Plant Circular RNA Database

Detail information of AT1G09340_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT1G09340_circ_g.4
					
						ID in PlantcircBase
						ath_circ_001653
					
						Alias
						Ath_circ_FC0271
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 3016035-3017266  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, MapSplice, PcircRNA_finder
					
						Parent gene
						
							AT1G09340						
					
						Parent gene annotation
						
							chloroplast RNA binding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G09340_circ_g.3 AT1G09340_circ_g.5 AT1G09340_circ_g.6 AT1G09340_circ_g.7 AT1G09340_circ_g.8 AT1G09340_circ_g.9 AT1G09340_circ_g.10 AT1G09340_circ_g.11 AT1G09340_circ_g.12 AT1G09340_circ_g.13 AT1G09340_circ_g.14 AT1G09340_circ_g.15 AT1G09340_circ_g.16 AT1G09340_circ_g.17 AT1G09340_circ_g.18 AT1G09340_circ_g.19 AT1G09340_circ_g.20 AT1G09340_circ_g.21 AT1G09340_circ_g.22 AT1G09340_circ_g.23 AT1G09340_circ_g.24 AT1G09340_circ_g.25 AT1G09340_circ_g.26 AT1G09340_circ_g.27 						
					
						Support reads
						125/2/NA
					
						Tissues
						aerial/seedlings/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
						AT1G09340.1:6
AT1G09340.2:6

General Information
CircRNA Name	AT1G09340_circ_g.4
ID in PlantcircBase	ath_circ_001653
Alias	Ath_circ_FC0271
Organism	Arabidpsis thaliana
Position	chr1: 3016035-3017266 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, MapSplice, PcircRNA_finder
Parent gene	AT1G09340
Parent gene annotation	chloroplast RNA binding
Parent gene strand	+
Alternative splicing	AT1G09340_circ_g.3 AT1G09340_circ_g.5 AT1G09340_circ_g.6 AT1G09340_circ_g.7 AT1G09340_circ_g.8 AT1G09340_circ_g.9 AT1G09340_circ_g.10 AT1G09340_circ_g.11 AT1G09340_circ_g.12 AT1G09340_circ_g.13 AT1G09340_circ_g.14 AT1G09340_circ_g.15 AT1G09340_circ_g.16 AT1G09340_circ_g.17 AT1G09340_circ_g.18 AT1G09340_circ_g.19 AT1G09340_circ_g.20 AT1G09340_circ_g.21 AT1G09340_circ_g.22 AT1G09340_circ_g.23 AT1G09340_circ_g.24 AT1G09340_circ_g.25 AT1G09340_circ_g.26 AT1G09340_circ_g.27
Support reads	125/2/NA
Tissues	aerial/seedlings/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	AT1G09340.1:6 AT1G09340.2:6

			
						 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  
						
							CAACCCCGTCGAAGAATGGTTTTTCCACCGTCTAAAGGCAGGTCGCCCAATCCCGGTTCCAAAC
TCTGGGATACAGATCTCACAACTCGGTCACGTTAAGtacaagaggaaggttcatcagccaaaag
gagcactctatgtttcagcgtcgagcgaaaagaagattctgataatgggtggtactcgattcat
tggtctgt

									
								

					

						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: 284
Transcript exons: 3016035-3016170,3017119-3017266
TACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCGAGCGAAAAGAAGA
TTCTGATAATGGGTGGTACTCGATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGG
ACATCAGGAAACTGGACTTCTATACGTCCTGTCTACATCTACGGTCCATTGAATTACAACCCCG
TCGAAGAATGGTTTTTCCACCGTCTAAAGGCAGGTCGCCCAATCCCGGTTCCAAACTCTGGGAT
ACAGATCTCACAACTCGGTCACGTTAAG
Transcript length: 651
Transcript exons: 3016035-3016169,3016248-3016334,3016458-3016548,3016660-
3016714,3016816-3016876,3017045-3017266
TACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCGAGCGAAAAGAAGA
TTCTGATAATGGGTGGTACTCGATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGG
ACATCAGGTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAATTGCCCGGTGAATCT
GACCAAGACTTTGCTGATTTCTCTTCTAAGATTCTTCACTTGAAAGGAGACAGAAAGGACTATG
ACTTTGTGAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACGGGAGGGA
GGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAGAGCAGTACATCTACTGTTCT
TCAGCTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAGGAGGATGCAGTTGATCCGA
AGAGCAGGCACAAGGGGAAGCTGGAGACTGAGAGCTTACTGCAATCAAAAGGTGTAAACTGGAC
TTCTATACGTCCTGTCTACATCTACGGTCCATTGAATTACAACCCCGTCGAAGAATGGTTTTTC
CACCGTCTAAAGGCAGGTCGCCCAATCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCG
GTCACGTTAAG
						
					

						Genomic sequence
						
							TACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCGAGCGAAAAGAAGA
TTCTGATAATGGGTGGTACTCGATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGG
ACATCAGGTTCCACTACCGATCAAACTCTCTTTTCAGCTAAAAATTTAGTTTCCGTTTCTGAGT
GACCAATGGTTGCTTTTGCAGGTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAAT
TGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAGGTATTACATGAATCCTTGTA
AAAAACTAGTATGCACACTCAAATATAATATACATTTCAGATGATAGGAACTTGGATGATTAGG
ATTCCAATAAAATAAATGATTTTTCTCGGCCTTTTCTAGATTCTTCACTTGAAAGGAGACAGAA
AGGACTATGACTTTGTGAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAA
CGGTAACAGCTAATCACTTTGTTCTTACTGTAAATTCAAGAATATCTAGTCTTTTGCCTTTGAC
AACAAAGATTTTAAGATTTCGTATAATTTATGCTCTCTTTTTTTCTCAGGGAGGGAGGCCGAAG
AAGTTGAGCCCATACTAGAAGCACTACCCAAACTAGAGCAGTAAGTAATACATAACATCTATCA
AGGCCTAGCTTGTTCATTTGGTTTATAGCTTTCAAAACATAGCCCTTCAAAATTTAAATCTTCC
GTTAATGTTATAGGTACATCTACTGTTCTTCAGCTGGTGTTTATCTGAAATCTGATATCTTGCC
ACATTGTGAGGTATGTAAAAGATATCTTATTCTTATTCCTGGAAGATATGAGCTTGTACTTTTC
TTGAATTAGCCATAGAATAGTATGATTATGTAATTTGATCATATGATGTCACCCAGAAGTTTAT
TATCTAAGGCCATTTGTAATAACTTTTTATTTGGGACATAACTGATGCAGGAGGATGCAGTTGA
TCCGAAGAGCAGGCACAAGGGGAAGCTGGAGACTGAGAGCTTACTGCAATCAAAAGGTGTAAAC
TGGACTTCTATACGTCCTGTCTACATCTACGGTCCATTGAATTACAACCCCGTCGAAGAATGGT
TTTTCCACCGTCTAAAGGCAGGTCGCCCAATCCCGGTTCCAAACTCTGGGATACAGATCTCACA
ACTCGGTCACGTTAAG
						
					

			
		

Sequences
Splice junction sequence	CAACCCCGTCGAAGAATGGTTTTTCCACCGTCTAAAGGCAGGTCGCCCAATCCCGGTTCCAAAC TCTGGGATACAGATCTCACAACTCGGTCACGTTAAGtacaagaggaaggttcatcagccaaaag gagcactctatgtttcagcgtcgagcgaaaagaagattctgataatgggtggtactcgattcat tggtctgt
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: 284 Transcript exons: 3016035-3016170,3017119-3017266 TACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCGAGCGAAAAGAAGA TTCTGATAATGGGTGGTACTCGATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGG ACATCAGGAAACTGGACTTCTATACGTCCTGTCTACATCTACGGTCCATTGAATTACAACCCCG TCGAAGAATGGTTTTTCCACCGTCTAAAGGCAGGTCGCCCAATCCCGGTTCCAAACTCTGGGAT ACAGATCTCACAACTCGGTCACGTTAAG Transcript length: 651 Transcript exons: 3016035-3016169,3016248-3016334,3016458-3016548,3016660- 3016714,3016816-3016876,3017045-3017266 TACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCGAGCGAAAAGAAGA TTCTGATAATGGGTGGTACTCGATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGG ACATCAGGTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAATTGCCCGGTGAATCT GACCAAGACTTTGCTGATTTCTCTTCTAAGATTCTTCACTTGAAAGGAGACAGAAAGGACTATG ACTTTGTGAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACGGGAGGGA GGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAGAGCAGTACATCTACTGTTCT TCAGCTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAGGAGGATGCAGTTGATCCGA AGAGCAGGCACAAGGGGAAGCTGGAGACTGAGAGCTTACTGCAATCAAAAGGTGTAAACTGGAC TTCTATACGTCCTGTCTACATCTACGGTCCATTGAATTACAACCCCGTCGAAGAATGGTTTTTC CACCGTCTAAAGGCAGGTCGCCCAATCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCG GTCACGTTAAG
Genomic sequence	TACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCGAGCGAAAAGAAGA TTCTGATAATGGGTGGTACTCGATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGG ACATCAGGTTCCACTACCGATCAAACTCTCTTTTCAGCTAAAAATTTAGTTTCCGTTTCTGAGT GACCAATGGTTGCTTTTGCAGGTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAAT TGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAGGTATTACATGAATCCTTGTA AAAAACTAGTATGCACACTCAAATATAATATACATTTCAGATGATAGGAACTTGGATGATTAGG ATTCCAATAAAATAAATGATTTTTCTCGGCCTTTTCTAGATTCTTCACTTGAAAGGAGACAGAA AGGACTATGACTTTGTGAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAA CGGTAACAGCTAATCACTTTGTTCTTACTGTAAATTCAAGAATATCTAGTCTTTTGCCTTTGAC AACAAAGATTTTAAGATTTCGTATAATTTATGCTCTCTTTTTTTCTCAGGGAGGGAGGCCGAAG AAGTTGAGCCCATACTAGAAGCACTACCCAAACTAGAGCAGTAAGTAATACATAACATCTATCA AGGCCTAGCTTGTTCATTTGGTTTATAGCTTTCAAAACATAGCCCTTCAAAATTTAAATCTTCC GTTAATGTTATAGGTACATCTACTGTTCTTCAGCTGGTGTTTATCTGAAATCTGATATCTTGCC ACATTGTGAGGTATGTAAAAGATATCTTATTCTTATTCCTGGAAGATATGAGCTTGTACTTTTC TTGAATTAGCCATAGAATAGTATGATTATGTAATTTGATCATATGATGTCACCCAGAAGTTTAT TATCTAAGGCCATTTGTAATAACTTTTTATTTGGGACATAACTGATGCAGGAGGATGCAGTTGA TCCGAAGAGCAGGCACAAGGGGAAGCTGGAGACTGAGAGCTTACTGCAATCAAAAGGTGTAAAC TGGACTTCTATACGTCCTGTCTACATCTACGGTCCATTGAATTACAACCCCGTCGAAGAATGGT TTTTCCACCGTCTAAAGGCAGGTCGCCCAATCCCGGTTCCAAACTCTGGGATACAGATCTCACA ACTCGGTCACGTTAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.369083671

Conservation Information
Conserved circRNAs	NA
PMCS	0.369083671

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3016107-3017263(+)
						
						Potential amino acid sequence
						
							MGGTRFIGLFLSRILVKEGHQVTLFTRGKSPIAKQLPGESDQDFADFSSKILHLKGDRKDYDFV
KSSLSAEGFDVVYDINGREAEEVEPILEALPKLEQYIYCSSAGVYLKSDILPHCEEDAVDPKSR
HKGKLETESLLQSKGVNWTSIRPVYIYGPLNYNPVEEWFFHRLKAGRPIPVPNSGIQISQLGHV
KYKRKVHQPKGALYVSASSEKKILIMGGTRFIGLFLSRILVKEGHQVTLFTRGKSPIAKQLPGE
SDQDFADFSSKILHLKGDRKDYDFVKSSLSAEGFDVVYDINGREAEEVEPILEALPKLEQYIYC
SSAGVYLKSDILPHCEEDAVDPKSRHKGKLETESLLQSKGVNWTSIRPVYIYGPLNYNPVEEWF
FHRLKAGRPIPVPNSGIQISQLGHVKYKRKVHQPKGALYVSASSEKKILIMGGTRFIGLFLSRI
LVKEGHQVTLFTRGKSPIAKQLPGESDQDFADFSSKILHLKGDRKDYDFVKSSLSAEGFDVVYD
INGREAEEVEPILEALPKLEQYIYCSSAGVYLKSDILPHCEEDAVDPKSRHKGKLETESLLQSK
GVNWTSIRPVYIYGPLNYNPVEEWFFHRLKAGRPIPVPNSGIQISQLGHVKYKRKVHQPKGALY
VSASSEKKILIMGGTRFIGLFLSRILVKEGHQVTLFTRGKSPIAKQLPGESDQDFADFSSKILH
LKGDRKDYDFVKSSLSAEGFDVVYDINGREAEEVEPILEALPKLEQYIYCSSAGVYLKSDILPH
CEEDAVDPKSRHKGKLETESLLQSKGVNWTSIRPVYIYGPLNYNPVEEWFFHRLKAGRPIPVPN
SGIQISQLGHVK(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3016107-3017263(+)
Potential amino acid sequence	MGGTRFIGLFLSRILVKEGHQVTLFTRGKSPIAKQLPGESDQDFADFSSKILHLKGDRKDYDFV KSSLSAEGFDVVYDINGREAEEVEPILEALPKLEQYIYCSSAGVYLKSDILPHCEEDAVDPKSR HKGKLETESLLQSKGVNWTSIRPVYIYGPLNYNPVEEWFFHRLKAGRPIPVPNSGIQISQLGHV KYKRKVHQPKGALYVSASSEKKILIMGGTRFIGLFLSRILVKEGHQVTLFTRGKSPIAKQLPGE SDQDFADFSSKILHLKGDRKDYDFVKSSLSAEGFDVVYDINGREAEEVEPILEALPKLEQYIYC SSAGVYLKSDILPHCEEDAVDPKSRHKGKLETESLLQSKGVNWTSIRPVYIYGPLNYNPVEEWF FHRLKAGRPIPVPNSGIQISQLGHVKYKRKVHQPKGALYVSASSEKKILIMGGTRFIGLFLSRI LVKEGHQVTLFTRGKSPIAKQLPGESDQDFADFSSKILHLKGDRKDYDFVKSSLSAEGFDVVYD INGREAEEVEPILEALPKLEQYIYCSSAGVYLKSDILPHCEEDAVDPKSRHKGKLETESLLQSK GVNWTSIRPVYIYGPLNYNPVEEWFFHRLKAGRPIPVPNSGIQISQLGHVKYKRKVHQPKGALY VSASSEKKILIMGGTRFIGLFLSRILVKEGHQVTLFTRGKSPIAKQLPGESDQDFADFSSKILH LKGDRKDYDFVKSSLSAEGFDVVYDINGREAEEVEPILEALPKLEQYIYCSSAGVYLKSDILPH CEEDAVDPKSRHKGKLETESLLQSKGVNWTSIRPVYIYGPLNYNPVEEWFFHRLKAGRPIPVPN SGIQISQLGHVK(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of AT1G09340_circ_g.4

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