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mmu_circGk5_396
Basic information of circular RNA
PanCircBase ID:
mmu_circGk5_396
mm39_Chr. Position ID:
chr9|96011053|96022723|+
Gene name:
Gk5
Transcript:
ENSMUST00000085217.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
2,3,4,5
Exon/intron offsets:
0,4388,8744,11538
Genomic length:
11670
Exon/intron sizes in nt:
94,76,94,132
Flanking exon/introns:
chr9:96001665-96011053|chr9:96022723-96027724
Splice length:
396
Other database IDs:
CIRCpedia: MMU_CIRCpedia_35299, circAtlas: mmu-Gk5_0004
circBase: hsa_circ_0122228, circAtlas: hsa-GK5_0012, CIRCpedia: HSA_CIRCpedia_105772
Human Ortholog IDs:
Mature spliced Sequence:
GTAGAAAATGTTTACCCTCAACCTGGCTGGGTTGAAATCGATCCTGATTCTCTCTGGGCTCAGTTTGTTGCCGTAATAAAAGATGCTGTCAAAGCTGCAGGGGTGCAGATGAATCAAATTGTCGGTCTTGGCATATCAACACAGAGAGCCACTTTCATTACATGGAACAAGAAAACAGGCCATCATTTTCACAACTTCATTAGCTGGCAAGACCTAAGGGCAGCTGAACTTGTAAAGTCCTGGAATAATTCTCTCATAATGAAGCTATTGCATGGGGCCACCCGAGTCCTTCATTTCTTCAGTAGAAGTAAAGTAATGCTAACGGTCAGCCGCTTCAATTTCAGCACCCAGCATGCCACCTTAAGATTGACCTGGATTTTACAAAACCTATCTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCCGCTTCAATTTCAGCA
59.76
GCAACAAACTGAGCCCAGAG
59.4
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCCGCTTCAATTTCAGCAC
59.76
GCAACAAACTGAGCCCAGAG
59.4
140
PCR template sequence:
CTTCAGTAGAAGTAAAGTAATGCTAACGGTCAGCCGCTTCAATTTCAGCACCCAGCATGCCACCTTAAGATTGACCTGGATTTTACAAAACCTATCTGAGGTAGAAAATGTTTACCCTCAACCTGGCTGGGTTGAAATCGATCCTGATTCTCTCTGGGCTCAGTTTGTTGCCGTAATAAAAGATGCTGTCAAAGCTGCAG
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-30e-5p(1), mmu-miR-30a-5p(1), mmu-miR-431-5p(1), mmu-miR-382-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAACCTATCTGAGGTAGAAAATGTTT
siRNA sets
AAACATTTTCTACCTCAGA, AACATTTTCTACCTCAGAT, ATTTTCTACCTCAGATAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGK5_396_ORF_1
0.8164
-0.068444491
0.713554187
684
ORF sequence:
ATGAATCAAATTGTCGGTCTTGGCATATCAACACAGAGAGCCACTTTCATTACATGGAACAAGAAAACAGGCCATCATTTTCACAACTTCATTAGCTGGCAAGACCTAAGGGCAGCTGAACTTGTAAAGTCCTGGAATAATTCTCTCATAATGAAGCTATTGCATGGGGCCACCCGAGTCCTTCATTTCTTCAGTAGAAGTAAAGTAATGCTAACGGTCAGCCGCTTCAATTTCAGCACCCAGCATGCCACCTTAAGATTGACCTGGATTTTACAAAACCTATCTGAGGTAGAAAATGTTTACCCTCAACCTGGCTGGGTTGAAATCGATCCTGATTCTCTCTGGGCTCAGTTTGTTGCCGTAATAAAAGATGCTGTCAAAGCTGCAGGGGTGCAGATGAATCAAATTGTCGGTCTTGGCATATCAACACAGAGAGCCACTTTCATTACATGGAACAAGAAAACAGGCCATCATTTTCACAACTTCATTAGCTGGCAAGACCTAAGGGCAGCTGAACTTGTAAAGTCCTGGAATAATTCTCTCATAATGAAGCTATTGCATGGGGCCACCCGAGTCCTTCATTTCTTCAGTAGAAGTAAAGTAATGCTAACGGTCAGCCGCTTCAATTTCAGCACCCAGCATGCCACCTTAAGATTGACCTGGATTTTACAAAACCTATCTGAG
Peptide sequence:
MNQIVGLGISTQRATFITWNKKTGHHFHNFISWQDLRAAELVKSWNNSLIMKLLHGATRVLHFFSRSKVMLTVSRFNFSTQHATLRLTWILQNLSEVENVYPQPGWVEIDPDSLWAQFVAVIKDAVKAAGVQMNQIVGLGISTQRATFITWNKKTGHHFHNFISWQDLRAAELVKSWNNSLIMKLLHGATRVLHFFSRSKVMLTVSRFNFSTQHATLRLTWILQNLSE
IRESfinder result
IRESfinder score
0.757413887
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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