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mmu_circPtpn13_549
Basic information of circular RNA
PanCircBase ID:
mmu_circPtpn13_549
mm39_Chr. Position ID:
chr5|103673619|103676768|+
Gene name:
Ptpn13
Transcript:
ENSMUST00000199412.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
11,12,13,14
Exon/intron offsets:
0,180,1242,3010
Genomic length:
3149
Exon/intron sizes in nt:
75,18,11,54,139
Flanking exon/introns:
chr5:103671655-103673619|chr5:103676768-103677513
Splice length:
549
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AATTTCTTTGGACCTGAGTTTGTGAAGATGACGGTTGAGCCATTTGTATCTTTGGATTTGCCACGGTCTATCCTCTCGCAGACCAAGAAGGGGAAGAGTGAGGACCAGCGGCGGAAAGTGAACATAAGGCTCCTGAGCGGGCAGCGGCTGGAGCTCACCTGCGACACCAAGACCATCTGCAAGGATGTGTTCGACATGGTGGTGGCGCACATCGGCTTGGTGGAGCACCATTTGTTTGCTCTCGCCACCCGCAAAGAGAATGAATATTTCTTTGTTGATCCTGACTTAAAATTAACCAAAGTGGCCCCGGAGGGGTGGAAGGAAGAACCGAAGAGAAAGGGCAAGGCCGCCGTTGACTTTACGTTGTTTTTCCGAATTAAATTTTTCATGGATGATGTTAGTCTGATACAACATGACCTCACGTGCCATCAGTATTACCTTCAGCTGAGGAAAGACCTTCTGGATGAGAGGGTGCACTGTGACGACGAGGCCGCCCTGCTTCTTGCATCCTTGGCTCTCCAGGCAGAGTATGGAGATTATCAGCCAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTTGCATCCTTGGCTCTCCA
60.03
CCCTTCTTGGTCTGCGAGAG
60.11
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGGATGAGAGGGTGCACTG
60.11
TCTGCGAGAGGATAGACCGT
59.82
172
PCR template sequence:
GAAAGACCTTCTGGATGAGAGGGTGCACTGTGACGACGAGGCCGCCCTGCTTCTTGCATCCTTGGCTCTCCAGGCAGAGTATGGAGATTATCAGCCAGAGAATTTCTTTGGACCTGAGTTTGTGAAGATGACGGTTGAGCCATTTGTATCTTTGGATTTGCCACGGTCTATCCTCTCGCAGACCAAGAAGGGGAAGAGTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-200b-3p(1), mmu-miR-128-3p(1), mmu-miR-362-5p(1), mmu-miR-300-3p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTATCAGCCAGAGAATTTCTTTGGAC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTPN13_549_ORF_1
1.1731
0.331621989
0.997520763
1071
ORF sequence:
ATGACGGTTGAGCCATTTGTATCTTTGGATTTGCCACGGTCTATCCTCTCGCAGACCAAGAAGGGGAAGAGTGAGGACCAGCGGCGGAAAGTGAACATAAGGCTCCTGAGCGGGCAGCGGCTGGAGCTCACCTGCGACACCAAGACCATCTGCAAGGATGTGTTCGACATGGTGGTGGCGCACATCGGCTTGGTGGAGCACCATTTGTTTGCTCTCGCCACCCGCAAAGAGAATGAATATTTCTTTGTTGATCCTGACTTAAAATTAACCAAAGTGGCCCCGGAGGGGTGGAAGGAAGAACCGAAGAGAAAGGGCAAGGCCGCCGTTGACTTTACGTTGTTTTTCCGAATTAAATTTTTCATGGATGATGTTAGTCTGATACAACATGACCTCACGTGCCATCAGTATTACCTTCAGCTGAGGAAAGACCTTCTGGATGAGAGGGTGCACTGTGACGACGAGGCCGCCCTGCTTCTTGCATCCTTGGCTCTCCAGGCAGAGTATGGAGATTATCAGCCAGAGAATTTCTTTGGACCTGAGTTTGTGAAGATGACGGTTGAGCCATTTGTATCTTTGGATTTGCCACGGTCTATCCTCTCGCAGACCAAGAAGGGGAAGAGTGAGGACCAGCGGCGGAAAGTGAACATAAGGCTCCTGAGCGGGCAGCGGCTGGAGCTCACCTGCGACACCAAGACCATCTGCAAGGATGTGTTCGACATGGTGGTGGCGCACATCGGCTTGGTGGAGCACCATTTGTTTGCTCTCGCCACCCGCAAAGAGAATGAATATTTCTTTGTTGATCCTGACTTAAAATTAACCAAAGTGGCCCCGGAGGGGTGGAAGGAAGAACCGAAGAGAAAGGGCAAGGCCGCCGTTGACTTTACGTTGTTTTTCCGAATTAAATTTTTCATGGATGATGTTAGTCTGATACAACATGACCTCACGTGCCATCAGTATTACCTTCAGCTGAGGAAAGACCTTCTGGATGAGAGGGTGCACTGTGACGACGAGGCCGCCCTGCTTCTTGCATCCTTGGCTCTCCAGGCAGAGTATGGAGATTATCAGCCAGAG
Peptide sequence:
MTVEPFVSLDLPRSILSQTKKGKSEDQRRKVNIRLLSGQRLELTCDTKTICKDVFDMVVAHIGLVEHHLFALATRKENEYFFVDPDLKLTKVAPEGWKEEPKRKGKAAVDFTLFFRIKFFMDDVSLIQHDLTCHQYYLQLRKDLLDERVHCDDEAALLLASLALQAEYGDYQPENFFGPEFVKMTVEPFVSLDLPRSILSQTKKGKSEDQRRKVNIRLLSGQRLELTCDTKTICKDVFDMVVAHIGLVEHHLFALATRKENEYFFVDPDLKLTKVAPEGWKEEPKRKGKAAVDFTLFFRIKFFMDDVSLIQHDLTCHQYYLQLRKDLLDERVHCDDEAALLLASLALQAEYGDYQPE
IRESfinder result
IRESfinder score
0.483981863
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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