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mmu_circSyt2_371
Basic information of circular RNA
PanCircBase ID:
mmu_circSyt2_371
mm39_Chr. Position ID:
chr1|134668572|134669714|+
Gene name:
Syt2
Transcript:
ENSMUST00000188842.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,4
Exon/intron offsets:
0,975
Genomic length:
1142
Exon/intron sizes in nt:
2,04,167
Flanking exon/introns:
chr1:134591736-134668572|chr1:134669714-134671247
Splice length:
371
Other database IDs:
circAtlas: mmu-Syt2_0013
Human Ortholog IDs:
Mature spliced Sequence:
CTATCCCCTCTGCCACCATGAGAAACATCTTCAAGAGGAACCAGGAGCCAAATGTGGCTCCGGCCACCACCACTGCCACAATGCCCCTTGCACCCGTCGCACCTGCCGACAACTCTACAGAGAGCACGGGTCCTGGGGAGAGCCAAGAAGACATGTTCGCCAAGCTGAAGGAGAAATTCTTCAATGAGATCAACAAGATCCCCTTGCCCCCCTGGGCTCTGATCGCCATGGCTGTGGTTGCTGGCCTCCTGCTGCTCACCTGTTGCTTCTGCATCTGTAAGAAGTGCTGCTGCAAGAAGAAGAAGAACAAGAAGGAGAAGGGCAAAGGCATGAAGAACGCCATGAACATGAAGGACATGAAAGGGGGCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGTAAGAAGTGCTGCTGCA
59.93
TTGGCTCCTGGTTCCTCTTG
59.6
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGTAAGAAGTGCTGCTGCA
59.93
TGGCTCCTGGTTCCTCTTGA
60.47
148
PCR template sequence:
CATCTGTAAGAAGTGCTGCTGCAAGAAGAAGAAGAACAAGAAGGAGAAGGGCAAAGGCATGAAGAACGCCATGAACATGAAGGACATGAAAGGGGGCCAGCTATCCCCTCTGCCACCATGAGAAACATCTTCAAGAGGAACCAGGAGCCAAATGTGGCTCCGGCCACCACCACTGCCACAATGCCCCTTGCACCCGTCGC
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-221-3p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-222-3p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
GAAAGGGGGCCAGCTATCCCCTCTGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSYT2_371_ORF_1
1.3174
0.454470063
0.852418705
375
ORF sequence:
ATGAGAAACATCTTCAAGAGGAACCAGGAGCCAAATGTGGCTCCGGCCACCACCACTGCCACAATGCCCCTTGCACCCGTCGCACCTGCCGACAACTCTACAGAGAGCACGGGTCCTGGGGAGAGCCAAGAAGACATGTTCGCCAAGCTGAAGGAGAAATTCTTCAATGAGATCAACAAGATCCCCTTGCCCCCCTGGGCTCTGATCGCCATGGCTGTGGTTGCTGGCCTCCTGCTGCTCACCTGTTGCTTCTGCATCTGTAAGAAGTGCTGCTGCAAGAAGAAGAAGAACAAGAAGGAGAAGGGCAAAGGCATGAAGAACGCCATGAACATGAAGGACATGAAAGGGGGCCAGCTATCCCCTCTGCCACCATGA
Peptide sequence:
MRNIFKRNQEPNVAPATTTATMPLAPVAPADNSTESTGPGESQEDMFAKLKEKFFNEINKIPLPPWALIAMAVVAGLLLLTCCFCICKKCCCKKKKNKKEKGKGMKNAMNMKDMKGGQLSPLPP
IRESfinder result
IRESfinder score
0.225590933
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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