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mmu_circPpp6r3_1211
Basic information of circular RNA
PanCircBase ID:
mmu_circPpp6r3_1211
mm39_Chr. Position ID:
chr19|3520970|3562041|-
Gene name:
Ppp6r3
Transcript:
ENSMUST00000025846.16
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
17,16,15,14,13,12,11,10,9,8,7
Exon/intron offsets:
0,1008,2798,13860,16005,19803,21395,22915,25551,36271,40958
Genomic length:
41071
Exon/intron sizes in nt:
13,15,59,88,61,16,65,10,00,00,00,00,00,000
Flanking exon/introns:
chr19:3519762-3520970|chr19:3562041-3564653
Splice length:
1211
Other database IDs:
CIRCpedia: MMU_CIRCpedia_223546, circAtlas: mmu-Ppp6r3_0050
Human Ortholog IDs:
Mature spliced Sequence:
CGGCATTCAAATGCCTCACAATCACTTTGTGAAATTGTTCGCCTGAGCAGAGACCAGATGTTACAAGTTCAGAACAGTACAGAGCCAGACCCCCTGCTTGCCACTCTAGAAAAGCAAGAAATTATTGAGCAGCTTCTGTCAAATATTTTTCACAAGGAGAAGAATGAATCGGCCATAGTCAGTGCAATTCAGATTTTGCTGACTTTGCTTGAGACTCGACGGCCAACGTTTGAAGGCCATATAGAAATCTGCCCCCCGGGCATGAGTCATTCAGCTTGTTCAGTTAACAAGAGTGTTCTTGAAGCCATCCGAGGAAGACTTGGATCTTTCCATGAACTCCTACTCGAGCCACCCAAGAAAAGTGTGATGAAGACTACATGGGGTATATTGGACCCACCTGTGGGGAATACTCGATTAAATGTCATTAGGTTGATATCCAGCCTGCTCCAAACCAATACCAGCAGCATAAATGGAGACCTGATGGAACTGAACAGCATTGGCGTCATATTGGATATGTTCTTCAAGTACACATGGAATAACTTTCTACACACGCAAGTGGAAATTTGCATTGCTCTCATTCTGGCCAGTCCTTTTGAGAATGCAGAGAATGGCACAATTACTGATCAAGACTCCACTGGTGACAATTTGTTATTGAAGCATCTTTTTCAAAAGTGTCAGTTAATAGAGCGAATACTTGAAGCCTGGGACACAAATGAGAAGAAACAGGCTGAAGGAGGACGACGGCATGGTTACATGGGACACCTTACGAGGATAGCTAACTGTATTGTGCACAGCACTGACAAGGGTCCGAACAGTGCGTTAGTACAGCAGCTCATCAAAGATCTTCCCGATGAAGTCAGGGAGCGGTGGGAGACGTTCTGCACGAACTCCTTAGGAGAGACGAACAAGAGGAACACGGTAGATCTAGCCTTTTCTGATTATCAGATGCAACAAATGACGTCCAATTTTATTGACCAGTTTGGCTTCAACGATGAGAAGTTTGCAGACCAAGACGACATTGGCAATGTTTCTTTTGATCGGGTGTCAGATATCAACTTTACTCTCAATACAAATGAAAGTGGAAATATTGCCCTGTTTGAAGCATGTTGTAAAGAACGGATACAACAATTTGATGATGGCGGCTCTGATGAAGAGGATATCTGGGAGGAGAAGCACATTGCATTTACTCCCGAATCCCAGAGGAGGTCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GATGATGGCGGCTCTGATGA
59.97
CATCTGGTCTCTGCTCAGGC
60.18
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGATGATGGCGGCTCTGATG
60.25
CATCTGGTCTCTGCTCAGGC
60.18
141
PCR template sequence:
AAGAACGGATACAACAATTTGATGATGGCGGCTCTGATGAAGAGGATATCTGGGAGGAGAAGCACATTGCATTTACTCCCGAATCCCAGAGGAGGTCCAGCGGCATTCAAATGCCTCACAATCACTTTGTGAAATTGTTCGCCTGAGCAGAGACCAGATGTTACAAGTTCAGAACAGTACAGAGCCAGACCCCCTGCTTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-32-5p(1), mmu-miR-375-3p(1), mmu-miR-92a-3p(1), mmu-miR-25-3p(1), mmu-miR-138-5p(1), mmu-miR-149-5p(1), mmu-miR-136-5p(1), mmu-miR-690(1), mmu-miR-802-5p(1), mmu-miR-207(1), mmu-miR-670-5p(1), mmu-miR-544-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAGGAGGTCCAGCGGCATTCAAATG
siRNA sets
TTTGAATGCCGCTGGACCT, TTGAATGCCGCTGGACCTC, CATTTGAATGCCGCTGGAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPPP6R3_1211_ORF_1
0.9966
0.159256427
0.997169119
1200
ORF sequence:
ATGTTACAAGTTCAGAACAGTACAGAGCCAGACCCCCTGCTTGCCACTCTAGAAAAGCAAGAAATTATTGAGCAGCTTCTGTCAAATATTTTTCACAAGGAGAAGAATGAATCGGCCATAGTCAGTGCAATTCAGATTTTGCTGACTTTGCTTGAGACTCGACGGCCAACGTTTGAAGGCCATATAGAAATCTGCCCCCCGGGCATGAGTCATTCAGCTTGTTCAGTTAACAAGAGTGTTCTTGAAGCCATCCGAGGAAGACTTGGATCTTTCCATGAACTCCTACTCGAGCCACCCAAGAAAAGTGTGATGAAGACTACATGGGGTATATTGGACCCACCTGTGGGGAATACTCGATTAAATGTCATTAGGTTGATATCCAGCCTGCTCCAAACCAATACCAGCAGCATAAATGGAGACCTGATGGAACTGAACAGCATTGGCGTCATATTGGATATGTTCTTCAAGTACACATGGAATAACTTTCTACACACGCAAGTGGAAATTTGCATTGCTCTCATTCTGGCCAGTCCTTTTGAGAATGCAGAGAATGGCACAATTACTGATCAAGACTCCACTGGTGACAATTTGTTATTGAAGCATCTTTTTCAAAAGTGTCAGTTAATAGAGCGAATACTTGAAGCCTGGGACACAAATGAGAAGAAACAGGCTGAAGGAGGACGACGGCATGGTTACATGGGACACCTTACGAGGATAGCTAACTGTATTGTGCACAGCACTGACAAGGGTCCGAACAGTGCGTTAGTACAGCAGCTCATCAAAGATCTTCCCGATGAAGTCAGGGAGCGGTGGGAGACGTTCTGCACGAACTCCTTAGGAGAGACGAACAAGAGGAACACGGTAGATCTAGCCTTTTCTGATTATCAGATGCAACAAATGACGTCCAATTTTATTGACCAGTTTGGCTTCAACGATGAGAAGTTTGCAGACCAAGACGACATTGGCAATGTTTCTTTTGATCGGGTGTCAGATATCAACTTTACTCTCAATACAAATGAAAGTGGAAATATTGCCCTGTTTGAAGCATGTTGTAAAGAACGGATACAACAATTTGATGATGGCGGCTCTGATGAAGAGGATATCTGGGAGGAGAAGCACATTGCATTTACTCCCGAATCCCAGAGGAGGTCCAGCGGCATTCAAATGCCTCACAATCACTTTGTGAAATTGTTCGCCTGA
Peptide sequence:
MLQVQNSTEPDPLLATLEKQEIIEQLLSNIFHKEKNESAIVSAIQILLTLLETRRPTFEGHIEICPPGMSHSACSVNKSVLEAIRGRLGSFHELLLEPPKKSVMKTTWGILDPPVGNTRLNVIRLISSLLQTNTSSINGDLMELNSIGVILDMFFKYTWNNFLHTQVEICIALILASPFENAENGTITDQDSTGDNLLLKHLFQKCQLIERILEAWDTNEKKQAEGGRRHGYMGHLTRIANCIVHSTDKGPNSALVQQLIKDLPDEVRERWETFCTNSLGETNKRNTVDLAFSDYQMQQMTSNFIDQFGFNDEKFADQDDIGNVSFDRVSDINFTLNTNESGNIALFEACCKERIQQFDDGGSDEEDIWEEKHIAFTPESQRRSSGIQMPHNHFVKLFA
IRESfinder result
IRESfinder score
0.638759241
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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