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mmu_circSycp2_846
Basic information of circular RNA
PanCircBase ID:
mmu_circSycp2_846
mm39_Chr. Position ID:
chr2|178010266|178019882|-
Gene name:
Sycp2
Transcript:
ENSMUST00000081134.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
25,24,23,22,21,20
Exon/intron offsets:
0,794,5881,6440,9165,9546
Genomic length:
9616
Exon/intron sizes in nt:
37,128,419,131,61,70
Flanking exon/introns:
chr2:178006699-178010266|chr2:178019882-178021192
Splice length:
846
Other database IDs:
circAtlas: mmu-Sycp2_0026
Human Ortholog IDs:
Mature spliced Sequence:
CATAACAAAACTACTGCTGTCATACAAAACAAACAATACGAGGATAATGAATCCCCAGACCAAAATTTCAATGAAATTGAGGACACTCTCTCTAATGTATCTTCTGCAGTGGGAAAAGTAGACAAGCCTGTATTGCCTGGTGTTTTAGACATCTCAAAAAATACAACACACTCCAGATGGGCATGTTGGACACCTGTAACAACTATCAAACTCTGCAATAACCAGAGAAGCCGTGCTTTACCTGGAGACACTTGTACCCAAGATACTGGTGTCAACAAAAAATGCACTAAACAAAAATCAGTATCAGATGATGATTCTGAAGAAACACAAAAGGGAAAATATAGTAAAGATGTAATCAAGTGTAACAAGTCAGATGAAGCAGAATTTTGTGAAAGAAACATTCAAGAACAAAATCATCCTAAATATTCACAAAAGAAAAATACTGCAAATGCAAAGAAGAGTGATTGGCATATTGAATCTGAAACTACTTATAAATCTGTACTCCTAAATAAGACAACTGAAGAATCTCTCATCTATAAGAAGACATGTGTATTGTCAAAAGATGTGAATACTACTATCTGTGATAAAAGCCCTTCTAGAAAAAGCAAGAGGAATCATACAAAATCAAGAAAGGAACTGATGTCTGAACTTACATCATGTGAGCTAGAAGAAATACCAGTGAGAGAAAATTCAAAAGGGAAAAGATTTACTGGTGCATCAGAATCCTTGATAAACCAAATTAGTAGGAGATATAACCCAAGTGATAGCATGATGTCAACAAGAAAACTGAAGGAGCCTCAGGATGGCAGTGGATTTTCAAAAAAACCTGATCTGCAGTTCAATAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGAAGGAGCCTCAGGATGG
59.53
AGAGAGAGTGTCCTCAATTTCA
56.49
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTCAGGATGGCAGTGGATT
59.45
AGAGAGAGTGTCCTCAATTTCA
56.49
144
PCR template sequence:
GAGATATAACCCAAGTGATAGCATGATGTCAACAAGAAAACTGAAGGAGCCTCAGGATGGCAGTGGATTTTCAAAAAAACCTGATCTGCAGTTCAATAAGCATAACAAAACTACTGCTGTCATACAAAACAAACAATACGAGGATAATGAATCCCCAGACCAAAATTTCAATGAAATTGAGGACACTCTCTCTAATGTAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-211-5p(1), mmu-miR-196a-5p(1), mmu-miR-676-3p(1), mmu-miR-541-5p(1), mmu-miR-324-3p(1), mmu-miR-5101(1), mmu-miR-1904(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCAGTTCAATAAGCATAACAAAACTA
siRNA sets
TTTGTTATGCTTATTGAAC,TTTTGTTATGCTTATTGAA,TTGTTATGCTTATTGAACT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSYCP2_846_ORF_1
0.8653
-0.037953722
0.977469774
1053
ORF sequence:
ATGTCTGAACTTACATCATGTGAGCTAGAAGAAATACCAGTGAGAGAAAATTCAAAAGGGAAAAGATTTACTGGTGCATCAGAATCCTTGATAAACCAAATTAGTAGGAGATATAACCCAAGTGATAGCATGATGTCAACAAGAAAACTGAAGGAGCCTCAGGATGGCAGTGGATTTTCAAAAAAACCTGATCTGCAGTTCAATAAGCATAACAAAACTACTGCTGTCATACAAAACAAACAATACGAGGATAATGAATCCCCAGACCAAAATTTCAATGAAATTGAGGACACTCTCTCTAATGTATCTTCTGCAGTGGGAAAAGTAGACAAGCCTGTATTGCCTGGTGTTTTAGACATCTCAAAAAATACAACACACTCCAGATGGGCATGTTGGACACCTGTAACAACTATCAAACTCTGCAATAACCAGAGAAGCCGTGCTTTACCTGGAGACACTTGTACCCAAGATACTGGTGTCAACAAAAAATGCACTAAACAAAAATCAGTATCAGATGATGATTCTGAAGAAACACAAAAGGGAAAATATAGTAAAGATGTAATCAAGTGTAACAAGTCAGATGAAGCAGAATTTTGTGAAAGAAACATTCAAGAACAAAATCATCCTAAATATTCACAAAAGAAAAATACTGCAAATGCAAAGAAGAGTGATTGGCATATTGAATCTGAAACTACTTATAAATCTGTACTCCTAAATAAGACAACTGAAGAATCTCTCATCTATAAGAAGACATGTGTATTGTCAAAAGATGTGAATACTACTATCTGTGATAAAAGCCCTTCTAGAAAAAGCAAGAGGAATCATACAAAATCAAGAAAGGAACTGATGTCTGAACTTACATCATGTGAGCTAGAAGAAATACCAGTGAGAGAAAATTCAAAAGGGAAAAGATTTACTGGTGCATCAGAATCCTTGATAAACCAAATTAGTAGGAGATATAACCCAAGTGATAGCATGATGTCAACAAGAAAACTGAAGGAGCCTCAGGATGGCAGTGGATTTTCAAAAAAACCTGATCTGCAGTTCAATAAG
Peptide sequence:
MSELTSCELEEIPVRENSKGKRFTGASESLINQISRRYNPSDSMMSTRKLKEPQDGSGFSKKPDLQFNKHNKTTAVIQNKQYEDNESPDQNFNEIEDTLSNVSSAVGKVDKPVLPGVLDISKNTTHSRWACWTPVTTIKLCNNQRSRALPGDTCTQDTGVNKKCTKQKSVSDDDSEETQKGKYSKDVIKCNKSDEAEFCERNIQEQNHPKYSQKKNTANAKKSDWHIESETTYKSVLLNKTTEESLIYKKTCVLSKDVNTTICDKSPSRKSKRNHTKSRKELMSELTSCELEEIPVRENSKGKRFTGASESLINQISRRYNPSDSMMSTRKLKEPQDGSGFSKKPDLQFNK
IRESfinder result
IRESfinder score
0.655656917
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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