Plant Circular RNA Database

Detail information of AT3G51460_circ_g.9

			
						 General Information
					
						CircRNA Name
						AT3G51460_circ_g.9
					
						ID in PlantcircBase
						ath_circ_026963
					
						Alias
						At_ciR594, Ath_circ_FC2333, AT3G51460_C2
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 19094437-19095353  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI, MapSplice, circRNA_finder, find_circ, circseq_cup, CIRI-full, CIRI2
					
						Parent gene
						
							AT3G51460						
					
						Parent gene annotation
						
							RHD4
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G51460_circ_g.1 AT3G51460_circ_g.2 AT3G51460_circ_g.3 AT3G51460_circ_g.4 AT3G51460_circ_g.5 AT3G51460_circ_g.6 AT3G51460_circ_g.7 AT3G51460_circ_g.8 AT3G51460_circ_g.10 3_circ_ag.11 AT3G51460_circ_g.12 AT3G51460_circ_g.13 AT3G51480_circ_g.1 AT3G51510_circ_g.1 AT3G51510_circ_g.2 AT3G51510_circ_g.3 AT3G51520_circ_g.1 AT3G51530_circ_g.1 AT3G51550_circ_g.1 AT3G51550_circ_g.2 AT3G51550_circ_g.3 AT3G51550_circ_g.4 AT3G51550_circ_g.5 AT3G51550_circ_g.6 AT3G51620_circ_g.1 AT3G51620_circ_g.2 AT3G51630_circ_g.1 3_circ_ag.2 3_circ_ag.3 3_circ_ag.4 AT3G51670_circ_g.1 AT3G51670_circ_g.2 AT3G51710_circ_g.1 AT3G51730_circ_g.1 AT3G51730_circ_g.2 AT3G51730_circ_g.3 AT3G51730_circ_g.4 AT3G51730_circ_g.5 AT3G51730_circ_g.6 AT3G51730_circ_g.7 AT3G51730_circ_g.8 AT3G51740_circ_g.1 AT3G51740_circ_g.2 AT3G51770_circ_g.1 AT3G51770_circ_g.2 AT3G51800_circ_g.1 AT3G51800_circ_g.2 AT3G51800_circ_g.3 AT3G51800_circ_g.4 AT3G51800_circ_g.5 AT3G51810_circ_g.1 AT3G51810_circ_g.2 AT3G51820_circ_g.1 AT3G51820_circ_g.2 AT3G51820_circ_g.3 AT3G51820_circ_g.4 AT3G51820_circ_g.5 AT3G51820_circ_g.6 AT3G51820_circ_g.7 AT3G51820_circ_g.8 AT3G51820_circ_g.9 AT3G51820_circ_g.10 AT3G51820_circ_g.11 AT3G51820_circ_g.12 AT3G51830_circ_g.1 AT3G51830_circ_g.2 AT3G51830_circ_g.3 AT3G51830_circ_g.4 AT3G51830_circ_g.5 AT3G51830_circ_g.6 AT3G51830_circ_g.7 AT3G51830_circ_g.8 AT3G51830_circ_g.9 AT3G51830_circ_g.10 AT3G51830_circ_g.11 AT3G51830_circ_g.12 						
					
						Support reads
						5/49
					
						Tissues
						leaf/root, aerial, inflorescences, seed
					
						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-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
						AT3G51460.1:4

General Information
CircRNA Name	AT3G51460_circ_g.9
ID in PlantcircBase	ath_circ_026963
Alias	At_ciR594, Ath_circ_FC2333, AT3G51460_C2
Organism	Arabidpsis thaliana
Position	chr3: 19094437-19095353 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRI, MapSplice, circRNA_finder, find_circ, circseq_cup, CIRI-full, CIRI2
Parent gene	AT3G51460
Parent gene annotation	RHD4
Parent gene strand	+
Alternative splicing	AT3G51460_circ_g.1 AT3G51460_circ_g.2 AT3G51460_circ_g.3 AT3G51460_circ_g.4 AT3G51460_circ_g.5 AT3G51460_circ_g.6 AT3G51460_circ_g.7 AT3G51460_circ_g.8 AT3G51460_circ_g.10 3_circ_ag.11 AT3G51460_circ_g.12 AT3G51460_circ_g.13 AT3G51480_circ_g.1 AT3G51510_circ_g.1 AT3G51510_circ_g.2 AT3G51510_circ_g.3 AT3G51520_circ_g.1 AT3G51530_circ_g.1 AT3G51550_circ_g.1 AT3G51550_circ_g.2 AT3G51550_circ_g.3 AT3G51550_circ_g.4 AT3G51550_circ_g.5 AT3G51550_circ_g.6 AT3G51620_circ_g.1 AT3G51620_circ_g.2 AT3G51630_circ_g.1 3_circ_ag.2 3_circ_ag.3 3_circ_ag.4 AT3G51670_circ_g.1 AT3G51670_circ_g.2 AT3G51710_circ_g.1 AT3G51730_circ_g.1 AT3G51730_circ_g.2 AT3G51730_circ_g.3 AT3G51730_circ_g.4 AT3G51730_circ_g.5 AT3G51730_circ_g.6 AT3G51730_circ_g.7 AT3G51730_circ_g.8 AT3G51740_circ_g.1 AT3G51740_circ_g.2 AT3G51770_circ_g.1 AT3G51770_circ_g.2 AT3G51800_circ_g.1 AT3G51800_circ_g.2 AT3G51800_circ_g.3 AT3G51800_circ_g.4 AT3G51800_circ_g.5 AT3G51810_circ_g.1 AT3G51810_circ_g.2 AT3G51820_circ_g.1 AT3G51820_circ_g.2 AT3G51820_circ_g.3 AT3G51820_circ_g.4 AT3G51820_circ_g.5 AT3G51820_circ_g.6 AT3G51820_circ_g.7 AT3G51820_circ_g.8 AT3G51820_circ_g.9 AT3G51820_circ_g.10 AT3G51820_circ_g.11 AT3G51820_circ_g.12 AT3G51830_circ_g.1 AT3G51830_circ_g.2 AT3G51830_circ_g.3 AT3G51830_circ_g.4 AT3G51830_circ_g.5 AT3G51830_circ_g.6 AT3G51830_circ_g.7 AT3G51830_circ_g.8 AT3G51830_circ_g.9 AT3G51830_circ_g.10 AT3G51830_circ_g.11 AT3G51830_circ_g.12
Support reads	5/49
Tissues	leaf/root, aerial, inflorescences, seed
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-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	AT3G51460.1:4

			
						 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  
						
							GCATAGGGTGCTTTTCTTGTAGAAACGGATAGCTGAGCGTCACTTTTTGGACCTTAGGAAAAAA
TATGGATCAGTTTTGGCAGTTGATCTCGTTAACAAGccattggaagagatattgttgacattac
tctgattgctaggagatgcactaggagaaacggtacttgtctctatgtgcttttttttacccat
tattcttc

						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: 332
Transcript exons: 19094437-19095353
CCATTGGAAGAGATATTGTTGACATTACTCTGATTGCTAGGAGATGCACTAGGAGAAACGGTAC
ACGTATGTGGAGAAGAGGAGCGGATCTTGATGGCTATGTTGCTAATTTTGTGGAGACTGAGCAA
ATTGTACAGATGAATGGGTATACGTCATCATTTGTTCAGGTCAGAGGATCCATGCCTTTTATGT
GGGAGCAGGTTGTAGATCTGACTTACAAGCCCAAGTTTGAAATTGTCCAACCTGAAGAAGCTAA
ACGGATAGCTGAGCGTCACTTTTTGGACCTTAGGAAAAAATATGGATCAGTTTTGGCAGTTGAT
CTCGTTAACAAG
						
						Genomic sequence
						
							CCATTGGAAGAGATATTGTTGACATTACTCTGATTGCTAGGAGATGCACTAGGAGAAACGGTAC
TTGTCTCTATGTGCTTTTTTTTACCCATTATTCTTCGATTTCAAGTTACTCAATCTTTTTTATT
GCATTAAAGCCTAGTGTGAATCTGTAAGTAGGTCAGTCATTTGTTTGACTGTTAGAATCTTTCT
ACTAGACATAGCAAGAAATTCAGATATTGACAGCACTTGATGGGACTTGTTTTTAAAATAGGAA
AGCATGATGTTTGGCACCTTAACTTCAGTTGAAACTTAATTCTTTTAGATAGATAAGAGAGATA
TATGTCCTTGCCTGCTGGAAATTTAAATGCTGAGTATTGTGTTGTGAATGTGTCTTCTCCCTTA
TCCTGGATCGTTTTACAAGGTACACGTATGTGGAGAAGAGGAGCGGATCTTGATGGCTATGTTG
CTAATTTTGTGGAGACTGAGCAAATTGTACAGATGAATGGGTATACGTCATCATTTGTTCAGGT
AGCTTTTCTTACATGCTTGCATATTGTGAATTCCCTTAATGCTGCAAATCTTTGGTCATTTTAT
AATTACCTTTTTTTTTCATACAACTTTTCTCGAGACTGAGTTATCCACGATTAAACTCTTAATG
TTATTTTGCTTCCTACATTTGCAGGTCAGAGGATCCATGCCTTTTATGTGGGAGCAGGTTGTAG
ATCTGACTTACAAGCCCAAGTTTGAAATTGTCCAACCTGAAGAAGCTGTGAGTACTAATTTCTG
ACTAATTACCTACTCTTTTAGTAATTTATCTATTTCTTTCAAGTAAATTGCATAGGGTGCTTTT
CTTGTAGAAACGGATAGCTGAGCGTCACTTTTTGGACCTTAGGAAAAAATATGGATCAGTTTTG
GCAGTTGATCTCGTTAACAAG

Sequences
Splice junction sequence	GCATAGGGTGCTTTTCTTGTAGAAACGGATAGCTGAGCGTCACTTTTTGGACCTTAGGAAAAAA TATGGATCAGTTTTGGCAGTTGATCTCGTTAACAAGccattggaagagatattgttgacattac tctgattgctaggagatgcactaggagaaacggtacttgtctctatgtgcttttttttacccat tattcttc
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: 332 Transcript exons: 19094437-19095353 CCATTGGAAGAGATATTGTTGACATTACTCTGATTGCTAGGAGATGCACTAGGAGAAACGGTAC ACGTATGTGGAGAAGAGGAGCGGATCTTGATGGCTATGTTGCTAATTTTGTGGAGACTGAGCAA ATTGTACAGATGAATGGGTATACGTCATCATTTGTTCAGGTCAGAGGATCCATGCCTTTTATGT GGGAGCAGGTTGTAGATCTGACTTACAAGCCCAAGTTTGAAATTGTCCAACCTGAAGAAGCTAA ACGGATAGCTGAGCGTCACTTTTTGGACCTTAGGAAAAAATATGGATCAGTTTTGGCAGTTGAT CTCGTTAACAAG
Genomic sequence	CCATTGGAAGAGATATTGTTGACATTACTCTGATTGCTAGGAGATGCACTAGGAGAAACGGTAC TTGTCTCTATGTGCTTTTTTTTACCCATTATTCTTCGATTTCAAGTTACTCAATCTTTTTTATT GCATTAAAGCCTAGTGTGAATCTGTAAGTAGGTCAGTCATTTGTTTGACTGTTAGAATCTTTCT ACTAGACATAGCAAGAAATTCAGATATTGACAGCACTTGATGGGACTTGTTTTTAAAATAGGAA AGCATGATGTTTGGCACCTTAACTTCAGTTGAAACTTAATTCTTTTAGATAGATAAGAGAGATA TATGTCCTTGCCTGCTGGAAATTTAAATGCTGAGTATTGTGTTGTGAATGTGTCTTCTCCCTTA TCCTGGATCGTTTTACAAGGTACACGTATGTGGAGAAGAGGAGCGGATCTTGATGGCTATGTTG CTAATTTTGTGGAGACTGAGCAAATTGTACAGATGAATGGGTATACGTCATCATTTGTTCAGGT AGCTTTTCTTACATGCTTGCATATTGTGAATTCCCTTAATGCTGCAAATCTTTGGTCATTTTAT AATTACCTTTTTTTTTCATACAACTTTTCTCGAGACTGAGTTATCCACGATTAAACTCTTAATG TTATTTTGCTTCCTACATTTGCAGGTCAGAGGATCCATGCCTTTTATGTGGGAGCAGGTTGTAG ATCTGACTTACAAGCCCAAGTTTGAAATTGTCCAACCTGAAGAAGCTGTGAGTACTAATTTCTG ACTAATTACCTACTCTTTTAGTAATTTATCTATTTCTTTCAAGTAAATTGCATAGGGTGCTTTT CTTGTAGAAACGGATAGCTGAGCGTCACTTTTTGGACCTTAGGAAAAAATATGGATCAGTTTTG GCAGTTGATCTCGTTAACAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.476579957

Conservation Information
Conserved circRNAs	NA
PMCS	0.476579957

			
						 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
						responsive to methyl jasmonate

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	responsive to methyl jasmonate

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017;Chen et al., 2017a;Liu et al., 2017;Zhang et al., 2019

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Detail information of AT3G51460_circ_g.9

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