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mmu_circRufy1_424
Basic information of circular RNA
PanCircBase ID:
mmu_circRufy1_424
mm39_Chr. Position ID:
chr11|50301392|50310549|-
Gene name:
Rufy1
Transcript:
ENSMUST00000020643.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
8,7,6,5,4
Exon/intron offsets:
0,3951,5674,6618,9055
Genomic length:
9157
Exon/intron sizes in nt:
70,66,62,124,102
Flanking exon/introns:
chr11:50298751-50301392|chr11:50310549-50311203
Splice length:
424
Other database IDs:
circAtlas: mmu-Rufy1_0012
circAtlas: hsa-RUFY1_0019, CIRCpedia: HSA_CIRCpedia_176803
Human Ortholog IDs:
Mature spliced Sequence:
GACAGCCGTGGGAAGAGGCAGAGCGTGGCTTTATCTTGCTCTCATGCAAAAGAAACTGGCAGATTATCTGAAAGTCCTCATAGACAACAAGCAGCTCCTAAGTGAGTTCTATGAGCCCGAGGCCTTAATGATGGAGGAGGAAGGAATGGTGATCGTGGGTCTGCTGGTGGGACTCAACGTTCTGGATGCCAACCTCTGCTTAAAGGGAGAAGACTTGGATTCTCAGGTCGGGGTGATTGACTTCTCTCTCTGTCTGAAGGACGCACAGGATCTTGACAGCGGCAGAGAGCATGAAAGAATTACCGATGTCCTTGATCAGAAAAATTACGTGGAGGAACTTAACCGGCACCTAAGCTGCACAGTTGGGGATCTTCAGACGAAGATAGATGGCTTGGAAAAGACGAACTCAAAGCTTCAAGAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACGTGGAGGAACTTAACCGG
59.68
AGAGCAAGATAAAGCCACGCT
60.07
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACGTGGAGGAACTTAACCGG
59.68
GAGAGCAAGATAAAGCCACGC
59.67
141
PCR template sequence:
TTACGTGGAGGAACTTAACCGGCACCTAAGCTGCACAGTTGGGGATCTTCAGACGAAGATAGATGGCTTGGAAAAGACGAACTCAAAGCTTCAAGAAGAGGACAGCCGTGGGAAGAGGCAGAGCGTGGCTTTATCTTGCTCTCATGCAAAAGAAACTGGCAGATTATCTGAAAGTCCTCATAGACAACAAGCAGCTCCTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-298-5p(1), mmu-miR-127-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCTTCAAGAAGAGGACAGCCGTGGGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRUFY1_424_ORF_1
1.2623
0.262293504
0.840780608
486
ORF sequence:
ATGCAAAAGAAACTGGCAGATTATCTGAAAGTCCTCATAGACAACAAGCAGCTCCTAAGTGAGTTCTATGAGCCCGAGGCCTTAATGATGGAGGAGGAAGGAATGGTGATCGTGGGTCTGCTGGTGGGACTCAACGTTCTGGATGCCAACCTCTGCTTAAAGGGAGAAGACTTGGATTCTCAGGTCGGGGTGATTGACTTCTCTCTCTGTCTGAAGGACGCACAGGATCTTGACAGCGGCAGAGAGCATGAAAGAATTACCGATGTCCTTGATCAGAAAAATTACGTGGAGGAACTTAACCGGCACCTAAGCTGCACAGTTGGGGATCTTCAGACGAAGATAGATGGCTTGGAAAAGACGAACTCAAAGCTTCAAGAAGAGGACAGCCGTGGGAAGAGGCAGAGCGTGGCTTTATCTTGCTCTCATGCAAAAGAAACTGGCAGATTATCTGAAAGTCCTCATAGACAACAAGCAGCTCCTAAGTGA
Peptide sequence:
MQKKLADYLKVLIDNKQLLSEFYEPEALMMEEEGMVIVGLLVGLNVLDANLCLKGEDLDSQVGVIDFSLCLKDAQDLDSGREHERITDVLDQKNYVEELNRHLSCTVGDLQTKIDGLEKTNSKLQEEDSRGKRQSVALSCSHAKETGRLSESPHRQQAAPK
IRESfinder result
IRESfinder score
0.498121948
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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