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mmu_circKdm5b_497
Basic information of circular RNA
PanCircBase ID:
mmu_circKdm5b_497
mm39_Chr. Position ID:
chr1|134535425|134541107|+
Gene name:
Kdm5b
Transcript:
ENSMUST00000047714.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
13,14,15
Exon/intron offsets:
0,1177,5500
Genomic length:
5682
Exon/intron sizes in nt:
12,01,95,182
Flanking exon/introns:
chr1:134533613-134535425|chr1:134541107-134541624
Splice length:
497
Other database IDs:
CIRCpedia: MMU_CIRCpedia_8133, circAtlas: mmu-Kdm5b_0003
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_362644
Human Ortholog IDs:
Mature spliced Sequence:
GTTTATCGAACGAATCAGTGTGCTGGGGAGTTTGTAATTACGTTTCCAAGAGCCTACCACAGTGGCTTCAACCAAGGTTTTAATTTTGCCGAGGCTGTTAACTTCTGCACTGTTGATTGGCTGCCATTGGGCCGCCAGTGTGTGGAGCATTATCGCTTGCTGCACCGTTATTGTGTCTTTTCCCACGATGAAATGATATGCAAAATGGCTTCTAAGGCTGATGTATTAGACGTTGTGGTAGCGTCAACTGTTCAGAAGGACATGGCCATCATGATCGAGGACGAGAAAGCTTTAAGGGAAACTGTTCGGAAATTGGGAGTAATTGATTCTGAAAGAATGGATTTTGAGCTGTTGCCAGATGATGAGCGGCAGTGTATAAAATGCAAAACTACATGCTTCATGTCTGCCATCTCCTGCTCTTGTAAACCTGGCCTACTTGTTTGCCTACATCATGTGAAAGAATTGTGTTCTTGCCCCCCGTATAAGTATAACCTGCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCATGTCTGCCATCTCCTGC
59.82
TTGGTTGAAGCCACTGTGGT
60.03
175
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CATGTCTGCCATCTCCTGCT
59.82
TTGGTTGAAGCCACTGTGGT
60.03
174
PCR template sequence:
TCATGTCTGCCATCTCCTGCTCTTGTAAACCTGGCCTACTTGTTTGCCTACATCATGTGAAAGAATTGTGTTCTTGCCCCCCGTATAAGTATAACCTGCGGTTTATCGAACGAATCAGTGTGCTGGGGAGTTTGTAATTACGTTTCCAAGAGCCTACCACAGTGGCTTCAACCAAGGTTTTAATTTTGCCGAGGCTGTTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-433-3p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGTATAACCTGCGGTTTATCGAACGA
siRNA sets
TCGTTCGATAAACCGCAGG, ATAAACCGCAGGTTATACT, GATAAACCGCAGGTTATAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKDM5B_497_ORF_1
0.7829
0.101153275
0.283149002
342
ORF sequence:
ATGATATGCAAAATGGCTTCTAAGGCTGATGTATTAGACGTTGTGGTAGCGTCAACTGTTCAGAAGGACATGGCCATCATGATCGAGGACGAGAAAGCTTTAAGGGAAACTGTTCGGAAATTGGGAGTAATTGATTCTGAAAGAATGGATTTTGAGCTGTTGCCAGATGATGAGCGGCAGTGTATAAAATGCAAAACTACATGCTTCATGTCTGCCATCTCCTGCTCTTGTAAACCTGGCCTACTTGTTTGCCTACATCATGTGAAAGAATTGTGTTCTTGCCCCCCGTATAAGTATAACCTGCGGTTTATCGAACGAATCAGTGTGCTGGGGAGTTTGTAA
Peptide sequence:
MICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCIKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYNLRFIERISVLGSL
IRESfinder result
IRESfinder score
0.57383029
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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