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mmu_ciKhdc4_549
Basic information of circular RNA
PanCircBase ID:
mmu_ciKhdc4_549
mm39_Chr. Position ID:
chr3|88618159|88618708|+
Gene name:
Khdc4
Transcript:
ENSMUST00000029696.11
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
13
Exon/intron offsets:
0
Genomic length:
549
Exon/intron sizes in nt:
549
Flanking exon/introns:
chr3:88618159-88618936
Splice length:
549
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGAGTACAGTGCAGCTGGGGGTGGGATGACAAGTAGGGGTGGAAACGGTTAGTCTTCTATCCCGGTGGTCAACCAGATTAATCCAATTTCAGTCATCTACTGGCTAATAACAACACTTTTTTTTTATTTTATTTAATTTGTAAGGACAGTATATAGCTTTCCGTTTTTAGCCATTCTGTGTCAGGAATAGAGTTGCCTAATTTATATTTTATACATCCCAGTGGCATTAAAGTCCTAGGAAATACTAATGATTGGGAGGTAATTTCAAAATCTTGTGCTCATTTTGTCTAATTGGGGGTCATCAGATGTAGATTTAGGAAAAGTTACTTTTCCTATGTGTTGGGAGCTGAGCTCATCACCCCACAGCATCCCTGCACTCTGCATCCTGTGCATGGGCTCGCTGTATTCCGTGCCTCTAGTTGATAAAAGTGAACAGAAGAAGAAAAAACGTTTTTCTTTTCTTCTTTTCTTTTAGCTCTTTAAGAGGTGAAATGTTAGTCTCCAGAGACTCACTTGCTAACTTTCCTTTTTTCTTTTCTTTTTTTTTT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGAGGTGAAATGTTAGTCTCCAGA
58.91
GGTTGACCACCGGGATAGAA
59.09
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGGTGAAATGTTAGTCTCCAGAGA
59.81
GGTTGACCACCGGGATAGAA
59.09
140
PCR template sequence:
CGTTTTTCTTTTCTTCTTTTCTTTTAGCTCTTTAAGAGGTGAAATGTTAGTCTCCAGAGACTCACTTGCTAACTTTCCTTTTTTCTTTTCTTTTTTTTTTGTGAGTACAGTGCAGCTGGGGGTGGGATGACAAGTAGGGGTGGAAACGGTTAGTCTTCTATCCCGGTGGTCAACCAGATTAATCCAATTTCAGTCATCTA
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-150-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTCTTTTTTTTTTGTGAGTACAGTGC
siRNA sets
TACTCACAAAAAAAAAAGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIKHDC4_549_ORF_3
0.6025
-0.495372023
0.003888312
87
ORF sequence:
ATGTTAGTCTCCAGAGACTCACTTGCTAACTTTCCTTTTTTCTTTTCTTTTTTTTTTGTGAGTACAGTGCAGCTGGGGGTGGGATGA
Peptide sequence:
MLVSRDSLANFPFFFSFFFVSTVQLGVG
IRESfinder result
IRESfinder score
0.93177463
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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