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mmu_circYbx3_311
Basic information of circular RNA
PanCircBase ID:
mmu_circYbx3_311
mm39_Chr. Position ID:
chr6|131356320|131361529|-
Gene name:
Ybx3
Transcript:
ENSMUST00000032309.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,1518,4143,5145
Genomic length:
5209
Exon/intron sizes in nt:
123,90,34,64
Flanking exon/introns:
chr6:131353143-131356320|chr6:131361529-131364980
Splice length:
311
Other database IDs:
CIRCpedia: MMU_CIRCpedia_7696, circAtlas: mmu-Ybx3_0002
CIRCpedia: HSA_CIRCpedia_70801
Human Ortholog IDs:
Mature spliced Sequence:
CCACCAAAGTCCTTGGCACTGTCAAATGGTTCAACGTCAGAAATGGATATGGATTTATAAACCGAAATGACACCAAAGAAGATGTGTTTGTACACCAGACGGCCATCAAGAAAAACAACCCACGCAAGTATCTGCGCAGTGTGGGGGATGGAGAAACTGTAGAGTTTGATGTAGTTGAAGGAGAAAAGGGTGCTGAAGCAGCAAACGTGACTGGCCCAGATGGAGTTCCTGTAGAAGGGAGTCGCTATGCTGCTGACCGGCGCCGGTACAGACGCGGCTACTATGGCAGGCGCCGTGGACCTCCCCGTAAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCCCAGATGGAGTTCCTGTAG
59.86
TCCATTTCTGACGTTGAACCA
57.8
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCCCAGATGGAGTTCCTGTA
58.8
TCCATTTCTGACGTTGAACCA
57.8
145
PCR template sequence:
TGGCCCAGATGGAGTTCCTGTAGAAGGGAGTCGCTATGCTGCTGACCGGCGCCGGTACAGACGCGGCTACTATGGCAGGCGCCGTGGACCTCCCCGTAATCCACCAAAGTCCTTGGCACTGTCAAATGGTTCAACGTCAGAAATGGATATGGATTTATAAACCGAAATGACACCAAAGAAGATGTGTTTGTACACCAGAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-434-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACCTCCCCGTAATCCACCAAAGTCCT
siRNA sets
TTTGGTGGATTACGGGGAG, GGACTTTGGTGGATTACGG, GACTTTGGTGGATTACGGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCYBX3_311_ORF_1
0.7553
-0.020755097
0.049091323
135
ORF sequence:
ATGCTGCTGACCGGCGCCGGTACAGACGCGGCTACTATGGCAGGCGCCGTGGACCTCCCCGTAATCCACCAAAGTCCTTGGCACTGTCAAATGGTTCAACGTCAGAAATGGATATGGATTTATAAACCGAAATGA
Peptide sequence:
MLLTGAGTDAATMAGAVDLPVIHQSPWHCQMVQRQKWIWIYKPK
IRESfinder result
IRESfinder score
0.208456409
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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