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mmu_circGlis3_616
Basic information of circular RNA
PanCircBase ID:
mmu_circGlis3_616
mm39_Chr. Position ID:
chr19|28261051|28331716|-
Gene name:
Glis3
Transcript:
ENSMUST00000162022.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
9,8,7,6
Exon/intron offsets:
0,15126,33602,70554
Genomic length:
70665
Exon/intron sizes in nt:
1,76,16,91,60,111
Flanking exon/introns:
chr19:28241444-28261051|chr19:28331716-28335190
Splice length:
616
Other database IDs:
CIRCpedia: MMU_CIRCpedia_15150, circAtlas: mmu-Glis3_0007
circAtlas: hsa-GLIS3_0009, CIRCpedia: HSA_CIRCpedia_111017
Human Ortholog IDs:
Mature spliced Sequence:
AAACCTTATGCTTGTCAAATTCCAGGATGTACAAAGCGCTACACAGACCCAAGCTCCCTCAGAAAGCACGTGAAGGCACATTCTTCCCGAGAGCAGCAAGCAAGGAAAAAGCTACGGTCTAGCACTGAGCTCCATCCAGATCTCCTCACAGACTGCCTCGCTGTGCAGCCCCTGCAGCCAGCCACGTCCCCTGGAGATGCTGCTGATCATACCGTGGGGCACTCCCCAGGGCCGGGGCCTGGGCCAGGGCCTGGGGCTGAACTCTATTCAGCTCCCATTTTCGCCAGCAATCATTCAACTCGAAGTGGAACAGCTGCTGGGGCTGGGCCACCCCCACATCCTGTCAGTCACCCTTCTCCAGGACATAATGTACAGGGGAGCCCCCACAACCCCTCCTCCCAGTTACCTCCACTCACAGCTGTGGACGCAGGCGCTGAGAGGTTTGCACCTCCGACTCCATCTCCTCACCACATCAGCCCGGGAAGAGTTCCAGCTCCTCCGTCACTGCTCCAGAGAGCACAGGCTCCCCACTCCCAGCAGCCACCAGGCTCACTCCTGAAGCCCTACCAGCCAGAAACCAACTCTTCTTTTCAGCCAAATGGTATCCATGTCCACG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCCCTACCAGCCAGAAAC
59.96
CTTGCTGCTCTCGGGAAGAA
60.04
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCCCTACCAGCCAGAAAC
59.96
GCTGCTCTCGGGAAGAATGT
60.11
155
PCR template sequence:
GCACAGGCTCCCCACTCCCAGCAGCCACCAGGCTCACTCCTGAAGCCCTACCAGCCAGAAACCAACTCTTCTTTTCAGCCAAATGGTATCCATGTCCACGAAACCTTATGCTTGTCAAATTCCAGGATGTACAAAGCGCTACACAGACCCAAGCTCCCTCAGAAAGCACGTGAAGGCACATTCTTCCCGAGAGCAGCAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-103-3p(1), mmu-miR-15b-5p(1), mmu-miR-19a-3p(1), mmu-miR-128-3p(1), mmu-miR-370-3p(1), mmu-miR-107-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
ATCCATGTCCACGAAACCTTATGCTT
siRNA sets
AAGCATAAGGTTTCGTGGA,TAAGGTTTCGTGGACATGG,AGCATAAGGTTTCGTGGAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGLIS3_616_ORF_1
0.9696
0.131902742
0.837320978
633
ORF sequence:
ATGGTATCCATGTCCACGAAACCTTATGCTTGTCAAATTCCAGGATGTACAAAGCGCTACACAGACCCAAGCTCCCTCAGAAAGCACGTGAAGGCACATTCTTCCCGAGAGCAGCAAGCAAGGAAAAAGCTACGGTCTAGCACTGAGCTCCATCCAGATCTCCTCACAGACTGCCTCGCTGTGCAGCCCCTGCAGCCAGCCACGTCCCCTGGAGATGCTGCTGATCATACCGTGGGGCACTCCCCAGGGCCGGGGCCTGGGCCAGGGCCTGGGGCTGAACTCTATTCAGCTCCCATTTTCGCCAGCAATCATTCAACTCGAAGTGGAACAGCTGCTGGGGCTGGGCCACCCCCACATCCTGTCAGTCACCCTTCTCCAGGACATAATGTACAGGGGAGCCCCCACAACCCCTCCTCCCAGTTACCTCCACTCACAGCTGTGGACGCAGGCGCTGAGAGGTTTGCACCTCCGACTCCATCTCCTCACCACATCAGCCCGGGAAGAGTTCCAGCTCCTCCGTCACTGCTCCAGAGAGCACAGGCTCCCCACTCCCAGCAGCCACCAGGCTCACTCCTGAAGCCCTACCAGCCAGAAACCAACTCTTCTTTTCAGCCAAATGGTATCCATGTCCAC
Peptide sequence:
MVSMSTKPYACQIPGCTKRYTDPSSLRKHVKAHSSREQQARKKLRSSTELHPDLLTDCLAVQPLQPATSPGDAADHTVGHSPGPGPGPGPGAELYSAPIFASNHSTRSGTAAGAGPPPHPVSHPSPGHNVQGSPHNPSSQLPPLTAVDAGAERFAPPTPSPHHISPGRVPAPPSLLQRAQAPHSQQPPGSLLKPYQPETNSSFQPNGIHVH
IRESfinder result
IRESfinder score
0.542279565
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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