top of page
mmu_circNek3_568
Basic information of circular RNA
PanCircBase ID:
mmu_circNek3_568
mm39_Chr. Position ID:
chr8|22636946|22648726|-
Gene name:
Nek3
Transcript:
ENSMUST00000033865.16
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
10,9,8,7,6,5
Exon/intron offsets:
0,1552,2930,10045,10219,11696
Genomic length:
11780
Exon/intron sizes in nt:
73,201,55,87,68,84
Flanking exon/introns:
chr8:22632955-22636946|chr8:22648726-22650207
Splice length:
568
Other database IDs:
circAtlas: mmu-Nek3_0001
Human Ortholog IDs:
Mature spliced Sequence:
ATACTTAATTGGTTTATACAAATTTGTCTTGGAGTAAATCACATTCATAAGAGACGTGTTTTACACAGAGATATCAAGTCGAAAAATGTCTTCCTCACCCACAATGGAAAAGTGAAATTGGGAGATTTTGGCTCTGCCCGTCTTCTCTCCAGTCCCATGGCGTTTGCATGCACGTACGTGGGAACACCTTATTATGTGCCTCCAGAAATCTGGGAGAACCTGCCTTACAACAATAAAAGTGACATCTGGTCCTTGGGATGCATTCTGTATGAACTCTGCGCTCTGAAGCATCCATTCCAGGCAAATAGTTGGAAAAACCTGATCCTGAAAATATGCCAGGGGCCCATCCACCCGCTGCCGGCTCTGTACTCCTGCAAGCTTCAGGGCCTGGTCAAGCAGATGCTGAAAAGGAACCCTTCCCACCGCCCCTCCGCCACAACCCTGCTCTGCAGGGGTAGCTTGGCTCCACTGGTCCCGAAGTGCTTGCCCCCTCAGATCATCAGAGAATATGGAGAACAGATATTAGATGAAATCAAAATATCCACGCCTAAGAATATGAAAAAACAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCCCCCTCAGATCATCAGA
60.03
GAGGAAGACATTTTTCGACTTGA
57.08
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCCCCCTCAGATCATCAGAG
59.31
TGAGGAAGACATTTTTCGACTTGA
58.64
180
PCR template sequence:
CTGGTCCCGAAGTGCTTGCCCCCTCAGATCATCAGAGAATATGGAGAACAGATATTAGATGAAATCAAAATATCCACGCCTAAGAATATGAAAAAACAGGATACTTAATTGGTTTATACAAATTTGTCTTGGAGTAAATCACATTCATAAGAGACGTGTTTTACACAGAGATATCAAGTCGAAAAATGTCTTCCTCACCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-7b-5p(1), mmu-miR-185-5p(1), mmu-miR-136-5p(1), mmu-miR-483-5p(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATGAAAAAACAGGATACTTAATTGGT
siRNA sets
TTAAGTATCCTGTTTTTTC, TAAGTATCCTGTTTTTTCA, AAGTATCCTGTTTTTTCAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNEK3_568_ORF_1
0.9054
0.155445566
0.520102448
420
ORF sequence:
ATGGCGTTTGCATGCACGTACGTGGGAACACCTTATTATGTGCCTCCAGAAATCTGGGAGAACCTGCCTTACAACAATAAAAGTGACATCTGGTCCTTGGGATGCATTCTGTATGAACTCTGCGCTCTGAAGCATCCATTCCAGGCAAATAGTTGGAAAAACCTGATCCTGAAAATATGCCAGGGGCCCATCCACCCGCTGCCGGCTCTGTACTCCTGCAAGCTTCAGGGCCTGGTCAAGCAGATGCTGAAAAGGAACCCTTCCCACCGCCCCTCCGCCACAACCCTGCTCTGCAGGGGTAGCTTGGCTCCACTGGTCCCGAAGTGCTTGCCCCCTCAGATCATCAGAGAATATGGAGAACAGATATTAGATGAAATCAAAATATCCACGCCTAAGAATATGAAAAAACAGGATACTTAA
Peptide sequence:
MAFACTYVGTPYYVPPEIWENLPYNNKSDIWSLGCILYELCALKHPFQANSWKNLILKICQGPIHPLPALYSCKLQGLVKQMLKRNPSHRPSATTLLCRGSLAPLVPKCLPPQIIREYGEQILDEIKISTPKNMKKQDT
IRESfinder result
IRESfinder score
0.611829501
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page