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mmu_ciKdm5a_500
Basic information of circular RNA
PanCircBase ID:
mmu_ciKdm5a_500
mm39_Chr. Position ID:
chr6|120366010|120366510|+
Gene name:
Kdm5a
Transcript:
ENSMUST00000135802.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
9
Exon/intron offsets:
0
Genomic length:
500
Exon/intron sizes in nt:
500
Flanking exon/introns:
chr6:120366010-120366513
Splice length:
500
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGAGTAGCTATCAATTTGGTTGGCTTAGAGAGAAACAACGATATTTTTCCTGTCAAGTTTTGTAGAAATCGGGAACAATATGAAAAAGGTTAGAGACTACCAAATCTTAAAATTAGAGACCTAATAATCTGTTTTGTTAGTTTCACTCTTTTTTGTTTTGTTTTTTGTTGTTTATGAAATGAGGTCTCACTATGTATGTAGCATTGGCAGGCAGGCCTGGACCTTAATCTGTAGACCAGGCTGGCCTGGAACTCAGAGAGATCCTCTTTCTCCTGGTGCTGGGATCAAAGGTATGTACCACCACAACTCCTAAGAAAAGCATTTTGATGTTTAAATTTTAATTATCTTTAGCTTTTCCCTCTTCTCAGTGGAGAGATAATAGGAGTTAATTCTGCTCTGAGAAATGGGTAATTTCTTTGTTTTTATCATGTTTTTGTTCAGTTTGTGTATTATGTTTCAGGAGATTATAATGAGTTAATTATCGTCTTTGGTTTTATTA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCATGTTTTTGTTCAGTTTGTGT
55.98
CCCGATTTCTACAAAACTTGACAGG
60.33
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCATGTTTTTGTTCAGTTTGTGT
55.98
TCCCGATTTCTACAAAACTTGACA
58.63
149
PCR template sequence:
AGAAATGGGTAATTTCTTTGTTTTTATCATGTTTTTGTTCAGTTTGTGTATTATGTTTCAGGAGATTATAATGAGTTAATTATCGTCTTTGGTTTTATTAGTGAGTAGCTATCAATTTGGTTGGCTTAGAGAGAAACAACGATATTTTTCCTGTCAAGTTTTGTAGAAATCGGGAACAATATGAAAAAGGTTAGAGACTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-494-3p(1), mmu-miR-369-3p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTGGTTTTATTAGTGAGTAGCTATC
siRNA sets
GCTACTCACTAATAAAACC, CTACTCACTAATAAAACCA, TACTCACTAATAAAACCAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.946954157
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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