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mmu_circSf3b1_471
Basic information of circular RNA
PanCircBase ID:
mmu_circSf3b1_471
mm39_Chr. Position ID:
chr1|55051260|55056042|-
Gene name:
Sf3b1
Transcript:
ENSMUST00000027127.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,5,4,3
Exon/intron offsets:
0,2381,4274,4677
Genomic length:
4782
Exon/intron sizes in nt:
17,18,01,15,105
Flanking exon/introns:
chr1:55046876-55051260|chr1:55056042-55058392
Splice length:
471
Other database IDs:
circBase: mmu_circ_0008801, CIRCpedia: MMU_CIRCpedia_23020, circAtlas: mmu-Sf3b1_0004
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_146386
Human Ortholog IDs:
Mature spliced Sequence:
GATGACGATGACTACTCATCATCCACGAGCTTGCTCGGTCAGAAGAAGCCTGGATATCATGCCCCCGTGGCGTTGCTTAATGATATACCACAGTCAACAGAGCAGTATGATCCATTTGCTGAGCATCGTCCTCCAAAGATTGCCGATCGGGAAGATGAATACAAAAAGCATAGGCGGACCATGATAATTTCCCCAGAGCGTCTTGATCCTTTTGCAGATGGAGGGAAGACTCCCGATCCTAAAATGAATGCTAGAACCTACATGGATGTTATGCGAGAACAACATTTGACTAAGGAAGAGAGAGAAATTAGGCAACAACTAGCAGAAAAAGCTAAAGCTGGAGAACTAAAAGTCGTCAATGGAGCAGCAGCATCCCAGCCTCCCTCAAAACGAAAACGGCGCTGGGATCAGACCGCTGACCAGACTCCTGGTGCCACTCCCAAAAAGCTATCGAGTTGGGATCAGGCAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGCCTCCCTCAAAACGAA
60.25
CCAGGCTTCTTCTGACCGAG
60.11
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTCAAAACGAAAACGGCGCT
60.32
CCAGGCTTCTTCTGACCGAG
60.11
141
PCR template sequence:
ATCCCAGCCTCCCTCAAAACGAAAACGGCGCTGGGATCAGACCGCTGACCAGACTCCTGGTGCCACTCCCAAAAAGCTATCGAGTTGGGATCAGGCAGAGGATGACGATGACTACTCATCATCCACGAGCTTGCTCGGTCAGAAGAAGCCTGGATATCATGCCCCCGTGGCGTTGCTTAATGATATACCACAGTCAACAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
NA
Interacting miRNAs (#binding sites)
NA
siRNAs for circular RNA silencing
Junction sequence
GGATCAGGCAGAGGATGACGATGACT
siRNA sets
AGTCATCGTCATCCTCTGC, GTCATCGTCATCCTCTGCC, CATCGTCATCCTCTGCCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSF3B1_471_ORF_1
1.1909
0.221353413
0.966215663
762
ORF sequence:
ATGATAATTTCCCCAGAGCGTCTTGATCCTTTTGCAGATGGAGGGAAGACTCCCGATCCTAAAATGAATGCTAGAACCTACATGGATGTTATGCGAGAACAACATTTGACTAAGGAAGAGAGAGAAATTAGGCAACAACTAGCAGAAAAAGCTAAAGCTGGAGAACTAAAAGTCGTCAATGGAGCAGCAGCATCCCAGCCTCCCTCAAAACGAAAACGGCGCTGGGATCAGACCGCTGACCAGACTCCTGGTGCCACTCCCAAAAAGCTATCGAGTTGGGATCAGGCAGAGGATGACGATGACTACTCATCATCCACGAGCTTGCTCGGTCAGAAGAAGCCTGGATATCATGCCCCCGTGGCGTTGCTTAATGATATACCACAGTCAACAGAGCAGTATGATCCATTTGCTGAGCATCGTCCTCCAAAGATTGCCGATCGGGAAGATGAATACAAAAAGCATAGGCGGACCATGATAATTTCCCCAGAGCGTCTTGATCCTTTTGCAGATGGAGGGAAGACTCCCGATCCTAAAATGAATGCTAGAACCTACATGGATGTTATGCGAGAACAACATTTGACTAAGGAAGAGAGAGAAATTAGGCAACAACTAGCAGAAAAAGCTAAAGCTGGAGAACTAAAAGTCGTCAATGGAGCAGCAGCATCCCAGCCTCCCTCAAAACGAAAACGGCGCTGGGATCAGACCGCTGACCAGACTCCTGGTGCCACTCCCAAAAAGCTATCGAGTTGGGATCAGGCAGAG
Peptide sequence:
MIISPERLDPFADGGKTPDPKMNARTYMDVMREQHLTKEEREIRQQLAEKAKAGELKVVNGAAASQPPSKRKRRWDQTADQTPGATPKKLSSWDQAEDDDDYSSSTSLLGQKKPGYHAPVALLNDIPQSTEQYDPFAEHRPPKIADREDEYKKHRRTMIISPERLDPFADGGKTPDPKMNARTYMDVMREQHLTKEEREIRQQLAEKAKAGELKVVNGAAASQPPSKRKRRWDQTADQTPGATPKKLSSWDQAE
IRESfinder result
IRESfinder score
0.323156774
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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