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mmu_circPtpn2_498
Basic information of circular RNA
PanCircBase ID:
mmu_circPtpn2_498
mm39_Chr. Position ID:
chr18|67810779|67814647|-
Gene name:
Ptpn2
Transcript:
ENSMUST00000120934.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
7,6,5
Exon/intron offsets:
0,3130,3733
Genomic length:
3868
Exon/intron sizes in nt:
15,32,10,135
Flanking exon/introns:
chr18:67808899-67810779|chr18:67814647-67821960
Splice length:
498
Other database IDs:
circAtlas: mmu-Ptpn2_0005
circAtlas: hsa-PTPN2_0008, CIRCpedia: HSA_CIRCpedia_178730
Human Ortholog IDs:
Mature spliced Sequence:
GTTAAATGTGCACAGTACTGGCCAACGGATGACAGAGAAATGGTGTTTAAGGAAACGGGATTCAGTGTGAAGCTCTTATCTGAAGATGTAAAATCATATTATACAGTACATCTACTACAGTTAGAAAATATCAATACTGGTGAAACCAGAACCATATCTCACTTCCATTATACCACCTGGCCAGATTTTGGGGTTCCAGAGTCACCAGCTTCATTTCTAAACTTCTTGTTTAAAGTTAGAGAATCTGGTTGTTTGACCCCTGACCATGGACCTGCAGTGATCCATTGCAGTGCGGGCATCGGGCGCTCTGGCACCTTCTCTCTTGTAGATACCTGTCTTGTTCTGATGGAAAAAGGAGAGGATGTTAATGTGAAACAATTATTACTGAATATGAGAAAGTATCGAATGGGACTTATTCAGACACCGGACCAACTCAGATTCTCCTACATGGCCATAATAGAAGGAGCAAAGTACACAAAAGGAGATTCAAATATACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGACACCGGACCAACTCAG
60.32
AGCTTCACACTGAATCCCGT
59.31
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCAGACACCGGACCAACTC
59.61
AGCTTCACACTGAATCCCGT
59.31
157
PCR template sequence:
GTATCGAATGGGACTTATTCAGACACCGGACCAACTCAGATTCTCCTACATGGCCATAATAGAAGGAGCAAAGTACACAAAAGGAGATTCAAATATACAGGTTAAATGTGCACAGTACTGGCCAACGGATGACAGAGAAATGGTGTTTAAGGAAACGGGATTCAGTGTGAAGCTCTTATCTGAAGATGTAAAATCATATT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-18a-5p(1), mmu-miR-138-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-127-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-697(1), mmu-miR-339-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTCAAATATACAGGTTAAATGTGCAC
siRNA sets
ATTTAACCTGTATATTTGA,TTTAACCTGTATATTTGAA,CATTTAACCTGTATATTTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTPN2_498_ORF_1
0.7378
-0.033013858
0.946681752
957
ORF sequence:
ATGGTGTTTAAGGAAACGGGATTCAGTGTGAAGCTCTTATCTGAAGATGTAAAATCATATTATACAGTACATCTACTACAGTTAGAAAATATCAATACTGGTGAAACCAGAACCATATCTCACTTCCATTATACCACCTGGCCAGATTTTGGGGTTCCAGAGTCACCAGCTTCATTTCTAAACTTCTTGTTTAAAGTTAGAGAATCTGGTTGTTTGACCCCTGACCATGGACCTGCAGTGATCCATTGCAGTGCGGGCATCGGGCGCTCTGGCACCTTCTCTCTTGTAGATACCTGTCTTGTTCTGATGGAAAAAGGAGAGGATGTTAATGTGAAACAATTATTACTGAATATGAGAAAGTATCGAATGGGACTTATTCAGACACCGGACCAACTCAGATTCTCCTACATGGCCATAATAGAAGGAGCAAAGTACACAAAAGGAGATTCAAATATACAGGTTAAATGTGCACAGTACTGGCCAACGGATGACAGAGAAATGGTGTTTAAGGAAACGGGATTCAGTGTGAAGCTCTTATCTGAAGATGTAAAATCATATTATACAGTACATCTACTACAGTTAGAAAATATCAATACTGGTGAAACCAGAACCATATCTCACTTCCATTATACCACCTGGCCAGATTTTGGGGTTCCAGAGTCACCAGCTTCATTTCTAAACTTCTTGTTTAAAGTTAGAGAATCTGGTTGTTTGACCCCTGACCATGGACCTGCAGTGATCCATTGCAGTGCGGGCATCGGGCGCTCTGGCACCTTCTCTCTTGTAGATACCTGTCTTGTTCTGATGGAAAAAGGAGAGGATGTTAATGTGAAACAATTATTACTGAATATGAGAAAGTATCGAATGGGACTTATTCAGACACCGGACCAACTCAGATTCTCCTACATGGCCATAATAGAAGGAGCAAAGTACACAAAAGGAGATTCAAATATACAG
Peptide sequence:
MVFKETGFSVKLLSEDVKSYYTVHLLQLENINTGETRTISHFHYTTWPDFGVPESPASFLNFLFKVRESGCLTPDHGPAVIHCSAGIGRSGTFSLVDTCLVLMEKGEDVNVKQLLLNMRKYRMGLIQTPDQLRFSYMAIIEGAKYTKGDSNIQVKCAQYWPTDDREMVFKETGFSVKLLSEDVKSYYTVHLLQLENINTGETRTISHFHYTTWPDFGVPESPASFLNFLFKVRESGCLTPDHGPAVIHCSAGIGRSGTFSLVDTCLVLMEKGEDVNVKQLLLNMRKYRMGLIQTPDQLRFSYMAIIEGAKYTKGDSNIQ
IRESfinder result
IRESfinder score
0.720815257
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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