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mmu_circSf1_498
Basic information of circular RNA
PanCircBase ID:
mmu_circSf1_498
mm39_Chr. Position ID:
chr19|6421647|6422655|+
Gene name:
Sf1
Transcript:
ENSMUST00000131252.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,6,7,8
Exon/intron offsets:
0,407,683,900
Genomic length:
1008
Exon/intron sizes in nt:
90,18,41,16,108
Flanking exon/introns:
chr19:6421449-6421647|chr19:6422655-6423602
Splice length:
498
Other database IDs:
CIRCpedia: MMU_CIRCpedia_25636, circAtlas: mmu-Sf1_0005
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GCCTCCAGCAACACGTGTGAGCGATAAAGTAATGATCCCCCAAGACGAATATCCAGAAATCAATTTTGTGGGGCTCCTAATTGGACCCAGAGGGAACACCCTGAAGAACATTGAGAAGGAATGCAACGCCAAGATCATGATTCGGGGGAAAGGATCAGTGAAAGAAGGGAAAGTTGGGCGTAAAGATGGTCAGATGTTGCCAGGCGAAGATGAGCCTCTTCATGCTCTAGTCACTGCCAATACGATGGAGAATGTCAAAAAGGCAGTAGAACAGATCAGAAACATCCTGAAGCAGGGTATTGAGACCCCAGAGGACCAGAACGATCTACGGAAAATGCAGCTTCGAGAGTTGGCTCGCTTGAATGGCACTCTACGGGAAGATGATAATAGGATCTTAAGGCCCTGGCAGAGCTCAGAGACGCGCAGCATTACCAATACTACTGTGTGTACCAAGTGTGGAGGGGCTGGTCACATTGCTTCTGATTGCAAATTTCAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGAGGGGCTGGTCACATTG
60.38
GTGTTCCCTCTGGGTCCAAT
59.3
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAGGGGCTGGTCACATTG
60.38
GTGTTCCCTCTGGGTCCAATT
59.92
140
PCR template sequence:
GGCCCTGGCAGAGCTCAGAGACGCGCAGCATTACCAATACTACTGTGTGTACCAAGTGTGGAGGGGCTGGTCACATTGCTTCTGATTGCAAATTTCAGAGGCCTCCAGCAACACGTGTGAGCGATAAAGTAATGATCCCCCAAGACGAATATCCAGAAATCAATTTTGTGGGGCTCCTAATTGGACCCAGAGGGAACACC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-5099(1)
siRNAs for circular RNA silencing
Junction sequence
GCAAATTTCAGAGGCCTCCAGCAACA
siRNA sets
TGTTGCTGGAGGCCTCTGA, GGAGGCCTCTGAAATTTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSF1_498_ORF_1
1.0795
0.30821173
0.992970304
963
ORF sequence:
ATGATCCCCCAAGACGAATATCCAGAAATCAATTTTGTGGGGCTCCTAATTGGACCCAGAGGGAACACCCTGAAGAACATTGAGAAGGAATGCAACGCCAAGATCATGATTCGGGGGAAAGGATCAGTGAAAGAAGGGAAAGTTGGGCGTAAAGATGGTCAGATGTTGCCAGGCGAAGATGAGCCTCTTCATGCTCTAGTCACTGCCAATACGATGGAGAATGTCAAAAAGGCAGTAGAACAGATCAGAAACATCCTGAAGCAGGGTATTGAGACCCCAGAGGACCAGAACGATCTACGGAAAATGCAGCTTCGAGAGTTGGCTCGCTTGAATGGCACTCTACGGGAAGATGATAATAGGATCTTAAGGCCCTGGCAGAGCTCAGAGACGCGCAGCATTACCAATACTACTGTGTGTACCAAGTGTGGAGGGGCTGGTCACATTGCTTCTGATTGCAAATTTCAGAGGCCTCCAGCAACACGTGTGAGCGATAAAGTAATGATCCCCCAAGACGAATATCCAGAAATCAATTTTGTGGGGCTCCTAATTGGACCCAGAGGGAACACCCTGAAGAACATTGAGAAGGAATGCAACGCCAAGATCATGATTCGGGGGAAAGGATCAGTGAAAGAAGGGAAAGTTGGGCGTAAAGATGGTCAGATGTTGCCAGGCGAAGATGAGCCTCTTCATGCTCTAGTCACTGCCAATACGATGGAGAATGTCAAAAAGGCAGTAGAACAGATCAGAAACATCCTGAAGCAGGGTATTGAGACCCCAGAGGACCAGAACGATCTACGGAAAATGCAGCTTCGAGAGTTGGCTCGCTTGAATGGCACTCTACGGGAAGATGATAATAGGATCTTAAGGCCCTGGCAGAGCTCAGAGACGCGCAGCATTACCAATACTACTGTGTGTACCAAGTGTGGAGGGGCTGGTCACATTGCTTCTGATTGCAAATTTCAG
Peptide sequence:
MIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGTLREDDNRILRPWQSSETRSITNTTVCTKCGGAGHIASDCKFQRPPATRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGTLREDDNRILRPWQSSETRSITNTTVCTKCGGAGHIASDCKFQ
IRESfinder result
IRESfinder score
0.345460989
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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