Plant Circular RNA Database

Detail information of AT3G28900_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT3G28900_circ_g.3
					
						ID in PlantcircBase
						ath_circ_024263
					
						Alias
						At_ciR4160
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 10903037-10904229  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ, circseq_cup, CIRI-full
					
						Parent gene
						
							AT3G28900						
					
						Parent gene annotation
						
							60S ribosomal protein L34-3
							
						Parent gene strand
						-
					
						Alternative splicing
						
							3_circ_ag.3 3_circ_ag.4 AT3G28830_circ_g.1 AT3G28860_circ_g.1 AT3G28860_circ_g.2 AT3G28860_circ_g.3 AT3G28860_circ_g.4 AT3G28860_circ_g.5 AT3G28860_circ_g.6 3_circ_ag.7 AT3G28900_circ_g.1 AT3G28900_circ_g.2 AT3G28910_circ_g.1 3_circ_ig.2 AT3G28930_circ_g.1 AT3G28930_circ_g.2 3_circ_ag.3 3_circ_ag.4 3_circ_ag.5 3_circ_ag.6 3_circ_ag.7 3_circ_ig.8 3_circ_ig.9 AT3G28940_circ_g.1 AT3G28940_circ_g.2 AT3G28940_circ_g.3 AT3G28940_circ_g.4 AT3G28950_circ_g.1 AT3G28970_circ_g.1 AT3G28970_circ_g.2 AT3G28970_circ_g.3 AT3G28970_circ_g.4 AT3G28980_circ_g.1 						
					
						Support reads
						4
					
						Tissues
						leaf
					
						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
						AT3G28900.1:2

General Information
CircRNA Name	AT3G28900_circ_g.3
ID in PlantcircBase	ath_circ_024263
Alias	At_ciR4160
Organism	Arabidpsis thaliana
Position	chr3: 10903037-10904229 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ, circseq_cup, CIRI-full
Parent gene	AT3G28900
Parent gene annotation	60S ribosomal protein L34-3
Parent gene strand	-
Alternative splicing	3_circ_ag.3 3_circ_ag.4 AT3G28830_circ_g.1 AT3G28860_circ_g.1 AT3G28860_circ_g.2 AT3G28860_circ_g.3 AT3G28860_circ_g.4 AT3G28860_circ_g.5 AT3G28860_circ_g.6 3_circ_ag.7 AT3G28900_circ_g.1 AT3G28900_circ_g.2 AT3G28910_circ_g.1 3_circ_ig.2 AT3G28930_circ_g.1 AT3G28930_circ_g.2 3_circ_ag.3 3_circ_ag.4 3_circ_ag.5 3_circ_ag.6 3_circ_ag.7 3_circ_ig.8 3_circ_ig.9 AT3G28940_circ_g.1 AT3G28940_circ_g.2 AT3G28940_circ_g.3 AT3G28940_circ_g.4 AT3G28950_circ_g.1 AT3G28970_circ_g.1 AT3G28970_circ_g.2 AT3G28970_circ_g.3 AT3G28970_circ_g.4 AT3G28980_circ_g.1
Support reads	4
Tissues	leaf
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	AT3G28900.1:2

			
						 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  
						
							AATTGAATAGAAAAGATTACCCCTTGGATTCTCTTGCCAGTAACAGGGCACTTAGGTCCACTAG
CTCTCTTGTTCGTCGTCTGGTAAGTCAATTTTCCACctctccctaacagcaactccagatagaa
caccaccatatgcacgattcactgtcctctcgttccttgccaaccttgaccttttgtactcagc
aggtctca

						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: 190
Transcript exons: 10903037-10903146,10904150-10904229
CTCTCCCTAACAGCAACTCCAGATAGAACACCACCATATGCACGATTCACTGTCCTCTCGTTCC
TTGCCAACCTTGACCTTTTGTACTCAGCAGGTCTCAAATGCGGAATCCCTTGGATTCTCTTGCC
AGTAACAGGGCACTTAGGTCCACTAGCTCTCTTGTTCGTCGTCTGGTAAGTCAATTTTCCAC
						
						Genomic sequence
						
							CTCTCCCTAACAGCAACTCCAGATAGAACACCACCATATGCACGATTCACTGTCCTCTCGTTCC
TTGCCAACCTTGACCTTTTGTACTCAGCAGGTCTCAAATGCGGAATCTGCAGAAAACAAACATA
GAAAGTAAAGCTTAAGAAACCATGCTAATTCAAAAAAAGGAATGTGTTTTTGAGGTTCTATTGA
GATTAAGCATATGAGTAACCCTTGATTATTCGATAAGAACCAGGGGCTGATCCAAGTAACTACC
AACTCATTATATACCAGGTACTAGTCTTCGACAAACACAATAGGAACAGAGAAAGCCAAATGAT
GCTCAACTTAAATTCAGGCTATCAAGTTATTGTTAGAATTAGCTGAAAGGAATACTAAGTCGAG
TAACCATGTAAACTTTGTTTCTCTATATCAATGGGCATGAAAGTAAGATATTTTTCACCATTTT
ACCAACTTAAGGAAAGCCTTCAACCAACAAAATTCTTGAATTCAATCCCTAAAGTGTCTATGTT
TTAATTTAAGTTCCAAATTTGGTCTCAATGCCAAAATAACCAATGTGTAACCCTTGGTCTCCAA
GACACATTATTCGTAAACAGAAACATAAACACGAACCAGAAAGCAGCTAATAGACCACAAGGGA
CATGAACCAAACTTGCATATCTTTAAGAGCAGGCTATCATCAAGTCAAGGTAAGAACTGGCTGA
AATGGACATGAAGTATAAATATATTACGACAAGTCTAGATCAATTTTAACTTTTATCCCTTGTG
GCTTTAGAGGCGACAAGTTTATACAAACATTGTTGTCCACTACACATAAACACGTACACTAACA
CCAACATTTACAAACTTTTATCCAAATATACTAAAGAAAACAGCTAGCACCACAAGAGACATGA
ACCGAATTTGAAACAGTCAGTCAAATTAAACTCAAACACGAACCCTAACACCAAAAGACACAAA
CTTTCTTGAAACAGAGAATCAAACTAAACTCAAAACACGAACCCTAACAGCAAAATGCACAATT
TCTTGATCCAGAGAATCTAACTAAACTCAAAACACGAACCCTAACAGCAAAATTCACCAACTTT
TTTGAAATTGAATAGAAAAGATTACCCCTTGGATTCTCTTGCCAGTAACAGGGCACTTAGGTCC
ACTAGCTCTCTTGTTCGTCGTCTGGTAAGTCAATTTTCCAC

Sequences
Splice junction sequence	AATTGAATAGAAAAGATTACCCCTTGGATTCTCTTGCCAGTAACAGGGCACTTAGGTCCACTAG CTCTCTTGTTCGTCGTCTGGTAAGTCAATTTTCCACctctccctaacagcaactccagatagaa caccaccatatgcacgattcactgtcctctcgttccttgccaaccttgaccttttgtactcagc aggtctca
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: 190 Transcript exons: 10903037-10903146,10904150-10904229 CTCTCCCTAACAGCAACTCCAGATAGAACACCACCATATGCACGATTCACTGTCCTCTCGTTCC TTGCCAACCTTGACCTTTTGTACTCAGCAGGTCTCAAATGCGGAATCCCTTGGATTCTCTTGCC AGTAACAGGGCACTTAGGTCCACTAGCTCTCTTGTTCGTCGTCTGGTAAGTCAATTTTCCAC
Genomic sequence	CTCTCCCTAACAGCAACTCCAGATAGAACACCACCATATGCACGATTCACTGTCCTCTCGTTCC TTGCCAACCTTGACCTTTTGTACTCAGCAGGTCTCAAATGCGGAATCTGCAGAAAACAAACATA GAAAGTAAAGCTTAAGAAACCATGCTAATTCAAAAAAAGGAATGTGTTTTTGAGGTTCTATTGA GATTAAGCATATGAGTAACCCTTGATTATTCGATAAGAACCAGGGGCTGATCCAAGTAACTACC AACTCATTATATACCAGGTACTAGTCTTCGACAAACACAATAGGAACAGAGAAAGCCAAATGAT GCTCAACTTAAATTCAGGCTATCAAGTTATTGTTAGAATTAGCTGAAAGGAATACTAAGTCGAG TAACCATGTAAACTTTGTTTCTCTATATCAATGGGCATGAAAGTAAGATATTTTTCACCATTTT ACCAACTTAAGGAAAGCCTTCAACCAACAAAATTCTTGAATTCAATCCCTAAAGTGTCTATGTT TTAATTTAAGTTCCAAATTTGGTCTCAATGCCAAAATAACCAATGTGTAACCCTTGGTCTCCAA GACACATTATTCGTAAACAGAAACATAAACACGAACCAGAAAGCAGCTAATAGACCACAAGGGA CATGAACCAAACTTGCATATCTTTAAGAGCAGGCTATCATCAAGTCAAGGTAAGAACTGGCTGA AATGGACATGAAGTATAAATATATTACGACAAGTCTAGATCAATTTTAACTTTTATCCCTTGTG GCTTTAGAGGCGACAAGTTTATACAAACATTGTTGTCCACTACACATAAACACGTACACTAACA CCAACATTTACAAACTTTTATCCAAATATACTAAAGAAAACAGCTAGCACCACAAGAGACATGA ACCGAATTTGAAACAGTCAGTCAAATTAAACTCAAACACGAACCCTAACACCAAAAGACACAAA CTTTCTTGAAACAGAGAATCAAACTAAACTCAAAACACGAACCCTAACAGCAAAATGCACAATT TCTTGATCCAGAGAATCTAACTAAACTCAAAACACGAACCCTAACAGCAAAATTCACCAACTTT TTTGAAATTGAATAGAAAAGATTACCCCTTGGATTCTCTTGCCAGTAACAGGGCACTTAGGTCC ACTAGCTCTCTTGTTCGTCGTCTGGTAAGTCAATTTTCCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.194468721

Conservation Information
Conserved circRNAs	NA
PMCS	0.194468721

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of AT3G28900_circ_g.3

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