Plant Circular RNA Database

Detail information of AT2G39810_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT2G39810_circ_g.4
					
						ID in PlantcircBase
						ath_circ_017536
					
						Alias
						Chr2:16614067|16615133
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 16614067-16615133  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ei-circRNA							
									
						Identification method
						CIRCexplorer; CIRI
					
						Parent gene
						
							AT2G39810						
					
						Parent gene annotation
						
							HOS1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT2G39810_circ_g.1 AT2G39810_circ_g.2 AT2G39810_circ_g.3 AT2G39810_circ_g.5 AT2G39810_circ_g.6 						
					
						Support reads
						16
					
						Tissues
						seedling
					
						Exon boundary  
						
							No-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-CA							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
						AT2G39810.2:2
AT2G39810.1:2

General Information
CircRNA Name	AT2G39810_circ_g.4
ID in PlantcircBase	ath_circ_017536
Alias	Chr2:16614067\|16615133
Organism	Arabidpsis thaliana
Position	chr2: 16614067-16615133 JBrowse»
Reference genome	TAIR10.38
Type	ei-circRNA
Identification method	CIRCexplorer; CIRI
Parent gene	AT2G39810
Parent gene annotation	HOS1
Parent gene strand	+
Alternative splicing	AT2G39810_circ_g.1 AT2G39810_circ_g.2 AT2G39810_circ_g.3 AT2G39810_circ_g.5 AT2G39810_circ_g.6
Support reads	16
Tissues	seedling
Exon boundary	No-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-CA 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	AT2G39810.2:2 AT2G39810.1:2

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							YES							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   
						
							Convergent:(F):GGACATAATGGTCTGGTGCATCA
(R):TCCTGACTGTATTCTGGCTCTCT.Divergent:(F):AGAGAGCCAGAATACAGTCAGGA
(R)CACACTACATATGCCAGCCACC
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	YES 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	Convergent:(F):GGACATAATGGTCTGGTGCATCA (R):TCCTGACTGTATTCTGGCTCTCT.Divergent:(F):AGAGAGCCAGAATACAGTCAGGA (R)CACACTACATATGCCAGCCACC 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  
						
							GGGAACTTCAGGATCTTATCCATTTGAGAATCTTAGAACTGCTGCTGACATGCTCTTTTTACAT
GGCGGTTCAGATTTGGTTGTTGCGAAGCAAGCAATTgataatcttgaaacaaaagagatgcaag
cgtggttagataaactcctaaggtgttccaaacaggtggctggcatatgtagtgtgctcgaagt
tatggaat

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							GATAATCTTGAAACAAAAGAGATGCAAGCGTGGTTAGATAAACTCCTAAGGTGTTCCAAACAGG
TGGCTGGCATATGTAGTGTGCTCGAAGTTATGGAATCAGCTTTTAAGGGTTCTGTGTCACCTCA
GCTTCAAGATGTGCAGACGCTGAGAGAGAACATTGGTAAAACAAAGCAGGTCAGCCATGATTTC
ATTTCATTGATATCCAAACAGTTTTGCAAAAGTATGCTTAAATAACTCTCTTTATCCCCCTTAG
AAATATCCGTTGTACATTGAAGTTTCCTACGTGCATTAATGTTTAGTTTGCCTCTGTCATAGAA
TGAGTTACTTGTTTTGTATACGGCTTGCAGTAAAGTTTGTACTGTAAAAGCTTTGCATTTAGAT
GTATGAAAGGCACGATAATGGTCTTCCATCATCAGCTTGGATCTGATTTTCTATCCCTAGCTTT
GTGACTTTATTCTTCTTTTCTTTTTTAATGTCATTGCATATTAGTGAATGTAGATGGGGTATAT
GTAACCTATCTTTATATGACATACTGAATAGTAAATGAGTATAACCTTATGGCTTCTGACCAGA
GAGTGTTTTAAATAGATCAGCTCTTTAGCTATTGGTGCAAGATCACTGAGCTTACGTGTGCTTA
CCCTATTCTTTTTATTTTATTTCAGCATTTGGACATAATGGTCTGGTGCATCAGACATGGATTT
CTGGATGATGTGAGGTCTCGATATTCGAATTTCACATCGTGGAATGCACTGGTAGGGGAAAGAA
AATCAAATGCAGTTAAGCGTGCATGGCCTGATGCTGTAGACCAGTCTTCAGATTGCAGTGTACA
GAGTGCTTCCCTCTTTATTGAGGATGCTTTAGAAAATCTTGAGAGAGAGCCAGAATACAGTCAG
GAAATAGGTGCCGACCTAGAAGTTGGACGTTTACAGAAGGATAAGAGATCATTTCTTAGGTCCA
AAATAGAGGGAACTTCAGGATCTTATCCATTTGAGAATCTTAGAACTGCTGCTGACATGCTCTT
TTTACATGGCGGTTCAGATTTGGTTGTTGCGAAGCAAGCAATT

Sequences
Splice junction sequence	GGGAACTTCAGGATCTTATCCATTTGAGAATCTTAGAACTGCTGCTGACATGCTCTTTTTACAT GGCGGTTCAGATTTGGTTGTTGCGAAGCAAGCAATTgataatcttgaaacaaaagagatgcaag cgtggttagataaactcctaaggtgttccaaacaggtggctggcatatgtagtgtgctcgaagt tatggaat
Assembled circRNA sequence	NA 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	NA
Genomic sequence	GATAATCTTGAAACAAAAGAGATGCAAGCGTGGTTAGATAAACTCCTAAGGTGTTCCAAACAGG TGGCTGGCATATGTAGTGTGCTCGAAGTTATGGAATCAGCTTTTAAGGGTTCTGTGTCACCTCA GCTTCAAGATGTGCAGACGCTGAGAGAGAACATTGGTAAAACAAAGCAGGTCAGCCATGATTTC ATTTCATTGATATCCAAACAGTTTTGCAAAAGTATGCTTAAATAACTCTCTTTATCCCCCTTAG AAATATCCGTTGTACATTGAAGTTTCCTACGTGCATTAATGTTTAGTTTGCCTCTGTCATAGAA TGAGTTACTTGTTTTGTATACGGCTTGCAGTAAAGTTTGTACTGTAAAAGCTTTGCATTTAGAT GTATGAAAGGCACGATAATGGTCTTCCATCATCAGCTTGGATCTGATTTTCTATCCCTAGCTTT GTGACTTTATTCTTCTTTTCTTTTTTAATGTCATTGCATATTAGTGAATGTAGATGGGGTATAT GTAACCTATCTTTATATGACATACTGAATAGTAAATGAGTATAACCTTATGGCTTCTGACCAGA GAGTGTTTTAAATAGATCAGCTCTTTAGCTATTGGTGCAAGATCACTGAGCTTACGTGTGCTTA CCCTATTCTTTTTATTTTATTTCAGCATTTGGACATAATGGTCTGGTGCATCAGACATGGATTT CTGGATGATGTGAGGTCTCGATATTCGAATTTCACATCGTGGAATGCACTGGTAGGGGAAAGAA AATCAAATGCAGTTAAGCGTGCATGGCCTGATGCTGTAGACCAGTCTTCAGATTGCAGTGTACA GAGTGCTTCCCTCTTTATTGAGGATGCTTTAGAAAATCTTGAGAGAGAGCCAGAATACAGTCAG GAAATAGGTGCCGACCTAGAAGTTGGACGTTTACAGAAGGATAAGAGATCATTTCTTAGGTCCA AAATAGAGGGAACTTCAGGATCTTATCCATTTGAGAATCTTAGAACTGCTGCTGACATGCTCTT TTTACATGGCGGTTCAGATTTGGTTGTTGCGAAGCAAGCAATT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.13544586

Conservation Information
Conserved circRNAs	NA
PMCS	0.13544586

			
						 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
						responsive to methyl jasmonate (validated)

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	responsive to methyl jasmonate (validated)

			
						 Other Information
					
						References
						Zhang et al., 2020

circRNA

Detail information of AT2G39810_circ_g.4

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