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mmu_circPtpn12_1897
Basic information of circular RNA
PanCircBase ID:
mmu_circPtpn12_1897
mm39_Chr. Position ID:
chr5|21202780|21234882|-
Gene name:
Ptpn12
Transcript:
ENSMUST00000030556.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
13,12,11,10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,3489,4640,4834,7566,11659,13902,16911,17928,21430,24235,31993
Genomic length:
32102
Exon/intron sizes in nt:
97,48,69,67,86,71,43,60,00,00,00,00,000
Flanking exon/introns:
chr5:21198296-21202780|chr5:21234882-21260646
Splice length:
1897
Other database IDs:
circAtlas: mmu-Ptpn12_0010
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_118209
Human Ortholog IDs:
Mature spliced Sequence:
CGATTGAGAAGATTGTCTACCAAATATAGAACAGAAAAGATTTATCCCACAGCCACTGGAGAAAAAGAAGAAAATGTTAAAAAGAACAGATATAAGGACATACTGCCATTTGATCACAGCCGAGTTAAGTTGACTTTGAAGACTCCATCCCAAGATTCAGATTATATCAATGCAAATTTTATTAAGGGTGTGTATGGGCCAAAAGCATATGTGGCAACCCAAGGGCCTTTGGCGAATACAGTCATAGACTTCTGGAGGATGATATGGGAGTATAATGTTGTGATCATCGTGATGGCCTGTCGAGAATTTGAGATGGGAAGGAAAAAGTGTGAGCGCTACTGGCCTTTGTATGGAGAAGATCCTATAACATTTGCACCATTTAAAATTTCTTGTGAAAATGAACAAGCAAGAACCGACTACTTCATCCGAACACTTTTACTTGAATTTCAAAATGAATCCCGTCGGCTCTATCAGTTTCATTACGTGAACTGGCCAGACCATGATGTTCCTTCGTCATTTGATTCTATTCTGGACATGATAAGCTTAATGAGGAAATACCAAGAACATGAAGATGTGCCTATTTGTATTCATTGCAGTGCAGGCTGTGGACGAACAGGTGCTATTTGTGCCATAGATTACACGTGGAACTTACTGAAAGCAGGGAAAATTCCAGAGGAATTTAATGTATTTAATTTAATACAAGAAATGAGAACACAGAGGCACTCGGCAGTACAAACAAAGGAGCAGTATGAACTTGTTCATAGGGCTATTGCTCAACTGTTTGAAAAACAGCTACAACTGTATGAAATTCATGGAGCACAGAAGATCGCTGATGGTAATGAAATTACCACTGGAACTATGGTCAGTTCCATTGATAGCGAGAAGCAAGACTCTCCTCCGCCAAAGCCACCGCGGACTCGAAGTTGCCTTGTAGAAGGGGATGCCAAGGAAGAAATACTACAGCCACCAGAACCTCACCCGGTGCCACCCATCCTGACGCCATCACCTCCTTCAGCCTTCCCAACCGTTACCACTGTGTGGCAGGACAGTGACAGGTACCACCCAAAGCCAGTGCTGCACATGGCCTCACCAGAGCAACACCCAGCCGACCTCAACAGAAGCTATGATAAATCAGCGGACCCAATGGGGAAAAGTGAATCAGCTATTGAGCACATAGATAAGAAGTTAGAGCGCAATTTAAGTTTTGAGATTAAGAAAGTCCCTCTCCAAGAAGGGCCCAAAAGTTTTGATGGGAACACACTCTTGAATAGGGGACATGCGATTAAAATTAAATCTGCTTCATCTTCTGTAGTTGACAGAACCTCTAAACCACAGGAGTTAAGTGCAGGTGCCCTAAAGGTTGATGATGTATCTCAGAATTCTTGCGCGGACTGTAGTGCGGCTCATTCACACAGAGCTGCTGAGTCGTCAGAGGAGTCCCAGAGCAACTCACACACACCTCCACGGCCAGACTGCTTGCCTCTCGATAAGAAAGGACACGTAACGTGGTCACTTCATGGACCTGAAAATGCCACACCTGTACCCGACTCACCTGACGGCAAATCCCCAGATAATCATTCTCAGACTCTGAAAACCGTGAGTTCCACACCCAACTCCACCGCAGAAGAGGAAGCCCACGATCTTACAGAGCACCACAACAGCTCCCCTCTGTTGAAAGCTCCCCTCAGCTTTACCAACCCTCTTCACTCTGACGACTCGGACTCAGACGGAGGGAGCTCTGATGGTGCTGTGACCAGGAACAAAACTAGCATTTCAACAGCAAGTGCCACAGTGTCTCCTGCCAGTAGTGCTGAGAGTGCTTGCACTAGGAGAGTATTGCCGATGTCCATTGCCAGACAGGAAGTAGCAGGCACGCCGCATTCAGGTGCTGAGAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTGAGAGTGCTTGCACTA
59.32
TCTCCAGTGGCTGTGGGATA
59.96
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TAGTGCTGAGAGTGCTTGCA
59.32
TCTCCAGTGGCTGTGGGATA
59.96
154
PCR template sequence:
CCTGCCAGTAGTGCTGAGAGTGCTTGCACTAGGAGAGTATTGCCGATGTCCATTGCCAGACAGGAAGTAGCAGGCACGCCGCATTCAGGTGCTGAGAAAGCGATTGAGAAGATTGTCTACCAAATATAGAACAGAAAAGATTTATCCCACAGCCACTGGAGAAAAAGAAGAAAATGTTAAAAAGAACAGATATAAGGACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
20
Interacting miRNAs (#binding sites)
mmu-miR-134-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-298-5p(1), mmu-miR-320-3p(1), mmu-miR-324-5p(1), mmu-miR-326-3p(1), mmu-miR-139-5p(1), mmu-miR-128-3p(1), mmu-miR-136-5p(1), mmu-miR-433-5p(1), mmu-miR-301b-3p(1), mmu-miR-183-5p(1), mmu-miR-301a-3p(1), mmu-miR-5101(1), mmu-miR-1199-5p(1), mmu-miR-574-5p(1), mmu-miR-296-3p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGTGCTGAGAAAGCGATTGAGAAGAT
siRNA sets
CTTCTCAATCGCTTTCTCA, TTCTCAATCGCTTTCTCAG, TCTTCTCAATCGCTTTCTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTPN12_1897_ORF_1
0.9365
0.12968738
0.999873717
1668
ORF sequence:
ATGATATGGGAGTATAATGTTGTGATCATCGTGATGGCCTGTCGAGAATTTGAGATGGGAAGGAAAAAGTGTGAGCGCTACTGGCCTTTGTATGGAGAAGATCCTATAACATTTGCACCATTTAAAATTTCTTGTGAAAATGAACAAGCAAGAACCGACTACTTCATCCGAACACTTTTACTTGAATTTCAAAATGAATCCCGTCGGCTCTATCAGTTTCATTACGTGAACTGGCCAGACCATGATGTTCCTTCGTCATTTGATTCTATTCTGGACATGATAAGCTTAATGAGGAAATACCAAGAACATGAAGATGTGCCTATTTGTATTCATTGCAGTGCAGGCTGTGGACGAACAGGTGCTATTTGTGCCATAGATTACACGTGGAACTTACTGAAAGCAGGGAAAATTCCAGAGGAATTTAATGTATTTAATTTAATACAAGAAATGAGAACACAGAGGCACTCGGCAGTACAAACAAAGGAGCAGTATGAACTTGTTCATAGGGCTATTGCTCAACTGTTTGAAAAACAGCTACAACTGTATGAAATTCATGGAGCACAGAAGATCGCTGATGGTAATGAAATTACCACTGGAACTATGGTCAGTTCCATTGATAGCGAGAAGCAAGACTCTCCTCCGCCAAAGCCACCGCGGACTCGAAGTTGCCTTGTAGAAGGGGATGCCAAGGAAGAAATACTACAGCCACCAGAACCTCACCCGGTGCCACCCATCCTGACGCCATCACCTCCTTCAGCCTTCCCAACCGTTACCACTGTGTGGCAGGACAGTGACAGGTACCACCCAAAGCCAGTGCTGCACATGGCCTCACCAGAGCAACACCCAGCCGACCTCAACAGAAGCTATGATAAATCAGCGGACCCAATGGGGAAAAGTGAATCAGCTATTGAGCACATAGATAAGAAGTTAGAGCGCAATTTAAGTTTTGAGATTAAGAAAGTCCCTCTCCAAGAAGGGCCCAAAAGTTTTGATGGGAACACACTCTTGAATAGGGGACATGCGATTAAAATTAAATCTGCTTCATCTTCTGTAGTTGACAGAACCTCTAAACCACAGGAGTTAAGTGCAGGTGCCCTAAAGGTTGATGATGTATCTCAGAATTCTTGCGCGGACTGTAGTGCGGCTCATTCACACAGAGCTGCTGAGTCGTCAGAGGAGTCCCAGAGCAACTCACACACACCTCCACGGCCAGACTGCTTGCCTCTCGATAAGAAAGGACACGTAACGTGGTCACTTCATGGACCTGAAAATGCCACACCTGTACCCGACTCACCTGACGGCAAATCCCCAGATAATCATTCTCAGACTCTGAAAACCGTGAGTTCCACACCCAACTCCACCGCAGAAGAGGAAGCCCACGATCTTACAGAGCACCACAACAGCTCCCCTCTGTTGAAAGCTCCCCTCAGCTTTACCAACCCTCTTCACTCTGACGACTCGGACTCAGACGGAGGGAGCTCTGATGGTGCTGTGACCAGGAACAAAACTAGCATTTCAACAGCAAGTGCCACAGTGTCTCCTGCCAGTAGTGCTGAGAGTGCTTGCACTAGGAGAGTATTGCCGATGTCCATTGCCAGACAGGAAGTAGCAGGCACGCCGCATTCAGGTGCTGAGAAAGCGATTGAGAAGATTGTCTACCAAATATAG
Peptide sequence:
MIWEYNVVIIVMACREFEMGRKKCERYWPLYGEDPITFAPFKISCENEQARTDYFIRTLLLEFQNESRRLYQFHYVNWPDHDVPSSFDSILDMISLMRKYQEHEDVPICIHCSAGCGRTGAICAIDYTWNLLKAGKIPEEFNVFNLIQEMRTQRHSAVQTKEQYELVHRAIAQLFEKQLQLYEIHGAQKIADGNEITTGTMVSSIDSEKQDSPPPKPPRTRSCLVEGDAKEEILQPPEPHPVPPILTPSPPSAFPTVTTVWQDSDRYHPKPVLHMASPEQHPADLNRSYDKSADPMGKSESAIEHIDKKLERNLSFEIKKVPLQEGPKSFDGNTLLNRGHAIKIKSASSSVVDRTSKPQELSAGALKVDDVSQNSCADCSAAHSHRAAESSEESQSNSHTPPRPDCLPLDKKGHVTWSLHGPENATPVPDSPDGKSPDNHSQTLKTVSSTPNSTAEEEAHDLTEHHNSSPLLKAPLSFTNPLHSDDSDSDGGSSDGAVTRNKTSISTASATVSPASSAESACTRRVLPMSIARQEVAGTPHSGAEKAIEKIVYQI
IRESfinder result
IRESfinder score
0.588339465
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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