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mmu_circAgo3_356

Basic information of circular RNA
PanCircBase ID:

mmu_circAgo3_356

mm39_Chr. Position ID:

chr4|126264055|126265619|-

Gene name:

Ago3

Transcript:

ENSMUST00000069097.13

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

3

Exon/intron indexes:

9,8,7

Exon/intron offsets:

0,1205,1476

Genomic length:

1564

Exon/intron sizes in nt:

120,148,88

Flanking exon/introns:

chr4:126262399-126264055|chr4:126265619-126270699

Splice length:

356

Other database IDs:

circBase: hsa_circ_0011641, circAtlas: hsa-AGO3_0010, CIRCpedia: HSA_CIRCpedia_31618

Human Ortholog IDs:
Mature spliced Sequence:

GTCTGAAAGTTGAAGTGACTCATTGTGGAACAATGAGACGGAAATACCGTGTTTGTAATGTAACGAGAAGGCCTGCCAGCCACCAAACCTTTCCTTTACAGCTAGAAAATGGCCAAACTGTGGAGAGGACTGTGGCTCAGTATTTCAGAGAAAAGTACACGCTGCAGCTGAAGTACCCACACCTTCCCTGCCTGCAAGTGGGGCAGGAGCAGAAGCATACATACCTGCCACTAGAAGTCTGTAATATTGTGGCTGGGCAAAGGTGTATCAAGAAACTAACGGACAATCAGACTTCTACAATGATAAAGGCAACAGCAAGATCTGCACCAGATAGACAAGAGGAAATTAGCAGATTG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

AAAGGCAACAGCAAGATCTG

56.61

AGGAAAGGTTTGGTGGCTGG

60.47

147

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

ACGGACAATCAGACTTCTACA

56.41

GGCAGGCCTTCTCGTTACAT

60.11

155

PCR template sequence:

GCAAAGGTGTATCAAGAAACTAACGGACAATCAGACTTCTACAATGATAAAGGCAACAGCAAGATCTGCACCAGATAGACAAGAGGAAATTAGCAGATTGGTCTGAAAGTTGAAGTGACTCATTGTGGAACAATGAGACGGAAATACCGTGTTTGTAATGTAACGAGAAGGCCTGCCAGCCACCAAACCTTTCCTTTACA

Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs

2

Interacting miRNAs (#binding sites)

mmu-miR-297a-5p(1), mmu-miR-1904(1)

siRNAs for circular RNA silencing
Junction sequence

AATTAGCAGATTGGTCTGAAAGTTGA

siRNA sets

TCAACTTTCAGACCAATCT

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCAGO3_356_ORF_1

0.8513

0.039689153

0.24360922

330

ORF sequence:

ATGAGACGGAAATACCGTGTTTGTAATGTAACGAGAAGGCCTGCCAGCCACCAAACCTTTCCTTTACAGCTAGAAAATGGCCAAACTGTGGAGAGGACTGTGGCTCAGTATTTCAGAGAAAAGTACACGCTGCAGCTGAAGTACCCACACCTTCCCTGCCTGCAAGTGGGGCAGGAGCAGAAGCATACATACCTGCCACTAGAAGTCTGTAATATTGTGGCTGGGCAAAGGTGTATCAAGAAACTAACGGACAATCAGACTTCTACAATGATAAAGGCAACAGCAAGATCTGCACCAGATAGACAAGAGGAAATTAGCAGATTGGTCTGA

Peptide sequence:

MRRKYRVCNVTRRPASHQTFPLQLENGQTVERTVAQYFREKYTLQLKYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIKATARSAPDRQEEISRLV

IRESfinder result

IRESfinder score

0.525661825

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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