Plant Circular RNA Database

Detail information of AT5G23490_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT5G23490_circ_g.4
					
						ID in PlantcircBase
						ath_circ_040040
					
						Alias
						Ath_circ_FC3476
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 7924423-7925937  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							AT5G23490						
					
						Parent gene annotation
						
							unknown protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							5_circ_ag.5 AT5G23490_circ_g.6 5_circ_ag.7 AT5G23490_circ_g.8 5_circ_ag.9 5_circ_ag.10 5_circ_ag.11 						
					
						Support reads
						2
					
						Tissues
						inflorescences, whole_plant
					
						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  
						
							GT-AG							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
						AT5G23490.1:7
AT5G23490.2:7
AT5G23490.4:7
AT5G23490.3:7

General Information
CircRNA Name	AT5G23490_circ_g.4
ID in PlantcircBase	ath_circ_040040
Alias	Ath_circ_FC3476
Organism	Arabidpsis thaliana
Position	chr5: 7924423-7925937 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	AT5G23490
Parent gene annotation	unknown protein
Parent gene strand	+
Alternative splicing	5_circ_ag.5 AT5G23490_circ_g.6 5_circ_ag.7 AT5G23490_circ_g.8 5_circ_ag.9 5_circ_ag.10 5_circ_ag.11
Support reads	2
Tissues	inflorescences, whole_plant
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	GT-AG 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	AT5G23490.1:7 AT5G23490.2:7 AT5G23490.4:7 AT5G23490.3:7

			
						 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  
						
							TAACCATTCCGTTTGGGCAACCGGCAGAACTTGTTATCATTGGTTCTGATGGTAGTGAACATTC
CTTACGAGCAGATAATGGATCGCCAGACCTTATCGGgtggagatgatgacccgttaccaggtat
agaggacctccaaatttcaggagaaccttatcctggacatgaacttcaggcttgtggttactcc
attaatgg

									
								

					

						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: 592
Transcript exons: 7924423-7924544,7924630-7924672,7924756-7924847,7925133-
7925181,7925394-7925464,7925550-7925663,7925837-7925937
GTGGAGATGATGACCCGTTACCAGGTATAGAGGACCTCCAAATTTCAGGAGAACCTTATCCTGG
ACATGAACTTCAGGCTTGTGGTTACTCCATTAATGGAACAACAAGTTGTAATTTTGAGTGGGTC
TGTCACCTAGAAGATGGATCTGTGAATTACATTGATGGAGCAAAGCAGCCAAATTACCTTGTCA
CTGCTGATGATGTTGATTTATATCTTGCTATTGAGGTTCAGCCTTTGGATGACAGGAACCGAAA
GGGGGAGCTTGTGAAGGTTTTTGCCAATGATAACCGCAAGATTGCTTGCCATCCAGATATGCAG
AGCAATATAGAGAAGACTCTTCATACTGGTCATGCTTCATACAAAGTTTCTCTTGCGGTTGGCT
TCGTGGATATATGGGAAGCAGCAACATTATCTATTAAGAGAGAAGGTTACAGCATCAAGTGTAT
TAGTGATCTCACAATTGCAGAAAAGTTCTCAGCATCTACTACTGTAACCATTCCGTTTGGGCAA
CCGGCAGAACTTGTTATCATTGGTTCTGATGGTAGTGAACATTCCTTACGAGCAGATAATGGAT
CGCCAGACCTTATCGG
						
					

						Genomic sequence
						
							GTGGAGATGATGACCCGTTACCAGGTATAGAGGACCTCCAAATTTCAGGAGAACCTTATCCTGG
ACATGAACTTCAGGCTTGTGGTTACTCCATTAATGGAACAACAAGTTGTAATTTTGAGGTGCGT
ACTAAATAAAAAACAGAATCGCTTCCTTACTTATGTTGAATTGCATCTAATCTATCTTCTTCTG
TTCTTCAATTTTCAGTGGGTCTGTCACCTAGAAGATGGATCTGTGAATTACATTGATGGTACAT
TCCCCTCCTGCTGAATTTTGTTTCTTATTTCTTTATATGGAAATAAGAATCTAGTCGTGAACGA
ACTTCTAATGCAGGAGCAAAGCAGCCAAATTACCTTGTCACTGCTGATGATGTTGATTTATATC
TTGCTATTGAGGTTCAGCCTTTGGATGACAGGAACCGAAAGGTTAATATTTTTTTGTATGAATG
AGATTATATGTTGAGTGGTTCTTTTCTGTGGAATACTGGAATCTTGATATGGATTTTAGTTTCC
ATTATTTACCTCAGCATTTTGTTTCGTCGGCTAGATTTCATGCTAAAATGTTGTAGGGGAAAAG
ATTCGCCTTTGGAAAGTACAGATACGATTTAACAGTTTTGTTAGATGTGCATACACTGTTGTTT
TCTGCTGATTGTTTTTCAGTTTTTTTTTTCATGTGGTTTGCAATATTCATTTGCTACTTTCTGA
TTTCAGGGGGAGCTTGTGAAGGTTTTTGCCAATGATAACCGCAAGATTGCTTGCCGTAAGTTAA
TCTGTTTACTTAGAGAATCACCCTCTTGCCACTTGTCTGTTTACGTCTTCATATTAAGATGTTA
CGTCTTTTATGCTCCCTGAGCTGTTTCTGGTTGGTTGTGTTAGAGAATGTTTCCCTTAAATCTG
AAGCATTCGTTGAGAACTTGATAATATTTATTCTGAGACCTAAATGTAACAGTAATCCTCTTTT
TACTTTGACAGATCCAGATATGCAGAGCAATATAGAGAAGACTCTTCATACTGGTCATGCTTCA
TACAAAGTTTCTCTTGCGGTATAACATTTACCATTTCAACTCGTTTATTTAGCCTATGTTCTCT
CTGGCTTTTCTTGGATTAATCCTTCACATGCATGGACAGGTTGGCTTCGTGGATATATGGGAAG
CAGCAACATTATCTATTAAGAGAGAAGGTTACAGCATCAAGTGTATTAGTGATCTCACAATTGC
AGAAAAGTTCTCAGCATCTACTACTGTAAGACTTATGCCTTATTTGTTTCTGTCCTTTTTTGTC
ATAAAATAAATCGCGCTTCTCTGTGAAACGTGTGGCGGTGTGGGTATGGAGAGAGCTTTGCATG
TTGAAAGAGTTATTAGATAGGTTCTGAACTTTGAACTAATATTTATATCCGTCTTGTGATACCT
ATGTAGGTAACCATTCCGTTTGGGCAACCGGCAGAACTTGTTATCATTGGTTCTGATGGTAGTG
AACATTCCTTACGAGCAGATAATGGATCGCCAGACCTTATCGG
						
					

			
		

Sequences
Splice junction sequence	TAACCATTCCGTTTGGGCAACCGGCAGAACTTGTTATCATTGGTTCTGATGGTAGTGAACATTC CTTACGAGCAGATAATGGATCGCCAGACCTTATCGGgtggagatgatgacccgttaccaggtat agaggacctccaaatttcaggagaaccttatcctggacatgaacttcaggcttgtggttactcc attaatgg
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: 592 Transcript exons: 7924423-7924544,7924630-7924672,7924756-7924847,7925133- 7925181,7925394-7925464,7925550-7925663,7925837-7925937 GTGGAGATGATGACCCGTTACCAGGTATAGAGGACCTCCAAATTTCAGGAGAACCTTATCCTGG ACATGAACTTCAGGCTTGTGGTTACTCCATTAATGGAACAACAAGTTGTAATTTTGAGTGGGTC TGTCACCTAGAAGATGGATCTGTGAATTACATTGATGGAGCAAAGCAGCCAAATTACCTTGTCA CTGCTGATGATGTTGATTTATATCTTGCTATTGAGGTTCAGCCTTTGGATGACAGGAACCGAAA GGGGGAGCTTGTGAAGGTTTTTGCCAATGATAACCGCAAGATTGCTTGCCATCCAGATATGCAG AGCAATATAGAGAAGACTCTTCATACTGGTCATGCTTCATACAAAGTTTCTCTTGCGGTTGGCT TCGTGGATATATGGGAAGCAGCAACATTATCTATTAAGAGAGAAGGTTACAGCATCAAGTGTAT TAGTGATCTCACAATTGCAGAAAAGTTCTCAGCATCTACTACTGTAACCATTCCGTTTGGGCAA CCGGCAGAACTTGTTATCATTGGTTCTGATGGTAGTGAACATTCCTTACGAGCAGATAATGGAT CGCCAGACCTTATCGG
Genomic sequence	GTGGAGATGATGACCCGTTACCAGGTATAGAGGACCTCCAAATTTCAGGAGAACCTTATCCTGG ACATGAACTTCAGGCTTGTGGTTACTCCATTAATGGAACAACAAGTTGTAATTTTGAGGTGCGT ACTAAATAAAAAACAGAATCGCTTCCTTACTTATGTTGAATTGCATCTAATCTATCTTCTTCTG TTCTTCAATTTTCAGTGGGTCTGTCACCTAGAAGATGGATCTGTGAATTACATTGATGGTACAT TCCCCTCCTGCTGAATTTTGTTTCTTATTTCTTTATATGGAAATAAGAATCTAGTCGTGAACGA ACTTCTAATGCAGGAGCAAAGCAGCCAAATTACCTTGTCACTGCTGATGATGTTGATTTATATC TTGCTATTGAGGTTCAGCCTTTGGATGACAGGAACCGAAAGGTTAATATTTTTTTGTATGAATG AGATTATATGTTGAGTGGTTCTTTTCTGTGGAATACTGGAATCTTGATATGGATTTTAGTTTCC ATTATTTACCTCAGCATTTTGTTTCGTCGGCTAGATTTCATGCTAAAATGTTGTAGGGGAAAAG ATTCGCCTTTGGAAAGTACAGATACGATTTAACAGTTTTGTTAGATGTGCATACACTGTTGTTT TCTGCTGATTGTTTTTCAGTTTTTTTTTTCATGTGGTTTGCAATATTCATTTGCTACTTTCTGA TTTCAGGGGGAGCTTGTGAAGGTTTTTGCCAATGATAACCGCAAGATTGCTTGCCGTAAGTTAA TCTGTTTACTTAGAGAATCACCCTCTTGCCACTTGTCTGTTTACGTCTTCATATTAAGATGTTA CGTCTTTTATGCTCCCTGAGCTGTTTCTGGTTGGTTGTGTTAGAGAATGTTTCCCTTAAATCTG AAGCATTCGTTGAGAACTTGATAATATTTATTCTGAGACCTAAATGTAACAGTAATCCTCTTTT TACTTTGACAGATCCAGATATGCAGAGCAATATAGAGAAGACTCTTCATACTGGTCATGCTTCA TACAAAGTTTCTCTTGCGGTATAACATTTACCATTTCAACTCGTTTATTTAGCCTATGTTCTCT CTGGCTTTTCTTGGATTAATCCTTCACATGCATGGACAGGTTGGCTTCGTGGATATATGGGAAG CAGCAACATTATCTATTAAGAGAGAAGGTTACAGCATCAAGTGTATTAGTGATCTCACAATTGC AGAAAAGTTCTCAGCATCTACTACTGTAAGACTTATGCCTTATTTGTTTCTGTCCTTTTTTGTC ATAAAATAAATCGCGCTTCTCTGTGAAACGTGTGGCGGTGTGGGTATGGAGAGAGCTTTGCATG TTGAAAGAGTTATTAGATAGGTTCTGAACTTTGAACTAATATTTATATCCGTCTTGTGATACCT ATGTAGGTAACCATTCCGTTTGGGCAACCGGCAGAACTTGTTATCATTGGTTCTGATGGTAGTG AACATTCCTTACGAGCAGATAATGGATCGCCAGACCTTATCGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.19520121

Conservation Information
Conserved circRNAs	NA
PMCS	0.19520121

			
						 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
						Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT5G23490_circ_g.4

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