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mmu_circScfd1_302
Basic information of circular RNA
PanCircBase ID:
mmu_circScfd1_302
mm39_Chr. Position ID:
chr12|51436064|51439053|+
Gene name:
Scfd1
Transcript:
ENSMUST00000219434.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
4,5,6
Exon/intron offsets:
0,1024,2901
Genomic length:
2989
Exon/intron sizes in nt:
91,123,88
Flanking exon/introns:
chr12:51433921-51436064|chr12:51439053-51440603
Splice length:
302
Other database IDs:
CIRCpedia: MMU_CIRCpedia_22069, circAtlas: mmu-Scfd1_0023
circBase: hsa_circ_0101541, circAtlas: hsa-SCFD1_0036, CIRCpedia: HSA_CIRCpedia_113372
Human Ortholog IDs:
Mature spliced Sequence:
CCTTTTGCACTCAGACCGAGATCCGATTCCAGATGTTCCTGCAGTGTACTTTGTGATGCCAACCGAAGAAAATATTGACAGACTGTGCCAGGATCTTCGAAATCAGCTCTATGAATCCTATTATTTAAATTTTATTTCTGCGATTTCAAGAAGTAAACTGGAAGACATTGCGAATGCAGCATTGGCCGCTAGTGCAGTCACACAAGTTGCCAAGGTTTTTGACCAGTATCTCAATTTTATTACTTTGGAAGATGACATGTTTGTATTATGTAATCAAAATAAGGAACTTGTTTCATATCGTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAAGTTGCCAAGGTTTTTGAC
56.71
ACACTGCAGGAACATCTGGA
58.94
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAAGTTGCCAAGGTTTTTGAC
56.71
GCAGGAACATCTGGAATCGGA
60.13
142
PCR template sequence:
CAAGTTGCCAAGGTTTTTGACCAGTATCTCAATTTTATTACTTTGGAAGATGACATGTTTGTATTATGTAATCAAAATAAGGAACTTGTTTCATATCGTGCCTTTTGCACTCAGACCGAGATCCGATTCCAGATGTTCCTGCAGTGTACTTTGTGATGCCAACCGAAGAAAATATTGACAGACTGTGCCAGGATCTTCGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-182-5p(1), mmu-miR-369-3p(1), mmu-miR-669d-5p(1), mmu-miR-350-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTTTCATATCGTGCCTTTTGCACTCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSCFD1_302_ORF_1
0.8387
0.052577143
0.2148305
303
ORF sequence:
ATGCCAACCGAAGAAAATATTGACAGACTGTGCCAGGATCTTCGAAATCAGCTCTATGAATCCTATTATTTAAATTTTATTTCTGCGATTTCAAGAAGTAAACTGGAAGACATTGCGAATGCAGCATTGGCCGCTAGTGCAGTCACACAAGTTGCCAAGGTTTTTGACCAGTATCTCAATTTTATTACTTTGGAAGATGACATGTTTGTATTATGTAATCAAAATAAGGAACTTGTTTCATATCGTGCCTTTTGCACTCAGACCGAGATCCGATTCCAGATGTTCCTGCAGTGTACTTTGTGA
Peptide sequence:
MPTEENIDRLCQDLRNQLYESYYLNFISAISRSKLEDIANAALAASAVTQVAKVFDQYLNFITLEDDMFVLCNQNKELVSYRAFCTQTEIRFQMFLQCTL
IRESfinder result
IRESfinder score
0.751169993
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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