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mmu_circSmchd1_242
Basic information of circular RNA
PanCircBase ID:
mmu_circSmchd1_242
mm39_Chr. Position ID:
chr17|71714161|71718909|-
Gene name:
Smchd1
Transcript:
ENSMUST00000127430.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
21,20
Exon/intron offsets:
0,4603
Genomic length:
4748
Exon/intron sizes in nt:
97,145
Flanking exon/introns:
chr17:71710165-71714161|chr17:71718909-71722029
Splice length:
242
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AGGGCAAGCCAGAAAAGTTTTCGTTTGGTCTTCTGGACTCTCCTTTCCGTGTTGGAGTTCCATTTAATATTCCTCTGGAGTTACAGGATGAATTTGGTCACACTACCCAACTATTGTCTGATATTGAGCCAGTTCTTGAAGCAAGTGGTCTGTCTTTACATTATGAAGGAATAACCAAAGGCCCGAATTGTGTAATTCAAGGTGTCGTAGCTAAAGGTCCAGTTAACTCTTGCCAGGGCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAAGGAATAACCAAAGGCCCG
59.25
TGGAACTCCAACACGGAAAGG
60.48
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAAGGAATAACCAAAGGCCCG
59.25
TGGAACTCCAACACGGAAAG
58.04
140
PCR template sequence:
AAGTGGTCTGTCTTTACATTATGAAGGAATAACCAAAGGCCCGAATTGTGTAATTCAAGGTGTCGTAGCTAAAGGTCCAGTTAACTCTTGCCAGGGCAAGAGGGCAAGCCAGAAAAGTTTTCGTTTGGTCTTCTGGACTCTCCTTTCCGTGTTGGAGTTCCATTTAATATTCCTCTGGAGTTACAGGATGAATTTGGTCA
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-149-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTGCCAGGGCAAGAGGGCAAGCCAGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.79857287
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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