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mmu_circPtpn13_1686
Basic information of circular RNA
PanCircBase ID:
mmu_circPtpn13_1686
mm39_Chr. Position ID:
chr5|103671432|103689252|+
Gene name:
Ptpn13
Transcript:
ENSMUST00000048957.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
10,11,12,13,14,15,16,17,18
Exon/intron offsets:
0,2187,2367,3429,5197,6081,9652,13147,17405
Genomic length:
17820
Exon/intron sizes in nt:
2,23,75,18,11,54,13,91,00,00,00,00,000
Flanking exon/introns:
chr5:103665435-103671432|chr5:103689252-103689387
Splice length:
1686
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TAGACAATATGAAACATCCCTCGAAGGCAACTTGATCAATCAGGACATAATGCTAAGGCGTCAAGAGGAAGAAATGATGCAGCTGCAAGCCAGGATGGCTCTCCGACAGTCGCGGCTCAGCCTGTATCCAGGGGACACCGTCAAAGCTTCCATGCTCGACATCTCTAGAGACCCCCTAAGGGAAATGGCCCTGGAGACAGCCATGACCCAGAGGAAGCTCAGGAATTTCTTTGGACCTGAGTTTGTGAAGATGACGGTTGAGCCATTTGTATCTTTGGATTTGCCACGGTCTATCCTCTCGCAGACCAAGAAGGGGAAGAGTGAGGACCAGCGGCGGAAAGTGAACATAAGGCTCCTGAGCGGGCAGCGGCTGGAGCTCACCTGCGACACCAAGACCATCTGCAAGGATGTGTTCGACATGGTGGTGGCGCACATCGGCTTGGTGGAGCACCATTTGTTTGCTCTCGCCACCCGCAAAGAGAATGAATATTTCTTTGTTGATCCTGACTTAAAATTAACCAAAGTGGCCCCGGAGGGGTGGAAGGAAGAACCGAAGAGAAAGGGCAAGGCCGCCGTTGACTTTACGTTGTTTTTCCGAATTAAATTTTTCATGGATGATGTTAGTCTGATACAACATGACCTCACGTGCCATCAGTATTACCTTCAGCTGAGGAAAGACCTTCTGGATGAGAGGGTGCACTGTGACGACGAGGCCGCCCTGCTTCTTGCATCCTTGGCTCTCCAGGCAGAGTATGGAGATTATCAGCCAGAGGTTCATGGCGTGTCCTACTTTCGCCTGGAACATTACCTGCCCGCCAGGGTGATGGAGAAGCTGGACGTGTCCTACATTAAAGAAGAGTTACCCAAACTGCATAACACCTATGCAGGCGCTTCCGAGAAGGAGACAGAGCTAGAGTTCTTAAAGGTCTGCCAAAGGCTGACAGAGTATGGAGTTCACTTTCACCGGGTACACCCTGAGAAGAAGTCACAGACAGGGATACTGCTGGGGGTCTGTTCCAAAGGTGTGCTGGTCTTTGAGGTTCACAATGGAGTCCGTGCCTTGGTCCTTCGCTTCCCGTGGAGGGAAACAAAAAAGATTTCCTTTTCAAAGAAGAAAATCACATTACAGAACACGTCAGATGGAATCAAGCATGCGTTCCAGACGGACAGCAGCAAGGCATGCCAGTACCTGCTGCACCTGTGCTCCTCCCAGCACAAGTTCCAATTGCAGATGAGGGCGCGGCAGAGCAACCAGGATGCCCAAGACATAGAGAGAGCTTCGTTTAGGAGCCTGAACCTGCAAGCAGAGTCTGTTAGAGGATTTAATATGGGCCGCGCAATCAGCACGGGCAGTCTGGCCAGCAGCACCATCAACAAACTTGCCGTCCGACCCCTGTCAGTTCAAGCTGAGATTCTGAAGAGGCTGTCCAGCTCAGAGTGGTCGCTTTACCAGCCCCTGCAGAACAGTTCAAAAGAGAAGACTGACAAAGCTTCCTGGGAGGAAAAGCCTAGAGGGATGAGCAAATCGTATCACGATCTCAGTCAGGCCTCTCTCTGTCCTCACCGGAAACAGGTCATTAACATGGAGGCCCTCCCACAAGCCTTTGCGGAGCTGGTGGGAAAACCCTTGTACCCGATGGCAAGATCTGACACAGAGTCACTGGCAGGACTCCCAAAGCTTGATAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGGAAAACCCTTGTACCCG
59.89
TTCCTCTTGACGCCTTAGCA
59.03
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGCTGGTGGGAAAACCCTT
60.18
TTCCTCTTGACGCCTTAGCA
59.03
147
PCR template sequence:
AGGCCCTCCCACAAGCCTTTGCGGAGCTGGTGGGAAAACCCTTGTACCCGATGGCAAGATCTGACACAGAGTCACTGGCAGGACTCCCAAAGCTTGATAATAGACAATATGAAACATCCCTCGAAGGCAACTTGATCAATCAGGACATAATGCTAAGGCGTCAAGAGGAAGAAATGATGCAGCTGCAAGCCAGGATGGCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-200b-3p(1), mmu-miR-216a-5p(1), mmu-miR-326-3p(1), mmu-miR-214-3p(1), mmu-miR-128-3p(1), mmu-miR-136-5p(1), mmu-miR-362-5p(1), mmu-miR-207(1), mmu-miR-300-3p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CAAAGCTTGATAATAGACAATATGAA
siRNA sets
TATTGTCTATTATCAAGCT, TTCATATTGTCTATTATCA, ATTGTCTATTATCAAGCTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTPN13_1686_ORF_1
1.153
0.293189216
1
3321
ORF sequence:
ATGCTAAGGCGTCAAGAGGAAGAAATGATGCAGCTGCAAGCCAGGATGGCTCTCCGACAGTCGCGGCTCAGCCTGTATCCAGGGGACACCGTCAAAGCTTCCATGCTCGACATCTCTAGAGACCCCCTAAGGGAAATGGCCCTGGAGACAGCCATGACCCAGAGGAAGCTCAGGAATTTCTTTGGACCTGAGTTTGTGAAGATGACGGTTGAGCCATTTGTATCTTTGGATTTGCCACGGTCTATCCTCTCGCAGACCAAGAAGGGGAAGAGTGAGGACCAGCGGCGGAAAGTGAACATAAGGCTCCTGAGCGGGCAGCGGCTGGAGCTCACCTGCGACACCAAGACCATCTGCAAGGATGTGTTCGACATGGTGGTGGCGCACATCGGCTTGGTGGAGCACCATTTGTTTGCTCTCGCCACCCGCAAAGAGAATGAATATTTCTTTGTTGATCCTGACTTAAAATTAACCAAAGTGGCCCCGGAGGGGTGGAAGGAAGAACCGAAGAGAAAGGGCAAGGCCGCCGTTGACTTTACGTTGTTTTTCCGAATTAAATTTTTCATGGATGATGTTAGTCTGATACAACATGACCTCACGTGCCATCAGTATTACCTTCAGCTGAGGAAAGACCTTCTGGATGAGAGGGTGCACTGTGACGACGAGGCCGCCCTGCTTCTTGCATCCTTGGCTCTCCAGGCAGAGTATGGAGATTATCAGCCAGAGGTTCATGGCGTGTCCTACTTTCGCCTGGAACATTACCTGCCCGCCAGGGTGATGGAGAAGCTGGACGTGTCCTACATTAAAGAAGAGTTACCCAAACTGCATAACACCTATGCAGGCGCTTCCGAGAAGGAGACAGAGCTAGAGTTCTTAAAGGTCTGCCAAAGGCTGACAGAGTATGGAGTTCACTTTCACCGGGTACACCCTGAGAAGAAGTCACAGACAGGGATACTGCTGGGGGTCTGTTCCAAAGGTGTGCTGGTCTTTGAGGTTCACAATGGAGTCCGTGCCTTGGTCCTTCGCTTCCCGTGGAGGGAAACAAAAAAGATTTCCTTTTCAAAGAAGAAAATCACATTACAGAACACGTCAGATGGAATCAAGCATGCGTTCCAGACGGACAGCAGCAAGGCATGCCAGTACCTGCTGCACCTGTGCTCCTCCCAGCACAAGTTCCAATTGCAGATGAGGGCGCGGCAGAGCAACCAGGATGCCCAAGACATAGAGAGAGCTTCGTTTAGGAGCCTGAACCTGCAAGCAGAGTCTGTTAGAGGATTTAATATGGGCCGCGCAATCAGCACGGGCAGTCTGGCCAGCAGCACCATCAACAAACTTGCCGTCCGACCCCTGTCAGTTCAAGCTGAGATTCTGAAGAGGCTGTCCAGCTCAGAGTGGTCGCTTTACCAGCCCCTGCAGAACAGTTCAAAAGAGAAGACTGACAAAGCTTCCTGGGAGGAAAAGCCTAGAGGGATGAGCAAATCGTATCACGATCTCAGTCAGGCCTCTCTCTGTCCTCACCGGAAACAGGTCATTAACATGGAGGCCCTCCCACAAGCCTTTGCGGAGCTGGTGGGAAAACCCTTGTACCCGATGGCAAGATCTGACACAGAGTCACTGGCAGGACTCCCAAAGCTTGATAATAGACAATATGAAACATCCCTCGAAGGCAACTTGATCAATCAGGACATAATGCTAAGGCGTCAAGAGGAAGAAATGATGCAGCTGCAAGCCAGGATGGCTCTCCGACAGTCGCGGCTCAGCCTGTATCCAGGGGACACCGTCAAAGCTTCCATGCTCGACATCTCTAGAGACCCCCTAAGGGAAATGGCCCTGGAGACAGCCATGACCCAGAGGAAGCTCAGGAATTTCTTTGGACCTGAGTTTGTGAAGATGACGGTTGAGCCATTTGTATCTTTGGATTTGCCACGGTCTATCCTCTCGCAGACCAAGAAGGGGAAGAGTGAGGACCAGCGGCGGAAAGTGAACATAAGGCTCCTGAGCGGGCAGCGGCTGGAGCTCACCTGCGACACCAAGACCATCTGCAAGGATGTGTTCGACATGGTGGTGGCGCACATCGGCTTGGTGGAGCACCATTTGTTTGCTCTCGCCACCCGCAAAGAGAATGAATATTTCTTTGTTGATCCTGACTTAAAATTAACCAAAGTGGCCCCGGAGGGGTGGAAGGAAGAACCGAAGAGAAAGGGCAAGGCCGCCGTTGACTTTACGTTGTTTTTCCGAATTAAATTTTTCATGGATGATGTTAGTCTGATACAACATGACCTCACGTGCCATCAGTATTACCTTCAGCTGAGGAAAGACCTTCTGGATGAGAGGGTGCACTGTGACGACGAGGCCGCCCTGCTTCTTGCATCCTTGGCTCTCCAGGCAGAGTATGGAGATTATCAGCCAGAGGTTCATGGCGTGTCCTACTTTCGCCTGGAACATTACCTGCCCGCCAGGGTGATGGAGAAGCTGGACGTGTCCTACATTAAAGAAGAGTTACCCAAACTGCATAACACCTATGCAGGCGCTTCCGAGAAGGAGACAGAGCTAGAGTTCTTAAAGGTCTGCCAAAGGCTGACAGAGTATGGAGTTCACTTTCACCGGGTACACCCTGAGAAGAAGTCACAGACAGGGATACTGCTGGGGGTCTGTTCCAAAGGTGTGCTGGTCTTTGAGGTTCACAATGGAGTCCGTGCCTTGGTCCTTCGCTTCCCGTGGAGGGAAACAAAAAAGATTTCCTTTTCAAAGAAGAAAATCACATTACAGAACACGTCAGATGGAATCAAGCATGCGTTCCAGACGGACAGCAGCAAGGCATGCCAGTACCTGCTGCACCTGTGCTCCTCCCAGCACAAGTTCCAATTGCAGATGAGGGCGCGGCAGAGCAACCAGGATGCCCAAGACATAGAGAGAGCTTCGTTTAGGAGCCTGAACCTGCAAGCAGAGTCTGTTAGAGGATTTAATATGGGCCGCGCAATCAGCACGGGCAGTCTGGCCAGCAGCACCATCAACAAACTTGCCGTCCGACCCCTGTCAGTTCAAGCTGAGATTCTGAAGAGGCTGTCCAGCTCAGAGTGGTCGCTTTACCAGCCCCTGCAGAACAGTTCAAAAGAGAAGACTGACAAAGCTTCCTGGGAGGAAAAGCCTAGAGGGATGAGCAAATCGTATCACGATCTCAGTCAGGCCTCTCTCTGTCCTCACCGGAAACAGGTCATTAACATGGAGGCCCTCCCACAAGCCTTTGCGGAGCTGGTGGGAAAACCCTTGTACCCGATGGCAAGATCTGACACAGAGTCACTGGCAGGACTCCCAAAGCTTGAT
Peptide sequence:
MLRRQEEEMMQLQARMALRQSRLSLYPGDTVKASMLDISRDPLREMALETAMTQRKLRNFFGPEFVKMTVEPFVSLDLPRSILSQTKKGKSEDQRRKVNIRLLSGQRLELTCDTKTICKDVFDMVVAHIGLVEHHLFALATRKENEYFFVDPDLKLTKVAPEGWKEEPKRKGKAAVDFTLFFRIKFFMDDVSLIQHDLTCHQYYLQLRKDLLDERVHCDDEAALLLASLALQAEYGDYQPEVHGVSYFRLEHYLPARVMEKLDVSYIKEELPKLHNTYAGASEKETELEFLKVCQRLTEYGVHFHRVHPEKKSQTGILLGVCSKGVLVFEVHNGVRALVLRFPWRETKKISFSKKKITLQNTSDGIKHAFQTDSSKACQYLLHLCSSQHKFQLQMRARQSNQDAQDIERASFRSLNLQAESVRGFNMGRAISTGSLASSTINKLAVRPLSVQAEILKRLSSSEWSLYQPLQNSSKEKTDKASWEEKPRGMSKSYHDLSQASLCPHRKQVINMEALPQAFAELVGKPLYPMARSDTESLAGLPKLDNRQYETSLEGNLINQDIMLRRQEEEMMQLQARMALRQSRLSLYPGDTVKASMLDISRDPLREMALETAMTQRKLRNFFGPEFVKMTVEPFVSLDLPRSILSQTKKGKSEDQRRKVNIRLLSGQRLELTCDTKTICKDVFDMVVAHIGLVEHHLFALATRKENEYFFVDPDLKLTKVAPEGWKEEPKRKGKAAVDFTLFFRIKFFMDDVSLIQHDLTCHQYYLQLRKDLLDERVHCDDEAALLLASLALQAEYGDYQPEVHGVSYFRLEHYLPARVMEKLDVSYIKEELPKLHNTYAGASEKETELEFLKVCQRLTEYGVHFHRVHPEKKSQTGILLGVCSKGVLVFEVHNGVRALVLRFPWRETKKISFSKKKITLQNTSDGIKHAFQTDSSKACQYLLHLCSSQHKFQLQMRARQSNQDAQDIERASFRSLNLQAESVRGFNMGRAISTGSLASSTINKLAVRPLSVQAEILKRLSSSEWSLYQPLQNSSKEKTDKASWEEKPRGMSKSYHDLSQASLCPHRKQVINMEALPQAFAELVGKPLYPMARSDTESLAGLPKLD
IRESfinder result
IRESfinder score
0.494121902
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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