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mmu_circApp_597

Basic information of circular RNA
PanCircBase ID:

mmu_circApp_597

mm39_Chr. Position ID:

chr16|84810514|84827253|-

Gene name:

App

Transcript:

ENSMUST00000227723.2

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

5

Exon/intron indexes:

13,12,11,10,9

Exon/intron offsets:

0,1605,11226,11796,16605

Genomic length:

16739

Exon/intron sizes in nt:

100,129,159,75,134

Flanking exon/introns:

chr16:84775173-84810514|chr16:84827253-84837138

Splice length:

597

Other database IDs:

circBase: mmu_circ_0000705, CIRCpedia: MMU_CIRCpedia_31915, circAtlas: mmu-App_0003

circBase: hsa_circ_0115728, circAtlas: hsa-APP_0006, CIRCpedia: HSA_CIRCpedia_35118

Human Ortholog IDs:
Mature spliced Sequence:

TTCCCACGACAGCAGCCAGCACCCCCGACGCCGTCGACAAGTACCTGGAGACACCCGGGGACGAGAACGAGCATGCCCATTTCCAGAAAGCCAAAGAGAGGCTGGAAGCCAAGCACCGAGAGAGAATGTCCCAGGTCATGAGAGAATGGGAAGAGGCAGAGCGTCAAGCCAAGAACTTGCCCAAAGCTGACAAGAAGGCCGTTATCCAGCATTTCCAGGAGAAAGTGGAATCTCTGGAACAGGAAGCAGCCAATGAGAGACAGCAGCTTGTAGAGACACACATGGCCAGAGTTGAAGCCATGCTCAATGACCGCCGCCGCCTGGCCCTCGAGAATTACATCACTGCACTGCAGGCGGTGCCCCCAAGGCCTCATCATGTGTTCAACATGCTGAAGAAGTACGTCCGTGCGGAGCAGAAAGACAGACAGCACACCCTAAAGCATTTTGAACATGTGCGCATGGTGGACCCCAAGAAAGCTGCTCAGATCCGGTCCCAGGTTATGACACACCTCCGTGTGATCTACGAGCGCATGAACCAGTCTCTGTCCCTGCTCTACAATGTCCCTGCGGTGGCTGAGGAGATTCAAGATGAAGTCG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CCTCCGTGTGATCTACGAGC

59.97

GGAAATGGGCATGCTCGTTC

59.9

173

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GAACCAGTCTCTGTCCCTGC

60.04

GGAAATGGGCATGCTCGTTC

59.9

149

PCR template sequence:

GTTATGACACACCTCCGTGTGATCTACGAGCGCATGAACCAGTCTCTGTCCCTGCTCTACAATGTCCCTGCGGTGGCTGAGGAGATTCAAGATGAAGTCGTTCCCACGACAGCAGCCAGCACCCCCGACGCCGTCGACAAGTACCTGGAGACACCCGGGGACGAGAACGAGCATGCCCATTTCCAGAAAGCCAAAGAGAG

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

8

Interacting miRNAs (#binding sites)

mmu-miR-135a-5p(1), mmu-miR-34c-5p(1), mmu-miR-152-3p(1), mmu-miR-342-5p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1), mmu-miR-1904(1)

siRNAs for circular RNA silencing
Junction sequence

CAAGATGAAGTCGTTCCCACGACAGC

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCAPP_597_ORF_1

1.2598

0.490090556

0.998867924

1068

ORF sequence:

ATGTCCCAGGTCATGAGAGAATGGGAAGAGGCAGAGCGTCAAGCCAAGAACTTGCCCAAAGCTGACAAGAAGGCCGTTATCCAGCATTTCCAGGAGAAAGTGGAATCTCTGGAACAGGAAGCAGCCAATGAGAGACAGCAGCTTGTAGAGACACACATGGCCAGAGTTGAAGCCATGCTCAATGACCGCCGCCGCCTGGCCCTCGAGAATTACATCACTGCACTGCAGGCGGTGCCCCCAAGGCCTCATCATGTGTTCAACATGCTGAAGAAGTACGTCCGTGCGGAGCAGAAAGACAGACAGCACACCCTAAAGCATTTTGAACATGTGCGCATGGTGGACCCCAAGAAAGCTGCTCAGATCCGGTCCCAGGTTATGACACACCTCCGTGTGATCTACGAGCGCATGAACCAGTCTCTGTCCCTGCTCTACAATGTCCCTGCGGTGGCTGAGGAGATTCAAGATGAAGTCGTTCCCACGACAGCAGCCAGCACCCCCGACGCCGTCGACAAGTACCTGGAGACACCCGGGGACGAGAACGAGCATGCCCATTTCCAGAAAGCCAAAGAGAGGCTGGAAGCCAAGCACCGAGAGAGAATGTCCCAGGTCATGAGAGAATGGGAAGAGGCAGAGCGTCAAGCCAAGAACTTGCCCAAAGCTGACAAGAAGGCCGTTATCCAGCATTTCCAGGAGAAAGTGGAATCTCTGGAACAGGAAGCAGCCAATGAGAGACAGCAGCTTGTAGAGACACACATGGCCAGAGTTGAAGCCATGCTCAATGACCGCCGCCGCCTGGCCCTCGAGAATTACATCACTGCACTGCAGGCGGTGCCCCCAAGGCCTCATCATGTGTTCAACATGCTGAAGAAGTACGTCCGTGCGGAGCAGAAAGACAGACAGCACACCCTAAAGCATTTTGAACATGTGCGCATGGTGGACCCCAAGAAAGCTGCTCAGATCCGGTCCCAGGTTATGACACACCTCCGTGTGATCTACGAGCGCATGAACCAGTCTCTGTCCCTGCTCTACAATGTCCCTGCGGTGGCTGAGGAGATTCAAGATGAAGTC

Peptide sequence:

MSQVMREWEEAERQAKNLPKADKKAVIQHFQEKVESLEQEAANERQQLVETHMARVEAMLNDRRRLALENYITALQAVPPRPHHVFNMLKKYVRAEQKDRQHTLKHFEHVRMVDPKKAAQIRSQVMTHLRVIYERMNQSLSLLYNVPAVAEEIQDEVVPTTAASTPDAVDKYLETPGDENEHAHFQKAKERLEAKHRERMSQVMREWEEAERQAKNLPKADKKAVIQHFQEKVESLEQEAANERQQLVETHMARVEAMLNDRRRLALENYITALQAVPPRPHHVFNMLKKYVRAEQKDRQHTLKHFEHVRMVDPKKAAQIRSQVMTHLRVIYERMNQSLSLLYNVPAVAEEIQDEV

IRESfinder result

IRESfinder score

0.187076899

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

RPF, cORF, m6A

mmu_circApp_001

Evidence
Peptide sequence:

MSLRWLRRFKMKSFPRQQPAPPTPSTSTWRHPGTRTSMPISRKPKRGWKPSTERECPRS*

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