top of page
mmu_circGart_300
Basic information of circular RNA
PanCircBase ID:
mmu_circGart_300
mm39_Chr. Position ID:
chr16|91433394|91434943|-
Gene name:
Gart
Transcript:
ENSMUST00000023684.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
9,8,7
Exon/intron offsets:
0,485,1423
Genomic length:
1549
Exon/intron sizes in nt:
86,88,126
Flanking exon/introns:
chr16:91433050-91433394|chr16:91434943-91435614
Splice length:
300
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TGCCTTTGCTTCACTGACGGGAAGACGGTGGCCGAAATGCCCCCAGCACAAGACCATAAGCGATTGCTGGATGGAGACGAAGGCCCCAACACCGGGGGGATGGGAGCCTACTGCCCAGCACCTCAGGTTTCTAAGGACTTGTTAGTAAAAATTAAGAACACTATTCTTCAGAGAGCAGTAGACGGCATGCAGCAGGAGGGTGCGCCGTACACAGGAATTCTTTATGCTGGTATAATGCTGACCAAAGATGGCCCAAAAGTGTTGGAGTTTAATTGCCGCTTTGGTGATCCGGAATGCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCGCCGTACACAGGAATTCT
60.74
TCGTCTCCATCCAGCAATCG
59.9
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCGCCGTACACAGGAATTCT
60.74
TTATGGTCTTGTGCTGGGGG
59.67
158
PCR template sequence:
TGCGCCGTACACAGGAATTCTTTATGCTGGTATAATGCTGACCAAAGATGGCCCAAAAGTGTTGGAGTTTAATTGCCGCTTTGGTGATCCGGAATGCCAGTGCCTTTGCTTCACTGACGGGAAGACGGTGGCCGAAATGCCCCCAGCACAAGACCATAAGCGATTGCTGGATGGAGACGAAGGCCCCAACACCGGGGGGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-338-3p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCCGGAATGCCAGTGCCTTTGCTTCA
siRNA sets
TGAAGCAAAGGCACTGGCA, GCAAAGGCACTGGCATTCC, CAAAGGCACTGGCATTCCG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGART_300_ORF_1
0.9454
0.231215361
0.819993454
564
ORF sequence:
ATGCCCCCAGCACAAGACCATAAGCGATTGCTGGATGGAGACGAAGGCCCCAACACCGGGGGGATGGGAGCCTACTGCCCAGCACCTCAGGTTTCTAAGGACTTGTTAGTAAAAATTAAGAACACTATTCTTCAGAGAGCAGTAGACGGCATGCAGCAGGAGGGTGCGCCGTACACAGGAATTCTTTATGCTGGTATAATGCTGACCAAAGATGGCCCAAAAGTGTTGGAGTTTAATTGCCGCTTTGGTGATCCGGAATGCCAGTGCCTTTGCTTCACTGACGGGAAGACGGTGGCCGAAATGCCCCCAGCACAAGACCATAAGCGATTGCTGGATGGAGACGAAGGCCCCAACACCGGGGGGATGGGAGCCTACTGCCCAGCACCTCAGGTTTCTAAGGACTTGTTAGTAAAAATTAAGAACACTATTCTTCAGAGAGCAGTAGACGGCATGCAGCAGGAGGGTGCGCCGTACACAGGAATTCTTTATGCTGGTATAATGCTGACCAAAGATGGCCCAAAAGTGTTGGAGTTTAATTGCCGCTTTGGTGATCCGGAATGCCAG
Peptide sequence:
MPPAQDHKRLLDGDEGPNTGGMGAYCPAPQVSKDLLVKIKNTILQRAVDGMQQEGAPYTGILYAGIMLTKDGPKVLEFNCRFGDPECQCLCFTDGKTVAEMPPAQDHKRLLDGDEGPNTGGMGAYCPAPQVSKDLLVKIKNTILQRAVDGMQQEGAPYTGILYAGIMLTKDGPKVLEFNCRFGDPECQ
IRESfinder result
IRESfinder score
0.35507817
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page