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mmu_circKlhl20_598
Basic information of circular RNA
PanCircBase ID:
mmu_circKlhl20_598
mm39_Chr. Position ID:
chr1|160917483|160918081|-
Gene name:
Klhl20
Transcript:
ENSMUST00000117467.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
1
Exon/intron indexes:
12
Exon/intron offsets:
0
Genomic length:
598
Exon/intron sizes in nt:
598
Flanking exon/introns:
chr1:160916694-160917483|chr1:160918081-160921250
Splice length:
598
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTTATACGGAGGGATGAATTACCGTCGGCTAGGAGGTGGTGTAGGAGTTATTAAAATGACACATTGTGAATCCCATATATGGTGAACACAGGAAAAAAATCTTGCATATGCTCCTTTATATTTGGAAGAGCCTTGACTTCGAAGCTTTGTACAGCTGGAGAAAACAATAGAACAAATTTTATTCTTTGCCGGTGCCTCAACATTCAGAAATACCCGTCTAAGGACGGAGCTCACCTGCAAAACGCCGCCTTTGCACAATGCCTTTCCGCTCTGTGCAGAAGAGTATTTATTTTTGGCTTTAATTTATCATGGAGTTTTGATGGGGATTTTTGTTTTTGTTTTGTTGGTTTGGGTCCTTTGGGCTTTTGTTGTTGTTATTGTTGTGTTGTTTTTAATTTTTTTTTTTTAACTTATCCTTCCTACCATGAAAAAAAAGGAGGGGGGAAAAAGGCAAAAATTCCAAGCTGCAAAATTTTCTTTGCTTTATAGGTTTTGGATTGGTTTTAAAGATCCTGGTAAGCGCAGAAGACCTATGTGTGACCTGATGTTATTCCTTTTAGACATATCTATACATCTGCAGAGATTGCCAGTGATGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGATCCTGGTAAGCGCAGA
58.8
ACTCCTACACCACCTCCTAGC
60.34
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TAAAGATCCTGGTAAGCGCAGA
59.24
TCCTACACCACCTCCTAGCC
60.03
140
PCR template sequence:
TGGTTTTAAAGATCCTGGTAAGCGCAGAAGACCTATGTGTGACCTGATGTTATTCCTTTTAGACATATCTATACATCTGCAGAGATTGCCAGTGATGAAGGTTATACGGAGGGATGAATTACCGTCGGCTAGGAGGTGGTGTAGGAGTTATTAAAATGACACATTGTGAATCCCATATATGGTGAACACAGGAAAAAAAT
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-340-5p(1), mmu-miR-377-3p(1), mmu-miR-190b-5p(1), mmu-miR-3065-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCCAGTGATGAAGGTTATACGGAGGG
siRNA sets
TATAACCTTCATCACTGGC, GTATAACCTTCATCACTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKLHL20_598_ORF_3
0.6754
-0.274283266
0.029564421
228
ORF sequence:
ATGAAAAAAAAGGAGGGGGGAAAAAGGCAAAAATTCCAAGCTGCAAAATTTTCTTTGCTTTATAGGTTTTGGATTGGTTTTAAAGATCCTGGTAAGCGCAGAAGACCTATGTGTGACCTGATGTTATTCCTTTTAGACATATCTATACATCTGCAGAGATTGCCAGTGATGAAGGTTATACGGAGGGATGAATTACCGTCGGCTAGGAGGTGGTGTAGGAGTTATTAA
Peptide sequence:
MKKKEGGKRQKFQAAKFSLLYRFWIGFKDPGKRRRPMCDLMLFLLDISIHLQRLPVMKVIRRDELPSARRWCRSY
IRESfinder result
IRESfinder score
0.811462211
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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