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mmu_circSt8sia6_351
Basic information of circular RNA
PanCircBase ID:
mmu_circSt8sia6_351
mm39_Chr. Position ID:
chr2|13670230|13677438|-
Gene name:
St8sia6
Transcript:
ENSMUST00000003509.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
7,6,5
Exon/intron offsets:
0,3365,7063
Genomic length:
7208
Exon/intron sizes in nt:
9,31,13,145
Flanking exon/introns:
chr2:13662101-13670230|chr2:13677438-13701638
Splice length:
351
Other database IDs:
circAtlas: mmu-St8sia6_0001
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
AGCAAAACTGGCTTCCTGTTGCGATGCCATTCAAGACTTCGTGGTTTCCCAGAACAACACTCCAGTGGGGACTAACATGAGCTACGAGGTGGAAAGCAAGAAACACATCCCCATTCGAGAGAACATTTTCCACATGTTTCCAGTGTCGCAGCCTTTTGTGGACTATCCCTATAACCAGTGTGCAGTGGTTGGTAATGGGGGAATTCTCAACAAGTCTCTCTGCGGAGCAGAAATTGATAAATCTGACTTCGTCTTCAGGTGTAACCTCCCCCCAATCACAGGGAGCGCTAGTAAAGATGTTGGAAGCAAAACAAATCTTGTGACTGTCAATCCCAGCATTATAACCCTGAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAATCACAGGGAGCGCTAGT
59.82
GTCCCCACTGGAGTGTTGTT
59.82
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAATCACAGGGAGCGCTAGT
59.82
GCTTTCCACCTCGTAGCTCA
59.75
176
PCR template sequence:
TCTTCAGGTGTAACCTCCCCCCAATCACAGGGAGCGCTAGTAAAGATGTTGGAAGCAAAACAAATCTTGTGACTGTCAATCCCAGCATTATAACCCTGAAAGCAAAACTGGCTTCCTGTTGCGATGCCATTCAAGACTTCGTGGTTTCCCAGAACAACACTCCAGTGGGGACTAACATGAGCTACGAGGTGGAAAGCAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-155-5p(1), mmu-miR-1198-5p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
TTATAACCCTGAAAGCAAAACTGGCT
siRNA sets
TTTTGCTTTCAGGGTTATA, AGCCAGTTTTGCTTTCAGG, TTTGCTTTCAGGGTTATAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCST8SIA6_351_ORF_1
1.1587
0.220688072
0.90892175
624
ORF sequence:
ATGAGCTACGAGGTGGAAAGCAAGAAACACATCCCCATTCGAGAGAACATTTTCCACATGTTTCCAGTGTCGCAGCCTTTTGTGGACTATCCCTATAACCAGTGTGCAGTGGTTGGTAATGGGGGAATTCTCAACAAGTCTCTCTGCGGAGCAGAAATTGATAAATCTGACTTCGTCTTCAGGTGTAACCTCCCCCCAATCACAGGGAGCGCTAGTAAAGATGTTGGAAGCAAAACAAATCTTGTGACTGTCAATCCCAGCATTATAACCCTGAAAGCAAAACTGGCTTCCTGTTGCGATGCCATTCAAGACTTCGTGGTTTCCCAGAACAACACTCCAGTGGGGACTAACATGAGCTACGAGGTGGAAAGCAAGAAACACATCCCCATTCGAGAGAACATTTTCCACATGTTTCCAGTGTCGCAGCCTTTTGTGGACTATCCCTATAACCAGTGTGCAGTGGTTGGTAATGGGGGAATTCTCAACAAGTCTCTCTGCGGAGCAGAAATTGATAAATCTGACTTCGTCTTCAGGTGTAACCTCCCCCCAATCACAGGGAGCGCTAGTAAAGATGTTGGAAGCAAAACAAATCTTGTGACTGTCAATCCCAGCATTATAACCCTG
Peptide sequence:
MSYEVESKKHIPIRENIFHMFPVSQPFVDYPYNQCAVVGNGGILNKSLCGAEIDKSDFVFRCNLPPITGSASKDVGSKTNLVTVNPSIITLKAKLASCCDAIQDFVVSQNNTPVGTNMSYEVESKKHIPIRENIFHMFPVSQPFVDYPYNQCAVVGNGGILNKSLCGAEIDKSDFVFRCNLPPITGSASKDVGSKTNLVTVNPSIITL
IRESfinder result
IRESfinder score
0.614057035
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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