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mmu_circFarsa_338
Basic information of circular RNA
PanCircBase ID:
mmu_circFarsa_338
mm39_Chr. Position ID:
chr8|85590686|85591181|+
Gene name:
Farsa
Transcript:
ENSMUST00000003906.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
5,6,7
Exon/intron offsets:
0,173,379
Genomic length:
495
Exon/intron sizes in nt:
93,129,116
Flanking exon/introns:
chr8:85588059-85590686|chr8:85591181-85594005
Splice length:
338
Other database IDs:
circBase: mmu_circ_0001705, CIRCpedia: MMU_CIRCpedia_31839, circAtlas: mmu-Farsa_0002
circBase: hsa_circ_0000896, circAtlas: hsa-FARSA_0001, CIRCpedia: HSA_CIRCpedia_24858
Human Ortholog IDs:
Mature spliced Sequence:
GATCCTGAAAACCTACTGGGTGAGCAAGGGCAAGGCCTTCAGCACAAGCGTGTCTAAGCAGGAGGCAGAGCTGAGCCCAGAGATGATCTCCAGTGGCTCTTGGAGGGACCGACCTTTCAAACCCTACAACTTCTCTGCCCGTGGTGTGCTCCCAGATAGTGGCCACCTGCACCCCTTGCTCAAGGTCCGCTCTCAGTTCCGACAAATCTTCTTGGAGATGGGGTTCACTGAGATGCCTACGGACAATTTCATTGAGAGCTCCTTCTGGAACTTTGATGCACTCTTTCAGCCTCAGCAGCACCCAGCACGTGACCAACATGATACTTTCTTCCTGCGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTCTTTCAGCCTCAGCAGCA
60.32
TCATCTCTGGGCTCAGCTCT
60.03
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTCTTTCAGCCTCAGCAGC
60.32
TCATCTCTGGGCTCAGCTCT
60.03
145
PCR template sequence:
ACGGACAATTTCATTGAGAGCTCCTTCTGGAACTTTGATGCACTCTTTCAGCCTCAGCAGCACCCAGCACGTGACCAACATGATACTTTCTTCCTGCGAGGATCCTGAAAACCTACTGGGTGAGCAAGGGCAAGGCCTTCAGCACAAGCGTGTCTAAGCAGGAGGCAGAGCTGAGCCCAGAGATGATCTCCAGTGGCTCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-326-3p(1), mmu-miR-24-3p(1), mmu-miR-382-5p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTCTTCCTGCGAGGATCCTGAAAACC
siRNA sets
TTTTCAGGATCCTCGCAGG, GTTTTCAGGATCCTCGCAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFARSA_338_ORF_1
0.6961
0.259611178
0.26935318
264
ORF sequence:
ATGATCTCCAGTGGCTCTTGGAGGGACCGACCTTTCAAACCCTACAACTTCTCTGCCCGTGGTGTGCTCCCAGATAGTGGCCACCTGCACCCCTTGCTCAAGGTCCGCTCTCAGTTCCGACAAATCTTCTTGGAGATGGGGTTCACTGAGATGCCTACGGACAATTTCATTGAGAGCTCCTTCTGGAACTTTGATGCACTCTTTCAGCCTCAGCAGCACCCAGCACGTGACCAACATGATACTTTCTTCCTGCGAGGATCCTGA
Peptide sequence:
MISSGSWRDRPFKPYNFSARGVLPDSGHLHPLLKVRSQFRQIFLEMGFTEMPTDNFIESSFWNFDALFQPQQHPARDQHDTFFLRGS
IRESfinder result
IRESfinder score
0.684700837
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
RPF, cORF, m6A
mmu_circFarsa_001
Evidence
Peptide sequence:
MISSGSWRDRPFKPYNFSARGVLPDSGHLHPLLKVRSQFRQIFLEMGFTEMPTDNFIESSFWNFDALFQPQQHPARDQHDTFFLRGS*
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