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mmu_circRfc1_847
Basic information of circular RNA
PanCircBase ID:
mmu_circRfc1_847
mm39_Chr. Position ID:
chr5|65453296|65476873|-
Gene name:
Rfc1
Transcript:
ENSMUST00000203581.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
8,7,6,5,4,3,2
Exon/intron offsets:
0,1445,5979,7022,15087,17004,23451
Genomic length:
23577
Exon/intron sizes in nt:
9,17,81,20,23,31,23,76,000
Flanking exon/introns:
chr5:65451278-65453296|chr5:65476873-65492866
Splice length:
847
Other database IDs:
circAtlas: mmu-Rfc1_0048
Human Ortholog IDs:
Mature spliced Sequence:
GACATTCGGAAATTCTTTGGGGTTATATCAAGTGGAAAAAAGCCTGTAAACGAGACAGTAAAGAATGAGAAGACAAAAGCTTCGGAGGGAACTGTCAAAGGAAAAAAGGGAGTCAAGGAGGCCAAGGTCAATAACTCCGGTAAAGAGGACGCCTCCAAACCAAAGCAGCACAGCAAGAAGAAGAGGATCATCAATGACTCAGACTCAGAGTCAGAGGAGACAGTACAGGTAAAAAATGCTAAAAAGAAATCAGAAAAATTGTCACTGTCTTATAAACCTGGTAAAGTCTCTCAGAAGGATCCTGTCACCTACGTCTCTGAGACAGATGAAGATGATGACTTTGTATGTAAAAAGGCAGCCTCCAAATCAAAAGAGAATGGAGTATCTACAAATAGTTACCTTGGAACATCAAACGTGAAAAAAAATGAAGAAAACGTTAAGACTAAGAACAAGCCGTTATCTCCAATAAAACTCACACCAACGTCAGTGCTCGACTATTTTGGAACTGAAAGTGTCCAGAGATCTGGGAAGAAGATGGTGACAAGCAAAAGGAAAGAACCAGATTTCTGCTTATCTTGCTTGATTTTCTTTGGAATACAGTCTTCTCAAAACACAGAGGATTCCAGATTAAATGATGAGGCCATCGCCAAGCAGCTGCAGCTGGATGAAGATGCAGAGCTGGAGAGGCAGTTGCATGAAGATGAAGAATTTGCAAGAACACTGGCCTTATTGGATGAAGAACCCAAGATCAAAAAGGCCCGAAAGGATTCTGAAGAGGGAGAAGAATCATTTTCATCTGTCCAAGATGATTTAAGCAAAGCAGAAAAGCAGAAAAGCCCTAATAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGAAAGGATTCTGAAGAGGGAGA
59.55
TCCCTCCGAAGCTTTTGTCT
58.94
178
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGATTCTGAAGAGGGAGAAGA
57.66
GACAGTTCCCTCCGAAGCTT
59.68
180
PCR template sequence:
ATCAAAAAGGCCCGAAAGGATTCTGAAGAGGGAGAAGAATCATTTTCATCTGTCCAAGATGATTTAAGCAAAGCAGAAAAGCAGAAAAGCCCTAATAAAGGACATTCGGAAATTCTTTGGGGTTATATCAAGTGGAAAAAAGCCTGTAAACGAGACAGTAAAGAATGAGAAGACAAAAGCTTCGGAGGGAACTGTCAAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-199a-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-136-5p(1), mmu-miR-34b-5p(1), mmu-miR-325-3p(1), mmu-miR-1199-5p(1), mmu-miR-466b-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
AGCCCTAATAAAGGACATTCGGAAAT
siRNA sets
ATTTCCGAATGTCCTTTAT, TTTCCGAATGTCCTTTATT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRFC1_847_ORF_1
0.779
0.196532354
0.430182204
381
ORF sequence:
ATGGTGACAAGCAAAAGGAAAGAACCAGATTTCTGCTTATCTTGCTTGATTTTCTTTGGAATACAGTCTTCTCAAAACACAGAGGATTCCAGATTAAATGATGAGGCCATCGCCAAGCAGCTGCAGCTGGATGAAGATGCAGAGCTGGAGAGGCAGTTGCATGAAGATGAAGAATTTGCAAGAACACTGGCCTTATTGGATGAAGAACCCAAGATCAAAAAGGCCCGAAAGGATTCTGAAGAGGGAGAAGAATCATTTTCATCTGTCCAAGATGATTTAAGCAAAGCAGAAAAGCAGAAAAGCCCTAATAAAGGACATTCGGAAATTCTTTGGGGTTATATCAAGTGGAAAAAAGCCTGTAAACGAGACAGTAAAGAATGA
Peptide sequence:
MVTSKRKEPDFCLSCLIFFGIQSSQNTEDSRLNDEAIAKQLQLDEDAELERQLHEDEEFARTLALLDEEPKIKKARKDSEEGEESFSSVQDDLSKAEKQKSPNKGHSEILWGYIKWKKACKRDSKE
IRESfinder result
IRESfinder score
0.448234415
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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