Plant Circular RNA Database

Detail information of AT5G23450_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT5G23450_circ_g.1
					
						ID in PlantcircBase
						ath_circ_040030
					
						Alias
						Ath_circ_FC3475
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 7905333-7907189  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							AT5G23450						
					
						Parent gene annotation
						
							Long-chain base (LCB) kinase 1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G23450_circ_g.2 AT5G23450_circ_g.3 AT5G23450_circ_g.4 						
					
						Support reads
						2
					
						Tissues
						whole_plant
					
						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
						AT5G23450.1:3
AT5G23450.3:3
AT5G23450.4:3
AT5G23450.5:3
AT5G23450.2:3

General Information
CircRNA Name	AT5G23450_circ_g.1
ID in PlantcircBase	ath_circ_040030
Alias	Ath_circ_FC3475
Organism	Arabidpsis thaliana
Position	chr5: 7905333-7907189 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	AT5G23450
Parent gene annotation	Long-chain base (LCB) kinase 1
Parent gene strand	-
Alternative splicing	AT5G23450_circ_g.2 AT5G23450_circ_g.3 AT5G23450_circ_g.4
Support reads	2
Tissues	whole_plant
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	AT5G23450.1:3 AT5G23450.3:3 AT5G23450.4:3 AT5G23450.5:3 AT5G23450.2:3

			
						 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  
						
							CAGTCCAAACTAACGAGTTATCAGAACCAGCAGGTACTATTCCAATTGGGATAGAAACTCCTTC
TTTCGGATTGCTTCGAGTAAGCAGACCATTAAGAACctttacacactcaacatacggaagagaa
aggtgtcgacctgtttgcaaaagtataaaaaacctcagtaacctcagtcttccacacccatgaa
ccaagagc

									
								

					

						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
						
							CTTTACACACTCAACATACGGAAGAGAAAGGTGTCGACCTGTTTGCAAAAGTATAAAAAACCTC
AGTAACCTCAGTCTTCCACACCCATGAACCAAGAGCATATCCATTGTACCATCATCATGTTCTG
AATTGGGAGCCACGACTTGGGAACTTTGCACAGTCCGACAAGCATGGTTACAGACCATGATGCC
GAGGAAATGTCCCTTTCTCGAAACCCATTTATCCTCAAATATTGGAGTGATGCTCTGTTTCCTC
AGTCCTGTCTCTATATCCTCAGGAGGACCAGGCAGCTCGATCGAATTTTCTACATCCCAAGCAG
ACGGTTCAGTGTCCCATTTGGGTCCTGCATCCCAGATTGGACCTGGATCAGATACAGTAGATGA
TATATCTTCCCTGTCTTGACCACCGGTATTCCCCCATGAACATCGAGTTGGAGGATCCTGCACG
GATGTTAACCCCATCCATCCTTTATCCATTCTTGACTTTGATCTTGTCCTTGGCCAATTAGGGG
TTGTTGACTGTGCTTGAGGATGAATAACCTCTGGCTCAGCCGTAACATCTCTTCTTCCAGAGGA
CAAGCGTTTCATTTTAGGATCTATTCCACGGACATATTCAGACGGCTCAGTGCTGGCATGTGTG
CTGCTACAAGTGTCTAATTCGCCTACGCTTGGGGTCATTATGGAGTCAATACTTGATAAACTGG
AGGCTCTAGGAAATCCTTCTCTGCTTGATCTCCTCATTACATCCGTGTAGAGATCTTGCATATC
CACAGCTTCCTTTTCAAGTCGAATTTTGCCTTCTGCATCCTCTTTTTGTGCCGGAAGATATTCC
ACTTCATAGCTATACTTCGGCAAACACATGAACTTGAGGAATCCAGCAACAAAGTAACGCAAAG
GACCAAACCGTTTTTGGTATTTTTCAGAGAGCTCCAAAACTGCAAATAGATAATGACAAGAAAA
ACCATGAAATTTAGTTATAGCAGGTGAATGCCACAAACATTATACAGTATTCATGAAGGTAATT
ATATGTGCAATAATCCTGACGTCAAACACGAGACAGCGTCCAATAGCTCAAACTAATACATCAA
ACACACACCGGAGCTGTTAAAGAAATGGAGAGAGATTTACAGCCTTTTGCACAAGTTCAATGTA
TTTGAGTTTATCCATGATACGTTTGAATAACTAGGCGATTTTCTGCTTCTAACTCATCATCAGA
AGAGTGCACATTCTGCAATATTCTATGAAATTATGTGTCTTGGGAGTCAGCATAGTGTTCACAC
TGTGCCAGTTAAAATATTTAGAAGATAAACTGAAAAATTACAGTAAGGAAGATTTAAAAACTCT
CCTCTAAAATGCATGAAAGATCTAAACAGTTGCAGACACGGTGAATGAAACAAAGAAGCTAGGA
ATACAGATTCAAACCTAACTACACTTGAGAAACTGTTTATCATTAGAAAATCATACAAGACAAA
GCACACAGGTATCCTCACTTACCATCGCTAACAAAACCATAGTAGGAAACAGTCATTCCAAAGT
GTATAATACCGGTATGAATCCATTCAACAGCAAAGACATCAGTAGCTGTTAGGCCACCCTAAAC
CAAAAAAAAAAAAATCTTTCACTGAGAAAATATTAATTAAGTAGAAGCTAATTAATGTTGGCGG
CTGGATAAAACAAAGCAGGGACCAATAGGATTTTAGGCGGGGTTACCTTCACAATAGAGAGTGC
TGCAGAAATAGGATCTCTTACACCAAGGACAGTCCAAACTAACGAGTTATCAGAACCAGCAGGT
ACTATTCCAATTGGGATAGAAACTCCTTCTTTCGGATTGCTTCGAGTAAGCAGACCATTAAGAA
C
						
					

			
		

Sequences
Splice junction sequence	CAGTCCAAACTAACGAGTTATCAGAACCAGCAGGTACTATTCCAATTGGGATAGAAACTCCTTC TTTCGGATTGCTTCGAGTAAGCAGACCATTAAGAACctttacacactcaacatacggaagagaa aggtgtcgacctgtttgcaaaagtataaaaaacctcagtaacctcagtcttccacacccatgaa ccaagagc
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	CTTTACACACTCAACATACGGAAGAGAAAGGTGTCGACCTGTTTGCAAAAGTATAAAAAACCTC AGTAACCTCAGTCTTCCACACCCATGAACCAAGAGCATATCCATTGTACCATCATCATGTTCTG AATTGGGAGCCACGACTTGGGAACTTTGCACAGTCCGACAAGCATGGTTACAGACCATGATGCC GAGGAAATGTCCCTTTCTCGAAACCCATTTATCCTCAAATATTGGAGTGATGCTCTGTTTCCTC AGTCCTGTCTCTATATCCTCAGGAGGACCAGGCAGCTCGATCGAATTTTCTACATCCCAAGCAG ACGGTTCAGTGTCCCATTTGGGTCCTGCATCCCAGATTGGACCTGGATCAGATACAGTAGATGA TATATCTTCCCTGTCTTGACCACCGGTATTCCCCCATGAACATCGAGTTGGAGGATCCTGCACG GATGTTAACCCCATCCATCCTTTATCCATTCTTGACTTTGATCTTGTCCTTGGCCAATTAGGGG TTGTTGACTGTGCTTGAGGATGAATAACCTCTGGCTCAGCCGTAACATCTCTTCTTCCAGAGGA CAAGCGTTTCATTTTAGGATCTATTCCACGGACATATTCAGACGGCTCAGTGCTGGCATGTGTG CTGCTACAAGTGTCTAATTCGCCTACGCTTGGGGTCATTATGGAGTCAATACTTGATAAACTGG AGGCTCTAGGAAATCCTTCTCTGCTTGATCTCCTCATTACATCCGTGTAGAGATCTTGCATATC CACAGCTTCCTTTTCAAGTCGAATTTTGCCTTCTGCATCCTCTTTTTGTGCCGGAAGATATTCC ACTTCATAGCTATACTTCGGCAAACACATGAACTTGAGGAATCCAGCAACAAAGTAACGCAAAG GACCAAACCGTTTTTGGTATTTTTCAGAGAGCTCCAAAACTGCAAATAGATAATGACAAGAAAA ACCATGAAATTTAGTTATAGCAGGTGAATGCCACAAACATTATACAGTATTCATGAAGGTAATT ATATGTGCAATAATCCTGACGTCAAACACGAGACAGCGTCCAATAGCTCAAACTAATACATCAA ACACACACCGGAGCTGTTAAAGAAATGGAGAGAGATTTACAGCCTTTTGCACAAGTTCAATGTA TTTGAGTTTATCCATGATACGTTTGAATAACTAGGCGATTTTCTGCTTCTAACTCATCATCAGA AGAGTGCACATTCTGCAATATTCTATGAAATTATGTGTCTTGGGAGTCAGCATAGTGTTCACAC TGTGCCAGTTAAAATATTTAGAAGATAAACTGAAAAATTACAGTAAGGAAGATTTAAAAACTCT CCTCTAAAATGCATGAAAGATCTAAACAGTTGCAGACACGGTGAATGAAACAAAGAAGCTAGGA ATACAGATTCAAACCTAACTACACTTGAGAAACTGTTTATCATTAGAAAATCATACAAGACAAA GCACACAGGTATCCTCACTTACCATCGCTAACAAAACCATAGTAGGAAACAGTCATTCCAAAGT GTATAATACCGGTATGAATCCATTCAACAGCAAAGACATCAGTAGCTGTTAGGCCACCCTAAAC CAAAAAAAAAAAAATCTTTCACTGAGAAAATATTAATTAAGTAGAAGCTAATTAATGTTGGCGG CTGGATAAAACAAAGCAGGGACCAATAGGATTTTAGGCGGGGTTACCTTCACAATAGAGAGTGC TGCAGAAATAGGATCTCTTACACCAAGGACAGTCCAAACTAACGAGTTATCAGAACCAGCAGGT ACTATTCCAATTGGGATAGAAACTCCTTCTTTCGGATTGCTTCGAGTAAGCAGACCATTAAGAA C

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.150295315

Conservation Information
Conserved circRNAs	NA
PMCS	0.150295315

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							7906861-7905335(-)
						
					

						Potential amino acid sequence
						
							MTVSYYGFVSDVLELSEKYQKRFGPLRYFVAGFLKFMCLPKYSYEVEYLPAQKEDAEGKIRLEK
EAVDMQDLYTDVMRRSSREGFPRASSLSSIDSIMTPSVGELDTCSSTHASTEPSEYVRGIDPKM
KRLSSGRRDVTAEPEVIHPQAQSTTPNWPRTRSKSRMDKGWMGLTSVQDPPTRCSWGNTGGQDR
EDISSTVSDPGPIWDAGPKWDTEPSAWDVENSIELPGPPEDIETGLRKQSITPIFEDKWVSRKG
HFLGIMVCNHACRTVQSSQVVAPNSEHDDGTMDMLLVHGCGRLRLLRFFILLQTGRHLSLPYVE
CVKVLNGLLTRSNPKEGVSIPIGIVPAGSDNSLVWTVLGVRDPISAALSIVKGGLTATDVFAVE
WIHTGIIHFGMTVSYYGFVSDVLELSEKYQKRFGPLRYFVAGFLKFMCLPKYSYEVEYLPAQKE
DAEGKIRLEKEAVDMQDLYTDVMRRSSREGFPRASSLSSIDSIMTPSVGELDTCSSTHASTEPS
EYVRGIDPKMKRLSSGRRDVTAEPEVIHPQAQSTTPNWPRTRSKSRMDKGWMGLTSVQDPPTRC
SWGNTGGQDREDISSTVSDPGPIWDAGPKWDTEPSAWDVENSIELPGPPEDIETGLRKQSITPI
FEDKWVSRKGHFLGIMVCNHACRTVQSSQVVAPNSEHDDGTMDMLLVHGCGRLRLLRFFILLQT
GRHLSLPYVECVKVLNGLLTRSNPKEGVSIPIGIVPAGSDNSLVWTVLGVRDPISAALSIVKGG
LTATDVFAVEWIHTGIIHFGMTVSYYGFVSDVLELSEKYQKRFGPLRYFVAGFLKFMCLPKYSY
EVEYLPAQKEDAEGKIRLEKEAVDMQDLYTDVMRRSSREGFPRASSLSSIDSIMTPSVGELDTC
SSTHASTEPSEYVRGIDPKMKRLSSGRRDVTAEPEVIHPQAQSTTPNWPRTRSKSRMDKGWMGL
TSVQDPPTRCSWGNTGGQDREDISSTVSDPGPIWDAGPKWDTEPSAWDVENSIELPGPPEDIET
GLRKQSITPIFEDKWVSRKGHFLGIMVCNHACRTVQSSQVVAPNSEHDDGTMDMLLVHGCGRLR
LLRFFILLQTGRHLSLPYVECVKVLNGLLTRSNPKEGVSIPIGIVPAGSDNSLVWTVLGVRDPI
SAALSIVKGGLTATDVFAVEWIHTGIIHFGMTVSYYGFVSDVLELSEKYQKRFGPLRYFVAGFL
KFMCLPKYSYEVEYLPAQKEDAEGKIRLEKEAVDMQDLYTDVMRRSSREGFPRASSLSSIDSIM
TPSVGELDTCSSTHASTEPSEYVRGIDPKMKRLSSGRRDVTAEPEVIHPQAQSTTPNWPRTRSK
SRMDKGWMGLTSVQDPPTRCSWGNTGGQDREDISSTVSDPGPIWDAGPKWDTEPSAWDVENSIE
LPGPPEDIETGLRKQSITPIFEDKWVSRKGHFLGIMVCNHACRTVQSSQVVAPNSEHDDGTMDM
LLVHGCGRLRLLRFFILLQTGRHLSLPYVECVK(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	7906861-7905335(-)
Potential amino acid sequence	MTVSYYGFVSDVLELSEKYQKRFGPLRYFVAGFLKFMCLPKYSYEVEYLPAQKEDAEGKIRLEK EAVDMQDLYTDVMRRSSREGFPRASSLSSIDSIMTPSVGELDTCSSTHASTEPSEYVRGIDPKM KRLSSGRRDVTAEPEVIHPQAQSTTPNWPRTRSKSRMDKGWMGLTSVQDPPTRCSWGNTGGQDR EDISSTVSDPGPIWDAGPKWDTEPSAWDVENSIELPGPPEDIETGLRKQSITPIFEDKWVSRKG HFLGIMVCNHACRTVQSSQVVAPNSEHDDGTMDMLLVHGCGRLRLLRFFILLQTGRHLSLPYVE CVKVLNGLLTRSNPKEGVSIPIGIVPAGSDNSLVWTVLGVRDPISAALSIVKGGLTATDVFAVE WIHTGIIHFGMTVSYYGFVSDVLELSEKYQKRFGPLRYFVAGFLKFMCLPKYSYEVEYLPAQKE DAEGKIRLEKEAVDMQDLYTDVMRRSSREGFPRASSLSSIDSIMTPSVGELDTCSSTHASTEPS EYVRGIDPKMKRLSSGRRDVTAEPEVIHPQAQSTTPNWPRTRSKSRMDKGWMGLTSVQDPPTRC SWGNTGGQDREDISSTVSDPGPIWDAGPKWDTEPSAWDVENSIELPGPPEDIETGLRKQSITPI FEDKWVSRKGHFLGIMVCNHACRTVQSSQVVAPNSEHDDGTMDMLLVHGCGRLRLLRFFILLQT GRHLSLPYVECVKVLNGLLTRSNPKEGVSIPIGIVPAGSDNSLVWTVLGVRDPISAALSIVKGG LTATDVFAVEWIHTGIIHFGMTVSYYGFVSDVLELSEKYQKRFGPLRYFVAGFLKFMCLPKYSY EVEYLPAQKEDAEGKIRLEKEAVDMQDLYTDVMRRSSREGFPRASSLSSIDSIMTPSVGELDTC SSTHASTEPSEYVRGIDPKMKRLSSGRRDVTAEPEVIHPQAQSTTPNWPRTRSKSRMDKGWMGL TSVQDPPTRCSWGNTGGQDREDISSTVSDPGPIWDAGPKWDTEPSAWDVENSIELPGPPEDIET GLRKQSITPIFEDKWVSRKGHFLGIMVCNHACRTVQSSQVVAPNSEHDDGTMDMLLVHGCGRLR LLRFFILLQTGRHLSLPYVECVKVLNGLLTRSNPKEGVSIPIGIVPAGSDNSLVWTVLGVRDPI SAALSIVKGGLTATDVFAVEWIHTGIIHFGMTVSYYGFVSDVLELSEKYQKRFGPLRYFVAGFL KFMCLPKYSYEVEYLPAQKEDAEGKIRLEKEAVDMQDLYTDVMRRSSREGFPRASSLSSIDSIM TPSVGELDTCSSTHASTEPSEYVRGIDPKMKRLSSGRRDVTAEPEVIHPQAQSTTPNWPRTRSK SRMDKGWMGLTSVQDPPTRCSWGNTGGQDREDISSTVSDPGPIWDAGPKWDTEPSAWDVENSIE LPGPPEDIETGLRKQSITPIFEDKWVSRKGHFLGIMVCNHACRTVQSSQVVAPNSEHDDGTMDM LLVHGCGRLRLLRFFILLQTGRHLSLPYVECVK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT5G23450_circ_g.1

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