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mmu_circPlekha6_374
Basic information of circular RNA
PanCircBase ID:
mmu_circPlekha6_374
mm39_Chr. Position ID:
chr1|133186746|133192471|+
Gene name:
Plekha6
Transcript:
ENSMUST00000212252.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
4,5,6,7
Exon/intron offsets:
0,1033,4788,5652
Genomic length:
5725
Exon/intron sizes in nt:
81,115,105,73
Flanking exon/introns:
chr1:133101544-133186746|chr1:133192471-133194303
Splice length:
374
Other database IDs:
circAtlas: mmu-Plekha6_0024
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
CCACAATGAAAGACGCAACACATTTCGACATCCAGTGACTGGCCAGATCCCAGAGGAGAACAAAAAGTTTGACTTGAAAACATCGGCCTTGGACATGTCCAACAAAACAGGTGGGAAACGTTCTGCTACCATCAACAGCGACATAGCCAACCACAACATGGTGTCTGAGGTTCCTCCAGAGCGGCCCAACATCCGGGCGACTCGAACTTCCCGAAAAGCCATTGCCTTTGGTAAACGCGCACACTCCATGAAGCGGAACCCCAATGCACCTGTTACCAAGGCGGGCTGGCTCTATAAGCAGGCCAGCTCCGGGGTGAAGCAGTGGAATAAGCGTTGGTTTGTCCTGGTGGATCGCTGCCTCTTTTACTACAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGGGGTGAAGCAGTGGAATA
59.75
ACATGTCCAAGGCCGATGTT
59.96
163
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCGTTGGTTTGTCCTGGT
60.4
ACATGTCCAAGGCCGATGTT
59.96
144
PCR template sequence:
ACCAAGGCGGGCTGGCTCTATAAGCAGGCCAGCTCCGGGGTGAAGCAGTGGAATAAGCGTTGGTTTGTCCTGGTGGATCGCTGCCTCTTTTACTACAAAGCCACAATGAAAGACGCAACACATTTCGACATCCAGTGACTGGCCAGATCCCAGAGGAGAACAAAAAGTTTGACTTGAAAACATCGGCCTTGGACATGTCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(1), mmu-miR-33-5p(1), mmu-miR-3105-3p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTTACTACAAAGCCACAATGAAAGA
siRNA sets
TTCATTGTGGCTTTGTAGT, TTTCATTGTGGCTTTGTAG, TCTTTCATTGTGGCTTTGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPLEKHA6_374_ORF_1
0.8129
0.381384477
0.526271041
318
ORF sequence:
ATGTCCAACAAAACAGGTGGGAAACGTTCTGCTACCATCAACAGCGACATAGCCAACCACAACATGGTGTCTGAGGTTCCTCCAGAGCGGCCCAACATCCGGGCGACTCGAACTTCCCGAAAAGCCATTGCCTTTGGTAAACGCGCACACTCCATGAAGCGGAACCCCAATGCACCTGTTACCAAGGCGGGCTGGCTCTATAAGCAGGCCAGCTCCGGGGTGAAGCAGTGGAATAAGCGTTGGTTTGTCCTGGTGGATCGCTGCCTCTTTTACTACAAAGCCACAATGAAAGACGCAACACATTTCGACATCCAGTGA
Peptide sequence:
MSNKTGGKRSATINSDIANHNMVSEVPPERPNIRATRTSRKAIAFGKRAHSMKRNPNAPVTKAGWLYKQASSGVKQWNKRWFVLVDRCLFYYKATMKDATHFDIQ
IRESfinder result
IRESfinder score
0.357414055
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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