Plant Circular RNA Database

Detail information of AT1G79950_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT1G79950_circ_g.1
					
						ID in PlantcircBase
						ath_circ_011165
					
						Alias
						1:30076559-30078052
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 30076559-30078052  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G79950						
					
						Parent gene annotation
						
							RAD3-like DNA-binding helicase protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G79950_circ_g.2 AT1G79950_circ_g.3 AT1G79950_circ_g.4 						
					
						Support reads
						2/2
					
						Tissues
						root;flower
					
						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
						AT1G79950.2:7
AT1G79950.3:7
AT1G79950.5:7
AT1G79950.7:7
AT1G79950.6:7
AT1G79950.4:7
AT1G79950.1:7

General Information
CircRNA Name	AT1G79950_circ_g.1
ID in PlantcircBase	ath_circ_011165
Alias	1:30076559-30078052
Organism	Arabidpsis thaliana
Position	chr1: 30076559-30078052 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G79950
Parent gene annotation	RAD3-like DNA-binding helicase protein
Parent gene strand	+
Alternative splicing	AT1G79950_circ_g.2 AT1G79950_circ_g.3 AT1G79950_circ_g.4
Support reads	2/2
Tissues	root;flower
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	AT1G79950.2:7 AT1G79950.3:7 AT1G79950.5:7 AT1G79950.7:7 AT1G79950.6:7 AT1G79950.4:7 AT1G79950.1:7

			
						 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  
						
							TCGTTTTTTCTGATTATTTCGTATATTGGCTATTGTTGACAGATTTGAACAACCATCCCAGCAA
TCCAAGATATCACTTTGGATACGACCTAACGTCAAGttaacttttctcgagtcgtgcctgaagg
actgctgatatttttcccttcctattaccttatggactcttgcattacattttggaaaaatggg
gtatggcc

									
								

					

						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
						
							TTAACTTTTCTCGAGTCGTGCCTGAAGGACTGCTGATATTTTTCCCTTCCTATTACCTTATGGA
CTCTTGCATTACATTTTGGAAAAATGGGGTATGGCCGTTGTTAATTTTCTCTTAAGTATGAAAA
AATGAGTACTCTTTAGCTTGTAAACCTACCGTTTTTTCATCATTCAGTGTTACAGAAACTCAAT
GACAGTATGGGAAAGAATTTGCAAGCTCAAGAAACCTGTCATTGAACCCAAGGATTCCTCCCTC
TTTCCTGCAGCAATGCGGGTGAGCAAGAGATGCCTCTGATCTACGTCTCTTGAATAGGATTAAT
TTAATCGTGTCTTGTATTTTTGTTAATGGTAGGACTTTTCAGAAAAATTGCAAGACAGAGCAAC
TTCGGGTGTGGTGTTTTTTGCCGTTTGTCGCGGTAAGGTATGTATTCTTCAACCTGTATAAATT
TTCTCCTGTATCCATATAGTATGTATGAGGATGCTGGTATAAAAGATAGGAGGTCAATAAGTTT
CTCTAGTGTAGTGTCTTCAGTATGGCTGGTCTCTCTGTTGTGTTGTCAGGTCAGCGAAGGACTG
GATTTTGCTGACGGTGCTGGCAGAGCTGTCGTCATTACTGGGTTACCTTATGCCAGGGTGACAG
ATCCTAGGGTTTGTCTGCTCTATCCTTTAATGTTTTGTTCTGAATTTGTATTTAGGCTCATTAG
CGAAATGGTAGCAAAAAACAGTTAGTGAACTGTTTTGTTCTTTTTCAGAGTTTCTTTCTCATTT
CTCTTCACTTTTATTTAAACTGGCACTGGGGGGCCACATAGCTTTAAATTTTATGCTGCTACTT
GTATTCCAGCATCATTAAACCATGTGTAAAACAGGTTAAATTGAAACGAGAGTTTCTGGATGAA
CAATCACAACTTGCAGATGTTAAGGTGAGTTCAATATTTATTTGATTATTGACACATCAAGGTA
TAATATTTCTTACAATTTTGTAGCTTCCAAGATCAACCCTACTATCTGGAAGCATGTGGTACAG
TCAAGAAGCCGCACGGGCTGTGAATCAAGCAATTGGACGTGTAATCCGCCATCGTCATGATTAT
GGAGCTATCATCTTTTGTGATGACAGGTTTTGTTCATGCTACCCGTGGCTTTTTTTTTCTGGTT
TCATGCAAGATTGTTCTTTTCGAGCATATATTCTGGGCATGATGCATGTAAAGATGTAGGCCTC
TTGTTTTTGGGCGAATAGATAGTGCATGAAATATTTTAGTTAAGGTACTGCCAATTTAAATTGA
GACGTATGCTCTTTATTTGAGATTGCTTTTGGTTGATATTGTGTCTGACATTCTCTTTCCTAAC
TTTACTTGCTATAGTTCTTAACTATCCTCCAAAAGACAATATACTCATTCTCGTTTTTTCTGAT
TATTTCGTATATTGGCTATTGTTGACAGATTTGAACAACCATCCCAGCAATCCAAGATATCACT
TTGGATACGACCTAACGTCAAG
						
					

			
		

Sequences
Splice junction sequence	TCGTTTTTTCTGATTATTTCGTATATTGGCTATTGTTGACAGATTTGAACAACCATCCCAGCAA TCCAAGATATCACTTTGGATACGACCTAACGTCAAGttaacttttctcgagtcgtgcctgaagg actgctgatatttttcccttcctattaccttatggactcttgcattacattttggaaaaatggg gtatggcc
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	TTAACTTTTCTCGAGTCGTGCCTGAAGGACTGCTGATATTTTTCCCTTCCTATTACCTTATGGA CTCTTGCATTACATTTTGGAAAAATGGGGTATGGCCGTTGTTAATTTTCTCTTAAGTATGAAAA AATGAGTACTCTTTAGCTTGTAAACCTACCGTTTTTTCATCATTCAGTGTTACAGAAACTCAAT GACAGTATGGGAAAGAATTTGCAAGCTCAAGAAACCTGTCATTGAACCCAAGGATTCCTCCCTC TTTCCTGCAGCAATGCGGGTGAGCAAGAGATGCCTCTGATCTACGTCTCTTGAATAGGATTAAT TTAATCGTGTCTTGTATTTTTGTTAATGGTAGGACTTTTCAGAAAAATTGCAAGACAGAGCAAC TTCGGGTGTGGTGTTTTTTGCCGTTTGTCGCGGTAAGGTATGTATTCTTCAACCTGTATAAATT TTCTCCTGTATCCATATAGTATGTATGAGGATGCTGGTATAAAAGATAGGAGGTCAATAAGTTT CTCTAGTGTAGTGTCTTCAGTATGGCTGGTCTCTCTGTTGTGTTGTCAGGTCAGCGAAGGACTG GATTTTGCTGACGGTGCTGGCAGAGCTGTCGTCATTACTGGGTTACCTTATGCCAGGGTGACAG ATCCTAGGGTTTGTCTGCTCTATCCTTTAATGTTTTGTTCTGAATTTGTATTTAGGCTCATTAG CGAAATGGTAGCAAAAAACAGTTAGTGAACTGTTTTGTTCTTTTTCAGAGTTTCTTTCTCATTT CTCTTCACTTTTATTTAAACTGGCACTGGGGGGCCACATAGCTTTAAATTTTATGCTGCTACTT GTATTCCAGCATCATTAAACCATGTGTAAAACAGGTTAAATTGAAACGAGAGTTTCTGGATGAA CAATCACAACTTGCAGATGTTAAGGTGAGTTCAATATTTATTTGATTATTGACACATCAAGGTA TAATATTTCTTACAATTTTGTAGCTTCCAAGATCAACCCTACTATCTGGAAGCATGTGGTACAG TCAAGAAGCCGCACGGGCTGTGAATCAAGCAATTGGACGTGTAATCCGCCATCGTCATGATTAT GGAGCTATCATCTTTTGTGATGACAGGTTTTGTTCATGCTACCCGTGGCTTTTTTTTTCTGGTT TCATGCAAGATTGTTCTTTTCGAGCATATATTCTGGGCATGATGCATGTAAAGATGTAGGCCTC TTGTTTTTGGGCGAATAGATAGTGCATGAAATATTTTAGTTAAGGTACTGCCAATTTAAATTGA GACGTATGCTCTTTATTTGAGATTGCTTTTGGTTGATATTGTGTCTGACATTCTCTTTCCTAAC TTTACTTGCTATAGTTCTTAACTATCCTCCAAAAGACAATATACTCATTCTCGTTTTTTCTGAT TATTTCGTATATTGGCTATTGTTGACAGATTTGAACAACCATCCCAGCAATCCAAGATATCACT TTGGATACGACCTAACGTCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.129398422

Conservation Information
Conserved circRNAs	NA
PMCS	0.129398422

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

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT1G79950_circ_g.1

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