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mmu_circAgap1_284

Basic information of circular RNA
PanCircBase ID:

mmu_circAgap1_284

mm39_Chr. Position ID:

chr1|89591382|89592911|+

Gene name:

Agap1

Transcript:

ENSMUST00000027521.15

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

2

Exon/intron indexes:

7,8

Exon/intron offsets:

0,1373

Genomic length:

1529

Exon/intron sizes in nt:

1,28,156

Flanking exon/introns:

chr1:89562016-89591382|chr1:89592911-89598900

Splice length:

284

Other database IDs:

CIRCpedia: MMU_CIRCpedia_33487, circAtlas: mmu-Agap1_0010

circBase: hsa_circ_0058805, circAtlas: hsa-AGAP1_0010, CIRCpedia: HSA_CIRCpedia_40119

Human Ortholog IDs:
Mature spliced Sequence:

TTGCCCAGAAGATCGTTGCCACAAGGAAGAAGCAGCAGCTATCCATAGGCCCCTGCAAGTCCTTACCCAACTCTCCAAGCCACTCGTCTGTGTGTTCTGCCCAAGTGTCCGCGGTACACATCAGCCAGACAAGTAACGGAGGTGGGAGTTTAAGTGACTACTCATCCTCTGTTCCTTCGACCCCAAGCACCAGCCAGAAAGAGCTTCGGATCGACGTCCCTCCCACTGCCAACACTCCAACGCCTGTCCGGAAGCAGTCCAAGCGCAGGTCCAACCTATTCACA

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CAGCCAGAAAGAGCTTCGGA

60.04

GGGCCTATGGATAGCTGCTG

60.04

146

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

AAGAGCTTCGGATCGACGTC

59.9

ACGAGTGGCTTGGAGAGTTG

59.97

173

PCR template sequence:

AAGCACCAGCCAGAAAGAGCTTCGGATCGACGTCCCTCCCACTGCCAACACTCCAACGCCTGTCCGGAAGCAGTCCAAGCGCAGGTCCAACCTATTCACATTGCCCAGAAGATCGTTGCCACAAGGAAGAAGCAGCAGCTATCCATAGGCCCCTGCAAGTCCTTACCCAACTCTCCAAGCCACTCGTCTGTGTGTTCTGC

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-122-5p(1), mmu-miR-138-5p(1), mmu-miR-705(1), mmu-miR-5101(1), mmu-miR-296-3p(1)

siRNAs for circular RNA silencing
Junction sequence

CAACCTATTCACATTGCCCAGAAGAT

siRNA sets

ATCTTCTGGGCAATGTGAA, TTCTGGGCAATGTGAATAG

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

NA

NA

NA

NA

NA

ORF sequence:

NA

Peptide sequence:

NA

IRESfinder result

IRESfinder score

0.406118596

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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