Plant Circular RNA Database

Detail information of AT1G19450_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT1G19450_circ_g.3
					
						ID in PlantcircBase
						ath_circ_003411
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 6732575-6734313  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							AT1G19450						
					
						Parent gene annotation
						
							Sugar transporter ERD6-like 4
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G19450_circ_g.1 AT1G19450_circ_g.2 AT1G19450_circ_g.4 AT1G19450_circ_g.5 						
					
						Support reads
						1
					
						Tissues
						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  
						
							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
						AT1G19450.1:11

General Information
CircRNA Name	AT1G19450_circ_g.3
ID in PlantcircBase	ath_circ_003411
Alias	NA
Organism	Arabidpsis thaliana
Position	chr1: 6732575-6734313 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	AT1G19450
Parent gene annotation	Sugar transporter ERD6-like 4
Parent gene strand	-
Alternative splicing	AT1G19450_circ_g.1 AT1G19450_circ_g.2 AT1G19450_circ_g.4 AT1G19450_circ_g.5
Support reads	1
Tissues	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	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	AT1G19450.1:11

			
						 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  
						
							ACAGAACAGTTCTTAAATAAAGATGGGACCTTCATACCTCTGATACAGTTAAACCAAGATCCTT
AGTAATGGCAGCTTGAGTTGGTGAGGAATAACCACActgaacaacgccaactccaaatgtcgcc
acattacttgatgtcaccccttagtgaatgataattgcaaacaaagaagcatagttagaaatct
gtttattc

									
								

					

						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
						
							CTGAACAACGCCAACTCCAAATGTCGCCACATTACTTGATGTCACCCCTTAGTGAATGATAATT
GCAAACAAAGAAGCATAGTTAGAAATCTGTTTATTCTATCTTAGGACCATTCCAATAATCAAAA
AAAACATATGACTCTACCTGCAGATTCAAAAATTGTACTCGAATAGAACAAGACACCATTGATT
CCTCCAAGTTGTTGAAGTGCAAGCAGCCCTATACCAACCTGTAACACAGATTACAGGAAAAGAG
TGAGTTTCTCTCATGTGTTGACAAAATTAGTTCAAGAGAGGTAAGAGAAATTGCACCATCAGTG
GGAAATAGTATCTCCTGCGCTTGAGGTCTACAAACCGAACTGCAGAACGTTTGCTAGATGATGC
CACAGATCTCTGCAGAGTGCATAAAATGAAAATTTTAAATAAGACAAGAAATCACATCAAAGCA
TTTCTTCAGTTTAGTCACTACCTTGATTTCATTAACCTCAACGGTAATATCAGTCTCAAATCCA
CGAAGAACTTGCAATGAAGTTTCGAAATCATCTGTCAAACCCATCTTTGCCTACAATTACAACA
CCAAAACAATTTAGGATAACCAATAATGCAACAAACTCAACAATATAAGCAATACGGTTGTAGA
GGCATACCAACCACCGAGGAGATTCAGGAATGAAAAAAAGACCCGGTATCAACAATGTACATGG
CAATACTCCTAAACATAAAGAAGACAAACAAGAAAGTGATTAGACTGTATCGATCAAAATAAAA
TAAAAACAGGTATAGTTTCTCCCAAGTCAAGTCAAAATGTTTTGTGAGTTACCCAAAACTGCAA
GAATTCTCCATGGAACAAAGAGACCGAGTAAATACGCCAGCATTATCCCAATTGTTACAGAAAG
CTATAAACACAAAACATTTATTGTTTAGTGTTAACATATGAATCAGCTCATAAAATGAAACATA
AAAATAGTGAAGCTAACTAAACATGACAAACCTGGTTAACTGAACCTAAGGCTCCTCTCATGGT
CTGTGGAGCGATCTCAGCTATATATACGGGAACCTAAAATCGCAATTCAAAGGTGTGTAATTAT
ATTGATCACTCCAAACAAACATTGCTGAAATCAAAGAAATAGTTGAATCTAATATTACCGTATA
GGAGATAATCCCAACTCCGAAGCCTTCTAACAATCTTCCCATGTAAAGAAAAGAAGTATCCTAA
ACAAAAACCAAGAACAACAACAACTTAGTAGGTATAGAGATAAGCCAAGAATATCAGAAACTTT
GAGAACACCAAAACACTCACTTTTGCAAATGATATCGAAAGCCATCCAATAATATTGGGAATTG
CAGCAATCATCAGAGACTGTCAAAAGGAAAGAAAAACACAGTAAATAAGATACAACAAGAAAGA
AGATGTTACATGACAAATTGTCACAGATGAGAACATGTTTTAGAATCAAGAAACAAAACTATTA
TACCCCTTTCCGTCCAACGTATTCAGCAATCTGACCACTCGCAATTGCTCCAACCATAGCACCC
ACATTGGATAGAGACCCAAACACAGAGTACTAAAACATCAAACAAGAAACCTAAAAGTCAGAAA
ATTACAGAACAAGAGTCTTTACAAAAAAAAAAAAAAAAAACAGAACAGTTCTTAAATAAAGATG
GGACCTTCATACCTCTGATACAGTTAAACCAAGATCCTTAGTAATGGCAGCTTGAGTTGGTGAG
GAATAACCACA
						
					

			
		

Sequences
Splice junction sequence	ACAGAACAGTTCTTAAATAAAGATGGGACCTTCATACCTCTGATACAGTTAAACCAAGATCCTT AGTAATGGCAGCTTGAGTTGGTGAGGAATAACCACActgaacaacgccaactccaaatgtcgcc acattacttgatgtcaccccttagtgaatgataattgcaaacaaagaagcatagttagaaatct gtttattc
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	CTGAACAACGCCAACTCCAAATGTCGCCACATTACTTGATGTCACCCCTTAGTGAATGATAATT GCAAACAAAGAAGCATAGTTAGAAATCTGTTTATTCTATCTTAGGACCATTCCAATAATCAAAA AAAACATATGACTCTACCTGCAGATTCAAAAATTGTACTCGAATAGAACAAGACACCATTGATT CCTCCAAGTTGTTGAAGTGCAAGCAGCCCTATACCAACCTGTAACACAGATTACAGGAAAAGAG TGAGTTTCTCTCATGTGTTGACAAAATTAGTTCAAGAGAGGTAAGAGAAATTGCACCATCAGTG GGAAATAGTATCTCCTGCGCTTGAGGTCTACAAACCGAACTGCAGAACGTTTGCTAGATGATGC CACAGATCTCTGCAGAGTGCATAAAATGAAAATTTTAAATAAGACAAGAAATCACATCAAAGCA TTTCTTCAGTTTAGTCACTACCTTGATTTCATTAACCTCAACGGTAATATCAGTCTCAAATCCA CGAAGAACTTGCAATGAAGTTTCGAAATCATCTGTCAAACCCATCTTTGCCTACAATTACAACA CCAAAACAATTTAGGATAACCAATAATGCAACAAACTCAACAATATAAGCAATACGGTTGTAGA GGCATACCAACCACCGAGGAGATTCAGGAATGAAAAAAAGACCCGGTATCAACAATGTACATGG CAATACTCCTAAACATAAAGAAGACAAACAAGAAAGTGATTAGACTGTATCGATCAAAATAAAA TAAAAACAGGTATAGTTTCTCCCAAGTCAAGTCAAAATGTTTTGTGAGTTACCCAAAACTGCAA GAATTCTCCATGGAACAAAGAGACCGAGTAAATACGCCAGCATTATCCCAATTGTTACAGAAAG CTATAAACACAAAACATTTATTGTTTAGTGTTAACATATGAATCAGCTCATAAAATGAAACATA AAAATAGTGAAGCTAACTAAACATGACAAACCTGGTTAACTGAACCTAAGGCTCCTCTCATGGT CTGTGGAGCGATCTCAGCTATATATACGGGAACCTAAAATCGCAATTCAAAGGTGTGTAATTAT ATTGATCACTCCAAACAAACATTGCTGAAATCAAAGAAATAGTTGAATCTAATATTACCGTATA GGAGATAATCCCAACTCCGAAGCCTTCTAACAATCTTCCCATGTAAAGAAAAGAAGTATCCTAA ACAAAAACCAAGAACAACAACAACTTAGTAGGTATAGAGATAAGCCAAGAATATCAGAAACTTT GAGAACACCAAAACACTCACTTTTGCAAATGATATCGAAAGCCATCCAATAATATTGGGAATTG CAGCAATCATCAGAGACTGTCAAAAGGAAAGAAAAACACAGTAAATAAGATACAACAAGAAAGA AGATGTTACATGACAAATTGTCACAGATGAGAACATGTTTTAGAATCAAGAAACAAAACTATTA TACCCCTTTCCGTCCAACGTATTCAGCAATCTGACCACTCGCAATTGCTCCAACCATAGCACCC ACATTGGATAGAGACCCAAACACAGAGTACTAAAACATCAAACAAGAAACCTAAAAGTCAGAAA ATTACAGAACAAGAGTCTTTACAAAAAAAAAAAAAAAAAACAGAACAGTTCTTAAATAAAGATG GGACCTTCATACCTCTGATACAGTTAAACCAAGATCCTTAGTAATGGCAGCTTGAGTTGGTGAG GAATAACCACA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.140745202

Conservation Information
Conserved circRNAs	NA
PMCS	0.140745202

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6734104-6732577(-)
						
						Potential amino acid sequence
						
							MVGAIASGQIAEYVGRKGSLMIAAIPNIIGWLSISFAKDTSFLYMGRLLEGFGVGIISYTVPVY
IAEIAPQTMRGALGSVNQLSVTIGIMLAYLLGLFVPWRILAVLGVLPCTLLIPGLFFIPESPRW
LAKMGLTDDFETSLQVLRGFETDITVEVNEIKRSVASSSKRSAVRFVDLKRRRYYFPLMVGIGL
LALQQLGGINGVLFYSSTIFESAGVTSSNVATFGVGVVQCGYSSPTQAAITKDLGLTVSEYSVF
GSLSNVGAMVGAIASGQIAEYVGRKGSLMIAAIPNIIGWLSISFAKDTSFLYMGRLLEGFGVGI
ISYTVPVYIAEIAPQTMRGALGSVNQLSVTIGIMLAYLLGLFVPWRILAVLGVLPCTLLIPGLF
FIPESPRWLAKMGLTDDFETSLQVLRGFETDITVEVNEIKRSVASSSKRSAVRFVDLKRRRYYF
PLMVGIGLLALQQLGGINGVLFYSSTIFESAGVTSSNVATFGVGVVQCGYSSPTQAAITKDLGL
TVSEYSVFGSLSNVGAMVGAIASGQIAEYVGRKGSLMIAAIPNIIGWLSISFAKDTSFLYMGRL
LEGFGVGIISYTVPVYIAEIAPQTMRGALGSVNQLSVTIGIMLAYLLGLFVPWRILAVLGVLPC
TLLIPGLFFIPESPRWLAKMGLTDDFETSLQVLRGFETDITVEVNEIKRSVASSSKRSAVRFVD
LKRRRYYFPLMVGIGLLALQQLGGINGVLFYSSTIFESAGVTSSNVATFGVGVVQCGYSSPTQA
AITKDLGLTVSEYSVFGSLSNVGAMVGAIASGQIAEYVGRKGSLMIAAIPNIIGWLSISFAKDT
SFLYMGRLLEGFGVGIISYTVPVYIAEIAPQTMRGALGSVNQLSVTIGIMLAYLLGLFVPWRIL
AVLGVLPCTLLIPGLFFIPESPRWLAKMGLTDDFETSLQVLRGFETDITVEVNEIKRSVASSSK
RSAVRFVDLKRRRYYFPLMVGIGLLALQQLGGINGVLFYSSTIFESAGVTSSNVATFGVGVVQ(
-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	6734104-6732577(-)
Potential amino acid sequence	MVGAIASGQIAEYVGRKGSLMIAAIPNIIGWLSISFAKDTSFLYMGRLLEGFGVGIISYTVPVY IAEIAPQTMRGALGSVNQLSVTIGIMLAYLLGLFVPWRILAVLGVLPCTLLIPGLFFIPESPRW LAKMGLTDDFETSLQVLRGFETDITVEVNEIKRSVASSSKRSAVRFVDLKRRRYYFPLMVGIGL LALQQLGGINGVLFYSSTIFESAGVTSSNVATFGVGVVQCGYSSPTQAAITKDLGLTVSEYSVF GSLSNVGAMVGAIASGQIAEYVGRKGSLMIAAIPNIIGWLSISFAKDTSFLYMGRLLEGFGVGI ISYTVPVYIAEIAPQTMRGALGSVNQLSVTIGIMLAYLLGLFVPWRILAVLGVLPCTLLIPGLF FIPESPRWLAKMGLTDDFETSLQVLRGFETDITVEVNEIKRSVASSSKRSAVRFVDLKRRRYYF PLMVGIGLLALQQLGGINGVLFYSSTIFESAGVTSSNVATFGVGVVQCGYSSPTQAAITKDLGL TVSEYSVFGSLSNVGAMVGAIASGQIAEYVGRKGSLMIAAIPNIIGWLSISFAKDTSFLYMGRL LEGFGVGIISYTVPVYIAEIAPQTMRGALGSVNQLSVTIGIMLAYLLGLFVPWRILAVLGVLPC TLLIPGLFFIPESPRWLAKMGLTDDFETSLQVLRGFETDITVEVNEIKRSVASSSKRSAVRFVD LKRRRYYFPLMVGIGLLALQQLGGINGVLFYSSTIFESAGVTSSNVATFGVGVVQCGYSSPTQA AITKDLGLTVSEYSVFGSLSNVGAMVGAIASGQIAEYVGRKGSLMIAAIPNIIGWLSISFAKDT SFLYMGRLLEGFGVGIISYTVPVYIAEIAPQTMRGALGSVNQLSVTIGIMLAYLLGLFVPWRIL AVLGVLPCTLLIPGLFFIPESPRWLAKMGLTDDFETSLQVLRGFETDITVEVNEIKRSVASSSK RSAVRFVDLKRRRYYFPLMVGIGLLALQQLGGINGVLFYSSTIFESAGVTSSNVATFGVGVVQ( -)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT1G19450_circ_g.3

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