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mmu_circFcho2_666
Basic information of circular RNA
PanCircBase ID:
mmu_circFcho2_666
mm39_Chr. Position ID:
chr13|98913896|98942905|-
Gene name:
Fcho2
Transcript:
ENSMUST00000099277.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
7,6,5,4,3,2
Exon/intron offsets:
0,7387,11974,12343,18904,28917
Genomic length:
29009
Exon/intron sizes in nt:
99,105,153,142,75,92
Flanking exon/introns:
chr13:98912425-98913896|chr13:98942905-98951583
Splice length:
666
Other database IDs:
CIRCpedia: MMU_CIRCpedia_35882, circAtlas: mmu-Fcho2_0029
circBase: hsa_circ_0129567, circAtlas: hsa-FCHO2_0049, CIRCpedia: HSA_CIRCpedia_136575
Human Ortholog IDs:
Mature spliced Sequence:
GGGGAAAAAAATAATGGCTTTGATGTACTGTACCATAATATGAAGCATGGACAGATATCAACTAAAGAACTAGCAGATTTTGTAAGAGAAAGAGCTACAATAGAAGAGGCATACTCCAGATCAATGACAAAACTAGCGAAATCTGCAAGCAATTATTCACAACTTGGAACATTTGCACCAATGTGGGATGTATTCAAAACATCTACAGAGAAATTAGCAAATTGTCATTTGGATCTTGTTAGAAAATTACAGGAATTAATAAAGGAAGTTCAGAAGTATGGAGAGGAGCAAGTCAAGTCTCATAAGAAGACTAAAGAAGAAGTCGCAGGGACTCTGGAAGCAGTCCAAGCCATTCAGAATATAACTCAGGCACTCCAGAAGTCGAAGGAAAATTACACTGCCAAATGTGTAGAACAGGAACGTCTGAAAAAGGAAGGAGCTACACAAAGAGAAATAGAAAAGGCAGCTGTTAAGTCTAAGAAAGCTACAGATACTTATAAACTTTATGTGGAAAAGTATGCATTAACAAAAGCAGATTTTGAGCAGAAGATGACAGAAACAGCCCAGAAATTTCAAGATATTGAAGAAACTCACCTCATTCACATAAAGGAAATTATCGGATCCTTGTCAAATGCTGTCAAGGAGATCCACTTACAGATCGGCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGGATCCTTGTCAAATGCTGT
58.91
AGCTCTTTCTCTTACAAAATCTGCT
58.76
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGGATCCTTGTCAAATGCTGTC
59.9
AGCTCTTTCTCTTACAAAATCTGCT
58.76
145
PCR template sequence:
GAAATTTCAAGATATTGAAGAAACTCACCTCATTCACATAAAGGAAATTATCGGATCCTTGTCAAATGCTGTCAAGGAGATCCACTTACAGATCGGCCAGGGGGAAAAAAATAATGGCTTTGATGTACTGTACCATAATATGAAGCATGGACAGATATCAACTAAAGAACTAGCAGATTTTGTAAGAGAAAGAGCTACAA
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-103-3p(1), mmu-miR-34c-5p(1), mmu-miR-19a-3p(1), mmu-miR-101b-3p(1), mmu-miR-382-5p(1), mmu-miR-34b-5p(1), mmu-miR-107-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACAGATCGGCCAGGGGGAAAAAAATA
siRNA sets
TATTTTTTTCCCCCTGGCC, ATTTTTTTCCCCCTGGCCG, TTTTTTTCCCCCTGGCCGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFCHO2_666_ORF_1
0.9566
0.076363105
0.997865997
1293
ORF sequence:
ATGAAGCATGGACAGATATCAACTAAAGAACTAGCAGATTTTGTAAGAGAAAGAGCTACAATAGAAGAGGCATACTCCAGATCAATGACAAAACTAGCGAAATCTGCAAGCAATTATTCACAACTTGGAACATTTGCACCAATGTGGGATGTATTCAAAACATCTACAGAGAAATTAGCAAATTGTCATTTGGATCTTGTTAGAAAATTACAGGAATTAATAAAGGAAGTTCAGAAGTATGGAGAGGAGCAAGTCAAGTCTCATAAGAAGACTAAAGAAGAAGTCGCAGGGACTCTGGAAGCAGTCCAAGCCATTCAGAATATAACTCAGGCACTCCAGAAGTCGAAGGAAAATTACACTGCCAAATGTGTAGAACAGGAACGTCTGAAAAAGGAAGGAGCTACACAAAGAGAAATAGAAAAGGCAGCTGTTAAGTCTAAGAAAGCTACAGATACTTATAAACTTTATGTGGAAAAGTATGCATTAACAAAAGCAGATTTTGAGCAGAAGATGACAGAAACAGCCCAGAAATTTCAAGATATTGAAGAAACTCACCTCATTCACATAAAGGAAATTATCGGATCCTTGTCAAATGCTGTCAAGGAGATCCACTTACAGATCGGCCAGGGGGAAAAAAATAATGGCTTTGATGTACTGTACCATAATATGAAGCATGGACAGATATCAACTAAAGAACTAGCAGATTTTGTAAGAGAAAGAGCTACAATAGAAGAGGCATACTCCAGATCAATGACAAAACTAGCGAAATCTGCAAGCAATTATTCACAACTTGGAACATTTGCACCAATGTGGGATGTATTCAAAACATCTACAGAGAAATTAGCAAATTGTCATTTGGATCTTGTTAGAAAATTACAGGAATTAATAAAGGAAGTTCAGAAGTATGGAGAGGAGCAAGTCAAGTCTCATAAGAAGACTAAAGAAGAAGTCGCAGGGACTCTGGAAGCAGTCCAAGCCATTCAGAATATAACTCAGGCACTCCAGAAGTCGAAGGAAAATTACACTGCCAAATGTGTAGAACAGGAACGTCTGAAAAAGGAAGGAGCTACACAAAGAGAAATAGAAAAGGCAGCTGTTAAGTCTAAGAAAGCTACAGATACTTATAAACTTTATGTGGAAAAGTATGCATTAACAAAAGCAGATTTTGAGCAGAAGATGACAGAAACAGCCCAGAAATTTCAAGATATTGAAGAAACTCACCTCATTCACATAAAGGAAATTATCGGATCCTTGTCAAATGCTGTCAAGGAGATCCACTTACAGATCGGCCAG
Peptide sequence:
MKHGQISTKELADFVRERATIEEAYSRSMTKLAKSASNYSQLGTFAPMWDVFKTSTEKLANCHLDLVRKLQELIKEVQKYGEEQVKSHKKTKEEVAGTLEAVQAIQNITQALQKSKENYTAKCVEQERLKKEGATQREIEKAAVKSKKATDTYKLYVEKYALTKADFEQKMTETAQKFQDIEETHLIHIKEIIGSLSNAVKEIHLQIGQGEKNNGFDVLYHNMKHGQISTKELADFVRERATIEEAYSRSMTKLAKSASNYSQLGTFAPMWDVFKTSTEKLANCHLDLVRKLQELIKEVQKYGEEQVKSHKKTKEEVAGTLEAVQAIQNITQALQKSKENYTAKCVEQERLKKEGATQREIEKAAVKSKKATDTYKLYVEKYALTKADFEQKMTETAQKFQDIEETHLIHIKEIIGSLSNAVKEIHLQIGQ
IRESfinder result
IRESfinder score
0.540100169
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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