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mmu_circPhtf1_1094
Basic information of circular RNA
PanCircBase ID:
mmu_circPhtf1_1094
mm39_Chr. Position ID:
chr3|103890261|103901218|+
Gene name:
Phtf1
Transcript:
ENSMUST00000117150.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
5,6,7,8,9,10,11
Exon/intron offsets:
0,2807,4481,5669,8092,8374,10735
Genomic length:
10957
Exon/intron sizes in nt:
1,59,15,71,35,16,01,74,00,000
Flanking exon/introns:
chr3:103889271-103890261|chr3:103901218-103903917
Splice length:
1094
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GCTCAACATTTGCCAAAGCCAAGCCTGAGATTCCATGGACCTCGCTCACTCGGAAGGGGCTTGTTCGAGTGGTGTTTTTCCCGTTGTTCAGCAGCTGGTGGATTCAGGTTACCTCTCTCAGAATCTTTGTTTGGTTGCTGCTACTTTACCTCATGCAAGTCACAGCGGTTGTGTTGTATCTCCTGATGCCTATTGTGAGCGCCAGTGAAGTGCTTGGACCCTTGTGCCTTATGCTACTCATGGGAACTGTCCACTGTCAGATTGTGTCGACTCAGATAACAAGGCCGTCAGGAAACAATGGAAATCGGAGAAGAAGAAAATTACGAAAAACTGTAAATGGTGATGGGAGCCGAGACAATGGAAATAACTCCCCTGATAAAGTCAGAGCAGTAGAAACTCTGGAGTCTGCATCCAGTGTTGGTGGTTTTTGGGGGACTCTCTTTGGCAACAGGATTAAAAGGGTGAAATTAGTATCTAACAAAGGTACTGAAACTGACAATGACTCAGGCTGTTTCCATCCTATCCTTAAGAAGAGACAGGGTCGACCCGAGATCAGAATGTGGCAAGCAAGAGAGAAAGCGAAGGTTTCGGATGGAGAAAAGTGCCGTAGGGAGGCTTATAGGCGTTTGGGTAATGGAATTTCAGACGATCTGTCAAGTGAGGAGGATGGTGAAGCACGGACACAGATGATATTATTGCGTAGGAGTGTGGAAGGGGCGTCAAGTGACAATGGTTATGAAGTTAAGAATAGAAGGTCAATACTTTCAAGGCACCTAAATTCTCAGGTAAAGAAAACCACAAGGTGGTGTCATATTGTTCGGGATTCAGATAGTCTGGCTGAATCAGAGTTTGAATCAGCAGTCTTCAGCCAGGGTTCTAGATCTGGTATGAGTGGTGGCTCTCGGAGCCTTAACTTGTCAAGAAGAGACTCAGAAAGCACCCGACATGACTCCGAGACTGAGGATATGTTATGGGATGACCTTCTCCATGGTCCAGAGTGCCGGTCATCTGTCACCAGTGACAGTGAGGGGGCTCATGTAAATACCATTCATTCAGGGACCAAACGTGACCCCAAAGAAGATGTTTTTCAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACAGTGAGGGGGCTCATGTA
60.25
ACGGGAAAAACACCACTCGA
59.82
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCGGTCATCTGTCACCAGTG
60.39
ACGGGAAAAACACCACTCGA
59.82
178
PCR template sequence:
AGAGTGCCGGTCATCTGTCACCAGTGACAGTGAGGGGGCTCATGTAAATACCATTCATTCAGGGACCAAACGTGACCCCAAAGAAGATGTTTTTCAGCAGGCTCAACATTTGCCAAAGCCAAGCCTGAGATTCCATGGACCTCGCTCACTCGGAAGGGGCTTGTTCGAGTGGTGTTTTTCCCGTTGTTCAGCAGCTGGTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-223-3p(1), mmu-miR-216a-5p(1), mmu-miR-182-5p(1), mmu-miR-335-3p(1), mmu-miR-532-5p(1), mmu-miR-3470b(1), mmu-miR-670-5p(1), mmu-miR-344-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGTTTTTCAGCAGGCTCAACATTTGC
siRNA sets
AAATGTTGAGCCTGCTGAA, GTTGAGCCTGCTGAAAAAC, CAAATGTTGAGCCTGCTGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPHTF1_1094_ORF_1
0.5871
0.002879034
0.981096297
1128
ORF sequence:
ATGCAAGTCACAGCGGTTGTGTTGTATCTCCTGATGCCTATTGTGAGCGCCAGTGAAGTGCTTGGACCCTTGTGCCTTATGCTACTCATGGGAACTGTCCACTGTCAGATTGTGTCGACTCAGATAACAAGGCCGTCAGGAAACAATGGAAATCGGAGAAGAAGAAAATTACGAAAAACTGTAAATGGTGATGGGAGCCGAGACAATGGAAATAACTCCCCTGATAAAGTCAGAGCAGTAGAAACTCTGGAGTCTGCATCCAGTGTTGGTGGTTTTTGGGGGACTCTCTTTGGCAACAGGATTAAAAGGGTGAAATTAGTATCTAACAAAGGTACTGAAACTGACAATGACTCAGGCTGTTTCCATCCTATCCTTAAGAAGAGACAGGGTCGACCCGAGATCAGAATGTGGCAAGCAAGAGAGAAAGCGAAGGTTTCGGATGGAGAAAAGTGCCGTAGGGAGGCTTATAGGCGTTTGGGTAATGGAATTTCAGACGATCTGTCAAGTGAGGAGGATGGTGAAGCACGGACACAGATGATATTATTGCGTAGGAGTGTGGAAGGGGCGTCAAGTGACAATGGTTATGAAGTTAAGAATAGAAGGTCAATACTTTCAAGGCACCTAAATTCTCAGGTAAAGAAAACCACAAGGTGGTGTCATATTGTTCGGGATTCAGATAGTCTGGCTGAATCAGAGTTTGAATCAGCAGTCTTCAGCCAGGGTTCTAGATCTGGTATGAGTGGTGGCTCTCGGAGCCTTAACTTGTCAAGAAGAGACTCAGAAAGCACCCGACATGACTCCGAGACTGAGGATATGTTATGGGATGACCTTCTCCATGGTCCAGAGTGCCGGTCATCTGTCACCAGTGACAGTGAGGGGGCTCATGTAAATACCATTCATTCAGGGACCAAACGTGACCCCAAAGAAGATGTTTTTCAGCAGGCTCAACATTTGCCAAAGCCAAGCCTGAGATTCCATGGACCTCGCTCACTCGGAAGGGGCTTGTTCGAGTGGTGTTTTTCCCGTTGTTCAGCAGCTGGTGGATTCAGGTTACCTCTCTCAGAATCTTTGTTTGGTTGCTGCTACTTTACCTCATGCAAGTCACAGCGGTTGTGTTGTATCTCCTGA
Peptide sequence:
MQVTAVVLYLLMPIVSASEVLGPLCLMLLMGTVHCQIVSTQITRPSGNNGNRRRRKLRKTVNGDGSRDNGNNSPDKVRAVETLESASSVGGFWGTLFGNRIKRVKLVSNKGTETDNDSGCFHPILKKRQGRPEIRMWQAREKAKVSDGEKCRREAYRRLGNGISDDLSSEEDGEARTQMILLRRSVEGASSDNGYEVKNRRSILSRHLNSQVKKTTRWCHIVRDSDSLAESEFESAVFSQGSRSGMSGGSRSLNLSRRDSESTRHDSETEDMLWDDLLHGPECRSSVTSDSEGAHVNTIHSGTKRDPKEDVFQQAQHLPKPSLRFHGPRSLGRGLFEWCFSRCSAAGGFRLPLSESLFGCCYFTSCKSQRLCCIS
IRESfinder result
IRESfinder score
0.558121111
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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