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mmu_circFhod3_1432
Basic information of circular RNA
PanCircBase ID:
mmu_circFhod3_1432
mm39_Chr. Position ID:
chr18|25102216|25193433|+
Gene name:
Fhod3
Transcript:
ENSMUST00000037097.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
6,7,8,9,10,11,12,13,14,15
Exon/intron offsets:
0,16054,20813,25256,32631,51502,53462,58905,87100,91166
Genomic length:
91217
Exon/intron sizes in nt:
95,112,95,144,242,96,357,105,135,51
Flanking exon/introns:
chr18:25037055-25102216|chr18:25193433-25199273
Splice length:
1432
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CTCTGGGTCAGATTATGTTGTATGTGGATGGGATGAATGGCGTCATCAACCACAGCGAGACCATCCAGTGGCTTTACACGCTCGTTGGGTCGAAGTTCCGCCTGGTAGTGAAGACAGCCCTGAAGCTTCTTCTGGTCTTTGTGGAGTATTCTGAGTCCAATGCACCACTTCTCATTCAGGCCGTTTCTGCTGTCGACACCAAAAGAGGTGTCAAACCCTGGTCCAACATCATGGAAATCTTGGAGGAAAAAGATGGAGTTGACACAGAGCTATTGGTTTATGCAATGACTCTAGTGAACAAGACACTGGCAGGACTGCCAGATCAAGACACCTTCTATGACGTAGTAGACTGCCTGGAAGAGCTGGGCATCGCCGCTGTGTCCCAAAGGCACTTGAACAAGAAAGGGACAGACCTGGACTTGCTGGAGCAGTTTAATATCTATGAGGTGGCACTCAGGCATGAAGATGGTGATGAGACAGCTGAGCCACCCCCCAGTGGGCACCGGGACCGGAGGAGGGCCAGCATGTGTTCTGGTGGCACTGTGGGTGAGCAACAGGGCCTTGACCGCAGAAGGAGCCGTAGACACTCAATCCAGAATATCAAGAGCCCACTGTCAGCTCCCACCAGCCCCTGCTCCCCGTCTGTTCCTGCCTTCAAACCCAGCCAAGTTCGAGACCTCTGTGAAAAGGATGAGGAGGAGGAGGAGGAAGAAGAACAGCCAATCACGGAGCCCAATTCAGAGGAGGAGAGAGAGGACGATGCCCAGTGTCAGGGCAAGGACAGCAAGGCCAGCTCTGCCTCCGGTCAGAGCTCCCCTGGGAAGGATGCTGCTCCTGAGAGTTCTGCACTCCATACCACCTCAAGTCCCACCTCACAGGGAAGGTGGCTTTCTGCCAGCACAGCAGCACGGAGCCCTGTGCTTGGTGGGACCTCTGGGCCTGAGGCCAGCCGGCCTGCTGCTCGCTTGCTACCTCCCAGCCCTGGCTTGGCCACTCGGCCCTCCACAGCACCAAAGGTGTCTCCAACCATAGACAAGCTGCCCTACGTGCCCCACAGCCCCTTCCACCTCTTCTCCTATGACTTTGAAGATTCACCCCTCCTCACCAAGGACAAGGGAGGAGACTCTCAGACAGAAAACAGATACAGCAATTTCAGCAGCAACTCTTTCCAATCCTCCAGACCCTCTCCTGGACCTAGTGGGTCCCCATCTTATGCATCATCCTTCTCATCCCCACAGGATACCAGGTCATCGCCAAGTGGCCTTCTCACATCCTCGTTCAGGCAGCACCAAGAGTCACTGGCAGCAGAGAGAGAGCGGAGGCGGCAAGAGAGAGAGGAAAGACTGCAGAGGATAGAACGGGAAGAAAGGAACAAATTCAACCGGGAATATCTAGACAAAAGGGAGGAGCAAAGGCAAGCAAGAGGAGAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GACTGCAGAGGATAGAACGGG
59.93
GGTCTCGCTGTGGTTGATGA
60.04
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GACTGCAGAGGATAGAACGGG
59.93
GATGGTCTCGCTGTGGTTGA
60.04
156
PCR template sequence:
GAGAGGAAAGACTGCAGAGGATAGAACGGGAAGAAAGGAACAAATTCAACCGGGAATATCTAGACAAAAGGGAGGAGCAAAGGCAAGCAAGAGGAGAAAGCTCTGGGTCAGATTATGTTGTATGTGGATGGGATGAATGGCGTCATCAACCACAGCGAGACCATCCAGTGGCTTTACACGCTCGTTGGGTCGAAGTTCCG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
18
Interacting miRNAs (#binding sites)
mmu-miR-204-5p(2), 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-33-5p(1), mmu-miR-328-3p(1), mmu-miR-709(1), mmu-miR-214-3p(1), mmu-let-7d-5p(1), mmu-miR-382-3p(1), mmu-miR-483-5p(1), mmu-miR-107-3p(1), mmu-miR-224-5p(1), mmu-miR-98-5p(1), mmu-miR-3061-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CAAGAGGAGAAAGCTCTGGGTCAGAT
siRNA sets
CTGACCCAGAGCTTTCTCC, ATCTGACCCAGAGCTTTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCFHOD3_1432_ORF_1
0.7987
0.257572639
0.999810779
1572
ORF sequence:
ATGTTGTATGTGGATGGGATGAATGGCGTCATCAACCACAGCGAGACCATCCAGTGGCTTTACACGCTCGTTGGGTCGAAGTTCCGCCTGGTAGTGAAGACAGCCCTGAAGCTTCTTCTGGTCTTTGTGGAGTATTCTGAGTCCAATGCACCACTTCTCATTCAGGCCGTTTCTGCTGTCGACACCAAAAGAGGTGTCAAACCCTGGTCCAACATCATGGAAATCTTGGAGGAAAAAGATGGAGTTGACACAGAGCTATTGGTTTATGCAATGACTCTAGTGAACAAGACACTGGCAGGACTGCCAGATCAAGACACCTTCTATGACGTAGTAGACTGCCTGGAAGAGCTGGGCATCGCCGCTGTGTCCCAAAGGCACTTGAACAAGAAAGGGACAGACCTGGACTTGCTGGAGCAGTTTAATATCTATGAGGTGGCACTCAGGCATGAAGATGGTGATGAGACAGCTGAGCCACCCCCCAGTGGGCACCGGGACCGGAGGAGGGCCAGCATGTGTTCTGGTGGCACTGTGGGTGAGCAACAGGGCCTTGACCGCAGAAGGAGCCGTAGACACTCAATCCAGAATATCAAGAGCCCACTGTCAGCTCCCACCAGCCCCTGCTCCCCGTCTGTTCCTGCCTTCAAACCCAGCCAAGTTCGAGACCTCTGTGAAAAGGATGAGGAGGAGGAGGAGGAAGAAGAACAGCCAATCACGGAGCCCAATTCAGAGGAGGAGAGAGAGGACGATGCCCAGTGTCAGGGCAAGGACAGCAAGGCCAGCTCTGCCTCCGGTCAGAGCTCCCCTGGGAAGGATGCTGCTCCTGAGAGTTCTGCACTCCATACCACCTCAAGTCCCACCTCACAGGGAAGGTGGCTTTCTGCCAGCACAGCAGCACGGAGCCCTGTGCTTGGTGGGACCTCTGGGCCTGAGGCCAGCCGGCCTGCTGCTCGCTTGCTACCTCCCAGCCCTGGCTTGGCCACTCGGCCCTCCACAGCACCAAAGGTGTCTCCAACCATAGACAAGCTGCCCTACGTGCCCCACAGCCCCTTCCACCTCTTCTCCTATGACTTTGAAGATTCACCCCTCCTCACCAAGGACAAGGGAGGAGACTCTCAGACAGAAAACAGATACAGCAATTTCAGCAGCAACTCTTTCCAATCCTCCAGACCCTCTCCTGGACCTAGTGGGTCCCCATCTTATGCATCATCCTTCTCATCCCCACAGGATACCAGGTCATCGCCAAGTGGCCTTCTCACATCCTCGTTCAGGCAGCACCAAGAGTCACTGGCAGCAGAGAGAGAGCGGAGGCGGCAAGAGAGAGAGGAAAGACTGCAGAGGATAGAACGGGAAGAAAGGAACAAATTCAACCGGGAATATCTAGACAAAAGGGAGGAGCAAAGGCAAGCAAGAGGAGAAAGCTCTGGGTCAGATTATGTTGTATGTGGATGGGATGAATGGCGTCATCAACCACAGCGAGACCATCCAGTGGCTTTACACGCTCGTTGGGTCGAAGTTCCGCCTGGTAGTGAAGACAGCCCTGAAGCTTCTTCTGGTCTTTGTGGAGTATTCTGA
Peptide sequence:
MLYVDGMNGVINHSETIQWLYTLVGSKFRLVVKTALKLLLVFVEYSESNAPLLIQAVSAVDTKRGVKPWSNIMEILEEKDGVDTELLVYAMTLVNKTLAGLPDQDTFYDVVDCLEELGIAAVSQRHLNKKGTDLDLLEQFNIYEVALRHEDGDETAEPPPSGHRDRRRASMCSGGTVGEQQGLDRRRSRRHSIQNIKSPLSAPTSPCSPSVPAFKPSQVRDLCEKDEEEEEEEEQPITEPNSEEEREDDAQCQGKDSKASSASGQSSPGKDAAPESSALHTTSSPTSQGRWLSASTAARSPVLGGTSGPEASRPAARLLPPSPGLATRPSTAPKVSPTIDKLPYVPHSPFHLFSYDFEDSPLLTKDKGGDSQTENRYSNFSSNSFQSSRPSPGPSGSPSYASSFSSPQDTRSSPSGLLTSSFRQHQESLAAERERRRQEREERLQRIEREERNKFNREYLDKREEQRQARGESSGSDYVVCGWDEWRHQPQRDHPVALHARWVEVPPGSEDSPEASSGLCGVF
IRESfinder result
IRESfinder score
0.455414395
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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