Plant Circular RNA Database

Detail information of AT1G50120_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT1G50120_circ_g.2
					
						ID in PlantcircBase
						ath_circ_006580
					
						Alias
						1:18562978-18564226
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 18562978-18564226  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G50120						
					
						Parent gene annotation
						
							Rgp1 (InterPro:IPR014848),  /.../globulin E-set (InterPro:IPR014
756)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G50120_circ_g.1 						
					
						Support reads
						1/1/1
					
						Tissues
						seedling;leaf;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
						AT1G50120.1:3
AT1G50120.2:3

General Information
CircRNA Name	AT1G50120_circ_g.2
ID in PlantcircBase	ath_circ_006580
Alias	1:18562978-18564226
Organism	Arabidpsis thaliana
Position	chr1: 18562978-18564226 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G50120
Parent gene annotation	Rgp1 (InterPro:IPR014848), /.../globulin E-set (InterPro:IPR014 756)
Parent gene strand	+
Alternative splicing	AT1G50120_circ_g.1
Support reads	1/1/1
Tissues	seedling;leaf;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	AT1G50120.1:3 AT1G50120.2:3

			
						 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  
						
							CAACCTGATGGGGCTCTCCAATTTTCTTACAGGTATTGTTCCAACCAGTACCATTCAGACAGAA
ATATATTGGAAAGAGATGGATGGGGACTCAGAATGGtaatggttcgagctatactcccacagat
tataccaccttcttataaaggtgctactttacgttacctttactacattaagagcacattatgc
ggaagatg

									
								

					

						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: 302
Transcript exons: 18562978-18563135,18563920-18563995,18564159-18564226
TAATGGTTCGAGCTATACTCCCACAGATTATACCACCTTCTTATAAAGGTGCTACTTTACGTTA
CCTTTACTACATTAAGAGCACATTATGCGGAAGATGGATGGCATTAGAAAACAGTCAATTTTAC
AAAGACTCAACACAAGATTTCATTGAAGTGGAGACTCGAATACCATTACAAGTATGGGTAATTC
AGAAGAACAATGGGCTGCTATTAGAGGAAGATCAAATCGATGGTATTGTTCCAACCAGTACCAT
TCAGACAGAAATATATTGGAAAGAGATGGATGGGGACTCAGAATGG
						
					

						Genomic sequence
						
							TAATGGTTCGAGCTATACTCCCACAGATTATACCACCTTCTTATAAAGGTGCTACTTTACGTTA
CCTTTACTACATTAAGAGCACATTATGCGGAAGATGGATGGCATTAGAAAACAGTCAATTTTAC
AAAGACTCAACACAAGATTTCATTGAAGTGGTTAGTTTACTTGACTTTCCGTGTTTTCTGTAGG
TGTTATATGTGTAAAACATTGTGTTTCGGTTACTTTGGTTGCTTGAACGCAATTTGTTTTCTAT
TCACCGGTGTGGAAAATATATAAACTGGGATAAACACAAACAATGTAGCTCTGTTGTGTTGAAA
CACGTCTCATGGTTCTTACTATAGTGCTAAGTCAGGCTGTATCCTTGGTTTTTAGTCTGCTTGA
TGCCTAATTGATAATAGAATCACACAACTTTGTATGAGTCATTCAACATTCTTAGATCATCTAG
CTTATTGTTTCTCTGTGGCGATGCAATGGAGATGCACCAGGGTTTATATGCAAACTATGAAGTT
GAAGCATGAGGTTTAAAGCGTAGCTTAGTCTAGATCTTCTTGGAAAACTTTTCAGTGTTACATG
TAGTTAGTTTTCTTTGGCCAATTTGTCACTGCAGTGAGTTTAGTAGTTCAGTCAGTTGATTATA
ACATCTTTCTAATCAAGTATAATTTGATACTTTCTGTCATCAAAATAATCTTGTTCCCCTGAAA
TTGGATGCCTTGATTCTGGAGTTGGTCTACGATTTAATCATGGTAATATGTCATAACTGAAGGT
CTAATTACATACCTCCTATGGCCTGATGCTTGATAGAAAATACTAAGTAAATGTATTTTGTGAT
AAGCCTCTTAATTTTTCTGAAATATAATATATTTTTCCCTTTTCCACTTGTATTTTATAGTTTG
CTGTTGGCATAAATTTGACTCCTGTAATCTTGTTATTTACCAACAGGAGACTCGAATACCATTA
CAAGTATGGGTAATTCAGAAGAACAATGGGCTGCTATTAGAGGAAGATCAAATCGATGGTAAGC
TTTTTTCTAAAATTTTGATTGGGAATTTTAAGTCAGAAGTCAAACTCTGTTTGTTTACAAGACA
ACAAGTTACAGGACGTCGGAAAGTTGTTTTCCCTCCTTTTTTTTGGATGACATTAGTGGTGCAA
CCTGATGGGGCTCTCCAATTTTCTTACAGGTATTGTTCCAACCAGTACCATTCAGACAGAAATA
TATTGGAAAGAGATGGATGGGGACTCAGAATGG
						
					

			
		

Sequences
Splice junction sequence	CAACCTGATGGGGCTCTCCAATTTTCTTACAGGTATTGTTCCAACCAGTACCATTCAGACAGAA ATATATTGGAAAGAGATGGATGGGGACTCAGAATGGtaatggttcgagctatactcccacagat tataccaccttcttataaaggtgctactttacgttacctttactacattaagagcacattatgc ggaagatg
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: 302 Transcript exons: 18562978-18563135,18563920-18563995,18564159-18564226 TAATGGTTCGAGCTATACTCCCACAGATTATACCACCTTCTTATAAAGGTGCTACTTTACGTTA CCTTTACTACATTAAGAGCACATTATGCGGAAGATGGATGGCATTAGAAAACAGTCAATTTTAC AAAGACTCAACACAAGATTTCATTGAAGTGGAGACTCGAATACCATTACAAGTATGGGTAATTC AGAAGAACAATGGGCTGCTATTAGAGGAAGATCAAATCGATGGTATTGTTCCAACCAGTACCAT TCAGACAGAAATATATTGGAAAGAGATGGATGGGGACTCAGAATGG
Genomic sequence	TAATGGTTCGAGCTATACTCCCACAGATTATACCACCTTCTTATAAAGGTGCTACTTTACGTTA CCTTTACTACATTAAGAGCACATTATGCGGAAGATGGATGGCATTAGAAAACAGTCAATTTTAC AAAGACTCAACACAAGATTTCATTGAAGTGGTTAGTTTACTTGACTTTCCGTGTTTTCTGTAGG TGTTATATGTGTAAAACATTGTGTTTCGGTTACTTTGGTTGCTTGAACGCAATTTGTTTTCTAT TCACCGGTGTGGAAAATATATAAACTGGGATAAACACAAACAATGTAGCTCTGTTGTGTTGAAA CACGTCTCATGGTTCTTACTATAGTGCTAAGTCAGGCTGTATCCTTGGTTTTTAGTCTGCTTGA TGCCTAATTGATAATAGAATCACACAACTTTGTATGAGTCATTCAACATTCTTAGATCATCTAG CTTATTGTTTCTCTGTGGCGATGCAATGGAGATGCACCAGGGTTTATATGCAAACTATGAAGTT GAAGCATGAGGTTTAAAGCGTAGCTTAGTCTAGATCTTCTTGGAAAACTTTTCAGTGTTACATG TAGTTAGTTTTCTTTGGCCAATTTGTCACTGCAGTGAGTTTAGTAGTTCAGTCAGTTGATTATA ACATCTTTCTAATCAAGTATAATTTGATACTTTCTGTCATCAAAATAATCTTGTTCCCCTGAAA TTGGATGCCTTGATTCTGGAGTTGGTCTACGATTTAATCATGGTAATATGTCATAACTGAAGGT CTAATTACATACCTCCTATGGCCTGATGCTTGATAGAAAATACTAAGTAAATGTATTTTGTGAT AAGCCTCTTAATTTTTCTGAAATATAATATATTTTTCCCTTTTCCACTTGTATTTTATAGTTTG CTGTTGGCATAAATTTGACTCCTGTAATCTTGTTATTTACCAACAGGAGACTCGAATACCATTA CAAGTATGGGTAATTCAGAAGAACAATGGGCTGCTATTAGAGGAAGATCAAATCGATGGTAAGC TTTTTTCTAAAATTTTGATTGGGAATTTTAAGTCAGAAGTCAAACTCTGTTTGTTTACAAGACA ACAAGTTACAGGACGTCGGAAAGTTGTTTTCCCTCCTTTTTTTTGGATGACATTAGTGGTGCAA CCTGATGGGGCTCTCCAATTTTCTTACAGGTATTGTTCCAACCAGTACCATTCAGACAGAAATA TATTGGAAAGAGATGGATGGGGACTCAGAATGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.173563417

Conservation Information
Conserved circRNAs	NA
PMCS	0.173563417

			
						 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 AT1G50120_circ_g.2

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