Plant Circular RNA Database

Detail information of AT4G22890_circ_g.10

			
						 General Information
					
						CircRNA Name
						AT4G22890_circ_g.10
					
						ID in PlantcircBase
						ath_circ_032249
					
						Alias
						4:12008378-12009185
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 12008378-12009185  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT4G22890						
					
						Parent gene annotation
						
							PGR5-LIKE A
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G22890_circ_g.1 AT4G22890_circ_g.2 AT4G22890_circ_g.3 AT4G22890_circ_g.4 AT4G22890_circ_g.5 AT4G22890_circ_g.6 AT4G22890_circ_g.7 AT4G22890_circ_g.8 AT4G22890_circ_g.9 						
					
						Support reads
						2
					
						Tissues
						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  
						
							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
						AT4G22890.2:4
AT4G22890.3:5
AT4G22890.4:5
AT4G22890.1:5
AT4G22890.5:5

General Information
CircRNA Name	AT4G22890_circ_g.10
ID in PlantcircBase	ath_circ_032249
Alias	4:12008378-12009185
Organism	Arabidpsis thaliana
Position	chr4: 12008378-12009185 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT4G22890
Parent gene annotation	PGR5-LIKE A
Parent gene strand	+
Alternative splicing	AT4G22890_circ_g.1 AT4G22890_circ_g.2 AT4G22890_circ_g.3 AT4G22890_circ_g.4 AT4G22890_circ_g.5 AT4G22890_circ_g.6 AT4G22890_circ_g.7 AT4G22890_circ_g.8 AT4G22890_circ_g.9
Support reads	2
Tissues	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	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	AT4G22890.2:4 AT4G22890.3:5 AT4G22890.4:5 AT4G22890.1:5 AT4G22890.5:5

			
						 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  
						
							TTGATTATCTCTGTTTTTAGCTGCGGAACCGCGATGGTGTATGACTCGGGTTCTAGGTTGATCA
CATTGCCAGAAGGAAGCCAAGCTTAAACCCTGTGAGattgatggtagcgacattgtgagcgagg
gtccaagatgcagtctccgtagtaaaaaggtaaatagaacataagattcattgttaatattaga
ttatagat

						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: 475
Transcript exons: 12008378-12008434,12008519-12008595,12008689-12008851,12
008931-12009028,12009106-12009185
ATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGTAAAAAGGTGTATA
GTGATCTCGCTGTAGATTATTTCAAAATGTTATTGTTGAATGTTCCAGCAACCGTTGTTGCTCT
CGGACTCTTTTTCTTCCTGGACGACATTACAGGTTTTGAGATCACATACATCATGGAGCTTCCA
GAACCATACAGTTTCATATTCACTTGGTTCGCTGCTGTGCCTGTGATTGTATATCTGGCTTTAT
CAATCACCAAATTGATCATCAAGGACTTCTTGATCTTGAAGGGTCCTTGTCCGAATTGTGGAAC
GGAAAACACCTCCTTCTTTGGAACAATTCTGTCAATCTCCAGCGGCGGCAAAACCAACACTGTC
AAATGCACCAACTGCGGAACCGCGATGGTGTATGACTCGGGTTCTAGGTTGATCACATTGCCAG
AAGGAAGCCAAGCTTAAACCCTGTGAG
						
						Genomic sequence
						
							ATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGTAAAAAGGTAAATA
GAACATAAGATTCATTGTTAATATTAGATTATAGATAGATACTAATTTTCAGTCTTTATGAACT
TCCTCAAATGTAGGTGTATAGTGATCTCGCTGTAGATTATTTCAAAATGTTATTGTTGAATGTT
CCAGCAACCGTTGTTGCTCTCGGACTGTGAGTCTCTATACCGAGTTTTCTATTCAAACATCCAA
ATCATATGAAACCCATATTTCGTCTTTGTTTATTCATTCAATTCTGTACTTGCAGCTTTTTCTT
CCTGGACGACATTACAGGTTTTGAGATCACATACATCATGGAGCTTCCAGAACCATACAGTTTC
ATATTCACTTGGTTCGCTGCTGTGCCTGTGATTGTATATCTGGCTTTATCAATCACCAAATTGA
TCATCAAGGACTTCTTGATCTTGAAGGTAAGAACCATTACCATTACTCAAGATTGCAAAAGAAA
AACATCAAAGAGCCTTTTTATGAATGTTTCTTGTTTCACAGGGTCCTTGTCCGAATTGTGGAAC
GGAAAACACCTCCTTCTTTGGAACAATTCTGTCAATCTCCAGCGGCGGCAAAACCAACACTGTC
AAATGCACCAAGTAAGATTTTACCTTCGAATATGGTTTCAAAAGTGTAACATATTACTATCTGA
TTCTTTGATTATCTCTGTTTTTAGCTGCGGAACCGCGATGGTGTATGACTCGGGTTCTAGGTTG
ATCACATTGCCAGAAGGAAGCCAAGCTTAAACCCTGTGAG

Sequences
Splice junction sequence	TTGATTATCTCTGTTTTTAGCTGCGGAACCGCGATGGTGTATGACTCGGGTTCTAGGTTGATCA CATTGCCAGAAGGAAGCCAAGCTTAAACCCTGTGAGattgatggtagcgacattgtgagcgagg gtccaagatgcagtctccgtagtaaaaaggtaaatagaacataagattcattgttaatattaga ttatagat
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: 475 Transcript exons: 12008378-12008434,12008519-12008595,12008689-12008851,12 008931-12009028,12009106-12009185 ATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGTAAAAAGGTGTATA GTGATCTCGCTGTAGATTATTTCAAAATGTTATTGTTGAATGTTCCAGCAACCGTTGTTGCTCT CGGACTCTTTTTCTTCCTGGACGACATTACAGGTTTTGAGATCACATACATCATGGAGCTTCCA GAACCATACAGTTTCATATTCACTTGGTTCGCTGCTGTGCCTGTGATTGTATATCTGGCTTTAT CAATCACCAAATTGATCATCAAGGACTTCTTGATCTTGAAGGGTCCTTGTCCGAATTGTGGAAC GGAAAACACCTCCTTCTTTGGAACAATTCTGTCAATCTCCAGCGGCGGCAAAACCAACACTGTC AAATGCACCAACTGCGGAACCGCGATGGTGTATGACTCGGGTTCTAGGTTGATCACATTGCCAG AAGGAAGCCAAGCTTAAACCCTGTGAG
Genomic sequence	ATTGATGGTAGCGACATTGTGAGCGAGGGTCCAAGATGCAGTCTCCGTAGTAAAAAGGTAAATA GAACATAAGATTCATTGTTAATATTAGATTATAGATAGATACTAATTTTCAGTCTTTATGAACT TCCTCAAATGTAGGTGTATAGTGATCTCGCTGTAGATTATTTCAAAATGTTATTGTTGAATGTT CCAGCAACCGTTGTTGCTCTCGGACTGTGAGTCTCTATACCGAGTTTTCTATTCAAACATCCAA ATCATATGAAACCCATATTTCGTCTTTGTTTATTCATTCAATTCTGTACTTGCAGCTTTTTCTT CCTGGACGACATTACAGGTTTTGAGATCACATACATCATGGAGCTTCCAGAACCATACAGTTTC ATATTCACTTGGTTCGCTGCTGTGCCTGTGATTGTATATCTGGCTTTATCAATCACCAAATTGA TCATCAAGGACTTCTTGATCTTGAAGGTAAGAACCATTACCATTACTCAAGATTGCAAAAGAAA AACATCAAAGAGCCTTTTTATGAATGTTTCTTGTTTCACAGGGTCCTTGTCCGAATTGTGGAAC GGAAAACACCTCCTTCTTTGGAACAATTCTGTCAATCTCCAGCGGCGGCAAAACCAACACTGTC AAATGCACCAAGTAAGATTTTACCTTCGAATATGGTTTCAAAAGTGTAACATATTACTATCTGA TTCTTTGATTATCTCTGTTTTTAGCTGCGGAACCGCGATGGTGTATGACTCGGGTTCTAGGTTG ATCACATTGCCAGAAGGAAGCCAAGCTTAAACCCTGTGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.239374672

Conservation Information
Conserved circRNAs	NA
PMCS	0.239374672

			
						 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 AT4G22890_circ_g.10

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