCTTTGAGACCAAGTTAATCAGCACATTAATTTACAAGCAAAGAATGGCTCAAGAAGTACTGACACATTTAAAGGAGCATCCTGATGCTTGGACACGGGTCGACACAATATTGGAGTTTTCGCAGAACATGAACACGAAATACTATGGACTACAGATTTTGGAAAATGTGATCAAAACAAGGTGGAAGATCCTTCCAAGGAACCAGTGTGAAGGAATAAAAAAATATGTTGTTGGTCTCATTATCAAGACATCCTCTGACCCAACTTGTGTAGAGAAAGAAAAGGTGTATATTGGGAAATTGAATATGATTCTTGTTCAGATACTTAAGCAAGAGTGGCCTAAGCATTGGCCAACTTTTATCAGTGACATTGTTGGAGCGAGTAGGACCAGTGAAAGTCTATGTCAAAATAATATGGTGATTCTTAAACTCTTGAGTGAAGAAGTGTTTGATTTCTCTAGTGGACAGATAACCCAAGTTAAAGCAAAGCATTTAAAAGACAGCATGTGCAATGAGTTTTCACAAATATTTCAGCTTTGTCAGTTTGTGATGGAAAATTCCCAAAATGCTCCCCTTGTTCATGCTACATTAGAAACACTGCTGAGATTTCTGAACTGGATTCCACTGGGATACATCTTTGAGACCAAGTTAATCAGCACATTAATTTACAAG
Peptide sequence:
MAQEVLTHLKEHPDAWTRVDTILEFSQNMNTKYYGLQILENVIKTRWKILPRNQCEGIKKYVVGLIIKTSSDPTCVEKEKVYIGKLNMILVQILKQEWPKHWPTFISDIVGASRTSESLCQNNMVILKLLSEEVFDFSSGQITQVKAKHLKDSMCNEFSQIFQLCQFVMENSQNAPLVHATLETLLRFLNWIPLGYIFETKLISTLIYKQRMAQEVLTHLKEHPDAWTRVDTILEFSQNMNTKYYGLQILENVIKTRWKILPRNQCEGIKKYVVGLIIKTSSDPTCVEKEKVYIGKLNMILVQILKQEWPKHWPTFISDIVGASRTSESLCQNNMVILKLLSEEVFDFSSGQITQVKAKHLKDSMCNEFSQIFQLCQFVMENSQNAPLVHATLETLLRFLNWIPLGYIFETKLISTLIYK
IRESfinder result
IRESfinder score
0.777527399
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page