Plant Circular RNA Database

Detail information of AT3G28860_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT3G28860_circ_g.1
					
						ID in PlantcircBase
						ath_circ_024254
					
						Alias
						3:10872589-10873729
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 10872589-10873729  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G28860						
					
						Parent gene annotation
						
							ABC transporter B family member 19
							
						Parent gene strand
						-
					
						Alternative splicing
						
							3_circ_ag.3 3_circ_ag.4 AT3G28830_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 AT3G28900_circ_g.3 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
						1/1
					
						Tissues
						root;flower
					
						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
						AT3G28860.1:2

General Information
CircRNA Name	AT3G28860_circ_g.1
ID in PlantcircBase	ath_circ_024254
Alias	3:10872589-10873729
Organism	Arabidpsis thaliana
Position	chr3: 10872589-10873729 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G28860
Parent gene annotation	ABC transporter B family member 19
Parent gene strand	-
Alternative splicing	3_circ_ag.3 3_circ_ag.4 AT3G28830_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 AT3G28900_circ_g.3 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	1/1
Tissues	root;flower
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	AT3G28860.1:2

			
						 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  
						
							CTTCATCTAGTAACAGAATCTTTGGGTCTTTCAACATCGCCCTAGCAATTGCAATTCTCTGCTT
CTGTCCACCTGAGAGTTGAACACCACGTTCTCCAACctgagcaaagttagcgaggactagaagt
gggaatgtgcctaagatgagaagtgagactctccattctactatgaaggcgactatgaaggatg
tgagaagt

									
								

					

						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: 1062
Transcript exons: 10872589-10872830,10872910-10873729
CTGAGCAAAGTTAGCGAGGACTAGAAGTGGGAATGTGCCTAAGATGAGAAGTGAGACTCTCCAT
TCTACTATGAAGGCGACTATGAAGGATGTGAGAAGTGAAGTCATGTTTTGTAGAATTACTGAGA
TTCTCTCGGCTATAGCGGATTTAACATCTGCTGCATCAGTAGCTAAACGTGCAGCGATCAGGCT
TGAGTTGTGTTCATCCTCATCGAACCAACCAACTTCGTTTCTCAAGATAGCTGAGAGCATCATT
CTTCTTACTCTTGTTGTGAGGTTTTCTCCCATGATGCTAAAGAAGTAATGTTGGATCAAATAAG
CACCCACAGCATAGAGACCAGCACCAATGTAGATGAAGACATACTCTTTTGTTTTCCTTTCCAT
TGAATCATAGTCTGTGTAGTAGAAGACTTCGATCATGTTGCTCATCACAATAGCAAATGTAGGA
CCAATGAAACCAGAAAGAATTGAGCCTACTGCTCCCATGATTGAGTAAGGCCATTCCGGTGAAT
TAAGCTTGAGAAGCCTGTAGAAGTAATTTTCAGGGGCACGAGTCTTTCGGTCAGTCTCTGCATT
TGAAATCATCTCTATCCGACCATCAGCTCCAGTGCTGTAAGAATAGCTCAGATTCCTCAAACTT
CCTGATCTTAAACTGAGTGATTTCGTTGACAGTGAATGGCTCAAACGGGTTGAACGAGTGCGAC
GAGTTGACGGGTTTGAGAAATCTCGAGTACCAACCATTTCCTGAAACCTGATGAGGGATGCGTA
AGCACCGGATTTGGCAATGAGTTCTTCATGTGTTCCGGTTTCAACAACTTGGCCTTGCTGTATC
ACGGCAATGGAATCAACATTTCTGATGGTGCAGAGACGATGAGCAACAACAACAGTGGTCCTCC
CCACCATGACTCTGTCTAAAGCTTCCTGAACAATGCTCTCAGAGCTAGCATCAAGAGCGCTTGT
AGCTTCATCTAGTAACAGAATCTTTGGGTCTTTCAACATCGCCCTAGCAATTGCAATTCTCTGC
TTCTGTCCACCTGAGAGTTGAACACCACGTTCTCCAAC
						
					

						Genomic sequence
						
							CTGAGCAAAGTTAGCGAGGACTAGAAGTGGGAATGTGCCTAAGATGAGAAGTGAGACTCTCCAT
TCTACTATGAAGGCGACTATGAAGGATGTGAGAAGTGAAGTCATGTTTTGTAGAATTACTGAGA
TTCTCTCGGCTATAGCGGATTTAACATCTGCTGCATCAGTAGCTAAACGTGCAGCGATCAGGCT
TGAGTTGTGTTCATCCTCATCGAACCAACCAACTTCGTTTCTCAAGATAGCTAAATAAGAACAA
TCAAGAAACCAAAATAAGAAATGGGAAAGTGATTTTAAGCAAATTCAGGAGATTTTGATACATA
CCTGAGAGCATCATTCTTCTTACTCTTGTTGTGAGGTTTTCTCCCATGATGCTAAAGAAGTAAT
GTTGGATCAAATAAGCACCCACAGCATAGAGACCAGCACCAATGTAGATGAAGACATACTCTTT
TGTTTTCCTTTCCATTGAATCATAGTCTGTGTAGTAGAAGACTTCGATCATGTTGCTCATCACA
ATAGCAAATGTAGGACCAATGAAACCAGAAAGAATTGAGCCTACTGCTCCCATGATTGAGTAAG
GCCATTCCGGTGAATTAAGCTTGAGAAGCCTGTAGAAGTAATTTTCAGGGGCACGAGTCTTTCG
GTCAGTCTCTGCATTTGAAATCATCTCTATCCGACCATCAGCTCCAGTGCTGTAAGAATAGCTC
AGATTCCTCAAACTTCCTGATCTTAAACTGAGTGATTTCGTTGACAGTGAATGGCTCAAACGGG
TTGAACGAGTGCGACGAGTTGACGGGTTTGAGAAATCTCGAGTACCAACCATTTCCTGAAACCT
GATGAGGGATGCGTAAGCACCGGATTTGGCAATGAGTTCTTCATGTGTTCCGGTTTCAACAACT
TGGCCTTGCTGTATCACGGCAATGGAATCAACATTTCTGATGGTGCAGAGACGATGAGCAACAA
CAACAGTGGTCCTCCCCACCATGACTCTGTCTAAAGCTTCCTGAACAATGCTCTCAGAGCTAGC
ATCAAGAGCGCTTGTAGCTTCATCTAGTAACAGAATCTTTGGGTCTTTCAACATCGCCCTAGCA
ATTGCAATTCTCTGCTTCTGTCCACCTGAGAGTTGAACACCACGTTCTCCAAC
						
					

			
		

Sequences
Splice junction sequence	CTTCATCTAGTAACAGAATCTTTGGGTCTTTCAACATCGCCCTAGCAATTGCAATTCTCTGCTT CTGTCCACCTGAGAGTTGAACACCACGTTCTCCAACctgagcaaagttagcgaggactagaagt gggaatgtgcctaagatgagaagtgagactctccattctactatgaaggcgactatgaaggatg tgagaagt
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: 1062 Transcript exons: 10872589-10872830,10872910-10873729 CTGAGCAAAGTTAGCGAGGACTAGAAGTGGGAATGTGCCTAAGATGAGAAGTGAGACTCTCCAT TCTACTATGAAGGCGACTATGAAGGATGTGAGAAGTGAAGTCATGTTTTGTAGAATTACTGAGA TTCTCTCGGCTATAGCGGATTTAACATCTGCTGCATCAGTAGCTAAACGTGCAGCGATCAGGCT TGAGTTGTGTTCATCCTCATCGAACCAACCAACTTCGTTTCTCAAGATAGCTGAGAGCATCATT CTTCTTACTCTTGTTGTGAGGTTTTCTCCCATGATGCTAAAGAAGTAATGTTGGATCAAATAAG CACCCACAGCATAGAGACCAGCACCAATGTAGATGAAGACATACTCTTTTGTTTTCCTTTCCAT TGAATCATAGTCTGTGTAGTAGAAGACTTCGATCATGTTGCTCATCACAATAGCAAATGTAGGA CCAATGAAACCAGAAAGAATTGAGCCTACTGCTCCCATGATTGAGTAAGGCCATTCCGGTGAAT TAAGCTTGAGAAGCCTGTAGAAGTAATTTTCAGGGGCACGAGTCTTTCGGTCAGTCTCTGCATT TGAAATCATCTCTATCCGACCATCAGCTCCAGTGCTGTAAGAATAGCTCAGATTCCTCAAACTT CCTGATCTTAAACTGAGTGATTTCGTTGACAGTGAATGGCTCAAACGGGTTGAACGAGTGCGAC GAGTTGACGGGTTTGAGAAATCTCGAGTACCAACCATTTCCTGAAACCTGATGAGGGATGCGTA AGCACCGGATTTGGCAATGAGTTCTTCATGTGTTCCGGTTTCAACAACTTGGCCTTGCTGTATC ACGGCAATGGAATCAACATTTCTGATGGTGCAGAGACGATGAGCAACAACAACAGTGGTCCTCC CCACCATGACTCTGTCTAAAGCTTCCTGAACAATGCTCTCAGAGCTAGCATCAAGAGCGCTTGT AGCTTCATCTAGTAACAGAATCTTTGGGTCTTTCAACATCGCCCTAGCAATTGCAATTCTCTGC TTCTGTCCACCTGAGAGTTGAACACCACGTTCTCCAAC
Genomic sequence	CTGAGCAAAGTTAGCGAGGACTAGAAGTGGGAATGTGCCTAAGATGAGAAGTGAGACTCTCCAT TCTACTATGAAGGCGACTATGAAGGATGTGAGAAGTGAAGTCATGTTTTGTAGAATTACTGAGA TTCTCTCGGCTATAGCGGATTTAACATCTGCTGCATCAGTAGCTAAACGTGCAGCGATCAGGCT TGAGTTGTGTTCATCCTCATCGAACCAACCAACTTCGTTTCTCAAGATAGCTAAATAAGAACAA TCAAGAAACCAAAATAAGAAATGGGAAAGTGATTTTAAGCAAATTCAGGAGATTTTGATACATA CCTGAGAGCATCATTCTTCTTACTCTTGTTGTGAGGTTTTCTCCCATGATGCTAAAGAAGTAAT GTTGGATCAAATAAGCACCCACAGCATAGAGACCAGCACCAATGTAGATGAAGACATACTCTTT TGTTTTCCTTTCCATTGAATCATAGTCTGTGTAGTAGAAGACTTCGATCATGTTGCTCATCACA ATAGCAAATGTAGGACCAATGAAACCAGAAAGAATTGAGCCTACTGCTCCCATGATTGAGTAAG GCCATTCCGGTGAATTAAGCTTGAGAAGCCTGTAGAAGTAATTTTCAGGGGCACGAGTCTTTCG GTCAGTCTCTGCATTTGAAATCATCTCTATCCGACCATCAGCTCCAGTGCTGTAAGAATAGCTC AGATTCCTCAAACTTCCTGATCTTAAACTGAGTGATTTCGTTGACAGTGAATGGCTCAAACGGG TTGAACGAGTGCGACGAGTTGACGGGTTTGAGAAATCTCGAGTACCAACCATTTCCTGAAACCT GATGAGGGATGCGTAAGCACCGGATTTGGCAATGAGTTCTTCATGTGTTCCGGTTTCAACAACT TGGCCTTGCTGTATCACGGCAATGGAATCAACATTTCTGATGGTGCAGAGACGATGAGCAACAA CAACAGTGGTCCTCCCCACCATGACTCTGTCTAAAGCTTCCTGAACAATGCTCTCAGAGCTAGC ATCAAGAGCGCTTGTAGCTTCATCTAGTAACAGAATCTTTGGGTCTTTCAACATCGCCCTAGCA ATTGCAATTCTCTGCTTCTGTCCACCTGAGAGTTGAACACCACGTTCTCCAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.580173026

Conservation Information
Conserved circRNAs	NA
PMCS	0.580173026

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

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT3G28860_circ_g.1

Address

Any questions?

Supported by