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mmu_circFhod3_800
Basic information of circular RNA
PanCircBase ID:
mmu_circFhod3_800
mm39_Chr. Position ID:
chr18|25134847|25161226|+
Gene name:
Fhod3
Transcript:
ENSMUST00000037097.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
10,11,12,13
Exon/intron offsets:
0,18871,20831,26274
Genomic length:
26379
Exon/intron sizes in nt:
24,29,63,57,105
Flanking exon/introns:
chr18:25127616-25134847|chr18:25161226-25189316
Splice length:
800
Other database IDs:
CIRCpedia: MMU_CIRCpedia_14348
circAtlas: hsa-FHOD3_0029, CIRCpedia: HSA_CIRCpedia_88373
Human Ortholog IDs:
Mature spliced Sequence:
GTGGCACTCAGGCATGAAGATGGTGATGAGACAGCTGAGCCACCCCCCAGTGGGCACCGGGACCGGAGGAGGGCCAGCATGTGTTCTGGTGGCACTGTGGGTGAGCAACAGGGCCTTGACCGCAGAAGGAGCCGTAGACACTCAATCCAGAATATCAAGAGCCCACTGTCAGCTCCCACCAGCCCCTGCTCCCCGTCTGTTCCTGCCTTCAAACCCAGCCAAGTTCGAGACCTCTGTGAAAAGGATGAGGAGGAGGAGGAGGAAGAAGAACAGCCAATCACGGAGCCCAATTCAGAGGAGGAGAGAGAGGACGATGCCCAGTGTCAGGGCAAGGACAGCAAGGCCAGCTCTGCCTCCGGTCAGAGCTCCCCTGGGAAGGATGCTGCTCCTGAGAGTTCTGCACTCCATACCACCTCAAGTCCCACCTCACAGGGAAGGTGGCTTTCTGCCAGCACAGCAGCACGGAGCCCTGTGCTTGGTGGGACCTCTGGGCCTGAGGCCAGCCGGCCTGCTGCTCGCTTGCTACCTCCCAGCCCTGGCTTGGCCACTCGGCCCTCCACAGCACCAAAGGTGTCTCCAACCATAGACAAGCTGCCCTACGTGCCCCACAGCCCCTTCCACCTCTTCTCCTATGACTTTGAAGATTCACCCCTCCTCACCAAGGACAAGGGAGGAGACTCTCAGACAGAAAACAGATACAGCAATTTCAGCAGCAACTCTTTCCAATCCTCCAGACCCTCTCCTGGACCTAGTGGGTCCCCATCTTATGCATCATCCTTCTCATCCCCACAGGATACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATCCTCCAGACCCTCTCCTG
59.74
ACAGTGCCACCAGAACACAT
59.82
173
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCCTCTCCTGGACCTAGTG
59.66
ACAGTGCCACCAGAACACAT
59.82
164
PCR template sequence:
GCAATTTCAGCAGCAACTCTTTCCAATCCTCCAGACCCTCTCCTGGACCTAGTGGGTCCCCATCTTATGCATCATCCTTCTCATCCCCACAGGATACCAGGTGGCACTCAGGCATGAAGATGGTGATGAGACAGCTGAGCCACCCCCCAGTGGGCACCGGGACCGGAGGAGGGCCAGCATGTGTTCTGGTGGCACTGTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-705(2), mmu-let-7a-5p(1), mmu-miR-103-3p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-328-3p(1), mmu-miR-709(1), mmu-miR-214-3p(1), mmu-let-7d-5p(1), mmu-miR-483-5p(1), mmu-miR-107-3p(1), mmu-miR-98-5p(1), mmu-miR-3061-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CACAGGATACCAGGTGGCACTCAGGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFHOD3_800_ORF_1
0.4838
0.163750507
0.996755696
1308
ORF sequence:
ATGTGTTCTGGTGGCACTGTGGGTGAGCAACAGGGCCTTGACCGCAGAAGGAGCCGTAGACACTCAATCCAGAATATCAAGAGCCCACTGTCAGCTCCCACCAGCCCCTGCTCCCCGTCTGTTCCTGCCTTCAAACCCAGCCAAGTTCGAGACCTCTGTGAAAAGGATGAGGAGGAGGAGGAGGAAGAAGAACAGCCAATCACGGAGCCCAATTCAGAGGAGGAGAGAGAGGACGATGCCCAGTGTCAGGGCAAGGACAGCAAGGCCAGCTCTGCCTCCGGTCAGAGCTCCCCTGGGAAGGATGCTGCTCCTGAGAGTTCTGCACTCCATACCACCTCAAGTCCCACCTCACAGGGAAGGTGGCTTTCTGCCAGCACAGCAGCACGGAGCCCTGTGCTTGGTGGGACCTCTGGGCCTGAGGCCAGCCGGCCTGCTGCTCGCTTGCTACCTCCCAGCCCTGGCTTGGCCACTCGGCCCTCCACAGCACCAAAGGTGTCTCCAACCATAGACAAGCTGCCCTACGTGCCCCACAGCCCCTTCCACCTCTTCTCCTATGACTTTGAAGATTCACCCCTCCTCACCAAGGACAAGGGAGGAGACTCTCAGACAGAAAACAGATACAGCAATTTCAGCAGCAACTCTTTCCAATCCTCCAGACCCTCTCCTGGACCTAGTGGGTCCCCATCTTATGCATCATCCTTCTCATCCCCACAGGATACCAGGTGGCACTCAGGCATGAAGATGGTGATGAGACAGCTGAGCCACCCCCCAGTGGGCACCGGGACCGGAGGAGGGCCAGCATGTGTTCTGGTGGCACTGTGGGTGAGCAACAGGGCCTTGACCGCAGAAGGAGCCGTAGACACTCAATCCAGAATATCAAGAGCCCACTGTCAGCTCCCACCAGCCCCTGCTCCCCGTCTGTTCCTGCCTTCAAACCCAGCCAAGTTCGAGACCTCTGTGAAAAGGATGAGGAGGAGGAGGAGGAAGAAGAACAGCCAATCACGGAGCCCAATTCAGAGGAGGAGAGAGAGGACGATGCCCAGTGTCAGGGCAAGGACAGCAAGGCCAGCTCTGCCTCCGGTCAGAGCTCCCCTGGGAAGGATGCTGCTCCTGAGAGTTCTGCACTCCATACCACCTCAAGTCCCACCTCACAGGGAAGGTGGCTTTCTGCCAGCACAGCAGCACGGAGCCCTGTGCTTGGTGGGACCTCTGGGCCTGAGGCCAGCCGGCCTGCTGCTCGCTTGCTACCTCCCAGCCCTGGCTTGGCCACTCGGCCCTCCACAGCACCAAAGGTGTCTCCAACCATAG
Peptide sequence:
MCSGGTVGEQQGLDRRRSRRHSIQNIKSPLSAPTSPCSPSVPAFKPSQVRDLCEKDEEEEEEEEQPITEPNSEEEREDDAQCQGKDSKASSASGQSSPGKDAAPESSALHTTSSPTSQGRWLSASTAARSPVLGGTSGPEASRPAARLLPPSPGLATRPSTAPKVSPTIDKLPYVPHSPFHLFSYDFEDSPLLTKDKGGDSQTENRYSNFSSNSFQSSRPSPGPSGSPSYASSFSSPQDTRWHSGMKMVMRQLSHPPVGTGTGGGPACVLVALWVSNRALTAEGAVDTQSRISRAHCQLPPAPAPRLFLPSNPAKFETSVKRMRRRRRKKNSQSRSPIQRRRERTMPSVRARTARPALPPVRAPLGRMLLLRVLHSIPPQVPPHREGGFLPAQQHGALCLVGPLGLRPAGLLLACYLPALAWPLGPPQHQRCLQP
IRESfinder result
IRESfinder score
0.479662473
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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