Plant Circular RNA Database

Detail information of AT2G22540_circ_g.6

			
						 General Information
					
						CircRNA Name
						AT2G22540_circ_g.6
					
						ID in PlantcircBase
						ath_circ_014386
					
						Alias
						At_ciR539, AT2G22540_C2
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 9581871-9582430  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI, KNIFE, MapSplice, PcircRNA_finder, find_circ, circseq_cup, CIRI-full, CIRI2
					
						Parent gene
						
							AT2G22540						
					
						Parent gene annotation
						
							At2g22540
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT2G22540_circ_g.1 AT2G22540_circ_g.2 AT2G22540_circ_g.3 AT2G22540_circ_g.4 AT2G22540_circ_g.5 AT2G22540_circ_g.7 AT2G22540_circ_g.8 AT2G22540_circ_g.9 AT2G22540_circ_g.10 AT2G22540_circ_g.11 AT2G22540_circ_g.12 AT2G22540_circ_g.13 						
					
						Support reads
						3/7/4
					
						Tissues
						NA/leaf/leaf, aerial, seed
					
						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
						AT2G22540.2:4
AT2G22540.1:4
AT2G22540.3:4

General Information
CircRNA Name	AT2G22540_circ_g.6
ID in PlantcircBase	ath_circ_014386
Alias	At_ciR539, AT2G22540_C2
Organism	Arabidpsis thaliana
Position	chr2: 9581871-9582430 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRI, KNIFE, MapSplice, PcircRNA_finder, find_circ, circseq_cup, CIRI-full, CIRI2
Parent gene	AT2G22540
Parent gene annotation	At2g22540
Parent gene strand	+
Alternative splicing	AT2G22540_circ_g.1 AT2G22540_circ_g.2 AT2G22540_circ_g.3 AT2G22540_circ_g.4 AT2G22540_circ_g.5 AT2G22540_circ_g.7 AT2G22540_circ_g.8 AT2G22540_circ_g.9 AT2G22540_circ_g.10 AT2G22540_circ_g.11 AT2G22540_circ_g.12 AT2G22540_circ_g.13
Support reads	3/7/4
Tissues	NA/leaf/leaf, aerial, seed
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	AT2G22540.2:4 AT2G22540.1:4 AT2G22540.3:4

			
						 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  
						
							TTTTGGCAGTTTCAAGATCCAAAATTTTCATCTTCTTCTCTTTTTTTTTGGTGTTCAGGGAATG
CAATTGATGGATGAGAACAAGCGGTTGAGGCAGCAActggttgagaacagtgatcacgcccgaa
tgagtaaagaaattgcggacaagagccaccgactaaggtacgttatatatgtatattctatgac
ttttgaac

						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: 249
Transcript exons: 9581871-9582430
CTGGTTGAGAACAGTGATCACGCCCGAATGAGTAAGGAAATTGCGGACAAGAGCCACCGACTAA
GGCAAATGAGAGGAGAGGAACTTCAAGGACTTGACATTGAAGAGCTTCAGCAGCTAGAGAAGGC
CCTTGAAACTGGTTTGACGCGTGTGATTGAAACAAAGAGTGACAAGATTATGAGTGAGATCAGC
GAACTTCAGAAAAAGGGAATGCAATTGATGGATGAGAACAAGCGGTTGAGGCAGCAA
						
						Genomic sequence
						
							CTGGTTGAGAACAGTGATCACGCCCGAATGAGTAAAGAAATTGCGGACAAGAGCCACCGACTAA
GGTACGTTATATATGTATATTCTATGACTTTTGAACTAACTATCATTTTCTAACTAATTTTTTT
TTTGATCAACCACTATCATTTTCTAACTGTGTGTTTACATGATCATATATAGGCAAATGAGAGG
AGAGGAACTTCAAGGACTTGACATTGAAGAGCTTCAGCAGCTAGAGAAGGCCCTTGAAACTGGT
TTGACGCGTGTGATTGAAACAAAGGTTGTTAAGAAAATTACTTGATACCATGTATAAGTTTCTC
TAAGCTTACGAGTATGCAATTTACTAATACGAGATGTGTTTGCAGAGTGACAAGATTATGAGTG
AGATCAGCGAACTTCAGAAAAAGGTAATAATTAACCAAAATAACGTTTATTCTTTACTTGATGA
TTTCAATATTAATTTTGGCAGTTTCAAGATCCAAAATTTTCATCTTCTTCTCTTTTTTTTTGGT
GTTCAGGGAATGCAATTGATGGATGAGAACAAGCGGTTGAGGCAGCAA

Sequences
Splice junction sequence	TTTTGGCAGTTTCAAGATCCAAAATTTTCATCTTCTTCTCTTTTTTTTTGGTGTTCAGGGAATG CAATTGATGGATGAGAACAAGCGGTTGAGGCAGCAActggttgagaacagtgatcacgcccgaa tgagtaaagaaattgcggacaagagccaccgactaaggtacgttatatatgtatattctatgac ttttgaac
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: 249 Transcript exons: 9581871-9582430 CTGGTTGAGAACAGTGATCACGCCCGAATGAGTAAGGAAATTGCGGACAAGAGCCACCGACTAA GGCAAATGAGAGGAGAGGAACTTCAAGGACTTGACATTGAAGAGCTTCAGCAGCTAGAGAAGGC CCTTGAAACTGGTTTGACGCGTGTGATTGAAACAAAGAGTGACAAGATTATGAGTGAGATCAGC GAACTTCAGAAAAAGGGAATGCAATTGATGGATGAGAACAAGCGGTTGAGGCAGCAA
Genomic sequence	CTGGTTGAGAACAGTGATCACGCCCGAATGAGTAAAGAAATTGCGGACAAGAGCCACCGACTAA GGTACGTTATATATGTATATTCTATGACTTTTGAACTAACTATCATTTTCTAACTAATTTTTTT TTTGATCAACCACTATCATTTTCTAACTGTGTGTTTACATGATCATATATAGGCAAATGAGAGG AGAGGAACTTCAAGGACTTGACATTGAAGAGCTTCAGCAGCTAGAGAAGGCCCTTGAAACTGGT TTGACGCGTGTGATTGAAACAAAGGTTGTTAAGAAAATTACTTGATACCATGTATAAGTTTCTC TAAGCTTACGAGTATGCAATTTACTAATACGAGATGTGTTTGCAGAGTGACAAGATTATGAGTG AGATCAGCGAACTTCAGAAAAAGGTAATAATTAACCAAAATAACGTTTATTCTTTACTTGATGA TTTCAATATTAATTTTGGCAGTTTCAAGATCCAAAATTTTCATCTTCTTCTCTTTTTTTTTGGT GTTCAGGGAATGCAATTGATGGATGAGAACAAGCGGTTGAGGCAGCAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.162414807

Conservation Information
Conserved circRNAs	NA
PMCS	0.162414807

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9581898-9582427(+)
						
						Potential amino acid sequence
						
							MSKEIADKSHRLRQMRGEELQGLDIEELQQLEKALETGLTRVIETKSDKIMSEISELQKKGMQL
MDENKRLRQQLVENSDHARMSKEIADKSHRLRQMRGEELQGLDIEELQQLEKALETGLTRVIET
KSDKIMSEISELQKKGMQLMDENKRLRQQLVENSDHARMSKEIADKSHRLRQMRGEELQGLDIE
ELQQLEKALETGLTRVIETKSDKIMSEISELQKKGMQLMDENKRLRQQLVENSDHARMSKEIAD
KSHRLRQMRGEELQGLDIEELQQLEKALETGLTRVIETKSDKIMSEISELQKKGMQLMDENKRL
RQQ(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to methyl jasmonate

Functional Information
Coding potential	Y
Potential coding position	9581898-9582427(+)
Potential amino acid sequence	MSKEIADKSHRLRQMRGEELQGLDIEELQQLEKALETGLTRVIETKSDKIMSEISELQKKGMQL MDENKRLRQQLVENSDHARMSKEIADKSHRLRQMRGEELQGLDIEELQQLEKALETGLTRVIET KSDKIMSEISELQKKGMQLMDENKRLRQQLVENSDHARMSKEIADKSHRLRQMRGEELQGLDIE ELQQLEKALETGLTRVIETKSDKIMSEISELQKKGMQLMDENKRLRQQLVENSDHARMSKEIAD KSHRLRQMRGEELQGLDIEELQQLEKALETGLTRVIETKSDKIMSEISELQKKGMQLMDENKRL RQQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to methyl jasmonate

			
						 Other Information
					
						References
						Sun et al., 2016;Ye et al., 2015;Chu et al., 2017;Liu et al., 2017;Zhang et al., 2019

circRNA

Detail information of AT2G22540_circ_g.6

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