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mmu_circAp4e1_401
Basic information of circular RNA
PanCircBase ID:
mmu_circAp4e1_401
mm39_Chr. Position ID:
chr2|126875449|126879779|+
Gene name:
Ap4e1
Transcript:
ENSMUST00000110394.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
6,7,8
Exon/intron offsets:
0,1514,4256
Genomic length:
4330
Exon/intron sizes in nt:
160,167,74
Flanking exon/introns:
chr2:126870213-126875449|chr2:126879779-126885340
Splice length:
401
Other database IDs:
circAtlas: mmu-Ap4e1_0001
circAtlas: hsa-AP4E1_0011, CIRCpedia: HSA_CIRCpedia_83202
Human Ortholog IDs:
Mature spliced Sequence:
GGAGATTATACGAAGAAAAGCAGTTCTGGCATTATACAAATTTTACCTCATTGCCCCCAATCAAGTACAGCACATCCACACTAAATTTCGGAAAGCGCTTTGTGACAGAGATGTTGGGGTCATGGCTGCCTCTTTGCACATATACCTTAGGATGATTAAGGAAAATGCTTCTGGCTATAAAGACTTGACGGAGAGTTTTGTAACAATTTTAAAGCAGGTGGTGGGCGGGAAGCTCCCGGTAGAGTTCAGTTACCACAGCGTGCCAGCACCATGGTTACAGATTCAGCTCCTGAGAATACTGGGACTGCTGGGGAAAGACGATGAAAGGACAAGTGAATTAATGTATGATGTTCTTGATGAATCCTTACGAAGAGCCGAGTTAAATCACAATGTCACTTACG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGCTGGGGAAAGACGATG
60.04
GCTGTACTTGATTGGGGGCA
60.32
169
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGCTGGGGAAAGACGATG
60.04
TGCTGTACTTGATTGGGGGC
60.32
170
PCR template sequence:
GGACTGCTGGGGAAAGACGATGAAAGGACAAGTGAATTAATGTATGATGTTCTTGATGAATCCTTACGAAGAGCCGAGTTAAATCACAATGTCACTTACGGGAGATTATACGAAGAAAAGCAGTTCTGGCATTATACAAATTTTACCTCATTGCCCCCAATCAAGTACAGCACATCCACACTAAATTTCGGAAAGCGCTT
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-let-7a-5p(1), mmu-let-7e-5p(1), mmu-let-7c-5p(1), mmu-miR-98-5p(1), mmu-miR-350-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AATGTCACTTACGGGAGATTATACGA
siRNA sets
TATAATCTCCCGTAAGTGA,ATAATCTCCCGTAAGTGAC,TAATCTCCCGTAAGTGACA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAP4E1_401_ORF_1
0.7288
0.048469091
0.361398055
435
ORF sequence:
ATGGCTGCCTCTTTGCACATATACCTTAGGATGATTAAGGAAAATGCTTCTGGCTATAAAGACTTGACGGAGAGTTTTGTAACAATTTTAAAGCAGGTGGTGGGCGGGAAGCTCCCGGTAGAGTTCAGTTACCACAGCGTGCCAGCACCATGGTTACAGATTCAGCTCCTGAGAATACTGGGACTGCTGGGGAAAGACGATGAAAGGACAAGTGAATTAATGTATGATGTTCTTGATGAATCCTTACGAAGAGCCGAGTTAAATCACAATGTCACTTACGGGAGATTATACGAAGAAAAGCAGTTCTGGCATTATACAAATTTTACCTCATTGCCCCCAATCAAGTACAGCACATCCACACTAAATTTCGGAAAGCGCTTTGTGACAGAGATGTTGGGGTCATGGCTGCCTCTTTGCACATATACCTTAGGATGA
Peptide sequence:
MAASLHIYLRMIKENASGYKDLTESFVTILKQVVGGKLPVEFSYHSVPAPWLQIQLLRILGLLGKDDERTSELMYDVLDESLRRAELNHNVTYGRLYEEKQFWHYTNFTSLPPIKYSTSTLNFGKRFVTEMLGSWLPLCTYTLG
IRESfinder result
IRESfinder score
0.553268413
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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