top of page
mmu_circNdel1_252
Basic information of circular RNA
PanCircBase ID:
mmu_circNdel1_252
mm39_Chr. Position ID:
chr11|68734646|68736250|-
Gene name:
Ndel1
Transcript:
ENSMUST00000018880.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,2
Exon/intron offsets:
0,1506
Genomic length:
1604
Exon/intron sizes in nt:
154,98
Flanking exon/introns:
chr11:68732994-68734646|chr11:68736250-68743767
Splice length:
252
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GCTTTCTTGATCATGGATGGTGAAGATATACCGGATTTTTCAAGTTTAAAGGAAGAAACTGCTTATTGGAAGGAACTTTCCTTGAAGTATAAGCAAAGCTTCCAGGAAGCTCGGGATGAGCTAGTTGAGTTCCAGGAAGGAAGCAGAGAGTTAGAAGCAGAGTTGGAGGCACAGTTAGTACAGGCTGAACAAAGAAATAGAGACCTGCAGGCTGATAACCAAAGACTGAAGTATGAAGTGGAGGCGTTAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAAGCAGAGTTGGAGGCACA
60.25
GGAAAGTTCCTTCCAATAAGCAGT
59.23
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCAGAGTTGGAGGCACAG
60.25
GGAAAGTTCCTTCCAATAAGCAGT
59.23
179
PCR template sequence:
AGAAGCAGAGTTGGAGGCACAGTTAGTACAGGCTGAACAAAGAAATAGAGACCTGCAGGCTGATAACCAAAGACTGAAGTATGAAGTGGAGGCGTTAAAGGCTTTCTTGATCATGGATGGTGAAGATATACCGGATTTTTCAAGTTTAAAGGAAGAAACTGCTTATTGGAAGGAACTTTCCTTGAAGTATAAGCAAAGCT
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-9-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGAGGCGTTAAAGGCTTTCTTGATCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNDEL1_252_ORF_1
0.9254
0.211994031
0.707482641
492
ORF sequence:
ATGGATGGTGAAGATATACCGGATTTTTCAAGTTTAAAGGAAGAAACTGCTTATTGGAAGGAACTTTCCTTGAAGTATAAGCAAAGCTTCCAGGAAGCTCGGGATGAGCTAGTTGAGTTCCAGGAAGGAAGCAGAGAGTTAGAAGCAGAGTTGGAGGCACAGTTAGTACAGGCTGAACAAAGAAATAGAGACCTGCAGGCTGATAACCAAAGACTGAAGTATGAAGTGGAGGCGTTAAAGGCTTTCTTGATCATGGATGGTGAAGATATACCGGATTTTTCAAGTTTAAAGGAAGAAACTGCTTATTGGAAGGAACTTTCCTTGAAGTATAAGCAAAGCTTCCAGGAAGCTCGGGATGAGCTAGTTGAGTTCCAGGAAGGAAGCAGAGAGTTAGAAGCAGAGTTGGAGGCACAGTTAGTACAGGCTGAACAAAGAAATAGAGACCTGCAGGCTGATAACCAAAGACTGAAGTATGAAGTGGAGGCGTTAAAG
Peptide sequence:
MDGEDIPDFSSLKEETAYWKELSLKYKQSFQEARDELVEFQEGSRELEAELEAQLVQAEQRNRDLQADNQRLKYEVEALKAFLIMDGEDIPDFSSLKEETAYWKELSLKYKQSFQEARDELVEFQEGSRELEAELEAQLVQAEQRNRDLQADNQRLKYEVEALK
IRESfinder result
IRESfinder score
0.55210233
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page