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mmu_circGart_461
Basic information of circular RNA
PanCircBase ID:
mmu_circGart_461
mm39_Chr. Position ID:
chr16|91438099|91440034|-
Gene name:
Gart
Transcript:
ENSMUST00000023684.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
4,3,2
Exon/intron offsets:
0,382,1745
Genomic length:
1935
Exon/intron sizes in nt:
1,75,96,190
Flanking exon/introns:
chr16:91436339-91438099|chr16:91440034-91443771
Splice length:
461
Other database IDs:
CIRCpedia: MMU_CIRCpedia_34160, circAtlas: mmu-Gart_0001
Human Ortholog IDs:
Mature spliced Sequence:
CAGGTGGTTGCATTTTGTTTCTGAATCCCTGCTTCGGAGACAGCCATGGCAGCCCGAGTTCTTGTCATCGGTAGCGGGGGAAGGGAACATACCCTGGCCTGGAAGCTCGCACAGTCTCCTCAGGTCAAGCAAGTGTTGGTTGCCCCAGGAAACGCAGGCACTGCGTGCGCTGGGAAGATCTCCAATGCTGCTGTCTCTGTCAATGATCACAGTGCCCTCGCTCAGTTCTGCAAGGATGAAAAGATTGAACTCGTAGTTGTCGGACCAGAGGCCCCTCTGGCTGCAGGAATTGTTGGGGACCTGACCTCTGCAGGAGTACGATGCTTTGGCCCCACAGCACAAGCAGCTCAATTAGAGTCCAGTAAGAAGTTTGCTAAAGAGTTTATGGACCGCCATGAAATCCCAACTGCACAGTGGAGAGCATTCACCAACCCTGAAGATGCCTGCAGCTTTATTACAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATCCCAACTGCACAGTGGAG
59.96
TATGTTCCCTTCCCCCGCTA
60.03
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCGCCATGAAATCCCAACT
59.96
TATGTTCCCTTCCCCCGCTA
60.03
164
PCR template sequence:
GTAAGAAGTTTGCTAAAGAGTTTATGGACCGCCATGAAATCCCAACTGCACAGTGGAGAGCATTCACCAACCCTGAAGATGCCTGCAGCTTTATTACAAGCAGGTGGTTGCATTTTGTTTCTGAATCCCTGCTTCGGAGACAGCCATGGCAGCCCGAGTTCTTGTCATCGGTAGCGGGGGAAGGGAACATACCCTGGCCT
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-322-5p(1), mmu-miR-541-5p(1), mmu-miR-362-5p(1), mmu-miR-107-3p(1), mmu-miR-680(1), mmu-miR-335-3p(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCTTTATTACAAGCAGGTGGTTGCAT
siRNA sets
ATGCAACCACCTGCTTGTA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGART_461_ORF_1
0.7582
0.101922305
0.803984371
672
ORF sequence:
ATGGCAGCCCGAGTTCTTGTCATCGGTAGCGGGGGAAGGGAACATACCCTGGCCTGGAAGCTCGCACAGTCTCCTCAGGTCAAGCAAGTGTTGGTTGCCCCAGGAAACGCAGGCACTGCGTGCGCTGGGAAGATCTCCAATGCTGCTGTCTCTGTCAATGATCACAGTGCCCTCGCTCAGTTCTGCAAGGATGAAAAGATTGAACTCGTAGTTGTCGGACCAGAGGCCCCTCTGGCTGCAGGAATTGTTGGGGACCTGACCTCTGCAGGAGTACGATGCTTTGGCCCCACAGCACAAGCAGCTCAATTAGAGTCCAGTAAGAAGTTTGCTAAAGAGTTTATGGACCGCCATGAAATCCCAACTGCACAGTGGAGAGCATTCACCAACCCTGAAGATGCCTGCAGCTTTATTACAAGCAGGTGGTTGCATTTTGTTTCTGAATCCCTGCTTCGGAGACAGCCATGGCAGCCCGAGTTCTTGTCATCGGTAGCGGGGGAAGGGAACATACCCTGGCCTGGAAGCTCGCACAGTCTCCTCAGGTCAAGCAAGTGTTGGTTGCCCCAGGAAACGCAGGCACTGCGTGCGCTGGGAAGATCTCCAATGCTGCTGTCTCTGTCAATGATCACAGTGCCCTCGCTCAGTTCTGCAAGGATGAAAAGATTGAACTCGTAG
Peptide sequence:
MAARVLVIGSGGREHTLAWKLAQSPQVKQVLVAPGNAGTACAGKISNAAVSVNDHSALAQFCKDEKIELVVVGPEAPLAAGIVGDLTSAGVRCFGPTAQAAQLESSKKFAKEFMDRHEIPTAQWRAFTNPEDACSFITSRWLHFVSESLLRRQPWQPEFLSSVAGEGNIPWPGSSHSLLRSSKCWLPQETQALRALGRSPMLLSLSMITVPSLSSARMKRLNS
IRESfinder result
IRESfinder score
0.456498829
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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