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mmu_circPatj_375_1
Basic information of circular RNA
PanCircBase ID:
mmu_circPatj_375_1
mm39_Chr. Position ID:
chr4|98423746|98457372|+
Gene name:
Patj
Transcript:
ENSMUST00000041284.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
26,27,28
Exon/intron offsets:
0,3449,33429
Genomic length:
33626
Exon/intron sizes in nt:
78,100,197
Flanking exon/introns:
chr4:98411738-98423746|chr4:98457372-98480169
Splice length:
375
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTCATCCCAACTGTGAATAACAAAGGCAAAACACCTGCCCCGAACCAGGATCAAAACACTCAAGAAAGGAAAGCTAAGAGGCACGGAACAGCTCCACCTCCAATGAAGCTGCCCCCGCCCTACAGAGCTCCATCTGCAGACATGGAGGGAAGTGAAGAAGACTGTGCGCTGACCGACAAAAAGATCAGGCAAAGATATGCAGACCTGCCGGGAGAACTACACATTATCGAACTGGAAAAGGACAAGAATGGACTGGGGCTCAGTCTCGCTGGCAATAAGGACAGGTCACGGATGAGCATCTTCGTGGTGGGGATTAATCCGGAGGGACCTGCTGCTGCAGACGGACGGATGCGGATTGGAGACGAGCTGCTAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGAGCATCTTCGTGGTGGG
60.11
GAGCTGTTCCGTGCCTCTTA
59.75
178
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATGAGCATCTTCGTGGTGGG
60.11
CTGTTCCGTGCCTCTTAGCT
59.75
175
PCR template sequence:
TAAGGACAGGTCACGGATGAGCATCTTCGTGGTGGGGATTAATCCGGAGGGACCTGCTGCTGCAGACGGACGGATGCGGATTGGAGACGAGCTGCTAGAGGTCATCCCAACTGTGAATAACAAAGGCAAAACACCTGCCCCGAACCAGGATCAAAACACTCAAGAAAGGAAAGCTAAGAGGCACGGAACAGCTCCACCTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-1199-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CGAGCTGCTAGAGGTCATCCCAACTG
siRNA sets
TTGGGATGACCTCTAGCAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPATJ_375_1_ORF_1
0.9838
0.387692179
0.944283019
648
ORF sequence:
ATGAAGCTGCCCCCGCCCTACAGAGCTCCATCTGCAGACATGGAGGGAAGTGAAGAAGACTGTGCGCTGACCGACAAAAAGATCAGGCAAAGATATGCAGACCTGCCGGGAGAACTACACATTATCGAACTGGAAAAGGACAAGAATGGACTGGGGCTCAGTCTCGCTGGCAATAAGGACAGGTCACGGATGAGCATCTTCGTGGTGGGGATTAATCCGGAGGGACCTGCTGCTGCAGACGGACGGATGCGGATTGGAGACGAGCTGCTAGAGGTCATCCCAACTGTGAATAACAAAGGCAAAACACCTGCCCCGAACCAGGATCAAAACACTCAAGAAAGGAAAGCTAAGAGGCACGGAACAGCTCCACCTCCAATGAAGCTGCCCCCGCCCTACAGAGCTCCATCTGCAGACATGGAGGGAAGTGAAGAAGACTGTGCGCTGACCGACAAAAAGATCAGGCAAAGATATGCAGACCTGCCGGGAGAACTACACATTATCGAACTGGAAAAGGACAAGAATGGACTGGGGCTCAGTCTCGCTGGCAATAAGGACAGGTCACGGATGAGCATCTTCGTGGTGGGGATTAATCCGGAGGGACCTGCTGCTGCAGACGGACGGATGCGGATTGGAGACGAGCTGCTAGAG
Peptide sequence:
MKLPPPYRAPSADMEGSEEDCALTDKKIRQRYADLPGELHIIELEKDKNGLGLSLAGNKDRSRMSIFVVGINPEGPAAADGRMRIGDELLEVIPTVNNKGKTPAPNQDQNTQERKAKRHGTAPPPMKLPPPYRAPSADMEGSEEDCALTDKKIRQRYADLPGELHIIELEKDKNGLGLSLAGNKDRSRMSIFVVGINPEGPAAADGRMRIGDELLE
IRESfinder result
IRESfinder score
0.241399629
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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