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mmu_circGart_809
Basic information of circular RNA
PanCircBase ID:
mmu_circGart_809
mm39_Chr. Position ID:
chr16|91424914|91427959|-
Gene name:
Gart
Transcript:
ENSMUST00000023684.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
16,15,14,13,12
Exon/intron offsets:
0,395,2016,2579,2950
Genomic length:
3045
Exon/intron sizes in nt:
153,252,199,110,95
Flanking exon/introns:
chr16:91422408-91424914|chr16:91427959-91430762
Splice length:
809
Other database IDs:
circAtlas: mmu-Gart_0018
CIRCpedia: HSA_CIRCpedia_35288
Human Ortholog IDs:
Mature spliced Sequence:
GGGCTTGACTTACAAGGACTCCGGAGTAGACATCGCAGCTGGAAATATGCTGGTTAAGAAAATTCAGCCTTTAGCAAAAGCCACCTCCAGACCAGGCTGCAGTGTTGACCTTGGGGGCTTTGCTGGTCTTTTTGATTTGAAAGCAGCTGGTTTCAAAGATCCTCTTCTGGCCTCTGGAACAGATGGTGTGGGAACTAAACTAAAGATTGCGCAGCTGTGCAATAAGCATGATTCCATCGGGCAGGATCTGGTGGCCATGTGTGTGAACGACATCCTCGCCCAGGGAGCAGAGCCCCTCTTCTTCCTTGACTACTTTTCCTGTGGGAAGCTCGACCTCAGTACAACTGAAGCCGTCATTGCTGGAATTGCTGCAGCTTGCCAGCAGGCTGGCTGTGCCCTGCTGGGTGGGGAGACAGCAGAGATGCCCAACATGTACCCTCCTGGAGAGTATGATCTTGCTGGGTTTGCTGTTGGTGCTATGGAGAGACACCAGAAGCTCCCTCAGCTAGAAAGGATCACCGAAGGGGATGCTGTTATTGGAGTGGCTTCATCTGGTCTTCACAGCAATGGGTTTAGCCTTGTGAGGAAAATCGTGGAGAGGTCTTCGCTCCAATACTCCTCCCCAGCACCTGGTGGTTGTGGAGATCAGACCTTAGGGGACTTACTTCTAACTCCAACCAGGATCTACAGCCATTCACTGCTGCCCATCATACGTTCAGGACGTGTCAAAGCTTTTGCTCATATCACTGGAGGCGGGTTGCTGGAAAACATCCCCAGAGTCCTCCCTCAGAAGTTTGGAGTAGATTTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTCATATCACTGGAGGCGGG
59.68
CTGGTCTGGAGGTGGCTTTT
59.89
167
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTCATATCACTGGAGGCGG
60.32
CTGGTCTGGAGGTGGCTTTT
59.89
168
PCR template sequence:
ATACGTTCAGGACGTGTCAAAGCTTTTGCTCATATCACTGGAGGCGGGTTGCTGGAAAACATCCCCAGAGTCCTCCCTCAGAAGTTTGGAGTAGATTTAGGGGCTTGACTTACAAGGACTCCGGAGTAGACATCGCAGCTGGAAATATGCTGGTTAAGAAAATTCAGCCTTTAGCAAAAGCCACCTCCAGACCAGGCTGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-32-5p(1), mmu-miR-211-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-324-5p(1), mmu-miR-25-3p(1), mmu-miR-214-3p(1), mmu-miR-363-3p(1), mmu-miR-676-3p(1), mmu-miR-194-5p(1), mmu-miR-690(1), mmu-miR-377-3p(1), mmu-miR-188-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGAGTAGATTTAGGGGCTTGACTTAC
siRNA sets
AAGCCCCTAAATCTACTCC, CAAGCCCCTAAATCTACTC, TAAGTCAAGCCCCTAAATC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGART_809_ORF_1
0.9968
0.163465367
0.942939614
771
ORF sequence:
ATGCTGGTTAAGAAAATTCAGCCTTTAGCAAAAGCCACCTCCAGACCAGGCTGCAGTGTTGACCTTGGGGGCTTTGCTGGTCTTTTTGATTTGAAAGCAGCTGGTTTCAAAGATCCTCTTCTGGCCTCTGGAACAGATGGTGTGGGAACTAAACTAAAGATTGCGCAGCTGTGCAATAAGCATGATTCCATCGGGCAGGATCTGGTGGCCATGTGTGTGAACGACATCCTCGCCCAGGGAGCAGAGCCCCTCTTCTTCCTTGACTACTTTTCCTGTGGGAAGCTCGACCTCAGTACAACTGAAGCCGTCATTGCTGGAATTGCTGCAGCTTGCCAGCAGGCTGGCTGTGCCCTGCTGGGTGGGGAGACAGCAGAGATGCCCAACATGTACCCTCCTGGAGAGTATGATCTTGCTGGGTTTGCTGTTGGTGCTATGGAGAGACACCAGAAGCTCCCTCAGCTAGAAAGGATCACCGAAGGGGATGCTGTTATTGGAGTGGCTTCATCTGGTCTTCACAGCAATGGGTTTAGCCTTGTGAGGAAAATCGTGGAGAGGTCTTCGCTCCAATACTCCTCCCCAGCACCTGGTGGTTGTGGAGATCAGACCTTAGGGGACTTACTTCTAACTCCAACCAGGATCTACAGCCATTCACTGCTGCCCATCATACGTTCAGGACGTGTCAAAGCTTTTGCTCATATCACTGGAGGCGGGTTGCTGGAAAACATCCCCAGAGTCCTCCCTCAGAAGTTTGGAGTAGATTTAGGGGCTTGA
Peptide sequence:
MLVKKIQPLAKATSRPGCSVDLGGFAGLFDLKAAGFKDPLLASGTDGVGTKLKIAQLCNKHDSIGQDLVAMCVNDILAQGAEPLFFLDYFSCGKLDLSTTEAVIAGIAAACQQAGCALLGGETAEMPNMYPPGEYDLAGFAVGAMERHQKLPQLERITEGDAVIGVASSGLHSNGFSLVRKIVERSSLQYSSPAPGGCGDQTLGDLLLTPTRIYSHSLLPIIRSGRVKAFAHITGGGLLENIPRVLPQKFGVDLGA
IRESfinder result
IRESfinder score
0.64028974
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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