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mmu_circNfx1_144
Basic information of circular RNA
PanCircBase ID:
mmu_circNfx1_144
mm39_Chr. Position ID:
chr4|41017971|41018489|+
Gene name:
Nfx1
Transcript:
ENSMUST00000098143.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
18,19
Exon/intron offsets:
0,476
Genomic length:
518
Exon/intron sizes in nt:
102,42
Flanking exon/introns:
chr4:41016150-41017971|chr4:41018489-41021748
Splice length:
144
Other database IDs:
CIRCpedia: MMU_CIRCpedia_19534, circAtlas: mmu-Nfx1_0015
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
AATAGTTGCTATTTCTATGGCCTCTAAAATAACGGACATGCAGCTTGGAGACTCAGTGGAGATCAGCAAGCTCATTACCAAGAAGGAAGTCCAACAAGCCAGGTTGCAGTGTGATGAGGAGTGTGCTGCCCTGGAAAGGAGAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGAAGTCCAACAAGCCAGG
59.89
CCACTGAGTCTCCAAGCTGC
60.67
120
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGAAGTCCAACAAGCCAGG
59.89
TCCACTGAGTCTCCAAGCTG
59.03
121
PCR template sequence:
CATTACCAAGAAGGAAGTCCAACAAGCCAGGTTGCAGTGTGATGAGGAGTGTGCTGCCCTGGAAAGGAGAAAAATAGTTGCTATTTCTATGGCCTCTAAAATAACGGACATGCAGCTTGGAGACTCAGTGGAGATCAGCAAGCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
NA
Interacting miRNAs (#binding sites)
NA
siRNAs for circular RNA silencing
Junction sequence
TGGAAAGGAGAAAAATAGTTGCTATT
siRNA sets
AACTATTTTTCTCCTTTCC, ATAGCAACTATTTTTCTCC, ACTATTTTTCTCCTTTCCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNFX1_144_ORF_1
1.141
0.319156987
0.531285506
270
ORF sequence:
ATGGCCTCTAAAATAACGGACATGCAGCTTGGAGACTCAGTGGAGATCAGCAAGCTCATTACCAAGAAGGAAGTCCAACAAGCCAGGTTGCAGTGTGATGAGGAGTGTGCTGCCCTGGAAAGGAGAAAAATAGTTGCTATTTCTATGGCCTCTAAAATAACGGACATGCAGCTTGGAGACTCAGTGGAGATCAGCAAGCTCATTACCAAGAAGGAAGTCCAACAAGCCAGGTTGCAGTGTGATGAGGAGTGTGCTGCCCTGGAAAGGAGA
Peptide sequence:
MASKITDMQLGDSVEISKLITKKEVQQARLQCDEECAALERRKIVAISMASKITDMQLGDSVEISKLITKKEVQQARLQCDEECAALERR
IRESfinder result
IRESfinder score
0.379075967
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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