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mmu_circKpna6_469
Basic information of circular RNA
PanCircBase ID:
mmu_circKpna6_469
mm39_Chr. Position ID:
chr4|129545380|129548180|-
Gene name:
Kpna6
Transcript:
ENSMUST00000102590.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
11,10,9,8
Exon/intron offsets:
0,1850,2254,2700
Genomic length:
2800
Exon/intron sizes in nt:
126,79,164,100
Flanking exon/introns:
chr4:129544604-129545380|chr4:129548180-129548657
Splice length:
469
Other database IDs:
CIRCpedia: MMU_CIRCpedia_7388, circAtlas: mmu-Kpna6_0008
Human Ortholog IDs:
Mature spliced Sequence:
ACTCCTTACTAAGTCCACACGACTGACAATGACACGGAATGCAGTCTGGGCCCTGTCAAACCTCTGCCGAGGCAAGAACCCTCCTCCAGAGTTTGCAAAGGTCTCTCCTTGTTTGCCTGTATTGTCCCGACTGCTCTTCAGCAGTGACTCAGACTTGCTGGCAGATGCTTGCTGGGCCCTCTCCTACCTGTCTGATGGCCCCAATGAGAAGATCCAGGCAGTCATAGACTCTGGAGTCTGCCGGAGATTGGTAGAGCTTCTGATGCACAACGATTACAAAGTGGCGTCTCCTGCCTTGAGAGCTGTGGGTAATATTGTCACTGGGGATGACATCCAGACCCAGGTCATTCTTAATTGTTCAGCCCTCCCTTGCCTCCTCCACCTACTGAGCAGCTCTAAGGAATCAATCCGGAAGGAAGCTTGCTGGACCATTTCAAACATCACTGCTGGCAACAGGGCTCAAATACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCACCTACTGAGCAGCTCT
59.96
CCAGACTGCATTCCGTGTCA
60.32
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGCCTCCTCCACCTACTGA
59.88
CCAGACTGCATTCCGTGTCA
60.32
149
PCR template sequence:
TTGCCTCCTCCACCTACTGAGCAGCTCTAAGGAATCAATCCGGAAGGAAGCTTGCTGGACCATTTCAAACATCACTGCTGGCAACAGGGCTCAAATACAGACTCCTTACTAAGTCCACACGACTGACAATGACACGGAATGCAGTCTGGGCCCTGTCAAACCTCTGCCGAGGCAAGAACCCTCCTCCAGAGTTTGCAAAG
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-203-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGCTCAAATACAGACTCCTTACTAAG
siRNA sets
TAAGGAGTCTGTATTTGAG, TTAGTAAGGAGTCTGTATT, GTAAGGAGTCTGTATTTGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKPNA6_469_ORF_1
0.8204
0.192474353
0.57847921
453
ORF sequence:
ATGACACGGAATGCAGTCTGGGCCCTGTCAAACCTCTGCCGAGGCAAGAACCCTCCTCCAGAGTTTGCAAAGGTCTCTCCTTGTTTGCCTGTATTGTCCCGACTGCTCTTCAGCAGTGACTCAGACTTGCTGGCAGATGCTTGCTGGGCCCTCTCCTACCTGTCTGATGGCCCCAATGAGAAGATCCAGGCAGTCATAGACTCTGGAGTCTGCCGGAGATTGGTAGAGCTTCTGATGCACAACGATTACAAAGTGGCGTCTCCTGCCTTGAGAGCTGTGGGTAATATTGTCACTGGGGATGACATCCAGACCCAGGTCATTCTTAATTGTTCAGCCCTCCCTTGCCTCCTCCACCTACTGAGCAGCTCTAAGGAATCAATCCGGAAGGAAGCTTGCTGGACCATTTCAAACATCACTGCTGGCAACAGGGCTCAAATACAGACTCCTTACTAA
Peptide sequence:
MTRNAVWALSNLCRGKNPPPEFAKVSPCLPVLSRLLFSSDSDLLADACWALSYLSDGPNEKIQAVIDSGVCRRLVELLMHNDYKVASPALRAVGNIVTGDDIQTQVILNCSALPCLLHLLSSSKESIRKEACWTISNITAGNRAQIQTPY
IRESfinder result
IRESfinder score
0.619881622
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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