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mmu_circRalgapb_325_2
Basic information of circular RNA
PanCircBase ID:
mmu_circRalgapb_325_2
mm39_Chr. Position ID:
chr2|158324284|158334933|+
Gene name:
Ralgapb
Transcript:
ENSMUST00000109486.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
26,27,28
Exon/intron offsets:
0,9999,10570
Genomic length:
10649
Exon/intron sizes in nt:
137,109,79
Flanking exon/introns:
chr2:158319683-158324284|chr2:158334933-158336544
Splice length:
325
Other database IDs:
circAtlas: mmu-Ralgapb_0007
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_34166
Human Ortholog IDs:
Mature spliced Sequence:
CTGATTCATTGGAAAGTAACATCTCAGACCAAGATAGTGACTCAAATATGGATCTTATGCCGGGAATTCTGAAGCAGCCACCCCTGACACTTGAGTTGGTCCCCAATCACACAGACAGTCTTAATTCCTCACAGAGGCTCAGTCCCAGTTCCAGAATGAAGAAGCTGCCTCAGGGTCGCCCTGTGCCCCCGCTTGGACCTGAGACAAGAGTATCTGTAGTCTGGGTGGAACGCTACGATGATATAGAAAACTTTCCACTCTCAGATCTGATGACAGAGATCAGCACTGGTGTAGAGACTACTGCAAATAGTAGCACTTCTCTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGACAGAGATCAGCACTGGTG
59.73
AACTCAAGTGTCAGGGGTGG
59.53
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGACAGAGATCAGCACTGGTG
59.73
CCAACTCAAGTGTCAGGGGT
59.53
154
PCR template sequence:
TGGAACGCTACGATGATATAGAAAACTTTCCACTCTCAGATCTGATGACAGAGATCAGCACTGGTGTAGAGACTACTGCAAATAGTAGCACTTCTCTGAGCTGATTCATTGGAAAGTAACATCTCAGACCAAGATAGTGACTCAAATATGGATCTTATGCCGGGAATTCTGAAGCAGCCACCCCTGACACTTGAGTTGGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-351-5p(1), mmu-miR-125a-5p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-499-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCACTTCTCTGAGCTGATTCATTGGA
siRNA sets
AATGAATCAGCTCAGAGAA, GAATCAGCTCAGAGAAGTG, ATGAATCAGCTCAGAGAAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRALGAPB_325_2_ORF_1
0.9999
0.137693947
0.309837716
282
ORF sequence:
ATGGATCTTATGCCGGGAATTCTGAAGCAGCCACCCCTGACACTTGAGTTGGTCCCCAATCACACAGACAGTCTTAATTCCTCACAGAGGCTCAGTCCCAGTTCCAGAATGAAGAAGCTGCCTCAGGGTCGCCCTGTGCCCCCGCTTGGACCTGAGACAAGAGTATCTGTAGTCTGGGTGGAACGCTACGATGATATAGAAAACTTTCCACTCTCAGATCTGATGACAGAGATCAGCACTGGTGTAGAGACTACTGCAAATAGTAGCACTTCTCTGAGCTGA
Peptide sequence:
MDLMPGILKQPPLTLELVPNHTDSLNSSQRLSPSSRMKKLPQGRPVPPLGPETRVSVVWVERYDDIENFPLSDLMTEISTGVETTANSSTSLS
IRESfinder result
IRESfinder score
0.630379863
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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