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mmu_circEfcab7_686
Basic information of circular RNA
PanCircBase ID:
mmu_circEfcab7_686
mm39_Chr. Position ID:
chr4|99719626|99735485|+
Gene name:
Efcab7
Transcript:
ENSMUST00000239516.1
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
2,3,4,5
Exon/intron offsets:
0,11870,13022,15663
Genomic length:
15859
Exon/intron sizes in nt:
19,12,12,87,196
Flanking exon/introns:
chr4:99717691-99719626|chr4:99735485-99735908
Splice length:
686
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CAGAATGGCCAGCAACCCTGGAAGTGATGCAGCTTTGGGTACTCAGAACCCACTGCTTTCTGGGAGTCCTCGAACAAAGAAATTCCCACTAACTGAACAGGAGGTGTTTTATATGAACTGTAGAGCCGCCTACTTAACTATCTTCAAAAGCAGCTTGGAAAACATTATTTCTAAAGATCAACTTTACCTAGCTCTTCAGCATGCAGGAAGAAATCCATCCCAAAAGACCATTAATAAGTATTGGACTCCTCAAACTGCCAAACTAAATTTTGATGATTTTTGTATAATTTTAAGCAAGGAAAAGCCTACTTCAAAAGCAGAATTGCTAAAATCATTTAAAAAATTAGATGTAAATGATGATGGTGCTATTCTACACTCTGACCTTCAGAAATATCTAACAAAGAGAGGTGAGAAGATGACTCAGGAAGAAGTGAATGCTGTCATAAATTTGGCTGATATAAATGCTAATGGAAAGTTTGACTACGTTAAGTTTTGTAAATTATACATGACAACCAGTGAGCAGTGTCTCAAGACTACACTAGAAAGACTGGAGGCCGACAGTAAACTGAGGCGTCAACAGTTTGGAAGCCACATGGAAGGGTCCCCTGAAAGGGGTCCGTCACCAGCACCAAAACCGTCACCTAGGGTCATAAGAAAAAATGACCAAGAAACATTCTCAAGCAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGAAAGGGGTCCGTCACC
60
CGAGGACTCCCAGAAAGCAG
60.11
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCGTCACCAGCACCAAAAC
61.1
CGAGGACTCCCAGAAAGCAG
60.11
143
PCR template sequence:
AGCCACATGGAAGGGTCCCCTGAAAGGGGTCCGTCACCAGCACCAAAACCGTCACCTAGGGTCATAAGAAAAAATGACCAAGAAACATTCTCAAGCAAAGCAGAATGGCCAGCAACCCTGGAAGTGATGCAGCTTTGGGTACTCAGAACCCACTGCTTTCTGGGAGTCCTCGAACAAAGAAATTCCCACTAACTGAACAG
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-miR-29a-3p(1), mmu-miR-139-5p(1), mmu-miR-540-3p(1), mmu-miR-1904(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTCTCAAGCAAAGCAGAATGGCCAGC
siRNA sets
CTGGCCATTCTGCTTTGCT, CATTCTGCTTTGCTTGAGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCEFCAB7_686_ORF_1
0.7554
-0.022646424
0.835129893
774
ORF sequence:
ATGGCCAGCAACCCTGGAAGTGATGCAGCTTTGGGTACTCAGAACCCACTGCTTTCTGGGAGTCCTCGAACAAAGAAATTCCCACTAACTGAACAGGAGGTGTTTTATATGAACTGTAGAGCCGCCTACTTAACTATCTTCAAAAGCAGCTTGGAAAACATTATTTCTAAAGATCAACTTTACCTAGCTCTTCAGCATGCAGGAAGAAATCCATCCCAAAAGACCATTAATAAGTATTGGACTCCTCAAACTGCCAAACTAAATTTTGATGATTTTTGTATAATTTTAAGCAAGGAAAAGCCTACTTCAAAAGCAGAATTGCTAAAATCATTTAAAAAATTAGATGTAAATGATGATGGTGCTATTCTACACTCTGACCTTCAGAAATATCTAACAAAGAGAGGTGAGAAGATGACTCAGGAAGAAGTGAATGCTGTCATAAATTTGGCTGATATAAATGCTAATGGAAAGTTTGACTACGTTAAGTTTTGTAAATTATACATGACAACCAGTGAGCAGTGTCTCAAGACTACACTAGAAAGACTGGAGGCCGACAGTAAACTGAGGCGTCAACAGTTTGGAAGCCACATGGAAGGGTCCCCTGAAAGGGGTCCGTCACCAGCACCAAAACCGTCACCTAGGGTCATAAGAAAAAATGACCAAGAAACATTCTCAAGCAAAGCAGAATGGCCAGCAACCCTGGAAGTGATGCAGCTTTGGGTACTCAGAACCCACTGCTTTCTGGGAGTCCTCGAACAAAGAAATTCCCACTAA
Peptide sequence:
MASNPGSDAALGTQNPLLSGSPRTKKFPLTEQEVFYMNCRAAYLTIFKSSLENIISKDQLYLALQHAGRNPSQKTINKYWTPQTAKLNFDDFCIILSKEKPTSKAELLKSFKKLDVNDDGAILHSDLQKYLTKRGEKMTQEEVNAVINLADINANGKFDYVKFCKLYMTTSEQCLKTTLERLEADSKLRRQQFGSHMEGSPERGPSPAPKPSPRVIRKNDQETFSSKAEWPATLEVMQLWVLRTHCFLGVLEQRNSH
IRESfinder result
IRESfinder score
0.593450442
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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