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mmu_circSvil_970
Basic information of circular RNA
PanCircBase ID:
mmu_circSvil_970
mm39_Chr. Position ID:
chr18|5037107|5049494|+
Gene name:
Svil
Transcript:
ENSMUST00000126977.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
2,3,4,5,6
Exon/intron offsets:
0,3040,9481,9656,11777
Genomic length:
12387
Exon/intron sizes in nt:
5,89,25,81,52,610
Flanking exon/introns:
chr18:4920874-5037107|chr18:5049494-5054017
Splice length:
970
Other database IDs:
CIRCpedia: MMU_CIRCpedia_21818, circAtlas: mmu-Svil_0011
Human Ortholog IDs:
Mature spliced Sequence:
ATTTCAACAAGAAAAACTTAGGATTCCAGGGATTCCCACATCAAAGAAAAGCTGCAAGCTTTCAGAAAGAGTTTTCTTTTGATGATAAAGAAGAGCCTGCCAACCACAGGAGAGGCCTTGATGTCAAGTGCTTAGCTGTGCTCCCTAAAGTTGCAGAATTAAGAAAAATCTTTGAACCAAAGAGGAAAGACTTTTTAGAAATGAAAAGAAAAGAAAGAATTGCTAGGCGCTTAGAAGGAATAGAAAATGACTCCCAGCCCATCCTGTTGCAGAGCTGCACAGGGCTAGTGACTCATCGGCTGCTAGAAGAAGACACACCCAGATACATGCGTGCCACAGACCCTGCAAGCCCTCATATTGGGCGATCCAAAGAAGAGGAAGACACTCCTGGGTCCTCCCTAGAAAAGCAAACTCCTTCTAAATACTGCATAGAAACCTCAGGCATCCATAGTTCGGGCTCCATGGACACCCACAGTCTGGAGTCCAAAGCGGAAAGGATCGCAAGATACAAAGCAGAGAGGAGGCGGCAGCTGGCCGAAAAGTACGGGCTGACCTTGGACCCAGAAGCTGACTCTGAATACTTGTCTCGATATGCCAAGTCTCGGAAGGACCCAGATGTGACTGAGAGACGAGGAAAAAGTGACAAGCAAGAAGAACAGAGCAAGGATGCCAATTCCCGGCACTCCAGGACAGAGTCAGGGCCCAGGACCAGCTTGGTGGCGTCCCAGGACTGTACCCCGCTGGGAAGCAATATGTCTGACCAGGAGCAGCTGCTCAATGTGGAGAACCAGAGAAGAGTCCAAGATCCCCCACTAGGAGAAGATGGCTCCTCTGCCTTCTTTTCTGAGCGAAGCATTTCCTTCCCCGAAGTGCCCAGGTCTCCAAAGCAGATACCCAGCTCACCACTGCAACAGCCAGCCTCCCCAAACCACCCCGGTGACTCACCACTGCCCACAGAGGCCCGAGCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCAGGTCTCCAAAGCAGAT
59.38
TGATGTGGGAATCCCTGGAA
58.32
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCCAGGTCTCCAAAGCAGAT
59.38
TTGATGTGGGAATCCCTGGA
58.32
142
PCR template sequence:
TGCCCAGGTCTCCAAAGCAGATACCCAGCTCACCACTGCAACAGCCAGCCTCCCCAAACCACCCCGGTGACTCACCACTGCCCACAGAGGCCCGAGCCAGATTTCAACAAGAAAAACTTAGGATTCCAGGGATTCCCACATCAAAGAAAAGCTGCAAGCTTTCAGAAAGAGTTTTCTTTTGATGATAAAGAAGAGCCTGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-34c-5p(1), mmu-miR-298-5p(1), mmu-miR-149-5p(1), mmu-miR-362-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
AGGCCCGAGCCAGATTTCAACAAGAA
siRNA sets
TTCTTGTTGAAATCTGGCT, TTGTTGAAATCTGGCTCGG, GTTGAAATCTGGCTCGGGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSVIL_970_ORF_1
0.6396
0.225150189
0.992422045
1116
ORF sequence:
ATGGCTCCTCTGCCTTCTTTTCTGAGCGAAGCATTTCCTTCCCCGAAGTGCCCAGGTCTCCAAAGCAGATACCCAGCTCACCACTGCAACAGCCAGCCTCCCCAAACCACCCCGGTGACTCACCACTGCCCACAGAGGCCCGAGCCAGATTTCAACAAGAAAAACTTAGGATTCCAGGGATTCCCACATCAAAGAAAAGCTGCAAGCTTTCAGAAAGAGTTTTCTTTTGATGATAAAGAAGAGCCTGCCAACCACAGGAGAGGCCTTGATGTCAAGTGCTTAGCTGTGCTCCCTAAAGTTGCAGAATTAAGAAAAATCTTTGAACCAAAGAGGAAAGACTTTTTAGAAATGAAAAGAAAAGAAAGAATTGCTAGGCGCTTAGAAGGAATAGAAAATGACTCCCAGCCCATCCTGTTGCAGAGCTGCACAGGGCTAGTGACTCATCGGCTGCTAGAAGAAGACACACCCAGATACATGCGTGCCACAGACCCTGCAAGCCCTCATATTGGGCGATCCAAAGAAGAGGAAGACACTCCTGGGTCCTCCCTAGAAAAGCAAACTCCTTCTAAATACTGCATAGAAACCTCAGGCATCCATAGTTCGGGCTCCATGGACACCCACAGTCTGGAGTCCAAAGCGGAAAGGATCGCAAGATACAAAGCAGAGAGGAGGCGGCAGCTGGCCGAAAAGTACGGGCTGACCTTGGACCCAGAAGCTGACTCTGAATACTTGTCTCGATATGCCAAGTCTCGGAAGGACCCAGATGTGACTGAGAGACGAGGAAAAAGTGACAAGCAAGAAGAACAGAGCAAGGATGCCAATTCCCGGCACTCCAGGACAGAGTCAGGGCCCAGGACCAGCTTGGTGGCGTCCCAGGACTGTACCCCGCTGGGAAGCAATATGTCTGACCAGGAGCAGCTGCTCAATGTGGAGAACCAGAGAAGAGTCCAAGATCCCCCACTAGGAGAAGATGGCTCCTCTGCCTTCTTTTCTGAGCGAAGCATTTCCTTCCCCGAAGTGCCCAGGTCTCCAAAGCAGATACCCAGCTCACCACTGCAACAGCCAGCCTCCCCAAACCACCCCGGTGACTCACCACTGCCCACAGAGGCCCGAGCC
Peptide sequence:
MAPLPSFLSEAFPSPKCPGLQSRYPAHHCNSQPPQTTPVTHHCPQRPEPDFNKKNLGFQGFPHQRKAASFQKEFSFDDKEEPANHRRGLDVKCLAVLPKVAELRKIFEPKRKDFLEMKRKERIARRLEGIENDSQPILLQSCTGLVTHRLLEEDTPRYMRATDPASPHIGRSKEEEDTPGSSLEKQTPSKYCIETSGIHSSGSMDTHSLESKAERIARYKAERRRQLAEKYGLTLDPEADSEYLSRYAKSRKDPDVTERRGKSDKQEEQSKDANSRHSRTESGPRTSLVASQDCTPLGSNMSDQEQLLNVENQRRVQDPPLGEDGSSAFFSERSISFPEVPRSPKQIPSSPLQQPASPNHPGDSPLPTEARA
IRESfinder result
IRESfinder score
0.382252581
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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