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mmu_circPhf3_1172
Basic information of circular RNA
PanCircBase ID:
mmu_circPhf3_1172
mm39_Chr. Position ID:
chr1|30845249|30859318|-
Gene name:
Phf3
Transcript:
ENSMUST00000186733.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
15,14,13,12,11,10,9,8
Exon/intron offsets:
0,2554,4514,5603,6848,7791,10299,13912
Genomic length:
14069
Exon/intron sizes in nt:
19,69,01,48,19,61,36,10,00,00,000
Flanking exon/introns:
chr1:30845023-30845249|chr1:30859318-30859763
Splice length:
1172
Other database IDs:
circBase: hsa_circ_0132068, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_150753
Human Ortholog IDs:
Mature spliced Sequence:
ACTTACAGATTCAAACCTGAAGATCCCAGAGGAAAAGGCAGCAAAGGTTGCCACAAAAATTGAAAAAGAACTTTTCTCTTTTTTTCGGGACACGGATGCCAAGTATAAGAATAAATATAGAAGCTTGATGTTTAATCTAAAAGATCCTAAAAACAATATATTATTTAAGAAAGTTCTAAAAGGAGAAGTAACCCCTGATCATCTTATAAGAATGAGCCCAGAAGAACTAGCCTCCAAAGAGCTGGCTGCGTGGAGACGAAGGGAGAACAGACACACCATAGAGATGATTGAGAAGGAACAGAGAGAAGTGGAAAGACGACCAATCACGAAAATAACTCACAAAGGTGAGATAGAAATCGAGAGTGACGCCCCGATGAAGGAGCAGGAAGCAGCCATCGAGATCCAGGAACCGTCAGCTAATAAGTCAATGGAGAAGCCAGATGTGTCTGAGAAACAAAAAGAAGAGGTTGACTCCACATCTAAAGACACCACTAGTCAACACAGACAGCATCTCTTTGACCTGAACTGCAAAATATGCATAGGTCGAATGGCACCACCTATAGATGATCTTTCTCCAAAAACTGTGAAAGTTGTTGTAGGAGGAGCCCGGAAACACTCAGACAACGAAGCAGAGAGTCTAGCAGATGCGTTGTCTTCAACTACGAATATTCTGACCTCTGACCTCTTTGAGGAGGAAAAGCAAGAATCTCCCAAGTCAACGTTTTCCCCCACTCCACGGCCAGAGATGCCTGGAACTGTGGAAGTTGAGTCAACCTTTCTGGCTCGATTGAACTTCATCTGGAAAGGTTTTATCAATATGCCCTCTGTGGCAAAGTTTGTTACCAAAGCCTACCCCGTGTCTGGATCCCCTGAGTACTTGACAGAGGACCTACCAGACAGCATTCAAGTAGGTGGCAGGATATCGCCTCAGACAGTTTGGGATTATGTGGAAAAAATAAAAGCATCAGGCACCAAGGAAATCTGTGTGGTTCGCTTCACACCAGTAACTGAAGAAGATCAGATTTCTTACACTTTGCTGTTTGCGTACTTCAGTAGCAGAAAGCGCTATGGTGTGGCTGCTAACAACATGAAGCAGGTTAAAGACATGTACCTCATTCCATTGGGCGCTGCAGATAAAATCCCACACCCTCTTGTGCCTTTTGATGGACCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCGCTGCAGATAAAATCCC
59.69
GGCATCCGTGTCCCGAAAAA
61.24
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGCGCTGCAGATAAAATCC
59.69
GGCATCCGTGTCCCGAAAAA
61.24
150
PCR template sequence:
GTGGCTGCTAACAACATGAAGCAGGTTAAAGACATGTACCTCATTCCATTGGGCGCTGCAGATAAAATCCCACACCCTCTTGTGCCTTTTGATGGACCTGACTTACAGATTCAAACCTGAAGATCCCAGAGGAAAAGGCAGCAAAGGTTGCCACAAAAATTGAAAAAGAACTTTTCTCTTTTTTTCGGGACACGGATGCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-26a-5p(1), mmu-miR-204-5p(1), mmu-miR-326-3p(1), mmu-miR-495-3p(1), mmu-miR-136-5p(1), mmu-miR-26b-5p(1), mmu-miR-680(1), mmu-miR-540-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
TTTGATGGACCTGACTTACAGATTCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPHF3_1172_ORF_1
0.8371
0.197346134
0.991431465
1065
ORF sequence:
ATGTTTAATCTAAAAGATCCTAAAAACAATATATTATTTAAGAAAGTTCTAAAAGGAGAAGTAACCCCTGATCATCTTATAAGAATGAGCCCAGAAGAACTAGCCTCCAAAGAGCTGGCTGCGTGGAGACGAAGGGAGAACAGACACACCATAGAGATGATTGAGAAGGAACAGAGAGAAGTGGAAAGACGACCAATCACGAAAATAACTCACAAAGGTGAGATAGAAATCGAGAGTGACGCCCCGATGAAGGAGCAGGAAGCAGCCATCGAGATCCAGGAACCGTCAGCTAATAAGTCAATGGAGAAGCCAGATGTGTCTGAGAAACAAAAAGAAGAGGTTGACTCCACATCTAAAGACACCACTAGTCAACACAGACAGCATCTCTTTGACCTGAACTGCAAAATATGCATAGGTCGAATGGCACCACCTATAGATGATCTTTCTCCAAAAACTGTGAAAGTTGTTGTAGGAGGAGCCCGGAAACACTCAGACAACGAAGCAGAGAGTCTAGCAGATGCGTTGTCTTCAACTACGAATATTCTGACCTCTGACCTCTTTGAGGAGGAAAAGCAAGAATCTCCCAAGTCAACGTTTTCCCCCACTCCACGGCCAGAGATGCCTGGAACTGTGGAAGTTGAGTCAACCTTTCTGGCTCGATTGAACTTCATCTGGAAAGGTTTTATCAATATGCCCTCTGTGGCAAAGTTTGTTACCAAAGCCTACCCCGTGTCTGGATCCCCTGAGTACTTGACAGAGGACCTACCAGACAGCATTCAAGTAGGTGGCAGGATATCGCCTCAGACAGTTTGGGATTATGTGGAAAAAATAAAAGCATCAGGCACCAAGGAAATCTGTGTGGTTCGCTTCACACCAGTAACTGAAGAAGATCAGATTTCTTACACTTTGCTGTTTGCGTACTTCAGTAGCAGAAAGCGCTATGGTGTGGCTGCTAACAACATGAAGCAGGTTAAAGACATGTACCTCATTCCATTGGGCGCTGCAGATAAAATCCCACACCCTCTTGTGCCTTTTGATGGACCTGACTTACAGATTCAAACCTGA
Peptide sequence:
MFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELASKELAAWRRRENRHTIEMIEKEQREVERRPITKITHKGEIEIESDAPMKEQEAAIEIQEPSANKSMEKPDVSEKQKEEVDSTSKDTTSQHRQHLFDLNCKICIGRMAPPIDDLSPKTVKVVVGGARKHSDNEAESLADALSSTTNILTSDLFEEEKQESPKSTFSPTPRPEMPGTVEVESTFLARLNFIWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTLLFAYFSSRKRYGVAANNMKQVKDMYLIPLGAADKIPHPLVPFDGPDLQIQT
IRESfinder result
IRESfinder score
0.602419766
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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