Plant Circular RNA Database

Detail information of AT1G75340_circ_g.6

			
						 General Information
					
						CircRNA Name
						AT1G75340_circ_g.6
					
						ID in PlantcircBase
						ath_circ_010285
					
						Alias
						At_ciR129
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 28269963-28270233  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI, CIRI-full, PcircRNA_finder, circseq_cup, find_circ
					
						Parent gene
						
							AT1G75340						
					
						Parent gene annotation
						
							Zinc finger CCCH domain-containing protein 16
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G75180_circ_g.1 1_circ_ag.2 AT1G75190_circ_g.1 AT1G75210_circ_g.1 AT1G75210_circ_g.2 AT1G75210_circ_g.3 AT1G75210_circ_g.4 AT1G75210_circ_g.5 AT1G75210_circ_g.6 AT1G75210_circ_g.7 AT1G75220_circ_g.1 AT1G75220_circ_g.2 AT1G75220_circ_g.3 AT1G75220_circ_g.4 AT1G75240_circ_g.1 1_circ_ag.2 1_circ_ag.3 AT1G75280_circ_g.1 1_circ_ag.2 AT1G75295_circ_g.1 AT1G75295_circ_g.2 AT1G75295_circ_g.3 AT1G75295_circ_g.4 AT1G75310_circ_g.1 AT1G75340_circ_g.1 AT1G75340_circ_g.2 AT1G75340_circ_g.3 AT1G75340_circ_g.4 AT1G75340_circ_g.5 AT1G75340_circ_g.7 AT1G75340_circ_g.8 AT1G75350_circ_g.1 AT1G75350_circ_g.2 AT1G75370_circ_g.1 AT1G75370_circ_g.2 AT1G75370_circ_g.3 AT1G75370_circ_g.4 AT1G75370_circ_g.5 AT1G75370_circ_g.6 AT1G75370_circ_g.7 AT1G75370_circ_g.8 AT1G75380_circ_g.1 AT1G75380_circ_g.2 AT1G75380_circ_g.3 AT1G75380_circ_g.4 AT1G75380_circ_g.5 AT1G75380_circ_g.6 AT1G75380_circ_g.7 AT1G75380_circ_g.8 AT1G75380_circ_g.9 AT1G75400_circ_g.1 AT1G75400_circ_g.2 						
					
						Support reads
						41/12
					
						Tissues
						leaf/root, aerial, inflorescences
					
						Exon boundary  
						
							Yes-Yes							"Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.

						Splicing signals  
						
							CT-AC							The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.

						Number of exons covered
						AT1G75340.1:2

General Information
CircRNA Name	AT1G75340_circ_g.6
ID in PlantcircBase	ath_circ_010285
Alias	At_ciR129
Organism	Arabidpsis thaliana
Position	chr1: 28269963-28270233 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRI, CIRI-full, PcircRNA_finder, circseq_cup, find_circ
Parent gene	AT1G75340
Parent gene annotation	Zinc finger CCCH domain-containing protein 16
Parent gene strand	-
Alternative splicing	AT1G75180_circ_g.1 1_circ_ag.2 AT1G75190_circ_g.1 AT1G75210_circ_g.1 AT1G75210_circ_g.2 AT1G75210_circ_g.3 AT1G75210_circ_g.4 AT1G75210_circ_g.5 AT1G75210_circ_g.6 AT1G75210_circ_g.7 AT1G75220_circ_g.1 AT1G75220_circ_g.2 AT1G75220_circ_g.3 AT1G75220_circ_g.4 AT1G75240_circ_g.1 1_circ_ag.2 1_circ_ag.3 AT1G75280_circ_g.1 1_circ_ag.2 AT1G75295_circ_g.1 AT1G75295_circ_g.2 AT1G75295_circ_g.3 AT1G75295_circ_g.4 AT1G75310_circ_g.1 AT1G75340_circ_g.1 AT1G75340_circ_g.2 AT1G75340_circ_g.3 AT1G75340_circ_g.4 AT1G75340_circ_g.5 AT1G75340_circ_g.7 AT1G75340_circ_g.8 AT1G75350_circ_g.1 AT1G75350_circ_g.2 AT1G75370_circ_g.1 AT1G75370_circ_g.2 AT1G75370_circ_g.3 AT1G75370_circ_g.4 AT1G75370_circ_g.5 AT1G75370_circ_g.6 AT1G75370_circ_g.7 AT1G75370_circ_g.8 AT1G75380_circ_g.1 AT1G75380_circ_g.2 AT1G75380_circ_g.3 AT1G75380_circ_g.4 AT1G75380_circ_g.5 AT1G75380_circ_g.6 AT1G75380_circ_g.7 AT1G75380_circ_g.8 AT1G75380_circ_g.9 AT1G75400_circ_g.1 AT1G75400_circ_g.2
Support reads	41/12
Tissues	leaf/root, aerial, inflorescences
Exon boundary	Yes-Yes "Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.
Splicing signals	CT-AC The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.
Number of exons covered	AT1G75340.1:2

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							NA							Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".

						PCR primers for BSS   
						
							NA							PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							NA							Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.

						PCR primers for FL   
						
							NA							 PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	NA Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".
PCR primers for BSS	NA PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	NA Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.
PCR primers for FL	NA PCR primers used in full-length (FL) sequence validation.

			
						 Sequences
					
						Splice junction sequence  
						
							GGAATATGGAGAAAGTTAGTACCTGACTCCACCAGCATTGGTATTGGGGAATGTAGTTTGTTGA
TTGAAGCTTGCAAAGGCATTCGGAGGTCCAGATGAActgagaccaccagcgttggtattggaga
atgcagtttgttgattatttgattgttgagtaaagcttgcaaaggggttcggaggtccagatga
actatgca

						Assembled circRNA sequence  
						
							Yes
The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).

						Full-length trsnacripts
						
							Transcript length: 169
Transcript exons: 28269963-28270057,28270160-28270233
CTGAGACCACCAGCGTTGGTATTGGAGAATGCAGTTTGTTGATTATTTGATTGTTGAGTAAAGC
TTGCAAAGGGGTTCGGAGGTCCAGATGAACTCTCCACCAGCATTGGTATTGGGGAATGTAGTTT
GTTGATTGAAGCTTGCAAAGGCATTCGGAGGTCCAGATGAA
Transcript length: 171
Transcript exons: 28269963-28270055,28270156-28270233
CTGAGACCACCAGCGTTGGTATTGGAGAATGCAGTTTGTTGATTATTTGATTGTTGAGTAAAGC
TTGCAAAGGGGTTCGGAGGTCCAGATGAACTGACTCCACCAGCATTGGTATTGGGGAATGTAGT
TTGTTGATTGAAGCTTGCAAAGGCATTCGGAGGTCCAGATGAA
Transcript length: 342
Transcript exons: 28269963-28270233
CTGAGACCACCAGCGTTGGTATTGGAGAATGCAGTTTGTTGATTATTTGATTGTTGAGTAAAGC
TTGCAAAGGGGTTCGGAGGTCCAGATGAACTGACTCCACCAGCATTGGTATTGGGGAATGTAGT
TTGTTGATTGAAGCTTGCAAAGGCATTCGGAGGTCCAGATGAACTGAGACCACCAGCGTTGGTA
TTGGAGAATGCAGTTTGTTGATTATTTGATTGTTGAGTAAAGCTTGCAAAGGGGTTCGGAGGTC
CAGATGAACTGACTCCACCAGCATTGGTATTGGGGAATGTAGTTTGTTGATTGAAGCTTGCAAG
GGCATTCGGAGGTCCAGATGAA
						
						Genomic sequence
						
							CTGAGACCACCAGCGTTGGTATTGGAGAATGCAGTTTGTTGATTATTTGATTGTTGAGTAAAGC
TTGCAAAGGGGTTCGGAGGTCCAGATGAACTATGCAGAGGAATAGTTGGCCAAAGAGAAATATG
GGAACCAAGAGGTTATAAAGGTAACACAAACTTGTTTGAATATGGAATATGGAGAAAGTTAGTA
CCTGACTCCACCAGCATTGGTATTGGGGAATGTAGTTTGTTGATTGAAGCTTGCAAAGGCATTC
GGAGGTCCAGATGAA

Sequences
Splice junction sequence	GGAATATGGAGAAAGTTAGTACCTGACTCCACCAGCATTGGTATTGGGGAATGTAGTTTGTTGA TTGAAGCTTGCAAAGGCATTCGGAGGTCCAGATGAActgagaccaccagcgttggtattggaga atgcagtttgttgattatttgattgttgagtaaagcttgcaaaggggttcggaggtccagatga actatgca
Assembled circRNA sequence	Yes The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).
Full-length trsnacripts	Transcript length: 169 Transcript exons: 28269963-28270057,28270160-28270233 CTGAGACCACCAGCGTTGGTATTGGAGAATGCAGTTTGTTGATTATTTGATTGTTGAGTAAAGC TTGCAAAGGGGTTCGGAGGTCCAGATGAACTCTCCACCAGCATTGGTATTGGGGAATGTAGTTT GTTGATTGAAGCTTGCAAAGGCATTCGGAGGTCCAGATGAA Transcript length: 171 Transcript exons: 28269963-28270055,28270156-28270233 CTGAGACCACCAGCGTTGGTATTGGAGAATGCAGTTTGTTGATTATTTGATTGTTGAGTAAAGC TTGCAAAGGGGTTCGGAGGTCCAGATGAACTGACTCCACCAGCATTGGTATTGGGGAATGTAGT TTGTTGATTGAAGCTTGCAAAGGCATTCGGAGGTCCAGATGAA Transcript length: 342 Transcript exons: 28269963-28270233 CTGAGACCACCAGCGTTGGTATTGGAGAATGCAGTTTGTTGATTATTTGATTGTTGAGTAAAGC TTGCAAAGGGGTTCGGAGGTCCAGATGAACTGACTCCACCAGCATTGGTATTGGGGAATGTAGT TTGTTGATTGAAGCTTGCAAAGGCATTCGGAGGTCCAGATGAACTGAGACCACCAGCGTTGGTA TTGGAGAATGCAGTTTGTTGATTATTTGATTGTTGAGTAAAGCTTGCAAAGGGGTTCGGAGGTC CAGATGAACTGACTCCACCAGCATTGGTATTGGGGAATGTAGTTTGTTGATTGAAGCTTGCAAG GGCATTCGGAGGTCCAGATGAA
Genomic sequence	CTGAGACCACCAGCGTTGGTATTGGAGAATGCAGTTTGTTGATTATTTGATTGTTGAGTAAAGC TTGCAAAGGGGTTCGGAGGTCCAGATGAACTATGCAGAGGAATAGTTGGCCAAAGAGAAATATG GGAACCAAGAGGTTATAAAGGTAACACAAACTTGTTTGAATATGGAATATGGAGAAAGTTAGTA CCTGACTCCACCAGCATTGGTATTGGGGAATGTAGTTTGTTGATTGAAGCTTGCAAAGGCATTC GGAGGTCCAGATGAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.382863293

Conservation Information
Conserved circRNAs	NA
PMCS	0.382863293

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							28270217-28269965(-)
						
						Potential amino acid sequence
						
							MPLQASINKLHSPIPMLVESVHLDLRTPLQALLNNQIINKLHSPIPTLVVSVHLDLRMPLQASI
NKLHSPIPMLVESVHLDLRTPLQALLNNQIINKLHSPIPTLVVSVHLDLRMPLQASINKLHSPI
PMLVESVHLDLRTPLQALLNNQIINKLHSPIPTLVVSVHLDLRMPLQASINKLHSPIPMLVESV
HLDLRTPLQALLNNQIINKLHSPIPTLVVS(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	28270217-28269965(-)
Potential amino acid sequence	MPLQASINKLHSPIPMLVESVHLDLRTPLQALLNNQIINKLHSPIPTLVVSVHLDLRMPLQASI NKLHSPIPMLVESVHLDLRTPLQALLNNQIINKLHSPIPTLVVSVHLDLRMPLQASINKLHSPI PMLVESVHLDLRTPLQALLNNQIINKLHSPIPTLVVSVHLDLRMPLQASINKLHSPIPMLVESV HLDLRTPLQALLNNQIINKLHSPIPTLVVS(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of AT1G75340_circ_g.6

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