Plant Circular RNA Database

Detail information of AT2G41440_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT2G41440_circ_g.3
					
						ID in PlantcircBase
						ath_circ_017796
					
						Alias
						AT2G41440_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 17272368-17272938  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, KNIFE, MapSplice, PcircRNA_finder, circRNA_finder, find_circ, CIRI-full, CIRI2
					
						Parent gene
						
							AT2G41440						
					
						Parent gene annotation
						
							unknown protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT2G41310_circ_g.1 2_circ_ag.2 AT2G41310_circ_g.3 AT2G41310_circ_g.4 AT2G41310_circ_g.5 AT2G41310_circ_g.6 AT2G41310_circ_g.7 AT2G41310_circ_g.8 AT2G41310_circ_g.9 AT2G41310_circ_g.10 AT2G41310_circ_g.11 AT2G41310_circ_g.12 AT2G41310_circ_g.13 AT2G41310_circ_g.14 AT2G41310_circ_g.15 AT2G41310_circ_g.16 AT2G41310_circ_g.17 AT2G41310_circ_g.18 AT2G41310_circ_g.19 AT2G41310_circ_g.20 AT2G41350_circ_g.1 AT2G41350_circ_g.2 AT2G41350_circ_g.3 AT2G41380_circ_g.1 AT2G41380_circ_g.2 AT2G41410_circ_g.1 AT2G41430_circ_g.1 AT2G41430_circ_g.2 AT2G41430_circ_g.3 AT2G41430_circ_g.4 AT2G41430_circ_g.5 AT2G41430_circ_g.6 AT2G41430_circ_g.7 AT2G41430_circ_g.8 AT2G41430_circ_g.9 2_circ_ag.10 AT2G41440_circ_g.1 AT2G41440_circ_g.2 AT2G41440_circ_g.4 AT2G41440_circ_g.5 AT2G41440_circ_g.6 AT2G41440_circ_g.7 AT2G41440_circ_g.8 AT2G41450_circ_g.1 AT2G41450_circ_g.2 2_circ_ag.3 AT2G41475_circ_g.1 AT2G41500_circ_g.1 AT2G41515_circ_g.1 AT2G41520_circ_g.1 AT2G41520_circ_g.2 AT2G41520_circ_g.3 AT2G41520_circ_g.4 						
					
						Support reads
						11/2
					
						Tissues
						root, leaf, inflorescences, whole_plant/seedlings
					
						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
						AT2G41440.3:3
AT2G41440.4:3
AT2G41440.1:3
AT2G41440.2:1

General Information
CircRNA Name	AT2G41440_circ_g.3
ID in PlantcircBase	ath_circ_017796
Alias	AT2G41440_C1
Organism	Arabidpsis thaliana
Position	chr2: 17272368-17272938 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, KNIFE, MapSplice, PcircRNA_finder, circRNA_finder, find_circ, CIRI-full, CIRI2
Parent gene	AT2G41440
Parent gene annotation	unknown protein
Parent gene strand	+
Alternative splicing	AT2G41310_circ_g.1 2_circ_ag.2 AT2G41310_circ_g.3 AT2G41310_circ_g.4 AT2G41310_circ_g.5 AT2G41310_circ_g.6 AT2G41310_circ_g.7 AT2G41310_circ_g.8 AT2G41310_circ_g.9 AT2G41310_circ_g.10 AT2G41310_circ_g.11 AT2G41310_circ_g.12 AT2G41310_circ_g.13 AT2G41310_circ_g.14 AT2G41310_circ_g.15 AT2G41310_circ_g.16 AT2G41310_circ_g.17 AT2G41310_circ_g.18 AT2G41310_circ_g.19 AT2G41310_circ_g.20 AT2G41350_circ_g.1 AT2G41350_circ_g.2 AT2G41350_circ_g.3 AT2G41380_circ_g.1 AT2G41380_circ_g.2 AT2G41410_circ_g.1 AT2G41430_circ_g.1 AT2G41430_circ_g.2 AT2G41430_circ_g.3 AT2G41430_circ_g.4 AT2G41430_circ_g.5 AT2G41430_circ_g.6 AT2G41430_circ_g.7 AT2G41430_circ_g.8 AT2G41430_circ_g.9 2_circ_ag.10 AT2G41440_circ_g.1 AT2G41440_circ_g.2 AT2G41440_circ_g.4 AT2G41440_circ_g.5 AT2G41440_circ_g.6 AT2G41440_circ_g.7 AT2G41440_circ_g.8 AT2G41450_circ_g.1 AT2G41450_circ_g.2 2_circ_ag.3 AT2G41475_circ_g.1 AT2G41500_circ_g.1 AT2G41515_circ_g.1 AT2G41520_circ_g.1 AT2G41520_circ_g.2 AT2G41520_circ_g.3 AT2G41520_circ_g.4
Support reads	11/2
Tissues	root, leaf, inflorescences, whole_plant/seedlings
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	AT2G41440.3:3 AT2G41440.4:3 AT2G41440.1:3 AT2G41440.2:1

			
						 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  
						
							TATCACAATCCCCTTCGATTTTGCAGAAGAAGGAAGCAGAGCATGATGCTGACGGTATGAGGAG
AGGGGTTTTGGTTCCTTGCAAATTCTCTGCCAGCAGgagaatgactgggaaggaagatattgtc
agcttcaccgagctgctagctcttcaaagtcaccttatggatgtccgatccattgtgctggagc
aaaaggtg

									
								

					

						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: 213
Transcript exons: 17272368-17272464,17272554-17272595,17272865-17272938
GAGAATGACTGGGAAGGAAGATATTGTCAGCTTCACCGAGCTGCTAGCTCTTCAAAGTCACCTT
ATGGATGTCCGATCCATTGTGCTGGAGCAAAAGAAGGAGGTAGAGCTGGAAGAAGCTGAAAGGC
CGCACAAACAGAAGAAGGAAGCAGAGCATGATGCTGACGGTATGAGGAGAGGGGTTTTGGTTCC
TTGCAAATTCTCTGCCAGCAG
Transcript length: 728
Transcript exons: 17272368-17272938
GAGAATGACTGGGAAGGAAGATATTGTCAGCTTCACCGAGCTGCTAGCTCTTCAAAGTCACCTT
ATGGATGTCCGATCCATTGTGCTGGAGCAAAAGAAGGAGGTAGAGCTGGAAGAAGCTGAAAGGC
CGCACAAACAGAAGAAGGAAGCAGAGCATGATGCTGACGGTATGAGGAGAGGGGTTTTGGTTCC
TTGCAAATTCTCTGCCAGCAGGAGAATGACTGGGAAGGAAGATATTGTCAGCTTCACCGAGCTG
CTAGCTCTTCAAAGTCACCTTATGGATGTCCGATCCATTGTGCTGGAGCAAAAGAAGGAGGTAG
AGCTGGAAGAAGCTGAAAGGCCGCACAAACAGAAGAAGGAAGCAGAGCATGATGCTGACGGTAT
GAGGAGAGGGGTTTTGGTTCCTTGCAAATTCTCTGCCAGCAGGAGAATGACTGGGAAGGAAGAT
ATTGTCAGCTTCACCGAGCTGCTAGCTCTTCAAAGTCACCTTATGGATGTCCGATCCATTGTGC
TGGAGCAAAAGGTGAAATAGGGGGAAATATTACTTGACTTTTTTTTTTTGTTTCCGTGTCGTTA
TTATCAAGAATTTTCTTTAACTATTGGCTATTGCAGAAGGAGGTAGAGCTGGAAGAAGCTGAAA
GGCCGCACAAACAGAAGAAGGAAGCAGAGCATGATGCTGACGGTATGAGGAGAGGGGTTTTGGT
TCCTTGCAAATTCTCTGCCAGCAG
						
					

						Genomic sequence
						
							GAGAATGACTGGGAAGGAAGATATTGTCAGCTTCACCGAGCTGCTAGCTCTTCAAAGTCACCTT
ATGGATGTCCGATCCATTGTGCTGGAGCAAAAGGTGAAATAGGGGGAAATATTACTTGACTTTT
TTTTTTTGTTTCCGTGTCGTTATTATCAAGAATTTTCTTTAACTATTGGCTATTGCAGAAGGAG
GTAGAGCTGGAAGAAGCTGAAAGGCCGCACAAACAGGTAAAGTATTCTAATTCTTAATTTAGCT
GTCTTCTTTTTTTTTGCCCTGTATCCAAATTTTTTTTGTTGAGGAAAGTCAGTTTTACCCTTTC
CAGTCTAAAATCTCTCACAAGGCCATTGCTTTTGCCTCTCCTTTTTTTCTTCTTAAAGTTCCTT
GTTGACCTTGCAAGTTCTTAAGCTTTCTCACCTTTTACTTCTTTCTTTCTTTTTTCTGTCTTCT
CGGGTAATTACGTATCTGACATATATCACAATCCCCTTCGATTTTGCAGAAGAAGGAAGCAGAG
CATGATGCTGACGGTATGAGGAGAGGGGTTTTGGTTCCTTGCAAATTCTCTGCCAGCAG
						
					

			
		

Sequences
Splice junction sequence	TATCACAATCCCCTTCGATTTTGCAGAAGAAGGAAGCAGAGCATGATGCTGACGGTATGAGGAG AGGGGTTTTGGTTCCTTGCAAATTCTCTGCCAGCAGgagaatgactgggaaggaagatattgtc agcttcaccgagctgctagctcttcaaagtcaccttatggatgtccgatccattgtgctggagc aaaaggtg
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: 213 Transcript exons: 17272368-17272464,17272554-17272595,17272865-17272938 GAGAATGACTGGGAAGGAAGATATTGTCAGCTTCACCGAGCTGCTAGCTCTTCAAAGTCACCTT ATGGATGTCCGATCCATTGTGCTGGAGCAAAAGAAGGAGGTAGAGCTGGAAGAAGCTGAAAGGC CGCACAAACAGAAGAAGGAAGCAGAGCATGATGCTGACGGTATGAGGAGAGGGGTTTTGGTTCC TTGCAAATTCTCTGCCAGCAG Transcript length: 728 Transcript exons: 17272368-17272938 GAGAATGACTGGGAAGGAAGATATTGTCAGCTTCACCGAGCTGCTAGCTCTTCAAAGTCACCTT ATGGATGTCCGATCCATTGTGCTGGAGCAAAAGAAGGAGGTAGAGCTGGAAGAAGCTGAAAGGC CGCACAAACAGAAGAAGGAAGCAGAGCATGATGCTGACGGTATGAGGAGAGGGGTTTTGGTTCC TTGCAAATTCTCTGCCAGCAGGAGAATGACTGGGAAGGAAGATATTGTCAGCTTCACCGAGCTG CTAGCTCTTCAAAGTCACCTTATGGATGTCCGATCCATTGTGCTGGAGCAAAAGAAGGAGGTAG AGCTGGAAGAAGCTGAAAGGCCGCACAAACAGAAGAAGGAAGCAGAGCATGATGCTGACGGTAT GAGGAGAGGGGTTTTGGTTCCTTGCAAATTCTCTGCCAGCAGGAGAATGACTGGGAAGGAAGAT ATTGTCAGCTTCACCGAGCTGCTAGCTCTTCAAAGTCACCTTATGGATGTCCGATCCATTGTGC TGGAGCAAAAGGTGAAATAGGGGGAAATATTACTTGACTTTTTTTTTTTGTTTCCGTGTCGTTA TTATCAAGAATTTTCTTTAACTATTGGCTATTGCAGAAGGAGGTAGAGCTGGAAGAAGCTGAAA GGCCGCACAAACAGAAGAAGGAAGCAGAGCATGATGCTGACGGTATGAGGAGAGGGGTTTTGGT TCCTTGCAAATTCTCTGCCAGCAG
Genomic sequence	GAGAATGACTGGGAAGGAAGATATTGTCAGCTTCACCGAGCTGCTAGCTCTTCAAAGTCACCTT ATGGATGTCCGATCCATTGTGCTGGAGCAAAAGGTGAAATAGGGGGAAATATTACTTGACTTTT TTTTTTTGTTTCCGTGTCGTTATTATCAAGAATTTTCTTTAACTATTGGCTATTGCAGAAGGAG GTAGAGCTGGAAGAAGCTGAAAGGCCGCACAAACAGGTAAAGTATTCTAATTCTTAATTTAGCT GTCTTCTTTTTTTTTGCCCTGTATCCAAATTTTTTTTGTTGAGGAAAGTCAGTTTTACCCTTTC CAGTCTAAAATCTCTCACAAGGCCATTGCTTTTGCCTCTCCTTTTTTTCTTCTTAAAGTTCCTT GTTGACCTTGCAAGTTCTTAAGCTTTCTCACCTTTTACTTCTTTCTTTCTTTTTTCTGTCTTCT CGGGTAATTACGTATCTGACATATATCACAATCCCCTTCGATTTTGCAGAAGAAGGAAGCAGAG CATGATGCTGACGGTATGAGGAGAGGGGTTTTGGTTCCTTGCAAATTCTCTGCCAGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.426526874

Conservation Information
Conserved circRNAs	NA
PMCS	0.426526874

			
						 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
						Chu et al., 2017;Pan et al., 2017;Liu et al., 2017;Zhang et al., 2019

circRNA

Detail information of AT2G41440_circ_g.3

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