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mmu_circDennd4c_269
Basic information of circular RNA
PanCircBase ID:
mmu_circDennd4c_269
mm39_Chr. Position ID:
chr4|86759221|86763214|+
Gene name:
Dennd4c
Transcript:
ENSMUST00000082026.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
30,31
Exon/intron offsets:
0,3842
Genomic length:
3993
Exon/intron sizes in nt:
1,18,151
Flanking exon/introns:
chr4:86758114-86759221|chr4:86763214-86766194
Splice length:
269
Other database IDs:
circBase: hsa_circ_0138420, circAtlas: hsa-DENND4C_0069, CIRCpedia: HSA_CIRCpedia_125502
Human Ortholog IDs:
Mature spliced Sequence:
CTTCCTCTATCATCTTTGTCCCAGGACAGCAAACTGGTGTATATTCAACTGCTGTGGGATAATATCAACCTTCATCAGGAACCAGGAGAACCTCTGTATGTCTCTTGGAGGAACTTGAATTCTGAGAAGAAGCCGTCACTTCTGTCAGAGCAGCAGCAGGCAGCCAGCGCTTTAGTGGAGACGATCAGGCAGAGCATCCAGCAGAATGACGTTCTCAAGCCCATCAACCTGCTTTCCCAGCAAATGAAGCCAGGCACGAAACGGCAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCAAGCCCATCAACCTGCTT
59.89
ACAGAGGTTCTCCTGGTTCCT
60.13
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCAAGCCCATCAACCTGCTT
59.89
AGAGGTTCTCCTGGTTCCTGA
59.85
150
PCR template sequence:
CTTTAGTGGAGACGATCAGGCAGAGCATCCAGCAGAATGACGTTCTCAAGCCCATCAACCTGCTTTCCCAGCAAATGAAGCCAGGCACGAAACGGCAGAGCTTCCTCTATCATCTTTGTCCCAGGACAGCAAACTGGTGTATATTCAACTGCTGTGGGATAATATCAACCTTCATCAGGAACCAGGAGAACCTCTGTATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-29b-1-5p(1), mmu-miR-188-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CGAAACGGCAGAGCTTCCTCTATCAT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDENND4C_269_ORF_1
0.8481
-0.113637409
0.042942844
144
ORF sequence:
ATGAAGCCAGGCACGAAACGGCAGAGCTTCCTCTATCATCTTTGTCCCAGGACAGCAAACTGGTGTATATTCAACTGCTGTGGGATAATATCAACCTTCATCAGGAACCAGGAGAACCTCTGTATGTCTCTTGGAGGAACTTGA
Peptide sequence:
MKPGTKRQSFLYHLCPRTANWCIFNCCGIISTFIRNQENLCMSLGGT
IRESfinder result
IRESfinder score
0.543077098
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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