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mmu_circPtprt_558
Basic information of circular RNA
PanCircBase ID:
mmu_circPtprt_558
mm39_Chr. Position ID:
chr2|161372356|161389335|-
Gene name:
Ptprt
Transcript:
ENSMUST00000109443.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
30,29,28,27
Exon/intron offsets:
0,3044,4032,16847
Genomic length:
16979
Exon/intron sizes in nt:
1,36,16,41,26,132
Flanking exon/introns:
chr2:161371489-161372356|chr2:161389335-161393666
Splice length:
558
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AGCCACAAGCAGCCTGCCGCCTTCGTGGTCACCCAGCATCCTCTACCCAACACGGTGGCAGACTTCTGGAGGCTGGTGTTTGATTATAATTGTTCATCTGTGGTGATGCTGAACGAGATGGATACTGCTCAGCTCTGTATGCAGTACTGGCCTGAGAAGACCTCCGGGTGTTATGGTCCCATCCAGGTGGAGTTTGTCTCTGCAGACATCGATGAGGACATCATCCACAGAATCTTCCGGATCTGTAACATGGCTCGGCCACAGGATGGTTATCGTATTGTCCAGCACCTCCAGTACATCGGCTGGCCTGCATACCGGGACACGCCCCCCTCTAAGCGCTCTCTGCTCAAAGTGGTCCGACGGCTGGAGAAATGGCAGGAGCAATACGACGGAAGAGAGGGGCGCACTGTGGTCCACTGCCTAAATGGGGGAGGCCGCAGTGGAACCTTCTGTGCTATCTGCAGTGTGTGTGAGATGATCCAGCAGCAGAACATTATTGACGTGTTCCACATTGTGAAAACCCTCCGCAACAACAAGTCCAACATGGTGGAGACGCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGAGATGATCCAGCAGCA
59.09
CACCAGCCTCCAGAAGTCTG
60.04
168
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGAGATGATCCAGCAGCA
59.09
GTTGGGTAGAGGATGCTGGG
59.82
141
PCR template sequence:
CTGCAGTGTGTGTGAGATGATCCAGCAGCAGAACATTATTGACGTGTTCCACATTGTGAAAACCCTCCGCAACAACAAGTCCAACATGGTGGAGACGCTGAGCCACAAGCAGCCTGCCGCCTTCGTGGTCACCCAGCATCCTCTACCCAACACGGTGGCAGACTTCTGGAGGCTGGTGTTTGATTATAATTGTTCATCTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-217-5p(1), mmu-miR-139-5p(1), mmu-miR-128-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGTGGAGACGCTGAGCCACAAGCAGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTPRT_558_ORF_1
1.0762
0.437566377
0.997031922
1011
ORF sequence:
ATGCTGAACGAGATGGATACTGCTCAGCTCTGTATGCAGTACTGGCCTGAGAAGACCTCCGGGTGTTATGGTCCCATCCAGGTGGAGTTTGTCTCTGCAGACATCGATGAGGACATCATCCACAGAATCTTCCGGATCTGTAACATGGCTCGGCCACAGGATGGTTATCGTATTGTCCAGCACCTCCAGTACATCGGCTGGCCTGCATACCGGGACACGCCCCCCTCTAAGCGCTCTCTGCTCAAAGTGGTCCGACGGCTGGAGAAATGGCAGGAGCAATACGACGGAAGAGAGGGGCGCACTGTGGTCCACTGCCTAAATGGGGGAGGCCGCAGTGGAACCTTCTGTGCTATCTGCAGTGTGTGTGAGATGATCCAGCAGCAGAACATTATTGACGTGTTCCACATTGTGAAAACCCTCCGCAACAACAAGTCCAACATGGTGGAGACGCTGAGCCACAAGCAGCCTGCCGCCTTCGTGGTCACCCAGCATCCTCTACCCAACACGGTGGCAGACTTCTGGAGGCTGGTGTTTGATTATAATTGTTCATCTGTGGTGATGCTGAACGAGATGGATACTGCTCAGCTCTGTATGCAGTACTGGCCTGAGAAGACCTCCGGGTGTTATGGTCCCATCCAGGTGGAGTTTGTCTCTGCAGACATCGATGAGGACATCATCCACAGAATCTTCCGGATCTGTAACATGGCTCGGCCACAGGATGGTTATCGTATTGTCCAGCACCTCCAGTACATCGGCTGGCCTGCATACCGGGACACGCCCCCCTCTAAGCGCTCTCTGCTCAAAGTGGTCCGACGGCTGGAGAAATGGCAGGAGCAATACGACGGAAGAGAGGGGCGCACTGTGGTCCACTGCCTAAATGGGGGAGGCCGCAGTGGAACCTTCTGTGCTATCTGCAGTGTGTGTGAGATGATCCAGCAGCAGAACATTATTGACGTGTTCCACATTGTGAAAACCCTCCGCAACAACAAGTCCAACATGGTGGAGACGCTG
Peptide sequence:
MLNEMDTAQLCMQYWPEKTSGCYGPIQVEFVSADIDEDIIHRIFRICNMARPQDGYRIVQHLQYIGWPAYRDTPPSKRSLLKVVRRLEKWQEQYDGREGRTVVHCLNGGGRSGTFCAICSVCEMIQQQNIIDVFHIVKTLRNNKSNMVETLSHKQPAAFVVTQHPLPNTVADFWRLVFDYNCSSVVMLNEMDTAQLCMQYWPEKTSGCYGPIQVEFVSADIDEDIIHRIFRICNMARPQDGYRIVQHLQYIGWPAYRDTPPSKRSLLKVVRRLEKWQEQYDGREGRTVVHCLNGGGRSGTFCAICSVCEMIQQQNIIDVFHIVKTLRNNKSNMVETL
IRESfinder result
IRESfinder score
0.397874964
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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