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mmu_circNedd4_229
Basic information of circular RNA
PanCircBase ID:
mmu_circNedd4_229
mm39_Chr. Position ID:
chr9|72647449|72650042|+
Gene name:
Nedd4
Transcript:
ENSMUST00000034740.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
24,25,26
Exon/intron offsets:
0,1460,2485
Genomic length:
2593
Exon/intron sizes in nt:
61,60,108
Flanking exon/introns:
chr9:72646810-72647449|chr9:72650042-72650821
Splice length:
229
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CCTTGTAATACAATGGCGATTTGTGAACCGTATCCAGAAGCAAATGGCAGCTTTTAAAGAGGGATTTTTTGAACTGATACCACAGGATCTCATCAAGATATTTGATGAAAATGAGCTAGAGCTTCTCATGTGTGGTCTGGGAGATGTGGATGTGAACGACTGGCGGGAACACACAAAATACAAAAATGGCTACAGCATGAACCACCAGGTCATCCACTGGTTCTGGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGTGGTCTGGGAGATGTGG
60.04
AGCTGCCATTTGCTTCTGGA
60.25
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGGTCTGGGAGATGTGGA
60.18
AGCTGCCATTTGCTTCTGGA
60.25
151
PCR template sequence:
GTGTGGTCTGGGAGATGTGGATGTGAACGACTGGCGGGAACACACAAAATACAAAAATGGCTACAGCATGAACCACCAGGTCATCCACTGGTTCTGGAAGCCTTGTAATACAATGGCGATTTGTGAACCGTATCCAGAAGCAAATGGCAGCTTTTAAAGAGGGATTTTTTGAACTGATACCACAGGATCTCATCAAGATA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-22-3p(1), mmu-miR-335-3p(1), mmu-miR-350-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGGTTCTGGAAGCCTTGTAATACAA
siRNA sets
TTGTATTACAAGGCTTCCA,ATTACAAGGCTTCCAGAAC,TATTACAAGGCTTCCAGAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNEDD4_229_ORF_1
0.9334
0.171367959
0.256579224
243
ORF sequence:
ATGGCAGCTTTTAAAGAGGGATTTTTTGAACTGATACCACAGGATCTCATCAAGATATTTGATGAAAATGAGCTAGAGCTTCTCATGTGTGGTCTGGGAGATGTGGATGTGAACGACTGGCGGGAACACACAAAATACAAAAATGGCTACAGCATGAACCACCAGGTCATCCACTGGTTCTGGAAGCCTTGTAATACAATGGCGATTTGTGAACCGTATCCAGAAGCAAATGGCAGCTTTTAA
Peptide sequence:
MAAFKEGFFELIPQDLIKIFDENELELLMCGLGDVDVNDWREHTKYKNGYSMNHQVIHWFWKPCNTMAICEPYPEANGSF
IRESfinder result
IRESfinder score
0.433604649
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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