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mmu_circNpm1_263
Basic information of circular RNA
PanCircBase ID:
mmu_circNpm1_263
mm39_Chr. Position ID:
chr11|33109933|33110921|-
Gene name:
Npm1
Transcript:
ENSMUST00000075641.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
6,5,4
Exon/intron offsets:
0,400,894
Genomic length:
988
Exon/intron sizes in nt:
62,107,94
Flanking exon/introns:
chr11:33107048-33109933|chr11:33110921-33111105
Splice length:
263
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTTTCCCTAGGGGGCTTTGAAATTACACCACCTGTGGTCTTACGGTTGAAGTGTGGTTCAGGGCCTGTGCACATTAGTGGACAGCATCTAGTAGCTGTAGAGGAAGATGCAGAGTCTGAAGATGAAGATGAGGAGGACGTAAAACTCTTAGGCATGTCTGGAAAGCGATCTGCTCCTGGAGGTGGTAACAAGGTTCCACAGAAAAAAGTAAAACTTGATGAAGATGATGAGGACGATGATGAGGACGATGAGGATGATGAGGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGCTCCTGGAGGTGGTAA
59.88
CTAATGTGCACAGGCCCTGA
60.04
172
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGCTCCTGGAGGTGGTAAC
59.75
CTAATGTGCACAGGCCCTGA
60.04
171
PCR template sequence:
AGCGATCTGCTCCTGGAGGTGGTAACAAGGTTCCACAGAAAAAAGTAAAACTTGATGAAGATGATGAGGACGATGATGAGGACGATGAGGATGATGAGGAGTTTCCCTAGGGGGCTTTGAAATTACACCACCTGTGGTCTTACGGTTGAAGTGTGGTTCAGGGCCTGTGCACATTAGTGGACAGCATCTAGTAGCTGTAG
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-125a-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGGATGATGAGGAGTTTCCCTAGGGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNPM1_263_ORF_1
1.1399
0.529629591
0.473965789
120
ORF sequence:
ATGTCTGGAAAGCGATCTGCTCCTGGAGGTGGTAACAAGGTTCCACAGAAAAAAGTAAAACTTGATGAAGATGATGAGGACGATGATGAGGACGATGAGGATGATGAGGAGTTTCCCTAG
Peptide sequence:
MSGKRSAPGGGNKVPQKKVKLDEDDEDDDEDDEDDEEFP
IRESfinder result
IRESfinder score
0.225292255
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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