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mmu_ciRab4b_240
Basic information of circular RNA
PanCircBase ID:
mmu_ciRab4b_240
mm39_Chr. Position ID:
chr7|26875342|26875582|-
Gene name:
Rab4b
Transcript:
ENSMUST00000093040.13
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
2
Exon/intron offsets:
0
Genomic length:
240
Exon/intron sizes in nt:
240
Flanking exon/introns:
chr7:26875318-26875582
Splice length:
240
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGAGTTTCTGGCAGGACCCTGGAACTGCGGATGTGGTCATGGTGTGGGTCAGTGGGGCAGCAGGTGGGGTAGGTAGCAGGTACCATTGACTAAAGCTAGTACTATAGGCTTGCCTCTAGCTTTGGTGGATGGTCTTTGCTAAGTTCTCTGCCAACCCAGCAGTGAGAATTGGGGTACAGAAAAGGAGGAAGAGGTCTGCAGGATGGGGGGGATTCCAGGAGCCCCTGCACTGCCCCCCC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGCAGTGAGAATTGGGGT
59.96
TACCTGCTACCTACCCCACC
60.03
167
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGCAGTGAGAATTGGGGT
59.96
GGTACCTGCTACCTACCCCA
60.03
169
PCR template sequence:
TAAGTTCTCTGCCAACCCAGCAGTGAGAATTGGGGTACAGAAAAGGAGGAAGAGGTCTGCAGGATGGGGGGGATTCCAGGAGCCCCTGCACTGCCCCCCCGTGAGTTTCTGGCAGGACCCTGGAACTGCGGATGTGGTCATGGTGTGGGTCAGTGGGGCAGCAGGTGGGGTAGGTAGCAGGTACCATTGACTAAAGCTAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-34c-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCACTGCCCCCCCGTGAGTTTCTGGC
siRNA sets
CAGAAACTCACGGGGGGGC,AAACTCACGGGGGGGCAGT,AGAAACTCACGGGGGGGCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRAB4B_240_ORF_1
0.6525
0.030011026
0.078149247
201
ORF sequence:
ATGGTCTTTGCTAAGTTCTCTGCCAACCCAGCAGTGAGAATTGGGGTACAGAAAAGGAGGAAGAGGTCTGCAGGATGGGGGGGATTCCAGGAGCCCCTGCACTGCCCCCCCGTGAGTTTCTGGCAGGACCCTGGAACTGCGGATGTGGTCATGGTGTGGGTCAGTGGGGCAGCAGGTGGGGTAGGTAGCAGGTACCATTGA
Peptide sequence:
MVFAKFSANPAVRIGVQKRRKRSAGWGGFQEPLHCPPVSFWQDPGTADVVMVWVSGAAGGVGSRYH
IRESfinder result
IRESfinder score
0.545531845
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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