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mmu_circGnpnat1_253
Basic information of circular RNA
PanCircBase ID:
mmu_circGnpnat1_253
mm39_Chr. Position ID:
chr14|45618393|45620913|-
Gene name:
Gnpnat1
Transcript:
ENSMUST00000046191.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
5,4,3
Exon/intron offsets:
0,619,2457
Genomic length:
2520
Exon/intron sizes in nt:
62,128,63
Flanking exon/introns:
chr14:45615943-45618393|chr14:45620913-45622037
Splice length:
253
Other database IDs:
circBase: hsa_circ_0031964
Human Ortholog IDs:
Mature spliced Sequence:
GTTTTTTTAAGGTATTGGGTCAGCTGACAGAGACTGGCGTCGTCAGCCCGGAACAGTTCATGAAATCTTTTGAGCATATGAAGAAGTCTGGAGATTACTACGTTACAGTTGTGGAAGATGTGACCCTAGGACAAATTGTGGCTACAGCAACTCTGATAATAGAACATAAATTTATCCATTCATGTGCTAAGAGAGGGAGAGTAGAAGATGTCGTCGTTAGTGACGAGTGCAGAGGGAAGCAACTCGGCAAACT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCATTCATGTGCTAAGAGAGGGA
59.86
CATGAACTGTTCCGGGCTGA
60.32
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCATTCATGTGCTAAGAGAGGGA
59.86
TCATGAACTGTTCCGGGCTG
60.32
141
PCR template sequence:
TGATAATAGAACATAAATTTATCCATTCATGTGCTAAGAGAGGGAGAGTAGAAGATGTCGTCGTTAGTGACGAGTGCAGAGGGAAGCAACTCGGCAAACTGTTTTTTTAAGGTATTGGGTCAGCTGACAGAGACTGGCGTCGTCAGCCCGGAACAGTTCATGAAATCTTTTGAGCATATGAAGAAGTCTGGAGATTACTA
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-223-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AACTCGGCAAACTGTTTTTTTAAGGT
siRNA sets
TTAAAAAAACAGTTTGCCG, TAAAAAAACAGTTTGCCGA, AAAAAAACAGTTTGCCGAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGNPNAT1_253_ORF_1
0.9432
0.107134293
0.285027392
297
ORF sequence:
ATGTCGTCGTTAGTGACGAGTGCAGAGGGAAGCAACTCGGCAAACTGTTTTTTTAAGGTATTGGGTCAGCTGACAGAGACTGGCGTCGTCAGCCCGGAACAGTTCATGAAATCTTTTGAGCATATGAAGAAGTCTGGAGATTACTACGTTACAGTTGTGGAAGATGTGACCCTAGGACAAATTGTGGCTACAGCAACTCTGATAATAGAACATAAATTTATCCATTCATGTGCTAAGAGAGGGAGAGTAGAAGATGTCGTCGTTAGTGACGAGTGCAGAGGGAAGCAACTCGGCAAA
Peptide sequence:
MSSLVTSAEGSNSANCFFKVLGQLTETGVVSPEQFMKSFEHMKKSGDYYVTVVEDVTLGQIVATATLIIEHKFIHSCAKRGRVEDVVVSDECRGKQLGK
IRESfinder result
IRESfinder score
0.505815852
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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