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mmu_ciKdm3b_705
Basic information of circular RNA
PanCircBase ID:
mmu_ciKdm3b_705
mm39_Chr. Position ID:
chr18|34966540|34967245|+
Gene name:
Kdm3b
Transcript:
ENSMUST00000043775.9
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
22
Exon/intron offsets:
0
Genomic length:
705
Exon/intron sizes in nt:
705
Flanking exon/introns:
chr18:34966540-34967269
Splice length:
705
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGGGCTGTGCCGGCAAGACTGGCTCCAGAGCTCCATGAGCTTGGATGGTTCCTTTTTCTCTCTAGTTTAGCTATAAATAGCGGGATCTAAAATCAGCTTTCCTGAGACCAGGCAAGCCTCAAATTCATAGATATCAGACTGTTTCTGCCTTGTTAATACTGAGAATAAAGCTGTGTGCGTGTGTGGTAGGTTAAAGGGCAGTTTACAGTAGTTGGGTGATCTCCTTCCACCATTGGATTCTGTGTATCAAACTCAGGCTACCAGGTTTGGTGGCAAGCACATATACCTGCCAAGCCATCTCCATTTTACCAGACTCCCCCACCTCCACCCCAACCCCTTTTTAAAGATTTTTATTAATTATGTATACAGCATTTTGCCTGCGTGTATGCCTGTATGCCAGAAGAGGGCAGCAGATCTCATGATAGATGGATATGAGCTACCAAAAGGTTGCTGGGGATTGAAGCCAGAACCTCTGGAAAAACATCTAGTATTCTTAATCTCTGAGCCATCTCTCCAGACCCTCTAGCCCTTGTTTTTAAATATATACTCATGTTTTGTAGTATTAACAGAACACAGTGGCATGTGCTATAGTTAGGAGGATTGCTCAAAGCCAGTATGGGAGACATAACACGTCTCACAAAAAAGGGGGGTGGGGGAGAAAGAAAAGAAGGAAGAAGGAAAAAAGAGATTGTGTTTGTTTTACT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGGGTGGGGGAGAAAGAAAA
59.51
AGCTGATTTTAGATCCCGCT
56.69
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGGTGGGGGAGAAAGAAAA
59.51
AAGCTGATTTTAGATCCCGCT
57.43
158
PCR template sequence:
TCAAAGCCAGTATGGGAGACATAACACGTCTCACAAAAAAGGGGGGTGGGGGAGAAAGAAAAGAAGGAAGAAGGAAAAAAGAGATTGTGTTTGTTTTACTGTGGGCTGTGCCGGCAAGACTGGCTCCAGAGCTCCATGAGCTTGGATGGTTCCTTTTTCTCTCTAGTTTAGCTATAAATAGCGGGATCTAAAATCAGCTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(1), mmu-miR-31-5p(1), mmu-miR-132-3p(1), mmu-miR-320-3p(1), mmu-miR-495-3p(1), mmu-miR-431-5p(1), mmu-miR-218-5p(1), mmu-miR-490-3p(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGTTTGTTTTACTGTGGGCTGTGCCG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIKDM3B_705_ORF_1
0.909
-0.215288704
0.04042959
180
ORF sequence:
ATGGGAGACATAACACGTCTCACAAAAAAGGGGGGTGGGGGAGAAAGAAAAGAAGGAAGAAGGAAAAAAGAGATTGTGTTTGTTTTACTGTGGGCTGTGCCGGCAAGACTGGCTCCAGAGCTCCATGAGCTTGGATGGTTCCTTTTTCTCTCTAGTTTAGCTATAAATAGCGGGATCTAA
Peptide sequence:
MGDITRLTKKGGGGERKEGRRKKEIVFVLLWAVPARLAPELHELGWFLFLSSLAINSGI
IRESfinder result
IRESfinder score
0.782989586
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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