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mmu_circSec61a2_455
Basic information of circular RNA
PanCircBase ID:
mmu_circSec61a2_455
mm39_Chr. Position ID:
chr2|5887391|5898032|-
Gene name:
Sec61a2
Transcript:
ENSMUST00000102981.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,237,3918,8709,10573
Genomic length:
10641
Exon/intron sizes in nt:
110,132,79,66,68
Flanking exon/introns:
chr2:5882819-5887391|chr2:5898032-5900067
Splice length:
455
Other database IDs:
circAtlas: mmu-Sec61a2_0001
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_696
Human Ortholog IDs:
Mature spliced Sequence:
TCAAGTTTTTAGAAGTTATTAAACCTTTCTGTGCAGTTCTACCAGAAATTCAGAAGCCTGAAAGGAAAATTCAGTTTAGAGAGAAGGTACTATGGACTGCTATAACACTCTTCATTTTCTTAGTATGCTGTCAGATTCCGCTGTTTGGGATCATGTCATCGGACTCTGCAGATCCCTTCTACTGGATGAGAGTTATTCTTGCATCCAACAGAGGAACATTGATGGAATTGGGTATTTCCCCAATTGTAACGTCTGGTTTGATTATGCAGTTGTTAGCTGGAGCCAAAATCATTGAAGTTGGAGACACACCCAAAGATAGAGCTCTGTTCAATGGAGCCCAGAAATTATTTGGTATGATCATTACCATTGGGCAAGCCATTGTGTATGTCATGACGGGGATGTACGGGGACCCTGCGGAAATGGGTGCTGGGATCTGTCTCCTTATCATTATTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CATTACCATTGGGCAAGCCA
58.81
TGGTAGAACTGCACAGAAAGGT
59.56
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCATTACCATTGGGCAAGCCA
60.27
TGGTAGAACTGCACAGAAAGGT
59.56
142
PCR template sequence:
GATCATTACCATTGGGCAAGCCATTGTGTATGTCATGACGGGGATGTACGGGGACCCTGCGGAAATGGGTGCTGGGATCTGTCTCCTTATCATTATTCAGTCAAGTTTTTAGAAGTTATTAAACCTTTCTGTGCAGTTCTACCAGAAATTCAGAAGCCTGAAAGGAAAATTCAGTTTAGAGAGAAGGTACTATGGACTGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-217-5p(1), mmu-miR-300-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TATCATTATTCAGTCAAGTTTTTAGA
siRNA sets
AAACTTGACTGAATAATGA, AAAACTTGACTGAATAATG, AAAAACTTGACTGAATAAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSEC61A2_455_ORF_1
1.1871
0.054857544
0.363698018
315
ORF sequence:
ATGTCATCGGACTCTGCAGATCCCTTCTACTGGATGAGAGTTATTCTTGCATCCAACAGAGGAACATTGATGGAATTGGGTATTTCCCCAATTGTAACGTCTGGTTTGATTATGCAGTTGTTAGCTGGAGCCAAAATCATTGAAGTTGGAGACACACCCAAAGATAGAGCTCTGTTCAATGGAGCCCAGAAATTATTTGGTATGATCATTACCATTGGGCAAGCCATTGTGTATGTCATGACGGGGATGTACGGGGACCCTGCGGAAATGGGTGCTGGGATCTGTCTCCTTATCATTATTCAGTCAAGTTTTTAG
Peptide sequence:
MSSDSADPFYWMRVILASNRGTLMELGISPIVTSGLIMQLLAGAKIIEVGDTPKDRALFNGAQKLFGMIITIGQAIVYVMTGMYGDPAEMGAGICLLIIIQSSF
IRESfinder result
IRESfinder score
0.726413283
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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