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mmu_circPtcd3_660
Basic information of circular RNA
PanCircBase ID:
mmu_circPtcd3_660
mm39_Chr. Position ID:
chr6|71865540|71872976|-
Gene name:
Ptcd3
Transcript:
ENSMUST00000082094.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
17,16,15,14,13,12,11,10
Exon/intron offsets:
0,784,1037,3912,4825,5730,6264,7348
Genomic length:
7436
Exon/intron sizes in nt:
107,29,93,51,145,86,61,88
Flanking exon/introns:
chr6:71862560-71865540|chr6:71872976-71874096
Splice length:
660
Other database IDs:
CIRCpedia: MMU_CIRCpedia_37149, circAtlas: mmu-Ptcd3_0023
circAtlas: hsa-PTCD3_0041
Human Ortholog IDs:
Mature spliced Sequence:
AGCACAAAACAATGCTGAGAGGATCTTCGCTTTAATGCCAGAGAAGAATGCACGCTCCTACTGCACGATGATCCGAGGGATGGTGAAGCACCGAGCTTATGCACAGGCACTGAACGTGTACACAGAGTTATTAAATAACAGACTTAGTGCTGATGTATATACCTTTAATGCATTGATTGAAGCAAAAACATTCATACTCAATGAGAAATTTGAGGAAAAATGGAATGATATACTGGATCTACTGAAACATATGGTTGCACAGAAAGTGAAACCAAATCTGCAGACTTTTAATACAATATTGAAAGGTCTCCGGAAGTGTTACTCACTTGGAAGGATACCAGCCTTACAGATACTACGTGAAATGAAACATATTGGAATAGAACCCTCACTTGCAACATACCATCATATTATTCACCTCTTTTATCCAAGAGATTTAAGCGCTATAAAAATGCCATCCCTCATCATCTATGATATCATGAATGAATTAGAGGGAAGAACATTTTCTCCACAGGACCTTGATGATGGTAGATTTTTTCAGTTGGCCATGAGTGTGTGTTCATCTCTCAGAGATTTAGAGCTTGCTTACCAAGTACACAGACTTTTAAACACGGGGGACAACCGGAAACTGGTCGGACATGATCCTCTACGTAAGGTATATTA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTTAAACACGGGGGACAACC
58.31
CCATCCCTCGGATCATCGTG
60.04
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTTAAACACGGGGGACAACC
58.31
CACCATCCCTCGGATCATCG
60.04
145
PCR template sequence:
CTCTCAGAGATTTAGAGCTTGCTTACCAAGTACACAGACTTTTAAACACGGGGGACAACCGGAAACTGGTCGGACATGATCCTCTACGTAAGGTATATTAAGCACAAAACAATGCTGAGAGGATCTTCGCTTTAATGCCAGAGAAGAATGCACGCTCCTACTGCACGATGATCCGAGGGATGGTGAAGCACCGAGCTTAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-143-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-190b-5p(1), mmu-miR-532-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GTAAGGTATATTAAGCACAAAACAAT
siRNA sets
TTTTGTGCTTAATATACCT, ATTGTTTTGTGCTTAATAT, TTTGTGCTTAATATACCTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTCD3_660_ORF_1
0.7985
-0.017827031
0.659867168
627
ORF sequence:
ATGCCAGAGAAGAATGCACGCTCCTACTGCACGATGATCCGAGGGATGGTGAAGCACCGAGCTTATGCACAGGCACTGAACGTGTACACAGAGTTATTAAATAACAGACTTAGTGCTGATGTATATACCTTTAATGCATTGATTGAAGCAAAAACATTCATACTCAATGAGAAATTTGAGGAAAAATGGAATGATATACTGGATCTACTGAAACATATGGTTGCACAGAAAGTGAAACCAAATCTGCAGACTTTTAATACAATATTGAAAGGTCTCCGGAAGTGTTACTCACTTGGAAGGATACCAGCCTTACAGATACTACGTGAAATGAAACATATTGGAATAGAACCCTCACTTGCAACATACCATCATATTATTCACCTCTTTTATCCAAGAGATTTAAGCGCTATAAAAATGCCATCCCTCATCATCTATGATATCATGAATGAATTAGAGGGAAGAACATTTTCTCCACAGGACCTTGATGATGGTAGATTTTTTCAGTTGGCCATGAGTGTGTGTTCATCTCTCAGAGATTTAGAGCTTGCTTACCAAGTACACAGACTTTTAAACACGGGGGACAACCGGAAACTGGTCGGACATGATCCTCTACGTAAGGTATATTAA
Peptide sequence:
MPEKNARSYCTMIRGMVKHRAYAQALNVYTELLNNRLSADVYTFNALIEAKTFILNEKFEEKWNDILDLLKHMVAQKVKPNLQTFNTILKGLRKCYSLGRIPALQILREMKHIGIEPSLATYHHIIHLFYPRDLSAIKMPSLIIYDIMNELEGRTFSPQDLDDGRFFQLAMSVCSSLRDLELAYQVHRLLNTGDNRKLVGHDPLRKVY
IRESfinder result
IRESfinder score
0.677386479
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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