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mmu_circXpo4_843
Basic information of circular RNA
PanCircBase ID:
mmu_circXpo4_843
mm39_Chr. Position ID:
chr14|57823323|57828536|-
Gene name:
Xpo4
Transcript:
ENSMUST00000174545.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
21,20,19,18,17
Exon/intron offsets:
0,713,2086,4074,4919
Genomic length:
5213
Exon/intron sizes in nt:
11,81,31,11,91,81,294
Flanking exon/introns:
chr14:57822149-57823323|chr14:57828536-57831284
Splice length:
843
Other database IDs:
CIRCpedia: MMU_CIRCpedia_217369, circAtlas: mmu-Xpo4_0031
Human Ortholog IDs:
Mature spliced Sequence:
GTTCTGCAGCCTCTTCAGCAGAGGTTCCTGAGAGTGATCAACCAAGAGAACTTTCAGCAGATGTGTCAGCAGGAGGAAGTCAAGCAGGAGATCACTGCCACATTGGAGGCCCTGTGTGGCATTGCTGAGGCCACCCAGATCGACAATGTAGCCATCCTTTTTAATTTTTTAATGGACTTCCTTAACAATTGCATTGGTTTAATGGAAGTTTACAAAAATACTCCAGAAACTGTCAATCTCATTATAGAAGTTTTTGTTGAAGTTGCACATAAACAAATATGCTATCTTGGAGAGTCCAAAGCTATGCATTTATACGAAGCCTGCCTTACTTTGTTACAAGTGTATTCTAAGAATAACTTAGGGCGGCAAAGGATAGACGTCACGGCGGAGGAAGAGCAGTACCAAGACCTGCTTCTCATCATGGAGCTTCTCACTAACCTTCTCTCAAAGGAGTTCATCGACTTTAGTGACACAGATGAAGTGTTTAGAGGACATGAGCCAGGACAAGCAGCAGGCAGATCTGTATCGGCAGCTGATGTCGTTTTATATGGAGTAAACCTAATTCTGCCCTTAATGTCACAAGATCTTTTGAAGTTTCCAACCCTTTGTAATCAATATTACAAACTGATCACATTTATTTGTGAGATTTTTCCTGAAAAGATACCGCAGCTTCCTGAGGATCTGTTTAAGAGTCTGATGTACTCCCTAGAACTAGGGATGACATCAATGAGTTCAGAAGTATGCCAGCTTTGTCTCGAGGCCTTGACACCATTAGCTGAACAATGTGCTAAAGCACAAGAAACGGATTCACCACTTTTTCTAGCAACACGACACTTCCTTAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGTCTCGAGGCCTTGACAC
59.97
TGCTTGACTTCCTCCTGCTG
59.96
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGTCTCGAGGCCTTGACAC
59.97
CCTGCTGACACATCTGCTGA
60.04
167
PCR template sequence:
CCAGCTTTGTCTCGAGGCCTTGACACCATTAGCTGAACAATGTGCTAAAGCACAAGAAACGGATTCACCACTTTTTCTAGCAACACGACACTTCCTTAAGGTTCTGCAGCCTCTTCAGCAGAGGTTCCTGAGAGTGATCAACCAAGAGAACTTTCAGCAGATGTGTCAGCAGGAGGAAGTCAAGCAGGAGATCACTGCCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-221-3p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-216a-5p(1), mmu-miR-222-3p(1), mmu-miR-149-5p(1), mmu-miR-22-3p(1), mmu-miR-34b-5p(1), mmu-miR-3065-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACACTTCCTTAAGGTTCTGCAGCCTC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCXPO4_843_ORF_1
0.9458
0.054454895
0.999782421
1626
ORF sequence:
ATGTGTCAGCAGGAGGAAGTCAAGCAGGAGATCACTGCCACATTGGAGGCCCTGTGTGGCATTGCTGAGGCCACCCAGATCGACAATGTAGCCATCCTTTTTAATTTTTTAATGGACTTCCTTAACAATTGCATTGGTTTAATGGAAGTTTACAAAAATACTCCAGAAACTGTCAATCTCATTATAGAAGTTTTTGTTGAAGTTGCACATAAACAAATATGCTATCTTGGAGAGTCCAAAGCTATGCATTTATACGAAGCCTGCCTTACTTTGTTACAAGTGTATTCTAAGAATAACTTAGGGCGGCAAAGGATAGACGTCACGGCGGAGGAAGAGCAGTACCAAGACCTGCTTCTCATCATGGAGCTTCTCACTAACCTTCTCTCAAAGGAGTTCATCGACTTTAGTGACACAGATGAAGTGTTTAGAGGACATGAGCCAGGACAAGCAGCAGGCAGATCTGTATCGGCAGCTGATGTCGTTTTATATGGAGTAAACCTAATTCTGCCCTTAATGTCACAAGATCTTTTGAAGTTTCCAACCCTTTGTAATCAATATTACAAACTGATCACATTTATTTGTGAGATTTTTCCTGAAAAGATACCGCAGCTTCCTGAGGATCTGTTTAAGAGTCTGATGTACTCCCTAGAACTAGGGATGACATCAATGAGTTCAGAAGTATGCCAGCTTTGTCTCGAGGCCTTGACACCATTAGCTGAACAATGTGCTAAAGCACAAGAAACGGATTCACCACTTTTTCTAGCAACACGACACTTCCTTAAGGTTCTGCAGCCTCTTCAGCAGAGGTTCCTGAGAGTGATCAACCAAGAGAACTTTCAGCAGATGTGTCAGCAGGAGGAAGTCAAGCAGGAGATCACTGCCACATTGGAGGCCCTGTGTGGCATTGCTGAGGCCACCCAGATCGACAATGTAGCCATCCTTTTTAATTTTTTAATGGACTTCCTTAACAATTGCATTGGTTTAATGGAAGTTTACAAAAATACTCCAGAAACTGTCAATCTCATTATAGAAGTTTTTGTTGAAGTTGCACATAAACAAATATGCTATCTTGGAGAGTCCAAAGCTATGCATTTATACGAAGCCTGCCTTACTTTGTTACAAGTGTATTCTAAGAATAACTTAGGGCGGCAAAGGATAGACGTCACGGCGGAGGAAGAGCAGTACCAAGACCTGCTTCTCATCATGGAGCTTCTCACTAACCTTCTCTCAAAGGAGTTCATCGACTTTAGTGACACAGATGAAGTGTTTAGAGGACATGAGCCAGGACAAGCAGCAGGCAGATCTGTATCGGCAGCTGATGTCGTTTTATATGGAGTAAACCTAATTCTGCCCTTAATGTCACAAGATCTTTTGAAGTTTCCAACCCTTTGTAATCAATATTACAAACTGATCACATTTATTTGTGAGATTTTTCCTGAAAAGATACCGCAGCTTCCTGAGGATCTGTTTAAGAGTCTGATGTACTCCCTAGAACTAGGGATGACATCAATGAGTTCAGAAGTATGCCAGCTTTGTCTCGAGGCCTTGACACCATTAGCTGAACAATGTGCTAAAGCACAAGAAACGGATTCACCACTTTTTCTAGCAACACGACACTTCCTTAAG
Peptide sequence:
MCQQEEVKQEITATLEALCGIAEATQIDNVAILFNFLMDFLNNCIGLMEVYKNTPETVNLIIEVFVEVAHKQICYLGESKAMHLYEACLTLLQVYSKNNLGRQRIDVTAEEEQYQDLLLIMELLTNLLSKEFIDFSDTDEVFRGHEPGQAAGRSVSAADVVLYGVNLILPLMSQDLLKFPTLCNQYYKLITFICEIFPEKIPQLPEDLFKSLMYSLELGMTSMSSEVCQLCLEALTPLAEQCAKAQETDSPLFLATRHFLKVLQPLQQRFLRVINQENFQQMCQQEEVKQEITATLEALCGIAEATQIDNVAILFNFLMDFLNNCIGLMEVYKNTPETVNLIIEVFVEVAHKQICYLGESKAMHLYEACLTLLQVYSKNNLGRQRIDVTAEEEQYQDLLLIMELLTNLLSKEFIDFSDTDEVFRGHEPGQAAGRSVSAADVVLYGVNLILPLMSQDLLKFPTLCNQYYKLITFICEIFPEKIPQLPEDLFKSLMYSLELGMTSMSSEVCQLCLEALTPLAEQCAKAQETDSPLFLATRHFLK
IRESfinder result
IRESfinder score
0.731975287
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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