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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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