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mmu_circPtpn13_3068
Basic information of circular RNA
PanCircBase ID:
mmu_circPtpn13_3068
mm39_Chr. Position ID:
chr5|103698090|103728618|+
Gene name:
Ptpn13
Transcript:
ENSMUST00000048957.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
20
Exon/intron indexes:
21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40
Exon/intron offsets:
0,524,822,4471,5863,7654,8912,9646,11707,12050,13786,14890,17801,19205,19473,22865,24854,28648,29473,30445
Genomic length:
30528
Exon/intron sizes in nt:
90,108,132,458,132,94,86,163,215,99,329,175,159,172,211,68,62,94,138,83
Flanking exon/introns:
chr5:103691330-103698090|chr5:103728618-103730604
Splice length:
3068
Other database IDs:
circAtlas: mmu-Ptpn13_0013
Human Ortholog IDs:
Mature spliced Sequence:
ATACACTGCACAAAAGATGGAGCATTGTTTCGTCACCAGAAAGGGAGATCACACTGGTGAACCTGAAGAAAGATCCAAAACACGGCTTAGGATTTCAAATTATCGGTGGGGAAAAAATGGGAAGACTGGATCTAGGAGTGTTTATCAGTGCAGTTACCCCTGGAGGACCTGCTGACCTGGATGGATGCTTAAAGCCTGGAGACCGTTTGATATCTGTGAACAGTGTGAGTCTGGAAGGGGTCAGTCACCACGCTGCAGTGGACATTCTGCAGAATGCACCTGAAGATGTGACACTTGTCATCTCCCAGCCAAAAGAAAAACCGTCCAAAGTGCCTTCTACTCCTGTTCATTTTGCCAATGGGATGAAAAGCTACACAAAGAAACCGGCATACATGCAGGACAGTGCTATGGACCCATCAGAGGACCAGCCCTGGCCACGGGGTACTCTGAGGCACATCCCAGAGAGTCCCTTCGGGCTGTCTGGGGGCCTGCGGGAGGGAAGCCTCAGTTCCCAAGATTCCAGGACTGAAAGTGCCAGCCTATCCCAGAGCCAAGTCAACGGCTTCTTTGCCAGCCACTTAGGCGACAGAGGCTGGCAGGAACCACAGCATAGCAGCCCATCGCCATCTGTGACAACCAAGGTCAACGAGAAGACCTTCTCCGACAGTAACCGAAGCAAGGCCAAGCGGCGAGGCATCTCCGATTTGATTGAACACCTCGACTGTGCTGATTCCGACAAAGACGATTCCACTTACACCAGCAGTCAAGACCATCAAACGTCAAAACAGGAACCTTCCTCCTCACTGAGTACATCGAACAAAACGAGCTTTCCAACCTCGTCTGCGTCACCTCCTAAGCCCGGAGACACGTTTGAGGTTGAGCTGGCTAAAACTGATGGCAGCCTGGGGATAAGTGTCACGGGAGGTGTGAATACCAGCGTCCGACATGGTGGTATTTATGTGAAAGCCATTATTCCCAAAGGAGCGGCAGAGTCAGATGGCAGAATTCACAAAGGTGATCGTGTGCTGGCTGTTAATGGAGTCAGTCTGGAAGGAGCTACCCACAAGCAAGCTGTGGAAACGTTAAGAAACACAGGGCAGGTGGTCCATCTGTTGTTAGAAAAGGGGCAGGTGCCAACATCTAGGGAACGGGATCCTGCAGGCCCACAGAGCCCCCCTCCAGACCAAGACGCCCAAAGACAAGCCCCGGAAAAGGTGGCGAAGCAAACACCCCATGTCAAAGACTACAGCTTTGTTACTGAAGATAATACATTTGAGGTCAAGCTGTTTAAAAATAGCTCAGGCCTTGGATTCAGTTTTTCTCGGGAAGATAATCTTATACCAGAACAAATAAATGGCAGCATAGTAAGGGTTAAAAAGCTCTTCCCTGGACAGCCGGCAGCAGAAAGTGGGAAAATCGATGTTGGAGATGTTATATTGAAAGTTAACGGAGCCCCCTTGAAGGGACTGTCTCAGCAGGACGTCATCTCTGCTCTCAGGGGAACAGCTCCAGAAGTGTCCTTGCTTCTCTGCAGACCGGCACCTGGTGTGCTACCAGAAATCGATACTACATTTTTGAACCCACTCTACTCTCCAGCAAACTCATTTCTAAACAGCAGTAAAGAGACTTCGCAGCCATCATCCTCAGTAGAGCAGGGTGCCAGCTCGGACGACAATGGGGTGTCTGGCAAAACCAAGAACCATTGCAGGGCTCCATCCAGGAGAGAGAGTTACAGCGACCACAGCGAGAGTGGAGAGGATGACTCCGTGAGAGCACCAGCCAAGATGCCAAATGTGACCCGAGTGGCAGCCTTTCCACACGAAGCACCGAGAAGCCAGGAAGAGTCCATATGTGCCATGTTTTACCTCCCTCGGAAAATACCCGGAAAGCTGGAGTCCGAGAGCAGCCATCCTCCTCCACTGGACGTGAGCCCTGGACAGACGTGCCAGCCCCCGGCAGAGTGTGCTCCGTCTGACGCCACTGGCAAACACTTTACACATCTTGCCTCTCAGCTGAGCAAAGAGGAAAACATAACAACCTTGAAAAATGACTTGGGAAACCACCTTGAGGATTCTGAGCTGGAAGTAGAGCTTCTCATTACCCTGGTTAAATCAGAAAAAGGAAGTCTGGGCTTTACAGTAACCAAAGGCAGTCAGAGTATTGGTTGTTATGTCCATGATGTCATACAGGATCCAGCCAAAGGTGACGGAAGGCTAAAGGCTGGAGACCGGCTTATAAAGGTTAATGATACAGACGTTACAAACATGACCCACACAGATGCAGTGAATCTGCTGCGAGCCGCACCCAAAACAGTCAGATTAGTTCTTGGGCGGATTCTGGAGTTACCCAGGATGCCAGTATTTCCCCATCTGCTGCCCGACATTACAGTCACATGCCACGGAGAGGAGTTAGGATTTTCCCTGTCTGGAGGTCAAGGCAGTCCACATGGAGTGGTGTATATTAGTGATATCAACCCAAGGTCAGCTGCAGCTGTTGACGGTAGTCTCCAGCTATTAGACATCATCCATTATGTGAACGGAGTCAGCACACAAGGAATGACCTTGGAAGATGCAAACAGGGCATTGGACCTGTCACTTCCTTCAGTGGTGCTGAAAGTAACAAGAGACGGTTGTCCAGTGGTGCCTACAACAAGAGCTGCCATTTCTGCGCCCAGGTTCACCAAAGCCAACGGCCTAACCAGCATGGAGCCTTCTGGACAGCCTGCACTCATGCCCAAGAACTCCTTCTCCAAGGTTAACGGGGAAGGAGTACATGAAGCTGTGTGCCCTGCAGGAGAAGGCTCGTCTTCTCAGATGAAGGAGTCAGCAGGCCTGACTGAAACCAAAGAATCTAACTCCCGGGATGATGACATCTATGATGATCCTCAAGAAGCTGAAGTTATCCAGTCCTTGCTGGATGTTGTGGACGAGGAAGCACAGAACCTCTTAAACCAGAGGCATGCCACCAGAAGAGCCTGTTCTCCAGATCCACTGAGGACGAATGGGGAGGCACCAGAAGAAGGAGATACCGACTATGATGGGTCTCCGCTACCTGAGGACGTCCCTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CACTGAGGACGAATGGGGAG
59.82
TCACCAGTGTGATCTCCCTT
57.97
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCCTGTTCTCCAGATCCACT
59.09
TCCCTTTCTGGTGACGAAACA
59.51
142
PCR template sequence:
AAGAGCCTGTTCTCCAGATCCACTGAGGACGAATGGGGAGGCACCAGAAGAAGGAGATACCGACTATGATGGGTCTCCGCTACCTGAGGACGTCCCTGAGATACACTGCACAAAAGATGGAGCATTGTTTCGTCACCAGAAAGGGAGATCACACTGGTGAACCTGAAGAAAGATCCAAAACACGGCTTAGGATTTCAAAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
25
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-429-3p(1), mmu-miR-375-3p(1), mmu-miR-200b-3p(1), mmu-miR-135a-5p(1), mmu-miR-31-5p(1), mmu-miR-200c-3p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-326-3p(1), mmu-miR-143-3p(1), mmu-miR-138-5p(1), mmu-miR-30b-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-96-5p(1), mmu-miR-370-3p(1), mmu-miR-183-5p(1), mmu-miR-27a-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-802-5p(1), mmu-miR-1187(1), mmu-miR-344d-3p(1), mmu-miR-207(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
GGACGTCCCTGAGATACACTGCACAA
siRNA sets
TTGTGCAGTGTATCTCAGG, TGTGCAGTGTATCTCAGGG, GTGCAGTGTATCTCAGGGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTPN13_3068_ORF_1
1.003
0.202015669
0.999999995
3012
ORF sequence:
ATGGGAAGACTGGATCTAGGAGTGTTTATCAGTGCAGTTACCCCTGGAGGACCTGCTGACCTGGATGGATGCTTAAAGCCTGGAGACCGTTTGATATCTGTGAACAGTGTGAGTCTGGAAGGGGTCAGTCACCACGCTGCAGTGGACATTCTGCAGAATGCACCTGAAGATGTGACACTTGTCATCTCCCAGCCAAAAGAAAAACCGTCCAAAGTGCCTTCTACTCCTGTTCATTTTGCCAATGGGATGAAAAGCTACACAAAGAAACCGGCATACATGCAGGACAGTGCTATGGACCCATCAGAGGACCAGCCCTGGCCACGGGGTACTCTGAGGCACATCCCAGAGAGTCCCTTCGGGCTGTCTGGGGGCCTGCGGGAGGGAAGCCTCAGTTCCCAAGATTCCAGGACTGAAAGTGCCAGCCTATCCCAGAGCCAAGTCAACGGCTTCTTTGCCAGCCACTTAGGCGACAGAGGCTGGCAGGAACCACAGCATAGCAGCCCATCGCCATCTGTGACAACCAAGGTCAACGAGAAGACCTTCTCCGACAGTAACCGAAGCAAGGCCAAGCGGCGAGGCATCTCCGATTTGATTGAACACCTCGACTGTGCTGATTCCGACAAAGACGATTCCACTTACACCAGCAGTCAAGACCATCAAACGTCAAAACAGGAACCTTCCTCCTCACTGAGTACATCGAACAAAACGAGCTTTCCAACCTCGTCTGCGTCACCTCCTAAGCCCGGAGACACGTTTGAGGTTGAGCTGGCTAAAACTGATGGCAGCCTGGGGATAAGTGTCACGGGAGGTGTGAATACCAGCGTCCGACATGGTGGTATTTATGTGAAAGCCATTATTCCCAAAGGAGCGGCAGAGTCAGATGGCAGAATTCACAAAGGTGATCGTGTGCTGGCTGTTAATGGAGTCAGTCTGGAAGGAGCTACCCACAAGCAAGCTGTGGAAACGTTAAGAAACACAGGGCAGGTGGTCCATCTGTTGTTAGAAAAGGGGCAGGTGCCAACATCTAGGGAACGGGATCCTGCAGGCCCACAGAGCCCCCCTCCAGACCAAGACGCCCAAAGACAAGCCCCGGAAAAGGTGGCGAAGCAAACACCCCATGTCAAAGACTACAGCTTTGTTACTGAAGATAATACATTTGAGGTCAAGCTGTTTAAAAATAGCTCAGGCCTTGGATTCAGTTTTTCTCGGGAAGATAATCTTATACCAGAACAAATAAATGGCAGCATAGTAAGGGTTAAAAAGCTCTTCCCTGGACAGCCGGCAGCAGAAAGTGGGAAAATCGATGTTGGAGATGTTATATTGAAAGTTAACGGAGCCCCCTTGAAGGGACTGTCTCAGCAGGACGTCATCTCTGCTCTCAGGGGAACAGCTCCAGAAGTGTCCTTGCTTCTCTGCAGACCGGCACCTGGTGTGCTACCAGAAATCGATACTACATTTTTGAACCCACTCTACTCTCCAGCAAACTCATTTCTAAACAGCAGTAAAGAGACTTCGCAGCCATCATCCTCAGTAGAGCAGGGTGCCAGCTCGGACGACAATGGGGTGTCTGGCAAAACCAAGAACCATTGCAGGGCTCCATCCAGGAGAGAGAGTTACAGCGACCACAGCGAGAGTGGAGAGGATGACTCCGTGAGAGCACCAGCCAAGATGCCAAATGTGACCCGAGTGGCAGCCTTTCCACACGAAGCACCGAGAAGCCAGGAAGAGTCCATATGTGCCATGTTTTACCTCCCTCGGAAAATACCCGGAAAGCTGGAGTCCGAGAGCAGCCATCCTCCTCCACTGGACGTGAGCCCTGGACAGACGTGCCAGCCCCCGGCAGAGTGTGCTCCGTCTGACGCCACTGGCAAACACTTTACACATCTTGCCTCTCAGCTGAGCAAAGAGGAAAACATAACAACCTTGAAAAATGACTTGGGAAACCACCTTGAGGATTCTGAGCTGGAAGTAGAGCTTCTCATTACCCTGGTTAAATCAGAAAAAGGAAGTCTGGGCTTTACAGTAACCAAAGGCAGTCAGAGTATTGGTTGTTATGTCCATGATGTCATACAGGATCCAGCCAAAGGTGACGGAAGGCTAAAGGCTGGAGACCGGCTTATAAAGGTTAATGATACAGACGTTACAAACATGACCCACACAGATGCAGTGAATCTGCTGCGAGCCGCACCCAAAACAGTCAGATTAGTTCTTGGGCGGATTCTGGAGTTACCCAGGATGCCAGTATTTCCCCATCTGCTGCCCGACATTACAGTCACATGCCACGGAGAGGAGTTAGGATTTTCCCTGTCTGGAGGTCAAGGCAGTCCACATGGAGTGGTGTATATTAGTGATATCAACCCAAGGTCAGCTGCAGCTGTTGACGGTAGTCTCCAGCTATTAGACATCATCCATTATGTGAACGGAGTCAGCACACAAGGAATGACCTTGGAAGATGCAAACAGGGCATTGGACCTGTCACTTCCTTCAGTGGTGCTGAAAGTAACAAGAGACGGTTGTCCAGTGGTGCCTACAACAAGAGCTGCCATTTCTGCGCCCAGGTTCACCAAAGCCAACGGCCTAACCAGCATGGAGCCTTCTGGACAGCCTGCACTCATGCCCAAGAACTCCTTCTCCAAGGTTAACGGGGAAGGAGTACATGAAGCTGTGTGCCCTGCAGGAGAAGGCTCGTCTTCTCAGATGAAGGAGTCAGCAGGCCTGACTGAAACCAAAGAATCTAACTCCCGGGATGATGACATCTATGATGATCCTCAAGAAGCTGAAGTTATCCAGTCCTTGCTGGATGTTGTGGACGAGGAAGCACAGAACCTCTTAAACCAGAGGCATGCCACCAGAAGAGCCTGTTCTCCAGATCCACTGAGGACGAATGGGGAGGCACCAGAAGAAGGAGATACCGACTATGATGGGTCTCCGCTACCTGAGGACGTCCCTGAGATACACTGCACAAAAGATGGAGCATTGTTTCGTCACCAGAAAGGGAGATCACACTGGTGA
Peptide sequence:
MGRLDLGVFISAVTPGGPADLDGCLKPGDRLISVNSVSLEGVSHHAAVDILQNAPEDVTLVISQPKEKPSKVPSTPVHFANGMKSYTKKPAYMQDSAMDPSEDQPWPRGTLRHIPESPFGLSGGLREGSLSSQDSRTESASLSQSQVNGFFASHLGDRGWQEPQHSSPSPSVTTKVNEKTFSDSNRSKAKRRGISDLIEHLDCADSDKDDSTYTSSQDHQTSKQEPSSSLSTSNKTSFPTSSASPPKPGDTFEVELAKTDGSLGISVTGGVNTSVRHGGIYVKAIIPKGAAESDGRIHKGDRVLAVNGVSLEGATHKQAVETLRNTGQVVHLLLEKGQVPTSRERDPAGPQSPPPDQDAQRQAPEKVAKQTPHVKDYSFVTEDNTFEVKLFKNSSGLGFSFSREDNLIPEQINGSIVRVKKLFPGQPAAESGKIDVGDVILKVNGAPLKGLSQQDVISALRGTAPEVSLLLCRPAPGVLPEIDTTFLNPLYSPANSFLNSSKETSQPSSSVEQGASSDDNGVSGKTKNHCRAPSRRESYSDHSESGEDDSVRAPAKMPNVTRVAAFPHEAPRSQEESICAMFYLPRKIPGKLESESSHPPPLDVSPGQTCQPPAECAPSDATGKHFTHLASQLSKEENITTLKNDLGNHLEDSELEVELLITLVKSEKGSLGFTVTKGSQSIGCYVHDVIQDPAKGDGRLKAGDRLIKVNDTDVTNMTHTDAVNLLRAAPKTVRLVLGRILELPRMPVFPHLLPDITVTCHGEELGFSLSGGQGSPHGVVYISDINPRSAAAVDGSLQLLDIIHYVNGVSTQGMTLEDANRALDLSLPSVVLKVTRDGCPVVPTTRAAISAPRFTKANGLTSMEPSGQPALMPKNSFSKVNGEGVHEAVCPAGEGSSSQMKESAGLTETKESNSRDDDIYDDPQEAEVIQSLLDVVDEEAQNLLNQRHATRRACSPDPLRTNGEAPEEGDTDYDGSPLPEDVPEIHCTKDGALFRHQKGRSHW
IRESfinder result
IRESfinder score
0.431389111
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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