Plant Circular RNA Database

Detail information of AT1G35220_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT1G35220_circ_g.1
					
						ID in PlantcircBase
						ath_circ_005702
					
						Alias
						At_ciR4414
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 12909274-12910340  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, find_circ
					
						Parent gene
						
							AT1G35220						
					
						Parent gene annotation
						
							unknown protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							1_circ_ag.2 AT1G34315_circ_g.1 AT1G34315_circ_g.2 AT1G34320_circ_g.1 AT1G34320_circ_g.2 AT1G34360_circ_g.1 AT1G34360_circ_g.2 AT1G34360_circ_g.3 AT1G34370_circ_g.1 AT1G34370_circ_g.2 AT1G34380_circ_g.1 1_circ_ag.2 AT1G34420_circ_g.1 AT1G34430_circ_g.1 AT1G34460_circ_g.1 AT1G34460_circ_g.2 AT1G34460_circ_g.3 AT1G34460_circ_g.4 AT1G34460_circ_g.5 AT1G34460_circ_g.6 AT1G34460_circ_g.7 AT1G34460_circ_g.8 AT1G34460_circ_g.9 AT1G34460_circ_g.10 AT1G34460_circ_g.11 AT1G34460_circ_g.12 AT1G34550_circ_g.1 AT1G34550_circ_g.2 AT1G34750_circ_g.1 AT1G34750_circ_g.2 AT1G34760_circ_g.1 AT1G34760_circ_g.2 AT1G34770_circ_g.1 AT1G34770_circ_g.2 AT1G34844_circ_g.1 AT1G35160_circ_g.1 AT1G35160_circ_g.2 1_circ_ag.3 1_circ_ag.4 AT1G35190_circ_g.1 AT1G35190_circ_g.2 AT1G35190_circ_g.3 AT1G35190_circ_g.4 AT1G35190_circ_g.5 AT1G35220_circ_g.2 1_circ_ag.3 1_circ_ag.4 1_circ_ag.5 1_circ_ag.6 AT1G35320_circ_g.1 1_circ_ig.2 1_circ_ig.3 1_circ_ig.4 1_circ_ig.5 1_circ_ig.6 AT1G35340_circ_g.1 AT1G35340_circ_g.2 AT1G35340_circ_g.3 AT1G35340_circ_g.4 AT1G35350_circ_g.1 AT1G35350_circ_g.2 AT1G35420_circ_g.1 AT1G35430_circ_g.1 AT1G35460_circ_g.1 AT1G35460_circ_g.2 AT1G35470_circ_g.1 AT1G35470_circ_g.2 AT1G35470_circ_g.3 AT1G35470_circ_g.4 AT1G35510_circ_g.1 AT1G35510_circ_g.2 AT1G35510_circ_g.3 						
					
						Support reads
						3/1
					
						Tissues
						leaf/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  
						
							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
						AT1G35220.3:4
AT1G35220.7:2
AT1G35220.6:3
AT1G35220.4:3
AT1G35220.2:4
AT1G35220.5:3
AT1G35220.1:4

General Information
CircRNA Name	AT1G35220_circ_g.1
ID in PlantcircBase	ath_circ_005702
Alias	At_ciR4414
Organism	Arabidpsis thaliana
Position	chr1: 12909274-12910340 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, find_circ
Parent gene	AT1G35220
Parent gene annotation	unknown protein
Parent gene strand	+
Alternative splicing	1_circ_ag.2 AT1G34315_circ_g.1 AT1G34315_circ_g.2 AT1G34320_circ_g.1 AT1G34320_circ_g.2 AT1G34360_circ_g.1 AT1G34360_circ_g.2 AT1G34360_circ_g.3 AT1G34370_circ_g.1 AT1G34370_circ_g.2 AT1G34380_circ_g.1 1_circ_ag.2 AT1G34420_circ_g.1 AT1G34430_circ_g.1 AT1G34460_circ_g.1 AT1G34460_circ_g.2 AT1G34460_circ_g.3 AT1G34460_circ_g.4 AT1G34460_circ_g.5 AT1G34460_circ_g.6 AT1G34460_circ_g.7 AT1G34460_circ_g.8 AT1G34460_circ_g.9 AT1G34460_circ_g.10 AT1G34460_circ_g.11 AT1G34460_circ_g.12 AT1G34550_circ_g.1 AT1G34550_circ_g.2 AT1G34750_circ_g.1 AT1G34750_circ_g.2 AT1G34760_circ_g.1 AT1G34760_circ_g.2 AT1G34770_circ_g.1 AT1G34770_circ_g.2 AT1G34844_circ_g.1 AT1G35160_circ_g.1 AT1G35160_circ_g.2 1_circ_ag.3 1_circ_ag.4 AT1G35190_circ_g.1 AT1G35190_circ_g.2 AT1G35190_circ_g.3 AT1G35190_circ_g.4 AT1G35190_circ_g.5 AT1G35220_circ_g.2 1_circ_ag.3 1_circ_ag.4 1_circ_ag.5 1_circ_ag.6 AT1G35320_circ_g.1 1_circ_ig.2 1_circ_ig.3 1_circ_ig.4 1_circ_ig.5 1_circ_ig.6 AT1G35340_circ_g.1 AT1G35340_circ_g.2 AT1G35340_circ_g.3 AT1G35340_circ_g.4 AT1G35350_circ_g.1 AT1G35350_circ_g.2 AT1G35420_circ_g.1 AT1G35430_circ_g.1 AT1G35460_circ_g.1 AT1G35460_circ_g.2 AT1G35470_circ_g.1 AT1G35470_circ_g.2 AT1G35470_circ_g.3 AT1G35470_circ_g.4 AT1G35510_circ_g.1 AT1G35510_circ_g.2 AT1G35510_circ_g.3
Support reads	3/1
Tissues	leaf/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	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	AT1G35220.3:4 AT1G35220.7:2 AT1G35220.6:3 AT1G35220.4:3 AT1G35220.2:4 AT1G35220.5:3 AT1G35220.1:4

			
						 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  
						
							TTATGACAGTATTCCAAACTTCAGTGCGGCAGATGCTTTCCGGCTTACAGGAATAGGGAGGAAT
GAGTTCATTGATATCATGAATAAATGCAGATCTAAGatagtgaaatttagggaagatgcagcac
actccagtaacaatagaggaccagttaatatcgaaagctgtaagagaagaatgtcaatgggaaa
acctccca

									
								

					

						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: 469
Transcript exons: 12909274-12909420,12909515-12909632,12910042-12910138,12
910234-12910340
ATAGTGAAATTTAGGGAAGATGCAGCACACTCCAGTAACAATAGAGGACCAGTTAATATCGAAA
GCTGTAAGAGAAGAATGTCAATGGGAAAACCTCCCAAAACGACTTCAATCGATCCTTGGGTCTA
AGGATGAATGGCATAGAAGGGTTACGGCGCATTGTATAAAGAAAAGACTCCTATGGAATACGTG
TTTTGCTTGTAAAGTTTGCAAAGAAGGTGAATATTATGAAGATATGATGCGTTACTTGCGAAAG
AATCTGGCGCTCTTTCCGTATCACCTTGCAGAGTATGTTTGCCGTGTGATGAGGATATCACCTT
TCAGATACTACTGTGATATGATATTTGAAGTCATGAGAAATGAGCAACCTTATGACAGTATTCC
AAACTTCAGTGCGGCAGATGCTTTCCGGCTTACAGGAATAGGGAGGAATGAGTTCATTGATATC
ATGAATAAATGCAGATCTAAG
Transcript length: 878
Transcript exons: 12909274-12909420,12909515-12910138,12910234-12910340
ATAGTGAAATTTAGGGAAGATGCAGCACACTCCAGTAACAATAGAGGACCAGTTAATATCGAAA
GCTGTAAGAGAAGAATGTCAATGGGAAAACCTCCCAAAACGACTTCAATCGATCCTTGGGTCTA
AGGATGAATGGCATAGAAGGGTTACGGCGCATTGTATAAAGAAAAGACTCCTATGGAATACGTG
TTTTGCTTGTAAAGTTTGCAAAGAAGGTGAATATTATGAAGATATGATGCGTTACTTGCGAAAG
AATCTGGCGGTGCGTGTTGATGGATTACTCTTTAAGAGGTCTTTTTGTTTTGATTGCATTCTAG
TGGAGAGTTACTAGCAAATCATTTTTCTGAAGTTTATTTTTGTTTGTGTTCGTTCCTCATTATA
TCTCATTTTCAATGGCTTTCTCACTGCGAATTTTTATGTACTATAGCGACAATGCATAAGAAAA
GGGTTTGGAATTGACAATAGTGGTTAACAAGGTTTATTTTAGATTTTAGATACCATAGTCTGTG
ATGCCAATTTATGAATATGTTTGCTACTCTGAAAGATAGCCGTGGGTTCAGATAGTCGATAGAA
AGAGAGAAACTTGGTGATCAAGGACGAAATATAGGGCATTGTTGTCTGTTACTGTCAGAGGATC
TCTAATCTTAATTGCTGTTAACAATTATCCGCAGCTCTTTCCGTATCACCTTGCAGAGTATGTT
TGCCGTGTGATGAGGATATCACCTTTCAGATACTACTGTGATATGATATTTGAAGTCATGAGAA
ATGAGCAACCTTATGACAGTATTCCAAACTTCAGTGCGGCAGATGCTTTCCGGCTTACAGGAAT
AGGGAGGAATGAGTTCATTGATATCATGAATAAATGCAGATCTAAG
						
					

						Genomic sequence
						
							ATAGTGAAATTTAGGGAAGATGCAGCACACTCCAGTAACAATAGAGGACCAGTTAATATCGAAA
GCTGTAAGAGAAGAATGTCAATGGGAAAACCTCCCAAAACGACTTCAATCGATCCTTGGGTCTA
AGGATGAATGGCATAGAAGGTTAGATTTTCTTTATGCTTTCTACTTGTAGTAGCTCGGTGCACG
GTGACATAGTTTACTTTGACATAGTTCACTGTTTTGATTGTTTGTGTAGGGTTACGGCGCATTG
TATAAAGAAAAGACTCCTATGGAATACGTGTTTTGCTTGTAAAGTTTGCAAAGAAGGTGAATAT
TATGAAGATATGATGCGTTACTTGCGAAAGAATCTGGCGGTGCGTGTTGATGGATTACTCTTTA
AGAGGTCTTTTTGTTTTGATTGCATTCTAGTGGAGAGTTACTAGCAAATCATTTTTCTGAAGTT
TATTTTTGTTTGTGTTCGTTCCTCATTATATCTCATTTTCAATGGCTTTCTCACTGCGAATTTT
TATGTACTATAGCGACAATGCATAAGAAAAGGGTTTGGAATTGACAATAGTGGTTAACAAGGTT
TATTTTAGATTTTAGATACCATAGTCTGTGATGCCAATTTATGAATATGTTTGCTACTCTGAAA
GATAGCCGTGGGTTCAGATAGTCGATAGAAAGAGAGAAACTTGGTGATCAAGGACGAAATATAG
GGCATTGTTGTCTGTTACTGTCAGAGGATCTCTAATCTTAATTGCTGTTAACAATTATCCGCAG
CTCTTTCCGTATCACCTTGCAGAGTATGTTTGCCGTGTGATGAGGATATCACCTTTCAGATACT
ACTGTGATATGATATTTGAAGTCATGAGAAATGGTATTTTTGTTTCTTTACTATATCGCTCATT
TTTCATTTACCTTAAATTCGAGCCAGTGATTTCGTCATTCCTCATTCCTTTTAATTTGACACAG
AGCAACCTTATGACAGTATTCCAAACTTCAGTGCGGCAGATGCTTTCCGGCTTACAGGAATAGG
GAGGAATGAGTTCATTGATATCATGAATAAATGCAGATCTAAG
						
					

			
		

Sequences
Splice junction sequence	TTATGACAGTATTCCAAACTTCAGTGCGGCAGATGCTTTCCGGCTTACAGGAATAGGGAGGAAT GAGTTCATTGATATCATGAATAAATGCAGATCTAAGatagtgaaatttagggaagatgcagcac actccagtaacaatagaggaccagttaatatcgaaagctgtaagagaagaatgtcaatgggaaa acctccca
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: 469 Transcript exons: 12909274-12909420,12909515-12909632,12910042-12910138,12 910234-12910340 ATAGTGAAATTTAGGGAAGATGCAGCACACTCCAGTAACAATAGAGGACCAGTTAATATCGAAA GCTGTAAGAGAAGAATGTCAATGGGAAAACCTCCCAAAACGACTTCAATCGATCCTTGGGTCTA AGGATGAATGGCATAGAAGGGTTACGGCGCATTGTATAAAGAAAAGACTCCTATGGAATACGTG TTTTGCTTGTAAAGTTTGCAAAGAAGGTGAATATTATGAAGATATGATGCGTTACTTGCGAAAG AATCTGGCGCTCTTTCCGTATCACCTTGCAGAGTATGTTTGCCGTGTGATGAGGATATCACCTT TCAGATACTACTGTGATATGATATTTGAAGTCATGAGAAATGAGCAACCTTATGACAGTATTCC AAACTTCAGTGCGGCAGATGCTTTCCGGCTTACAGGAATAGGGAGGAATGAGTTCATTGATATC ATGAATAAATGCAGATCTAAG Transcript length: 878 Transcript exons: 12909274-12909420,12909515-12910138,12910234-12910340 ATAGTGAAATTTAGGGAAGATGCAGCACACTCCAGTAACAATAGAGGACCAGTTAATATCGAAA GCTGTAAGAGAAGAATGTCAATGGGAAAACCTCCCAAAACGACTTCAATCGATCCTTGGGTCTA AGGATGAATGGCATAGAAGGGTTACGGCGCATTGTATAAAGAAAAGACTCCTATGGAATACGTG TTTTGCTTGTAAAGTTTGCAAAGAAGGTGAATATTATGAAGATATGATGCGTTACTTGCGAAAG AATCTGGCGGTGCGTGTTGATGGATTACTCTTTAAGAGGTCTTTTTGTTTTGATTGCATTCTAG TGGAGAGTTACTAGCAAATCATTTTTCTGAAGTTTATTTTTGTTTGTGTTCGTTCCTCATTATA TCTCATTTTCAATGGCTTTCTCACTGCGAATTTTTATGTACTATAGCGACAATGCATAAGAAAA GGGTTTGGAATTGACAATAGTGGTTAACAAGGTTTATTTTAGATTTTAGATACCATAGTCTGTG ATGCCAATTTATGAATATGTTTGCTACTCTGAAAGATAGCCGTGGGTTCAGATAGTCGATAGAA AGAGAGAAACTTGGTGATCAAGGACGAAATATAGGGCATTGTTGTCTGTTACTGTCAGAGGATC TCTAATCTTAATTGCTGTTAACAATTATCCGCAGCTCTTTCCGTATCACCTTGCAGAGTATGTT TGCCGTGTGATGAGGATATCACCTTTCAGATACTACTGTGATATGATATTTGAAGTCATGAGAA ATGAGCAACCTTATGACAGTATTCCAAACTTCAGTGCGGCAGATGCTTTCCGGCTTACAGGAAT AGGGAGGAATGAGTTCATTGATATCATGAATAAATGCAGATCTAAG
Genomic sequence	ATAGTGAAATTTAGGGAAGATGCAGCACACTCCAGTAACAATAGAGGACCAGTTAATATCGAAA GCTGTAAGAGAAGAATGTCAATGGGAAAACCTCCCAAAACGACTTCAATCGATCCTTGGGTCTA AGGATGAATGGCATAGAAGGTTAGATTTTCTTTATGCTTTCTACTTGTAGTAGCTCGGTGCACG GTGACATAGTTTACTTTGACATAGTTCACTGTTTTGATTGTTTGTGTAGGGTTACGGCGCATTG TATAAAGAAAAGACTCCTATGGAATACGTGTTTTGCTTGTAAAGTTTGCAAAGAAGGTGAATAT TATGAAGATATGATGCGTTACTTGCGAAAGAATCTGGCGGTGCGTGTTGATGGATTACTCTTTA AGAGGTCTTTTTGTTTTGATTGCATTCTAGTGGAGAGTTACTAGCAAATCATTTTTCTGAAGTT TATTTTTGTTTGTGTTCGTTCCTCATTATATCTCATTTTCAATGGCTTTCTCACTGCGAATTTT TATGTACTATAGCGACAATGCATAAGAAAAGGGTTTGGAATTGACAATAGTGGTTAACAAGGTT TATTTTAGATTTTAGATACCATAGTCTGTGATGCCAATTTATGAATATGTTTGCTACTCTGAAA GATAGCCGTGGGTTCAGATAGTCGATAGAAAGAGAGAAACTTGGTGATCAAGGACGAAATATAG GGCATTGTTGTCTGTTACTGTCAGAGGATCTCTAATCTTAATTGCTGTTAACAATTATCCGCAG CTCTTTCCGTATCACCTTGCAGAGTATGTTTGCCGTGTGATGAGGATATCACCTTTCAGATACT ACTGTGATATGATATTTGAAGTCATGAGAAATGGTATTTTTGTTTCTTTACTATATCGCTCATT TTTCATTTACCTTAAATTCGAGCCAGTGATTTCGTCATTCCTCATTCCTTTTAATTTGACACAG AGCAACCTTATGACAGTATTCCAAACTTCAGTGCGGCAGATGCTTTCCGGCTTACAGGAATAGG GAGGAATGAGTTCATTGATATCATGAATAAATGCAGATCTAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.300384452

Conservation Information
Conserved circRNAs	NA
PMCS	0.300384452

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of AT1G35220_circ_g.1

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