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mmu_circNup160_235

Basic information of circular RNA
PanCircBase ID:

mmu_circNup160_235

mm39_Chr. Position ID:

chr2|90553680|90554079|+

Gene name:

Nup160

Transcript:

ENSMUST00000057481.7

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

2

Exon/intron indexes:

31,32

Exon/intron offsets:

0,275

Genomic length:

399

Exon/intron sizes in nt:

1,11,124

Flanking exon/introns:

chr2:90552434-90553680|chr2:90554079-90555945

Splice length:

235

Other database IDs:

CIRCpedia: MMU_CIRCpedia_213301

circBase: hsa_circ_0022062, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_4650

Human Ortholog IDs:
Mature spliced Sequence:

CCAATCGGCAAATTGAAATTCTGGAATTGGAAGATCTCGAGAAAGAATATTCTTTAGCTCGCATTCGCCTCACGTTGGCTCGGCATGATCCATCAGTGATTGCCATTGCAGGAAGTTCATCAGCAAAGGAGATGAGCGCACTCTTGGTTCAGGCTGGCCTCTTTGATACTGCCATATCACTCTGTCAGACTTTTACTCTTCCATTAACACCAGTCTTTGAAGGGCTTGCTTTCAA

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

GTTCAGGCTGGCCTCTTTGA

60.25

TGAGGCGAATGCGAGCTAAA

60.11

161

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GTTCAGGCTGGCCTCTTTGA

60.25

AGGCGAATGCGAGCTAAAGA

59.82

159

PCR template sequence:

GCGCACTCTTGGTTCAGGCTGGCCTCTTTGATACTGCCATATCACTCTGTCAGACTTTTACTCTTCCATTAACACCAGTCTTTGAAGGGCTTGCTTTCAACCAATCGGCAAATTGAAATTCTGGAATTGGAAGATCTCGAGAAAGAATATTCTTTAGCTCGCATTCGCCTCACGTTGGCTCGGCATGATCCATCAGTGAT

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

GGCTTGCTTTCAACCAATCGGCAAAT

siRNA sets

TTGCCGATTGGTTGAAAGC, TTTGCCGATTGGTTGAAAG, ATTTGCCGATTGGTTGAAA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCNUP160_235_ORF_1

0.8994

-0.17068794

0.031877951

120

ORF sequence:

ATGAGCGCACTCTTGGTTCAGGCTGGCCTCTTTGATACTGCCATATCACTCTGTCAGACTTTTACTCTTCCATTAACACCAGTCTTTGAAGGGCTTGCTTTCAACCAATCGGCAAATTGA

Peptide sequence:

MSALLVQAGLFDTAISLCQTFTLPLTPVFEGLAFNQSAN

IRESfinder result

IRESfinder score

0.851510228

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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Institute of Life sciences, Bhubaneswar, India

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