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mmu_circCask_365
Basic information of circular RNA
PanCircBase ID:
mmu_circCask_365
mm39_Chr. Position ID:
chrX|13399578|13404080|-
Gene name:
Cask
Transcript:
ENSMUST00000156096.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
22,21,20
Exon/intron offsets:
0,4246,4421
Genomic length:
4502
Exon/intron sizes in nt:
203,81,81
Flanking exon/introns:
chrX:13392320-13399578|chrX:13404080-13410752
Splice length:
365
Other database IDs:
circAtlas: mmu-Cask_0025
Human Ortholog IDs:
Mature spliced Sequence:
TGTTTGATCAATTAGATCTTGTCACATATGAAGAAGTAGTCAAACTGCCAGCATTCAAAAGGAAAACATTAGTCTTATTAGGTGCACATGGTGTTGGAAGAAGACACATAAAAAATACCCTCATCACAAAGCACCCGGACCGGTTTGCGTACCCTATTCCACATACAACCAGACCTCCAAAGAAAGATGAAGAAAATGGCAAGAATTATTACTTTGTATCTCATGACCAAATGATGCAAGACATCTCAAATAACGAATACTTGGAGTATGGCAGCCATGAGGATGCAATGTACGGGACAAAACTGGAGACCATTCGGAAAATCCATGAGCAGGGGCTGATTGCGATTCTGGACGTGGAGCCTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGGGACAAAACTGGAGACCA
59.89
TTCCAACACCATGTGCACCT
60.11
172
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACGGGACAAAACTGGAGACC
59.89
TTCCAACACCATGTGCACCT
60.11
173
PCR template sequence:
GTATGGCAGCCATGAGGATGCAATGTACGGGACAAAACTGGAGACCATTCGGAAAATCCATGAGCAGGGGCTGATTGCGATTCTGGACGTGGAGCCTCAGTGTTTGATCAATTAGATCTTGTCACATATGAAGAAGTAGTCAAACTGCCAGCATTCAAAAGGAAAACATTAGTCTTATTAGGTGCACATGGTGTTGGAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-297a-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CGTGGAGCCTCAGTGTTTGATCAATT
siRNA sets
ATTGATCAAACACTGAGGC,AATTGATCAAACACTGAGG,TTGATCAAACACTGAGGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCASK_365_ORF_1
1.1477
0.394545021
0.394055595
150
ORF sequence:
ATGATGCAAGACATCTCAAATAACGAATACTTGGAGTATGGCAGCCATGAGGATGCAATGTACGGGACAAAACTGGAGACCATTCGGAAAATCCATGAGCAGGGGCTGATTGCGATTCTGGACGTGGAGCCTCAGTGTTTGATCAATTAG
Peptide sequence:
MMQDISNNEYLEYGSHEDAMYGTKLETIRKIHEQGLIAILDVEPQCLIN
IRESfinder result
IRESfinder score
0.347712253
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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