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mmu_circFrmd4b_295
Basic information of circular RNA
PanCircBase ID:
mmu_circFrmd4b_295
mm39_Chr. Position ID:
chr6|97300615|97306525|-
Gene name:
Frmd4b
Transcript:
ENSMUST00000113355.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
12,11,10,9
Exon/intron offsets:
0,1778,4578,5826
Genomic length:
5910
Exon/intron sizes in nt:
87,58,66,84
Flanking exon/introns:
chr6:97287700-97300615|chr6:97306525-97330142
Splice length:
295
Other database IDs:
circBase: mmu_circ_0013632, CIRCpedia: MMU_CIRCpedia_35563, circAtlas: mmu-Frmd4b_0006
circBase: hsa_circ_0124536, circAtlas: hsa-FRMD4B_0005, CIRCpedia: HSA_CIRCpedia_124465
Human Ortholog IDs:
Mature spliced Sequence:
CGATGAGAATGCCAGGAAAGACTTGAAGACACTGCCAGTCTTTCCAACCAAAACCCTTCAGGAACATCCATCCCTCGCTTACTGTGAGGACAGAGTGATTGAGCATTATTTGAAAATCAAAGGTCTCACTCGGGGTCAAGCTGTGGTCCAGTATATGAAAATAGTAGAAGCCCTACCAACGTATGGAGTCCATTACTATGCAGTGAAGGATAAGCAGGGACTTCCATGGTGGCTTGGTATCAGCTACAAAGGAATCGGCCAGTATGACTTACAAGACAAGGTGAAGCCTCGCAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GACTTCCATGGTGGCTTGGT
60.25
TCCTCACAGTAAGCGAGGGA
59.96
167
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GACTTCCATGGTGGCTTGGT
60.25
GTCCTCACAGTAAGCGAGGG
59.83
168
PCR template sequence:
CTATGCAGTGAAGGATAAGCAGGGACTTCCATGGTGGCTTGGTATCAGCTACAAAGGAATCGGCCAGTATGACTTACAAGACAAGGTGAAGCCTCGCAAACGATGAGAATGCCAGGAAAGACTTGAAGACACTGCCAGTCTTTCCAACCAAAACCCTTCAGGAACATCCATCCCTCGCTTACTGTGAGGACAGAGTGATT
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-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-217-5p(1), mmu-miR-185-5p(1), mmu-miR-351-5p(1), mmu-miR-34b-5p(1), mmu-miR-335-3p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAAGCCTCGCAAACGATGAGAATGCC
siRNA sets
CATTCTCATCGTTTGCGAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFRMD4B_295_ORF_1
0.6946
0.203203298
0.111687199
147
ORF sequence:
ATGAAAATAGTAGAAGCCCTACCAACGTATGGAGTCCATTACTATGCAGTGAAGGATAAGCAGGGACTTCCATGGTGGCTTGGTATCAGCTACAAAGGAATCGGCCAGTATGACTTACAAGACAAGGTGAAGCCTCGCAAACGATGA
Peptide sequence:
MKIVEALPTYGVHYYAVKDKQGLPWWLGISYKGIGQYDLQDKVKPRKR
IRESfinder result
IRESfinder score
0.515712795
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
RPF, cORF, m6A
mmu_circFrmd4b_001
Evidence
Peptide sequence:
MKIVEALPTYGVHYYAVKDKQGLPWWLGISYKGIGQYDLQDKVKPRKR*
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