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mmu_circ5330434G04Rik_302
Basic information of circular RNA
PanCircBase ID:
mmu_circ5330434G04Rik_302
mm39_Chr. Position ID:
chrX|104421621|104426555|-
Gene name:
5330434G04Rik
Transcript:
ENSMUST00000130264.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,2
Exon/intron offsets:
0,4737
Genomic length:
4934
Exon/intron sizes in nt:
1,05,197
Flanking exon/introns:
chrX:104419443-104421621|chrX:104426555-104431487
Splice length:
302
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGCACAGTGAGGCACAGAATCAGTTGTAGAAGCACTTCAGGGAATTCGGATACTATTTTGTGGCCTGGCAAGATCAGCAGCCTTACTATCTTAGTCCCTGCCAGTCATCAGCTTCTGGTTTCCCTGTTATCCTGCTGCTCCCTAGAATGCAGCTATTAAGTGGCCTAAGAGCCAGCACCTTCACGGAGTAGCAAAGGAATGGGACAGAAGACTCCAGCTACAATGGGAATCAACCAGTGTCTATGTTGTACAGCCTGTTCCAGCAGTCCCAGTTGCCTAAAGGCCTAGCTATCAGAATAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTACAGCCTGTTCCAGCAG
59.96
GTAAGGCTGCTGATCTTGCC
58.98
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTACAGCCTGTTCCAGCAGT
59.96
GTAAGGCTGCTGATCTTGCC
58.98
141
PCR template sequence:
GGACAGAAGACTCCAGCTACAATGGGAATCAACCAGTGTCTATGTTGTACAGCCTGTTCCAGCAGTCCCAGTTGCCTAAAGGCCTAGCTATCAGAATAAGGTGCACAGTGAGGCACAGAATCAGTTGTAGAAGCACTTCAGGGAATTCGGATACTATTTTGTGGCCTGGCAAGATCAGCAGCCTTACTATCTTAGTCCCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-214-3p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTATCAGAATAAGGTGCACAGTGAGG
siRNA sets
ACTGTGCACCTTATTCTGA, TCACTGTGCACCTTATTCT, CACTGTGCACCTTATTCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRC5330434G04RIK_302_ORF_1
0.8828
-0.141163581
0.068349809
219
ORF sequence:
ATGTTGTACAGCCTGTTCCAGCAGTCCCAGTTGCCTAAAGGCCTAGCTATCAGAATAAGGTGCACAGTGAGGCACAGAATCAGTTGTAGAAGCACTTCAGGGAATTCGGATACTATTTTGTGGCCTGGCAAGATCAGCAGCCTTACTATCTTAGTCCCTGCCAGTCATCAGCTTCTGGTTTCCCTGTTATCCTGCTGCTCCCTAGAATGCAGCTATTAA
Peptide sequence:
MLYSLFQQSQLPKGLAIRIRCTVRHRISCRSTSGNSDTILWPGKISSLTILVPASHQLLVSLLSCCSLECSY
IRESfinder result
IRESfinder score
0.63812676
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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