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mmu_circNedd4l_450
Basic information of circular RNA
PanCircBase ID:
mmu_circNedd4l_450
mm39_Chr. Position ID:
chr18|65305345|65307313|+
Gene name:
Nedd4l
Transcript:
ENSMUST00000235343.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
14,15,16
Exon/intron offsets:
0,641,1770
Genomic length:
1968
Exon/intron sizes in nt:
13,21,20,198
Flanking exon/introns:
chr18:65300644-65305345|chr18:65307313-65311989
Splice length:
450
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_24089
Human Ortholog IDs:
Mature spliced Sequence:
CCATCAGTGGCCTATGTACATACCACGCCGGGCCTGCCTTCAGGCTGGGAAGAAAGAAAGGATGCAAAGGGACGCACATACTATGTCAATCATAACAATCGAACCACAACTTGGACTCGGCCAATCATGCAGCTTGCAGAAGACGGTGCCTCCGGATCAGCCACAAACAGTAACAACCACCTAGTCGAACCCCAGATCCGCCGGCCCCGTAGCCTCAGCTCGCCAACAGTAACTTTATCTGCCCCACTGGAGGGTGCCAAGGATTCACCCATCCGCCGTGCCGTGAAAGATACCCTTTCCAATCCACAGTCCCCTCAGCCATCACCTTACAACTCCCCCAAACCACAACACAAAGTCACACAGAGCTTCCTGCCACCAGGCTGGGAGATGAGGATAGCCCCCAACGGCCGACCCTTCTTCATTGACCATAACACAAAGACTACAACCTGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTCACACAGAGCTTCCTGC
59.97
AGTATGTGCGTCCCTTTGCA
59.96
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GATGAGGATAGCCCCCAACG
59.96
AGTATGTGCGTCCCTTTGCA
59.96
146
PCR template sequence:
CAAAGTCACACAGAGCTTCCTGCCACCAGGCTGGGAGATGAGGATAGCCCCCAACGGCCGACCCTTCTTCATTGACCATAACACAAAGACTACAACCTGGCCATCAGTGGCCTATGTACATACCACGCCGGGCCTGCCTTCAGGCTGGGAAGAAAGAAAGGATGCAAAGGGACGCACATACTATGTCAATCATAACAATC
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-211-5p(1), mmu-miR-204-5p(1), mmu-miR-362-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GACTACAACCTGGCCATCAGTGGCCT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNEDD4L_450_ORF_1
0.4771
0.254036626
0.904401392
774
ORF sequence:
ATGCAGCTTGCAGAAGACGGTGCCTCCGGATCAGCCACAAACAGTAACAACCACCTAGTCGAACCCCAGATCCGCCGGCCCCGTAGCCTCAGCTCGCCAACAGTAACTTTATCTGCCCCACTGGAGGGTGCCAAGGATTCACCCATCCGCCGTGCCGTGAAAGATACCCTTTCCAATCCACAGTCCCCTCAGCCATCACCTTACAACTCCCCCAAACCACAACACAAAGTCACACAGAGCTTCCTGCCACCAGGCTGGGAGATGAGGATAGCCCCCAACGGCCGACCCTTCTTCATTGACCATAACACAAAGACTACAACCTGGCCATCAGTGGCCTATGTACATACCACGCCGGGCCTGCCTTCAGGCTGGGAAGAAAGAAAGGATGCAAAGGGACGCACATACTATGTCAATCATAACAATCGAACCACAACTTGGACTCGGCCAATCATGCAGCTTGCAGAAGACGGTGCCTCCGGATCAGCCACAAACAGTAACAACCACCTAGTCGAACCCCAGATCCGCCGGCCCCGTAGCCTCAGCTCGCCAACAGTAACTTTATCTGCCCCACTGGAGGGTGCCAAGGATTCACCCATCCGCCGTGCCGTGAAAGATACCCTTTCCAATCCACAGTCCCCTCAGCCATCACCTTACAACTCCCCCAAACCACAACACAAAGTCACACAGAGCTTCCTGCCACCAGGCTGGGAGATGAGGATAGCCCCCAACGGCCGACCCTTCTTCATTGACCATAACACAAAGACTACAACCTGG
Peptide sequence:
MQLAEDGASGSATNSNNHLVEPQIRRPRSLSSPTVTLSAPLEGAKDSPIRRAVKDTLSNPQSPQPSPYNSPKPQHKVTQSFLPPGWEMRIAPNGRPFFIDHNTKTTTWPSVAYVHTTPGLPSGWEERKDAKGRTYYVNHNNRTTTWTRPIMQLAEDGASGSATNSNNHLVEPQIRRPRSLSSPTVTLSAPLEGAKDSPIRRAVKDTLSNPQSPQPSPYNSPKPQHKVTQSFLPPGWEMRIAPNGRPFFIDHNTKTTTW
IRESfinder result
IRESfinder score
0.466025063
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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