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mmu_circKdm6a_339
Basic information of circular RNA
PanCircBase ID:
mmu_circKdm6a_339
mm39_Chr. Position ID:
chrX|18065396|18089116|+
Gene name:
Kdm6a
Transcript:
ENSMUST00000044484.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
3,4,5,6
Exon/intron offsets:
0,9578,17780,23599
Genomic length:
23720
Exon/intron sizes in nt:
1,09,50,59,121
Flanking exon/introns:
chrX:18029686-18065396|chrX:18089116-18100098
Splice length:
339
Other database IDs:
circBase: mmu_circ_0016238, CIRCpedia: MMU_CIRCpedia_12439, circAtlas: mmu-Kdm6a_0001
circBase: hsa_circ_0140320, circAtlas: hsa-KDM6A_0002, CIRCpedia: HSA_CIRCpedia_65870
Human Ortholog IDs:
Mature spliced Sequence:
GCTGTTCGCTGCTACGAATCTCTAATCTTAAAAGCTGAAGGGAAAGTGGAGTCTGATTTCTTTTGTCAATTAGGTCACTTCAACCTCTTATTGGAAGATTATCCAAAAGCATTATCTGCATACCAGAGGTACTACAGTTTACAGTCTGATTACTGGAAGAATGCTGCCTTTTTATATGGTCTTGGTTTGGTCTACTTCCATTACAATGCATTTCAGTGGGCTATTAAAGCATTTCAGGAGGTGCTTTATGTCGATCCCAGCTTTTGTCGAGCCAAGGAAATTCATTTACGACTTGGGCTTATGTTCAAAGTGAACACAGACTATGAGTCTAGTTTAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCGATCCCAGCTTTTGTCGA
59.39
GACTCCACTTTCCCTTCAGCT
59.65
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCGATCCCAGCTTTTGTCGA
59.39
AGACTCCACTTTCCCTTCAGC
59.65
143
PCR template sequence:
GGTGCTTTATGTCGATCCCAGCTTTTGTCGAGCCAAGGAAATTCATTTACGACTTGGGCTTATGTTCAAAGTGAACACAGACTATGAGTCTAGTTTAAAGGCTGTTCGCTGCTACGAATCTCTAATCTTAAAAGCTGAAGGGAAAGTGGAGTCTGATTTCTTTTGTCAATTAGGTCACTTCAACCTCTTATTGGAAGATT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-155-5p(1), mmu-miR-103-3p(1), mmu-miR-33-5p(1), mmu-miR-203-3p(1), mmu-miR-320-3p(1), mmu-miR-503-5p(1), mmu-miR-192-5p(1), mmu-miR-215-5p(1), mmu-miR-107-3p(1), mmu-miR-383-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GTCTAGTTTAAAGGCTGTTCGCTGCT
siRNA sets
AACAGCCTTTAAACTAGAC,GAACAGCCTTTAAACTAGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKDM6A_339_ORF_1
0.8213
0.05900941
0.318078697
378
ORF sequence:
ATGTTCAAAGTGAACACAGACTATGAGTCTAGTTTAAAGGCTGTTCGCTGCTACGAATCTCTAATCTTAAAAGCTGAAGGGAAAGTGGAGTCTGATTTCTTTTGTCAATTAGGTCACTTCAACCTCTTATTGGAAGATTATCCAAAAGCATTATCTGCATACCAGAGGTACTACAGTTTACAGTCTGATTACTGGAAGAATGCTGCCTTTTTATATGGTCTTGGTTTGGTCTACTTCCATTACAATGCATTTCAGTGGGCTATTAAAGCATTTCAGGAGGTGCTTTATGTCGATCCCAGCTTTTGTCGAGCCAAGGAAATTCATTTACGACTTGGGCTTATGTTCAAAGTGAACACAGACTATGAGTCTAGTTTAAAG
Peptide sequence:
MFKVNTDYESSLKAVRCYESLILKAEGKVESDFFCQLGHFNLLLEDYPKALSAYQRYYSLQSDYWKNAAFLYGLGLVYFHYNAFQWAIKAFQEVLYVDPSFCRAKEIHLRLGLMFKVNTDYESSLK
IRESfinder result
IRESfinder score
0.841102109
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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