Plant Circular RNA Database

Detail information of AT2G17820_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT2G17820_circ_g.2
					
						ID in PlantcircBase
						ath_circ_013645
					
						Alias
						At_ciR2639
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 7743440-7744712  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							AT2G17820						
					
						Parent gene annotation
						
							Histidine kinase 1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT2G17820_circ_g.1 						
					
						Support reads
						3
					
						Tissues
						leaf
					
						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  
						
							CT-AC							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
						AT2G17820.1:2

General Information
CircRNA Name	AT2G17820_circ_g.2
ID in PlantcircBase	ath_circ_013645
Alias	At_ciR2639
Organism	Arabidpsis thaliana
Position	chr2: 7743440-7744712 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ
Parent gene	AT2G17820
Parent gene annotation	Histidine kinase 1
Parent gene strand	-
Alternative splicing	AT2G17820_circ_g.1
Support reads	3
Tissues	leaf
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	CT-AC 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	AT2G17820.1:2

			
						 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  
						
							GATCTACAGTGTCAGGAGTACTCAAAATCAAGTACAGTCTCATAAGAGTCCCTAAGCCATTCTT
CTGCACTACTTTGATTTCTCCACCCATTTTGTTAACctggcagtccatgaggatcaagtcataa
ggcgaggaattccgtaaactagtctcccgagttgtaactttgttagcggtttcttcttcgaacg
atttgtgt

						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
						
							CTGGCAGTCCATGAGGATCAAGTCATAAGGCGAGGAATTCCGTAAACTAGTCTCCCGAGTTGTA
ACTTTGTTAGCGGTTTCTTCTTCGAACGATTTGTGTTCTTCAGTTGGAGCTTGAGCATTGATAG
ACTTGTAGTTGAGGGAATCAACTGCTTGTTGTCCATCCCAGACTGCAGTTACAGTTGCTCCCAT
TTTCTCAAGCATTATGGTGGCTACTCGTTGAAGAACGGGTGTATCCTCTGCCAGCAAGATCCTT
ATACCTTCAAGAGATTTCTGATTCTTTCCATCCAACGCAATTCCTGAATACAGCCGATCCTTCC
AATCTTCTTCTTCTGGGTTCTTTTGAGTCATACTTGCAGATGTTGAGTCATCATTGCTGGTAGT
GGCATCGATGAGATAGTTCTTAAGCACTGGAGAGTGCAAGGTGCTTGGTTTAACAGATTTATCT
ACTTGTTTCTCGCCAGATGTCTCCGAGGAATCATCGGAACTGCAAGTGTCGAATTGTGTTGGAT
CAATTTCTAAGCAATCGTGGGATTCATCACTTCCGTTTCCTCTGTTTCTTAAGTCATTACACAA
GCCTCTCTTCCGGTTTTTTATTACAGCCTCCAGAATCTGGATCATTTTGGCCTTGTACAACGGT
TTGTTAACCATCATGACATGCCCTTTTCGTCTAAGTTCTGTTTTAACTGTATTGGAGGTGTCAT
GCTTCAGTAGCCAAGCAAACTTTGCTTTGTTGGAGAATCTGTCGAGGTAGTTAAGCTGTTCCTT
CCATATATTTGTGGTGAGATCAAGTACTCCGATATCCACCACTATGACAAACACAGGGTTCTTG
ATTTCTACTATATTTGAAAGCTCTGCTCTCAGTGGATCAGATATATTGTGCTGTGAATCAAAGC
TGTTGTCACGGCTTCCCGTCTCCAAGAGGTCTCTAATGATCTGAGTCAGCTCGTTCCAGTCTGA
TGCTTCAACAGTTGCAATGCCGTGTTTTCGCAACCACTTTGATGTGATCATTCTTGCTGTACTT
CCATACATGGAAAGCATAACCTGTAGCATTCAAAACCATTAACACTTTCACAAACACATAAGCT
TTAATTTATGATGCATTCGTCATTATTTCTTTCCCAAATTTACTTACCACGAGACCGTATTTGG
AGAAATCTGGCTGGATGTTTTGATCTACAGTGTCAGGAGTACTCAAAATCAAGTACAGTCTCAT
AAGAGTCCCTAAGCCATTCTTCTGCACTACTTTGATTTCTCCACCCATTTTGTTAAC

Sequences
Splice junction sequence	GATCTACAGTGTCAGGAGTACTCAAAATCAAGTACAGTCTCATAAGAGTCCCTAAGCCATTCTT CTGCACTACTTTGATTTCTCCACCCATTTTGTTAACctggcagtccatgaggatcaagtcataa ggcgaggaattccgtaaactagtctcccgagttgtaactttgttagcggtttcttcttcgaacg atttgtgt
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	CTGGCAGTCCATGAGGATCAAGTCATAAGGCGAGGAATTCCGTAAACTAGTCTCCCGAGTTGTA ACTTTGTTAGCGGTTTCTTCTTCGAACGATTTGTGTTCTTCAGTTGGAGCTTGAGCATTGATAG ACTTGTAGTTGAGGGAATCAACTGCTTGTTGTCCATCCCAGACTGCAGTTACAGTTGCTCCCAT TTTCTCAAGCATTATGGTGGCTACTCGTTGAAGAACGGGTGTATCCTCTGCCAGCAAGATCCTT ATACCTTCAAGAGATTTCTGATTCTTTCCATCCAACGCAATTCCTGAATACAGCCGATCCTTCC AATCTTCTTCTTCTGGGTTCTTTTGAGTCATACTTGCAGATGTTGAGTCATCATTGCTGGTAGT GGCATCGATGAGATAGTTCTTAAGCACTGGAGAGTGCAAGGTGCTTGGTTTAACAGATTTATCT ACTTGTTTCTCGCCAGATGTCTCCGAGGAATCATCGGAACTGCAAGTGTCGAATTGTGTTGGAT CAATTTCTAAGCAATCGTGGGATTCATCACTTCCGTTTCCTCTGTTTCTTAAGTCATTACACAA GCCTCTCTTCCGGTTTTTTATTACAGCCTCCAGAATCTGGATCATTTTGGCCTTGTACAACGGT TTGTTAACCATCATGACATGCCCTTTTCGTCTAAGTTCTGTTTTAACTGTATTGGAGGTGTCAT GCTTCAGTAGCCAAGCAAACTTTGCTTTGTTGGAGAATCTGTCGAGGTAGTTAAGCTGTTCCTT CCATATATTTGTGGTGAGATCAAGTACTCCGATATCCACCACTATGACAAACACAGGGTTCTTG ATTTCTACTATATTTGAAAGCTCTGCTCTCAGTGGATCAGATATATTGTGCTGTGAATCAAAGC TGTTGTCACGGCTTCCCGTCTCCAAGAGGTCTCTAATGATCTGAGTCAGCTCGTTCCAGTCTGA TGCTTCAACAGTTGCAATGCCGTGTTTTCGCAACCACTTTGATGTGATCATTCTTGCTGTACTT CCATACATGGAAAGCATAACCTGTAGCATTCAAAACCATTAACACTTTCACAAACACATAAGCT TTAATTTATGATGCATTCGTCATTATTTCTTTCCCAAATTTACTTACCACGAGACCGTATTTGG AGAAATCTGGCTGGATGTTTTGATCTACAGTGTCAGGAGTACTCAAAATCAAGTACAGTCTCAT AAGAGTCCCTAAGCCATTCTTCTGCACTACTTTGATTTCTCCACCCATTTTGTTAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.131902527

Conservation Information
Conserved circRNAs	NA
PMCS	0.131902527

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							7744704-7743442(-)
						
					

						Potential amino acid sequence
						
							MGGEIKVVQKNGLGTLMRLYLILSTPDTVDQNIQPDFSKYGLVVMLSMYGSTARMITSKWLRKH
GIATVEASDWNELTQIIRDLLETGSRDNSFDSQHNISDPLRAELSNIVEIKNPVFVIVVDIGVL
DLTTNIWKEQLNYLDRFSNKAKFAWLLKHDTSNTVKTELRRKGHVMMVNKPLYKAKMIQILEAV
IKNRKRGLCNDLRNRGNGSDESHDCLEIDPTQFDTCSSDDSSETSGEKQVDKSVKPSTLHSPVL
KNYLIDATTSNDDSTSASMTQKNPEEEDWKDRLYSGIALDGKNQKSLEGIRILLAEDTPVLQRV
ATIMLEKMGATVTAVWDGQQAVDSLNYKSINAQAPTEEHKSFEEETANKVTTRETSLRNSSPYD
LILMDCQVNKMGGEIKVVQKNGLGTLMRLYLILSTPDTVDQNIQPDFSKYGLVVMLSMYGSTAR
MITSKWLRKHGIATVEASDWNELTQIIRDLLETGSRDNSFDSQHNISDPLRAELSNIVEIKNPV
FVIVVDIGVLDLTTNIWKEQLNYLDRFSNKAKFAWLLKHDTSNTVKTELRRKGHVMMVNKPLYK
AKMIQILEAVIKNRKRGLCNDLRNRGNGSDESHDCLEIDPTQFDTCSSDDSSETSGEKQVDKSV
KPSTLHSPVLKNYLIDATTSNDDSTSASMTQKNPEEEDWKDRLYSGIALDGKNQKSLEGIRILL
AEDTPVLQRVATIMLEKMGATVTAVWDGQQAVDSLNYKSINAQAPTEEHKSFEEETANKVTTRE
TSLRNSSPYDLILMDCQVNKMGGEIKVVQKNGLGTLMRLYLILSTPDTVDQNIQPDFSKYGLVV
MLSMYGSTARMITSKWLRKHGIATVEASDWNELTQIIRDLLETGSRDNSFDSQHNISDPLRAEL
SNIVEIKNPVFVIVVDIGVLDLTTNIWKEQLNYLDRFSNKAKFAWLLKHDTSNTVKTELRRKGH
VMMVNKPLYKAKMIQILEAVIKNRKRGLCNDLRNRGNGSDESHDCLEIDPTQFDTCSSDDSSET
SGEKQVDKSVKPSTLHSPVLKNYLIDATTSNDDSTSASMTQKNPEEEDWKDRLYSGIALDGKNQ
KSLEGIRILLAEDTPVLQRVATIMLEKMGATVTAVWDGQQAVDSLNYKSINAQAPTEEHKSFEE
ETANKVTTRETSLRNSSPYDLILMDCQVNKMGGEIKVVQKNGLGTLMRLYLILSTPDTVDQNIQ
PDFSKYGLVVMLSMYGSTARMITSKWLRKHGIATVEASDWNELTQIIRDLLETGSRDNSFDSQH
NISDPLRAELSNIVEIKNPVFVIVVDIGVLDLTTNIWKEQLNYLDRFSNKAKFAWLLKHDTSNT
VKTELRRKGHVMMVNKPLYKAKMIQILEAVIKNRKRGLCNDLRNRGNGSDESHDCLEIDPTQFD
TCSSDDSSETSGEKQVDKSVKPSTLHSPVLKNYLIDATTSNDDSTSASMTQKNPEEEDWKDRLY
SGIALDGKNQKSLEGIRILLAEDTPVLQRVATIMLEKMGATVTAVWDGQQAVDSLNYKSINAQA
PTEEHKSFEEETANKVTTRETSLRNSSPYDLILMDCQ(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	7744704-7743442(-)
Potential amino acid sequence	MGGEIKVVQKNGLGTLMRLYLILSTPDTVDQNIQPDFSKYGLVVMLSMYGSTARMITSKWLRKH GIATVEASDWNELTQIIRDLLETGSRDNSFDSQHNISDPLRAELSNIVEIKNPVFVIVVDIGVL DLTTNIWKEQLNYLDRFSNKAKFAWLLKHDTSNTVKTELRRKGHVMMVNKPLYKAKMIQILEAV IKNRKRGLCNDLRNRGNGSDESHDCLEIDPTQFDTCSSDDSSETSGEKQVDKSVKPSTLHSPVL KNYLIDATTSNDDSTSASMTQKNPEEEDWKDRLYSGIALDGKNQKSLEGIRILLAEDTPVLQRV ATIMLEKMGATVTAVWDGQQAVDSLNYKSINAQAPTEEHKSFEEETANKVTTRETSLRNSSPYD LILMDCQVNKMGGEIKVVQKNGLGTLMRLYLILSTPDTVDQNIQPDFSKYGLVVMLSMYGSTAR MITSKWLRKHGIATVEASDWNELTQIIRDLLETGSRDNSFDSQHNISDPLRAELSNIVEIKNPV FVIVVDIGVLDLTTNIWKEQLNYLDRFSNKAKFAWLLKHDTSNTVKTELRRKGHVMMVNKPLYK AKMIQILEAVIKNRKRGLCNDLRNRGNGSDESHDCLEIDPTQFDTCSSDDSSETSGEKQVDKSV KPSTLHSPVLKNYLIDATTSNDDSTSASMTQKNPEEEDWKDRLYSGIALDGKNQKSLEGIRILL AEDTPVLQRVATIMLEKMGATVTAVWDGQQAVDSLNYKSINAQAPTEEHKSFEEETANKVTTRE TSLRNSSPYDLILMDCQVNKMGGEIKVVQKNGLGTLMRLYLILSTPDTVDQNIQPDFSKYGLVV MLSMYGSTARMITSKWLRKHGIATVEASDWNELTQIIRDLLETGSRDNSFDSQHNISDPLRAEL SNIVEIKNPVFVIVVDIGVLDLTTNIWKEQLNYLDRFSNKAKFAWLLKHDTSNTVKTELRRKGH VMMVNKPLYKAKMIQILEAVIKNRKRGLCNDLRNRGNGSDESHDCLEIDPTQFDTCSSDDSSET SGEKQVDKSVKPSTLHSPVLKNYLIDATTSNDDSTSASMTQKNPEEEDWKDRLYSGIALDGKNQ KSLEGIRILLAEDTPVLQRVATIMLEKMGATVTAVWDGQQAVDSLNYKSINAQAPTEEHKSFEE ETANKVTTRETSLRNSSPYDLILMDCQVNKMGGEIKVVQKNGLGTLMRLYLILSTPDTVDQNIQ PDFSKYGLVVMLSMYGSTARMITSKWLRKHGIATVEASDWNELTQIIRDLLETGSRDNSFDSQH NISDPLRAELSNIVEIKNPVFVIVVDIGVLDLTTNIWKEQLNYLDRFSNKAKFAWLLKHDTSNT VKTELRRKGHVMMVNKPLYKAKMIQILEAVIKNRKRGLCNDLRNRGNGSDESHDCLEIDPTQFD TCSSDDSSETSGEKQVDKSVKPSTLHSPVLKNYLIDATTSNDDSTSASMTQKNPEEEDWKDRLY SGIALDGKNQKSLEGIRILLAEDTPVLQRVATIMLEKMGATVTAVWDGQQAVDSLNYKSINAQA PTEEHKSFEEETANKVTTRETSLRNSSPYDLILMDCQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of AT2G17820_circ_g.2

Address

Any questions?

Supported by