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mmu_circSde2_484
Basic information of circular RNA
PanCircBase ID:
mmu_circSde2_484
mm39_Chr. Position ID:
chr1|180689922|180690406|+
Gene name:
Sde2
Transcript:
ENSMUST00000038091.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
1
Exon/intron indexes:
6
Exon/intron offsets:
0
Genomic length:
484
Exon/intron sizes in nt:
484
Flanking exon/introns:
chr1:180688783-180689922|chr1:180690406-180693636
Splice length:
484
Other database IDs:
circAtlas: mmu-Sde2_0003
circBase: hsa_circ_0112235, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_30323
Human Ortholog IDs:
Mature spliced Sequence:
GTTGGGCATGGATGGGCTGGAGGCTGCCGAGGGGTCCAGTACTGGAAGCTCAGAGGACAGCTCAGAGGATGACAGTGAGGATGCTCCTGGGACTTCGGAGCAGAGCTGCTGTGCTCGGGAAGACGGCATTGATGCTGTAGAGGTGGCAGCCGACCGACCTGGCAGTCCTCGGAGCTCGGCCTCTGGTACACACTCTGAGTCACCTGAAAAGCTTCAGTGCCCCGTGACCGAGCCTGGGCAGGGCATTTTGGAGAACACAGGAACTGAGCCAGGAGAGACCTCTGACAAGGAGTGCAACGAGAGGAAGACAGTCACAGACCCAGAGGAGACGCCAGCAAGGAAGGAAACAGAGAGTCATGAGGCCACAGAAAAGGACCAAAAGACAGGAATGTCTGGTGGGGACAGAGCTGCCATGGTTTTGTCTGGAGAAGACAGGAAAAGTGTCCCTGCTGCTAATCTGGAGGGAAACAACTCAGGAGACACA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGAATGTCTGGTGGGGACAG
60.04
GCTGTCCTCTGAGCTTCCAG
60.11
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAATGTCTGGTGGGGACAG
60.04
GAGCTGTCCTCTGAGCTTCC
59.82
162
PCR template sequence:
AGGAATGTCTGGTGGGGACAGAGCTGCCATGGTTTTGTCTGGAGAAGACAGGAAAAGTGTCCCTGCTGCTAATCTGGAGGGAAACAACTCAGGAGACACAGTTGGGCATGGATGGGCTGGAGGCTGCCGAGGGGTCCAGTACTGGAAGCTCAGAGGACAGCTCAGAGGATGACAGTGAGGATGCTCCTGGGACTTCGGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-214-3p(1), mmu-miR-24-3p(1), mmu-miR-149-5p(1), mmu-miR-127-5p(1), mmu-miR-484(1), mmu-miR-540-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTCAGGAGACACAGTTGGGCATGGAT
siRNA sets
ATGCCCAACTGTGTCTCCT, ATCCATGCCCAACTGTGTC, CATGCCCAACTGTGTCTCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSDE2_484_ORF_1
1.0199
0.302781472
0.907647028
612
ORF sequence:
ATGAGGCCACAGAAAAGGACCAAAAGACAGGAATGTCTGGTGGGGACAGAGCTGCCATGGTTTTGTCTGGAGAAGACAGGAAAAGTGTCCCTGCTGCTAATCTGGAGGGAAACAACTCAGGAGACACAGTTGGGCATGGATGGGCTGGAGGCTGCCGAGGGGTCCAGTACTGGAAGCTCAGAGGACAGCTCAGAGGATGACAGTGAGGATGCTCCTGGGACTTCGGAGCAGAGCTGCTGTGCTCGGGAAGACGGCATTGATGCTGTAGAGGTGGCAGCCGACCGACCTGGCAGTCCTCGGAGCTCGGCCTCTGGTACACACTCTGAGTCACCTGAAAAGCTTCAGTGCCCCGTGACCGAGCCTGGGCAGGGCATTTTGGAGAACACAGGAACTGAGCCAGGAGAGACCTCTGACAAGGAGTGCAACGAGAGGAAGACAGTCACAGACCCAGAGGAGACGCCAGCAAGGAAGGAAACAGAGAGTCATGAGGCCACAGAAAAGGACCAAAAGACAGGAATGTCTGGTGGGGACAGAGCTGCCATGGTTTTGTCTGGAGAAGACAGGAAAAGTGTCCCTGCTGCTAATCTGGAGGGAAACAACTCAGGAGACACA
Peptide sequence:
MRPQKRTKRQECLVGTELPWFCLEKTGKVSLLLIWRETTQETQLGMDGLEAAEGSSTGSSEDSSEDDSEDAPGTSEQSCCAREDGIDAVEVAADRPGSPRSSASGTHSESPEKLQCPVTEPGQGILENTGTEPGETSDKECNERKTVTDPEETPARKETESHEATEKDQKTGMSGGDRAAMVLSGEDRKSVPAANLEGNNSGDT
IRESfinder result
IRESfinder score
0.281252774
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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