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mmu_circFarp2_544
Basic information of circular RNA
PanCircBase ID:
mmu_circFarp2_544
mm39_Chr. Position ID:
chr1|93531099|93535392|+
Gene name:
Farp2
Transcript:
ENSMUST00000120301.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
15,16,17,18
Exon/intron offsets:
0,832,1964,4055
Genomic length:
4293
Exon/intron sizes in nt:
9,01,34,82,238
Flanking exon/introns:
chr1:93527823-93531099|chr1:93535392-93537697
Splice length:
544
Other database IDs:
CIRCpedia: MMU_CIRCpedia_34551, circAtlas: mmu-Farp2_0006
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_135465
Human Ortholog IDs:
Mature spliced Sequence:
CACATGCCAGAAGATGAGGCCTATTTCATAGCCAAGGAGATTCTCGCTACAGAACGAACCTATCTGAAGGATTTAGAAGTTATCACTGTGTGGTTCCGGAGCGTGCTGATCAAGGAGGAGGCCATGCCTGCAGCCCTGATGGCCCTGCTTTTCTCCAACATTGATCCAGTCTACGAGTTCCACAGAGGCTTCCTTCACGAGGTGGAACAGAGGCTGGCACTCTGGGAAGGGCCCTCCAGTGCCCACTTAAAAGGTGATCACCAGCGAATCGGGGACATCCTCCTCAGGAACATGCGTCAGTTAAAGGAATTTACTAGCTACTTCCAAAGACACGATGAGGTCCTAACAGAACTGGAAAAGGCCACAAAACACTGTAAAAAGCTGGAGGCAGTCTACAAAGAGTTTGAGCTCCAAAAGGTCTGCTACCTGCCTCTCAACACATTCCTGCTGAAGCCCGTCCAGAGGCTAGTCCACTACCGTCTGCTGCTGAGCCGGCTGTGTGCTCACTACTCTCCTGGGCACCGCGACTATGCCGACTGCCATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTAGTCCACTACCGTCTGC
59.9
AGGTTCGTTCTGTAGCGAGA
58.47
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTAGTCCACTACCGTCTGC
59.9
TCCGGAACCACACAGTGATA
58.37
180
PCR template sequence:
CTGCTGAAGCCCGTCCAGAGGCTAGTCCACTACCGTCTGCTGCTGAGCCGGCTGTGTGCTCACTACTCTCCTGGGCACCGCGACTATGCCGACTGCCATGCACATGCCAGAAGATGAGGCCTATTTCATAGCCAAGGAGATTCTCGCTACAGAACGAACCTATCTGAAGGATTTAGAAGTTATCACTGTGTGGTTCCGGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-15a-5p(1), mmu-miR-1a-3p(1), mmu-miR-15b-5p(1), mmu-miR-709(1), mmu-miR-24-3p(1), mmu-miR-377-3p(1), mmu-miR-3061-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCCGACTGCCATGCACATGCCAGAAG
siRNA sets
CATGTGCATGGCAGTCGGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFARP2_544_ORF_1
1.2684
0.344618161
0.925940798
558
ORF sequence:
ATGCCAGAAGATGAGGCCTATTTCATAGCCAAGGAGATTCTCGCTACAGAACGAACCTATCTGAAGGATTTAGAAGTTATCACTGTGTGGTTCCGGAGCGTGCTGATCAAGGAGGAGGCCATGCCTGCAGCCCTGATGGCCCTGCTTTTCTCCAACATTGATCCAGTCTACGAGTTCCACAGAGGCTTCCTTCACGAGGTGGAACAGAGGCTGGCACTCTGGGAAGGGCCCTCCAGTGCCCACTTAAAAGGTGATCACCAGCGAATCGGGGACATCCTCCTCAGGAACATGCGTCAGTTAAAGGAATTTACTAGCTACTTCCAAAGACACGATGAGGTCCTAACAGAACTGGAAAAGGCCACAAAACACTGTAAAAAGCTGGAGGCAGTCTACAAAGAGTTTGAGCTCCAAAAGGTCTGCTACCTGCCTCTCAACACATTCCTGCTGAAGCCCGTCCAGAGGCTAGTCCACTACCGTCTGCTGCTGAGCCGGCTGTGTGCTCACTACTCTCCTGGGCACCGCGACTATGCCGACTGCCATGCACATGCCAGAAGATGA
Peptide sequence:
MPEDEAYFIAKEILATERTYLKDLEVITVWFRSVLIKEEAMPAALMALLFSNIDPVYEFHRGFLHEVEQRLALWEGPSSAHLKGDHQRIGDILLRNMRQLKEFTSYFQRHDEVLTELEKATKHCKKLEAVYKEFELQKVCYLPLNTFLLKPVQRLVHYRLLLSRLCAHYSPGHRDYADCHAHARR
IRESfinder result
IRESfinder score
0.382953092
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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