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mmu_circSmurf2_659
Basic information of circular RNA
PanCircBase ID:
mmu_circSmurf2_659
mm39_Chr. Position ID:
chr11|106726895|106740658|-
Gene name:
Smurf2
Transcript:
ENSMUST00000103067.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
12,11,10,9,8
Exon/intron offsets:
0,3118,5530,9913,13678
Genomic length:
13763
Exon/intron sizes in nt:
115,104,196,159,85
Flanking exon/introns:
chr11:106724749-106726895|chr11:106740658-106743272
Splice length:
659
Other database IDs:
circAtlas: mmu-Smurf2_0052
Human Ortholog IDs:
Mature spliced Sequence:
AACAAAGGACAACGCAGCAGGGTCAGGTATATTTCTTACATACTCAGACTGGTGTGAGCACATGGCATGATCCACGAGTGCCTAGGGATCTTAGCAACATCAATTGTGAAGAGCTCGGTCCTTTGCCTCCTGGATGGGAGATCCGCAATACCGCAACAGGAAGAGTTTATTTCGTTGACCATAACAACAGAACAACACAATTTACAGATCCCCGGCTCTCTGCTAACTTGCATTTAGTTTTAAATCGTCAGAACCAGTTGAAAGACCAACAGCAACAGCAAGTGGTGCCATTGTGTCCCGATGACACTGAGTGTCTGACAGTGCCAAGATACAAGCGAGATTTGGTTCAAAAACTAAAAATCTTGCGGCAAGAACTTTCCCAACAGCAGCCTCAAGCTGGCCACTGCCGTATTGAGGTGTCTAGGGAAGAGATTTTTGAGGAATCATATAGACAGGTCATGAAAATGAGGCCAAAAGATCTATGGAAGCGATTAATGATAAAATTTCGTGGAGAAGAAGGTCTTGACTATGGAGGAGTTGCCAGGGAATGGTTGTATCTCCTGTCACATGAAATGTTGAATCCTTACTATGGTCTCTTCCAGTATTCTAGAGATGATATCTACACATTGCAGATCAATCCTGATTCTGCAGTTAATCCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTTACTATGGTCTCTTCCAGT
57.79
CCATGTGCTCACACCAGTCT
59.96
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTTACTATGGTCTCTTCCAGT
57.79
TAGGCACTCGTGGATCATGC
59.9
163
PCR template sequence:
CCTGTCACATGAAATGTTGAATCCTTACTATGGTCTCTTCCAGTATTCTAGAGATGATATCTACACATTGCAGATCAATCCTGATTCTGCAGTTAATCCGAACAAAGGACAACGCAGCAGGGTCAGGTATATTTCTTACATACTCAGACTGGTGTGAGCACATGGCATGATCCACGAGTGCCTAGGGATCTTAGCAACAT
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-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-181b-5p(1), mmu-miR-434-3p(1), mmu-miR-96-5p(1), mmu-miR-183-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGCAGTTAATCCGAACAAAGGACAAC
siRNA sets
TTTGTTCGGATTAACTGCA, CTTTGTTCGGATTAACTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMURF2_659_ORF_1
0.4975
-0.036578363
0.066824611
258
ORF sequence:
ATGAAAATGAGGCCAAAAGATCTATGGAAGCGATTAATGATAAAATTTCGTGGAGAAGAAGGTCTTGACTATGGAGGAGTTGCCAGGGAATGGTTGTATCTCCTGTCACATGAAATGTTGAATCCTTACTATGGTCTCTTCCAGTATTCTAGAGATGATATCTACACATTGCAGATCAATCCTGATTCTGCAGTTAATCCGAACAAAGGACAACGCAGCAGGGTCAGGTATATTTCTTACATACTCAGACTGGTGTGA
Peptide sequence:
MKMRPKDLWKRLMIKFRGEEGLDYGGVAREWLYLLSHEMLNPYYGLFQYSRDDIYTLQINPDSAVNPNKGQRSRVRYISYILRLV
IRESfinder result
IRESfinder score
0.615196693
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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