Plant Circular RNA Database

Detail information of AT4G12720_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT4G12720_circ_g.2
					
						ID in PlantcircBase
						ath_circ_030580
					
						Alias
						At_ciR1511, Ath_circ_FC2613
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 7487686-7488295  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ, CIRI-full
					
						Parent gene
						
							AT4G12720						
					
						Parent gene annotation
						
							MutT/nudix family protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G12720_circ_g.1 AT4G12720_circ_g.3 AT4G12720_circ_g.4 AT4G12720_circ_g.5 AT4G12720_circ_g.6 						
					
						Support reads
						8
					
						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  
						
							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
						AT4G12720.2:3
AT4G12720.5:3
AT4G12720.1:3
AT4G12720.6:2
AT4G12720.4:3
AT4G12720.3:3

General Information
CircRNA Name	AT4G12720_circ_g.2
ID in PlantcircBase	ath_circ_030580
Alias	At_ciR1511, Ath_circ_FC2613
Organism	Arabidpsis thaliana
Position	chr4: 7487686-7488295 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ, CIRI-full
Parent gene	AT4G12720
Parent gene annotation	MutT/nudix family protein
Parent gene strand	+
Alternative splicing	AT4G12720_circ_g.1 AT4G12720_circ_g.3 AT4G12720_circ_g.4 AT4G12720_circ_g.5 AT4G12720_circ_g.6
Support reads	8
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	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	AT4G12720.2:3 AT4G12720.5:3 AT4G12720.1:3 AT4G12720.6:2 AT4G12720.4:3 AT4G12720.3:3

			
						 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  
						
							GCTTGTATCTTGGATCTCTGAAACTCCTGATACAATCCCAGCCAATGCTTCTCATGTTGTAGGT
GCTGGTGCTTTGGTCATCAACAAAAATACTAAAGAGctgatttttgtgataagaagattgattg
agatgggtactagagctcagcagattcctttacttgaaggtgagactgataattacgatggtgt
tactgtaa

									
								

					

						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: 381
Transcript exons: 7487686-7487859,7488005-7488070,7488155-7488295
CTGATTTTTGTGATAAGAAGATTGATTGAGATGGGTACTAGAGCTCAGCAGATTCCTTTACTTG
AAGGTGAGACTGATAATTACGATGGTGTTACTGTAACCATGGTGGAACCTATGGATTCTGAGGT
TTTTACTGAAAGTCTTAGGGCTTCTCTTTCGCATTGGAGAGAAGAGGGGAAGAAGGGAATTTGG
ATAAAGCTGCCTCTTGGATTGGCTAATCTTGTGGAGGCTGCAGTTAGTGAAGGATTTAGATATC
ACCACGCGGAGCCTGAGTACTTGATGCTTGTATCTTGGATCTCTGAAACTCCTGATACAATCCC
AGCCAATGCTTCTCATGTTGTAGGTGCTGGTGCTTTGGTCATCAACAAAAATACTAAAGAG
Transcript length: 477
Transcript exons: 7487686-7488295
CTGATTTTTGTGATAAGAAGATTGATTGAGATGGGTACTAGAGCTCAGCAGATTCCTTTACTTG
AAGGGGAAGAAGGGAATTTGGATAAAGCTGCCTCTTGGATTGGCTAATCTTGTGGAGGCTGCAG
TTAGTGAAGGATTTAGATATCACCACGCGGAGCCTGAGTGCTGGTGCTTTGGTCATCAACAAAA
ATACTAAAGAGCTGATTTTTGTGATAAGAAGATTGATTGAGATGGGTACTAGAGCTCAGCAGAT
TCCTTTACTTGAAGGGGAAGAAGGGAATTTGGATAAAGCTGCCTCTTGGATTGGCTAATCTTGT
GGAGGCTGCAGTTAGTGAAGGATTTAGATATCACCACGCGGAGCCTGAGTACTTGATGCTTGTA
TCTTGGATCTCTGAAACTCCTGATACAATCCCAGCCAATGCTTCTCATGTTGTAGGTGCTGGTG
CTTTGGTCATCAACAAAAATACTAAAGAG
						
					

						Genomic sequence
						
							CTGATTTTTGTGATAAGAAGATTGATTGAGATGGGTACTAGAGCTCAGCAGATTCCTTTACTTG
AAGGTGAGACTGATAATTACGATGGTGTTACTGTAACCATGGTGGAACCTATGGATTCTGAGGT
TTTTACTGAAAGTCTTAGGGCTTCTCTTTCGCATTGGAGAGAAGAGGTATTAACAATATATATA
ACTCAGATTCAAGCCTTATTGTTTGATTGTACTGATAACTGATAAACTTCTGAGATATGATATG
AGCTCTTAAGAGTTTAGAGGATTGTGATAACATGAGGACTTAGTCAGAGTTTATGATTTGCAGG
GGAAGAAGGGAATTTGGATAAAGCTGCCTCTTGGATTGGCTAATCTTGTGGAGGCTGCAGTTAG
TGTAAGTTTTATATGAGGATTTGGATTGACGTTAGTTATTGTGATGATTAGTTGAATATCTTCT
TGTGTTTGGTGATTTTTTCAGGAAGGATTTAGATATCACCACGCGGAGCCTGAGTACTTGATGC
TTGTATCTTGGATCTCTGAAACTCCTGATACAATCCCAGCCAATGCTTCTCATGTTGTAGGTGC
TGGTGCTTTGGTCATCAACAAAAATACTAAAGAG
						
					

			
		

Sequences
Splice junction sequence	GCTTGTATCTTGGATCTCTGAAACTCCTGATACAATCCCAGCCAATGCTTCTCATGTTGTAGGT GCTGGTGCTTTGGTCATCAACAAAAATACTAAAGAGctgatttttgtgataagaagattgattg agatgggtactagagctcagcagattcctttacttgaaggtgagactgataattacgatggtgt tactgtaa
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: 381 Transcript exons: 7487686-7487859,7488005-7488070,7488155-7488295 CTGATTTTTGTGATAAGAAGATTGATTGAGATGGGTACTAGAGCTCAGCAGATTCCTTTACTTG AAGGTGAGACTGATAATTACGATGGTGTTACTGTAACCATGGTGGAACCTATGGATTCTGAGGT TTTTACTGAAAGTCTTAGGGCTTCTCTTTCGCATTGGAGAGAAGAGGGGAAGAAGGGAATTTGG ATAAAGCTGCCTCTTGGATTGGCTAATCTTGTGGAGGCTGCAGTTAGTGAAGGATTTAGATATC ACCACGCGGAGCCTGAGTACTTGATGCTTGTATCTTGGATCTCTGAAACTCCTGATACAATCCC AGCCAATGCTTCTCATGTTGTAGGTGCTGGTGCTTTGGTCATCAACAAAAATACTAAAGAG Transcript length: 477 Transcript exons: 7487686-7488295 CTGATTTTTGTGATAAGAAGATTGATTGAGATGGGTACTAGAGCTCAGCAGATTCCTTTACTTG AAGGGGAAGAAGGGAATTTGGATAAAGCTGCCTCTTGGATTGGCTAATCTTGTGGAGGCTGCAG TTAGTGAAGGATTTAGATATCACCACGCGGAGCCTGAGTGCTGGTGCTTTGGTCATCAACAAAA ATACTAAAGAGCTGATTTTTGTGATAAGAAGATTGATTGAGATGGGTACTAGAGCTCAGCAGAT TCCTTTACTTGAAGGGGAAGAAGGGAATTTGGATAAAGCTGCCTCTTGGATTGGCTAATCTTGT GGAGGCTGCAGTTAGTGAAGGATTTAGATATCACCACGCGGAGCCTGAGTACTTGATGCTTGTA TCTTGGATCTCTGAAACTCCTGATACAATCCCAGCCAATGCTTCTCATGTTGTAGGTGCTGGTG CTTTGGTCATCAACAAAAATACTAAAGAG
Genomic sequence	CTGATTTTTGTGATAAGAAGATTGATTGAGATGGGTACTAGAGCTCAGCAGATTCCTTTACTTG AAGGTGAGACTGATAATTACGATGGTGTTACTGTAACCATGGTGGAACCTATGGATTCTGAGGT TTTTACTGAAAGTCTTAGGGCTTCTCTTTCGCATTGGAGAGAAGAGGTATTAACAATATATATA ACTCAGATTCAAGCCTTATTGTTTGATTGTACTGATAACTGATAAACTTCTGAGATATGATATG AGCTCTTAAGAGTTTAGAGGATTGTGATAACATGAGGACTTAGTCAGAGTTTATGATTTGCAGG GGAAGAAGGGAATTTGGATAAAGCTGCCTCTTGGATTGGCTAATCTTGTGGAGGCTGCAGTTAG TGTAAGTTTTATATGAGGATTTGGATTGACGTTAGTTATTGTGATGATTAGTTGAATATCTTCT TGTGTTTGGTGATTTTTTCAGGAAGGATTTAGATATCACCACGCGGAGCCTGAGTACTTGATGC TTGTATCTTGGATCTCTGAAACTCCTGATACAATCCCAGCCAATGCTTCTCATGTTGTAGGTGC TGGTGCTTTGGTCATCAACAAAAATACTAAAGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.210154291

Conservation Information
Conserved circRNAs	NA
PMCS	0.210154291

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							7487716-7488292(+)
						
						Potential amino acid sequence
						
							MGTRAQQIPLLEGETDNYDGVTVTMVEPMDSEVFTESLRASLSHWREEGKKGIWIKLPLGLANL
VEAAVSEGFRYHHAEPEYLMLVSWISETPDTIPANASHVVGAGALVINKNTKELIFVIRRLIEM
GTRAQQIPLLEGETDNYDGVTVTMVEPMDSEVFTESLRASLSHWREEGKKGIWIKLPLGLANLV
EAAVSEGFRYHHAEPEYLMLVSWISETPDTIPANASHVVGAGALVINKNTKELIFVIRRLIEMG
TRAQQIPLLEGETDNYDGVTVTMVEPMDSEVFTESLRASLSHWREEGKKGIWIKLPLGLANLVE
AAVSEGFRYHHAEPEYLMLVSWISETPDTIPANASHVVGAGALVINKNTKELIFVIRRLIEMGT
RAQQIPLLEGETDNYDGVTVTMVEPMDSEVFTESLRASLSHWREEGKKGIWIKLPLGLANLVEA
AVSEGFRYHHAEPEYLMLVSWISETPDTIPANASHVVGAGALVINKNTKE(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	7487716-7488292(+)
Potential amino acid sequence	MGTRAQQIPLLEGETDNYDGVTVTMVEPMDSEVFTESLRASLSHWREEGKKGIWIKLPLGLANL VEAAVSEGFRYHHAEPEYLMLVSWISETPDTIPANASHVVGAGALVINKNTKELIFVIRRLIEM GTRAQQIPLLEGETDNYDGVTVTMVEPMDSEVFTESLRASLSHWREEGKKGIWIKLPLGLANLV EAAVSEGFRYHHAEPEYLMLVSWISETPDTIPANASHVVGAGALVINKNTKELIFVIRRLIEMG TRAQQIPLLEGETDNYDGVTVTMVEPMDSEVFTESLRASLSHWREEGKKGIWIKLPLGLANLVE AAVSEGFRYHHAEPEYLMLVSWISETPDTIPANASHVVGAGALVINKNTKELIFVIRRLIEMGT RAQQIPLLEGETDNYDGVTVTMVEPMDSEVFTESLRASLSHWREEGKKGIWIKLPLGLANLVEA AVSEGFRYHHAEPEYLMLVSWISETPDTIPANASHVVGAGALVINKNTKE(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chen et al., 2017a

circRNA

Detail information of AT4G12720_circ_g.2

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