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mmu_circMdm4_489
Basic information of circular RNA
PanCircBase ID:
mmu_circMdm4_489
mm39_Chr. Position ID:
chr1|132922240|132931628|-
Gene name:
Mdm4
Transcript:
ENSMUST00000186617.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
10,9,8,7
Exon/intron offsets:
0,2060,6780,9288
Genomic length:
9388
Exon/intron sizes in nt:
81,14,71,61,100
Flanking exon/introns:
chr1:132890894-132922240|chr1:132931628-132932391
Splice length:
489
Other database IDs:
CIRCpedia: MMU_CIRCpedia_7910, circAtlas: mmu-Mdm4_0011
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_371215
Human Ortholog IDs:
Mature spliced Sequence:
CACGGTGCAACAGAATACTCCAATCCCAGAAAAAGAACTGAAGAAGAGGATACTCACACACTGCCTACCTCACGACATAAATGCAGAGACTCCAGAGCAGATGAAGACTTGATAGAACATTTATCTCAAGATGAGACATCTAGGCTTGACCTTGATTTTGAGGAGTGGGACGTTGCTGGCCTGCCTTGGTGGTTTCTAGGGAATTTGAGAAACAACTGTATTCCTAAAAGTAATGGCTCAACTGATTTACAGACAAATCAGGATATAGGTACTGCCATTGTTTCAGACACTACGGATGATTTGTGGTTTTTAAATGAGACCGTGTCAGAGCAATTAGGTGTTGGAATAAAAGTTGAAGCTGCTAATTCTGAGCAAACAAGTGAAGTAGGGAAAACAAGTAACAAGAAGACGGTGGAGGTGGGAAAGGATGATGATCTTGAGGACTCCAGGTCCTTGAGCGATGATACTGACGTGGAACTTACCTCTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGTGGAGGTGGGAAAGGATG
60.03
GTCGTGAGGTAGGCAGTGTG
60.39
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGTGGAGGTGGGAAAGGATG
60.03
ATGTCGTGAGGTAGGCAGTG
59.47
157
PCR template sequence:
GAAAACAAGTAACAAGAAGACGGTGGAGGTGGGAAAGGATGATGATCTTGAGGACTCCAGGTCCTTGAGCGATGATACTGACGTGGAACTTACCTCTGAGCACGGTGCAACAGAATACTCCAATCCCAGAAAAAGAACTGAAGAAGAGGATACTCACACACTGCCTACCTCACGACATAAATGCAGAGACTCCAGAGCAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-34a-5p(2), mmu-let-7a-5p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-miR-34c-5p(1), mmu-let-7c-5p(1), mmu-miR-98-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTTACCTCTGAGCACGGTGCAACAG
siRNA sets
TTGCACCGTGCTCAGAGGT, TGTTGCACCGTGCTCAGAG, GTTGCACCGTGCTCAGAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMDM4_489_ORF_1
1.1216
0.091255913
0.143124573
141
ORF sequence:
ATGATACTGACGTGGAACTTACCTCTGAGCACGGTGCAACAGAATACTCCAATCCCAGAAAAAGAACTGAAGAAGAGGATACTCACACACTGCCTACCTCACGACATAAATGCAGAGACTCCAGAGCAGATGAAGACTTGA
Peptide sequence:
MILTWNLPLSTVQQNTPIPEKELKKRILTHCLPHDINAETPEQMKT
IRESfinder result
IRESfinder score
0.566681156
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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