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mmu_circUrgcp_161
Basic information of circular RNA
PanCircBase ID:
mmu_circUrgcp_161
mm39_Chr. Position ID:
chr11|5672801|5676418|-
Gene name:
Urgcp
Transcript:
ENSMUST00000093362.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
5,4,3
Exon/intron offsets:
0,309,3546
Genomic length:
3617
Exon/intron sizes in nt:
39,51,71
Flanking exon/introns:
chr11:5668263-5672801|chr11:5676418-5676830
Splice length:
161
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GCATTCAGATCTGGGAGAAGTGGCCCCAGAAGTAAAACCTTCAGACAGCCAAACATCTGTGGCAATTGCAGATTTGGAATGGAGAGAAATGGAAGGAGATGACTGCGGGTTCCATTATGGAGATGGTACAAACGAGGCTCAGGACAATGACTTCCCCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGATGACTGCGGGTTCCAT
59.82
CCACAGATGTTTGGCTGTCTG
59.46
128
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGGAGATGACTGCGGGTTC
59.75
CCACAGATGTTTGGCTGTCTG
59.46
131
PCR template sequence:
GAGAGAAATGGAAGGAGATGACTGCGGGTTCCATTATGGAGATGGTACAAACGAGGCTCAGGACAATGACTTCCCCACAGGCATTCAGATCTGGGAGAAGTGGCCCCAGAAGTAAAACCTTCAGACAGCCAAACATCTGTGGCAATTGCAGATTTGGAAT
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-207(1)
siRNAs for circular RNA silencing
Junction sequence
GACTTCCCCACAGGCATTCAGATCTG
siRNA sets
GATCTGAATGCCTGTGGGG, AGATCTGAATGCCTGTGGG, ATCTGAATGCCTGTGGGGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCURGCP_161_ORF_1
0.9849
-0.155624493
0.053928632
165
ORF sequence:
ATGACTGCGGGTTCCATTATGGAGATGGTACAAACGAGGCTCAGGACAATGACTTCCCCACAGGCATTCAGATCTGGGAGAAGTGGCCCCAGAAGTAAAACCTTCAGACAGCCAAACATCTGTGGCAATTGCAGATTTGGAATGGAGAGAAATGGAAGGAGATGA
Peptide sequence:
MTAGSIMEMVQTRLRTMTSPQAFRSGRSGPRSKTFRQPNICGNCRFGMERNGRR
IRESfinder result
IRESfinder score
0.398699392
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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