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mmu_circSmyd2_357
Basic information of circular RNA
PanCircBase ID:
mmu_circSmyd2_357
mm39_Chr. Position ID:
chr1|189621011|189629680|-
Gene name:
Smyd2
Transcript:
ENSMUST00000027897.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
7,6,5,4
Exon/intron offsets:
0,2585,7756,8608
Genomic length:
8669
Exon/intron sizes in nt:
103,68,125,61
Flanking exon/introns:
chr1:189618828-189621011|chr1:189629680-189632014
Splice length:
357
Other database IDs:
circAtlas: mmu-Smyd2_0010
Human Ortholog IDs:
Mature spliced Sequence:
AAAATCCACCCAGAGAGGACACCTTCAGAGAAATTGTTGGCTGTGAGGGAGTTTGAGTCACATCTGGACAAGCTAGACAACGAGAAGAAAGATCTCATCCAGAGTGACATCGCCGCTCTCCACCAGTTCTACTCCAAGTACCTGGAATTCCCTGACCACAGCAGTCTCGTGGTGCTCTTCGCCCAGGTGAACTGTAATGGCTTCACTATTGAAGATGAAGAGCTCTCCCATTTGGGATCGGCGATATTCCCTGATGTTGCATTGATGAATCACAGCTGCTGCCCGAATGTCATTGTGACCTACAAAGGGACCCTGGCAGAAGTCAGAGCTGTACAGGAGATCCACCCAGGAGACGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGCTGCCCGAATGTCATTG
59.9
ACTCAAACTCCCTCACAGCC
59.6
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GATGAATCACAGCTGCTGCC
59.62
CTCAAACTCCCTCACAGCCA
59.6
151
PCR template sequence:
TGCATTGATGAATCACAGCTGCTGCCCGAATGTCATTGTGACCTACAAAGGGACCCTGGCAGAAGTCAGAGCTGTACAGGAGATCCACCCAGGAGACGAGAAAATCCACCCAGAGAGGACACCTTCAGAGAAATTGTTGGCTGTGAGGGAGTTTGAGTCACATCTGGACAAGCTAGACAACGAGAAGAAAGATCTCATCC
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-211-5p(1), mmu-miR-204-5p(1), mmu-miR-29b-3p(1), mmu-miR-666-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCCAGGAGACGAGAAAATCCACCCAG
siRNA sets
GATTTTCTCGTCTCCTGGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMYD2_357_ORF_1
1.2736
0.376529073
0.869376695
450
ORF sequence:
ATGAATCACAGCTGCTGCCCGAATGTCATTGTGACCTACAAAGGGACCCTGGCAGAAGTCAGAGCTGTACAGGAGATCCACCCAGGAGACGAGAAAATCCACCCAGAGAGGACACCTTCAGAGAAATTGTTGGCTGTGAGGGAGTTTGAGTCACATCTGGACAAGCTAGACAACGAGAAGAAAGATCTCATCCAGAGTGACATCGCCGCTCTCCACCAGTTCTACTCCAAGTACCTGGAATTCCCTGACCACAGCAGTCTCGTGGTGCTCTTCGCCCAGGTGAACTGTAATGGCTTCACTATTGAAGATGAAGAGCTCTCCCATTTGGGATCGGCGATATTCCCTGATGTTGCATTGATGAATCACAGCTGCTGCCCGAATGTCATTGTGACCTACAAAGGGACCCTGGCAGAAGTCAGAGCTGTACAGGAGATCCACCCAGGAGACGAG
Peptide sequence:
MNHSCCPNVIVTYKGTLAEVRAVQEIHPGDEKIHPERTPSEKLLAVREFESHLDKLDNEKKDLIQSDIAALHQFYSKYLEFPDHSSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIHPGDE
IRESfinder result
IRESfinder score
0.473407889
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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