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mmu_ciCpne3_521
Basic information of circular RNA
PanCircBase ID:
mmu_ciCpne3_521
mm39_Chr. Position ID:
chr4|19532533|19533054|-
Gene name:
Cpne3
Transcript:
ENSMUST00000029885.5
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
10
Exon/intron offsets:
0
Genomic length:
521
Exon/intron sizes in nt:
521
Flanking exon/introns:
chr4:19532532-19533054
Splice length:
521
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTAACACTAAGTTTTCTAACATAGGCTGTTAGATGGTGCCTCCCCCACTCTGTTTTGCTGCACTCCTTTAATGCCAGGTTGACTCTGTAATGAAATTTACCCAATCTGTTTCCTATGACTTCCTCATGGACCATTTAGGTTCATCATGGAAGTTTGACTTAGTTAGTGAGTTGATGAGTGCTCTCCTCTTTAGAGAAAATAGATATGTATAAGCTAGTGGTTATCCTACAGTAATTTAAGAAATAGAAACATGCATATAAGAACAGCCCCTAATATGGGCCATTCATAGGATGAATGATTCATGATTCTTCAGTCTGGAAAGAGAAGAACAGGTTGTTTTCATGATGAATTCAGTTCAATTGTTTGTAGAAATGCTGTGGTCATTTGTTAGGAGATGGCAGTAATAGGTTCTGGGATGATTTGGGGTCTTGTACCTGGAAACTTTCTTGGACCTCAAGCTCAGATAGGTAGCCCTTTTCTCTCTTTGGTAAGAACTCCTGTCTGTCGTTTCTTGGTA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCTGGAAACTTTCTTGGACCT
59.49
GTGCAGCAAAACAGAGTGGG
59.97
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCTGGAAACTTTCTTGGACCT
59.49
AGCAAAACAGAGTGGGGGAG
59.89
148
PCR template sequence:
GATTTGGGGTCTTGTACCTGGAAACTTTCTTGGACCTCAAGCTCAGATAGGTAGCCCTTTTCTCTCTTTGGTAAGAACTCCTGTCTGTCGTTTCTTGGTAGTAAGTAACACTAAGTTTTCTAACATAGGCTGTTAGATGGTGCCTCCCCCACTCTGTTTTGCTGCACTCCTTTAATGCCAGGTTGACTCTGTAATGAAAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-3087-3p(1), mmu-miR-323-3p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCGTTTCTTGGTAGTAAGTAACACTA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CICPNE3_521_ORF_1
0.9001
-0.359841562
0.019504251
159
ORF sequence:
ATGGCAGTAATAGGTTCTGGGATGATTTGGGGTCTTGTACCTGGAAACTTTCTTGGACCTCAAGCTCAGATAGGTAGCCCTTTTCTCTCTTTGGTAAGAACTCCTGTCTGTCGTTTCTTGGTAGTAAGTAACACTAAGTTTTCTAACATAGGCTGTTAG
Peptide sequence:
MAVIGSGMIWGLVPGNFLGPQAQIGSPFLSLVRTPVCRFLVVSNTKFSNIGC
IRESfinder result
IRESfinder score
0.839027501
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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