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mmu_circKdm5b_1126
Basic information of circular RNA
PanCircBase ID:
mmu_circKdm5b_1126
mm39_Chr. Position ID:
chr1|134530187|134541749|+
Gene name:
Kdm5b
Transcript:
ENSMUST00000047714.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
10,11,12,13,14,15,16
Exon/intron offsets:
0,1992,3263,5238,6415,10738,11437
Genomic length:
11562
Exon/intron sizes in nt:
15,91,82,16,31,20,19,50,00,000
Flanking exon/introns:
chr1:134528491-134530187|chr1:134541749-134543655
Splice length:
1126
Other database IDs:
circAtlas: mmu-Kdm5b_0031
Human Ortholog IDs:
Mature spliced Sequence:
ATGGTTCCCACAGAGCTGGTGGAGAAGGAGTTTTGGCGGCTCGTAAGCACTATTGAAGAAGACGTCACGGTGGAGTATGGAGCTGATATTGCTTCAAAAGAGTTTGGCAGTGGCTTTCCTGTTCGAGATGGGAAAATCAAGATTTCTCCTGAGGAAGAGGAATACCTGGATAGTGGCTGGAATTTGAACAACATGCCAGTGATGGAGCAGTCTGTCCTTGCTCATATTACTGCTGATATATGTGGCATGAAACTCCCCTGGTTGTATGTGGGCATGTGCTTTTCTTCATTCTGTTGGCACATTGAAGACCACTGGAGCTATTCAATCAACTACCTACACTGGGGTGAGCCAAAAACCTGGTATGGAGTTCCAGGCTACGCTGCTGAGCAGCTAGAAAACGTGATGAAGAAGCTCGCTCCTGAGCTCTTTGTGTCCCAGCCGGACCTGCTCCACCAGCTGGTGACCATCATGAACCCCAACACTCTGATGACTCATGAAGTGCCTGTTTATCGAACGAATCAGTGTGCTGGGGAGTTTGTAATTACGTTTCCAAGAGCCTACCACAGTGGCTTCAACCAAGGTTTTAATTTTGCCGAGGCTGTTAACTTCTGCACTGTTGATTGGCTGCCATTGGGCCGCCAGTGTGTGGAGCATTATCGCTTGCTGCACCGTTATTGTGTCTTTTCCCACGATGAAATGATATGCAAAATGGCTTCTAAGGCTGATGTATTAGACGTTGTGGTAGCGTCAACTGTTCAGAAGGACATGGCCATCATGATCGAGGACGAGAAAGCTTTAAGGGAAACTGTTCGGAAATTGGGAGTAATTGATTCTGAAAGAATGGATTTTGAGCTGTTGCCAGATGATGAGCGGCAGTGTATAAAATGCAAAACTACATGCTTCATGTCTGCCATCTCCTGCTCTTGTAAACCTGGCCTACTTGTTTGCCTACATCATGTGAAAGAATTGTGTTCTTGCCCCCCGTATAAGTATAACCTGCGGTATAGATACACTCTGGATGATCTCTATCCAATGATGAATGCATTAAAGCTTCGAGCAGAGTCTTACAATGAATGGGCCTTAAATGTGAATGAAGCCTTGGAAGCAAAGATCAATAAGAAGAAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCTTCGAGCAGAGTCTTACA
58.84
CCACCGTGACGTCTTCTTCA
59.97
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCTTCGAGCAGAGTCTTACA
58.84
CTCCATACTCCACCGTGACG
59.9
160
PCR template sequence:
TATCCAATGATGAATGCATTAAAGCTTCGAGCAGAGTCTTACAATGAATGGGCCTTAAATGTGAATGAAGCCTTGGAAGCAAAGATCAATAAGAAGAAAAATGGTTCCCACAGAGCTGGTGGAGAAGGAGTTTTGGCGGCTCGTAAGCACTATTGAAGAAGACGTCACGGTGGAGTATGGAGCTGATATTGCTTCAAAAG
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-433-3p(2), mmu-let-7a-5p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-138-5p(1), mmu-let-7d-5p(1), mmu-miR-207(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AATAAGAAGAAAAATGGTTCCCACAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKDM5B_1126_ORF_1
0.9548
0.191161634
0.996954738
1182
ORF sequence:
ATGGTTCCCACAGAGCTGGTGGAGAAGGAGTTTTGGCGGCTCGTAAGCACTATTGAAGAAGACGTCACGGTGGAGTATGGAGCTGATATTGCTTCAAAAGAGTTTGGCAGTGGCTTTCCTGTTCGAGATGGGAAAATCAAGATTTCTCCTGAGGAAGAGGAATACCTGGATAGTGGCTGGAATTTGAACAACATGCCAGTGATGGAGCAGTCTGTCCTTGCTCATATTACTGCTGATATATGTGGCATGAAACTCCCCTGGTTGTATGTGGGCATGTGCTTTTCTTCATTCTGTTGGCACATTGAAGACCACTGGAGCTATTCAATCAACTACCTACACTGGGGTGAGCCAAAAACCTGGTATGGAGTTCCAGGCTACGCTGCTGAGCAGCTAGAAAACGTGATGAAGAAGCTCGCTCCTGAGCTCTTTGTGTCCCAGCCGGACCTGCTCCACCAGCTGGTGACCATCATGAACCCCAACACTCTGATGACTCATGAAGTGCCTGTTTATCGAACGAATCAGTGTGCTGGGGAGTTTGTAATTACGTTTCCAAGAGCCTACCACAGTGGCTTCAACCAAGGTTTTAATTTTGCCGAGGCTGTTAACTTCTGCACTGTTGATTGGCTGCCATTGGGCCGCCAGTGTGTGGAGCATTATCGCTTGCTGCACCGTTATTGTGTCTTTTCCCACGATGAAATGATATGCAAAATGGCTTCTAAGGCTGATGTATTAGACGTTGTGGTAGCGTCAACTGTTCAGAAGGACATGGCCATCATGATCGAGGACGAGAAAGCTTTAAGGGAAACTGTTCGGAAATTGGGAGTAATTGATTCTGAAAGAATGGATTTTGAGCTGTTGCCAGATGATGAGCGGCAGTGTATAAAATGCAAAACTACATGCTTCATGTCTGCCATCTCCTGCTCTTGTAAACCTGGCCTACTTGTTTGCCTACATCATGTGAAAGAATTGTGTTCTTGCCCCCCGTATAAGTATAACCTGCGGTATAGATACACTCTGGATGATCTCTATCCAATGATGAATGCATTAAAGCTTCGAGCAGAGTCTTACAATGAATGGGCCTTAAATGTGAATGAAGCCTTGGAAGCAAAGATCAATAAGAAGAAAAATGGTTCCCACAGAGCTGGTGGAGAAGGAGTTTTGGCGGCTCGTAAGCACTATTGA
Peptide sequence:
MVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKISPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCIKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYNLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEAKINKKKNGSHRAGGEGVLAARKHY
IRESfinder result
IRESfinder score
0.562490788
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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