Plant Circular RNA Database

Detail information of AT1G05890_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT1G05890_circ_g.4
					
						ID in PlantcircBase
						ath_circ_000893
					
						Alias
						1:1780174-1781799
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 1780174-1781799  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G05890						
					
						Parent gene annotation
						
							RING/U-box superfamily protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G05890_circ_g.2 AT1G05890_circ_g.3 AT1G05890_circ_g.5 AT1G05890_circ_g.6 AT1G05890_circ_g.7 AT1G05890_circ_g.8 AT1G05890_circ_g.9 AT1G05890_circ_g.10 AT1G05890_circ_g.11 AT1G05890_circ_g.12 AT1G05890_circ_g.13 AT1G05890_circ_g.14 						
					
						Support reads
						1/1
					
						Tissues
						root;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
						AT1G05890.1:5
AT1G05890.2:5

General Information
CircRNA Name	AT1G05890_circ_g.4
ID in PlantcircBase	ath_circ_000893
Alias	1:1780174-1781799
Organism	Arabidpsis thaliana
Position	chr1: 1780174-1781799 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G05890
Parent gene annotation	RING/U-box superfamily protein
Parent gene strand	+
Alternative splicing	AT1G05890_circ_g.2 AT1G05890_circ_g.3 AT1G05890_circ_g.5 AT1G05890_circ_g.6 AT1G05890_circ_g.7 AT1G05890_circ_g.8 AT1G05890_circ_g.9 AT1G05890_circ_g.10 AT1G05890_circ_g.11 AT1G05890_circ_g.12 AT1G05890_circ_g.13 AT1G05890_circ_g.14
Support reads	1/1
Tissues	root;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	AT1G05890.1:5 AT1G05890.2:5

			
						 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  
						
							GTGGTGTCCTGCCCCAGGATGTGAACATGCAATTGATTTTGCTGGTGGGACCGAAAGTTATGAT
GTTTCGTGCTTGTGTTCGCATAGCTTTTGCTGGAATagtaattatgttgttctcaaggaagaag
atattcgcaggcatcagaacgatgatgttgggcgagtttccgcggtcctctccataaccgatgt
cgaagcaa

									
								

					

						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
						
							AGTAATTATGTTGTTCTCAAGGAAGAAGATATTCGCAGGCATCAGAACGATGATGTTGGGCGAG
TTTCCGCGGTCCTCTCCATAACCGATGTCGAAGCAAGTACTTTGCTTCTTCACTATCACTGGTA
AAATCCCTTTTACATTTACTGTGTGATTTTGTTATAAATCTTTCTGTTTCCTTTGTTTTCGATG
ATATATCCACGACATTGTTTATCCTCTAGTTGTTTCAAAACGACTTTTCTCTTCCATGGGATTG
TTTTGATCTGCTACATTTAATGGACTCTATATTGATGTCCAAACTAGTGTCTTTCTCTAGTTTC
CTAATGCTCCTGAGAAATGTTTCTTTTTTTAGGAGTGTCAGTAAAGTTAATGATGAATGGTTTG
CGGATGAGGAGAGAGTTCGCAGAACTGTTGGCATATTAGAGGGACCTGTTGTTACAACACCTGA
TGGCAGAGAAGTAATTCCTTTAATTCTCGACTCGGAATTGTTTTCTATAATTCTCGCTTGGTAA
ATCATGTTTCACTGACGCATGATTTGATGTTTAGTTTACATGTGGAATATGCTTTGATTCCTAC
ACTCTTGAGGAAATTGTATCGGTTTCTTGTGGTCATCCTTTCTGCGCTACATGTTGGACAGGTA
TGTTTTTTCCCTCCATTATCGTTAGATGCTTACATCTGTAGCTTCTTCAGAAACAGCGATTGTT
GATTTATTACTTTCCTTGGATTTATCTGAGTGTTTATTTAGTTAGCATTTCGGTTTACACATTT
TAAAAGATATTTGCCTATGAATTTAATTGTTAAGCTTTAGTTTCCTTCATGTCTGGAATGCGTA
GATCTAAGTTTTATATACTGTTTTTCCTACTAAAACATCTCTTTTCTGATACCTTTCGTTTTAT
ACTGTGCACTTTTGTAGGTTATATAAGCACAACCATCAATGATGGCCCAGGCTGTTTGATGCTA
AAATGTCCCGACCCTTCTTGTCCTGCTGCTATTGGTCGAGATATGATCGATAAGTTGGCTTCTA
AGGAAGACAAGGAGAAGTATTATAGATATTTTCTTAGATCTTATGTCGAAGTCAACAGAGAGGT
AAGCTTCCAAGATAATATATATTCAGACTGCATATCTTCATGCAAGAAGCATAAACTACTTGAT
GCTCTTGCGAGTTCTTTCGATCCGTCTATATAGTTTAAACTTTAAAATTCAGTTTATCCGCGTG
TCCTCCCTATGATGCTTTAATTGACTCCAATTTCCAGGAAGCTTTTACTTCTCTATACTGGCTA
TTACAATTTTTAGCATATACTAGTATTGGTCGAAGATTTTCTCTGTCTCCAGATTTACCTAATT
TTTCCTCTTCTTAATCTTGTATGGAATGGCGTCCAGCTTTTCTTCTTGAATTACATCACAATAA
TCCCAACGTATTTCAATGCATTTGCTTTGAGCAAAGTACTACTTTGTCATCAGTTTTTGTGTCT
TTGTGTGTCTAGTTTGAAATATTGCTCGTATTTGTTTTTTCTGTTTCAGATGAAGTGGTGTCCT
GCCCCAGGATGTGAACATGCAATTGATTTTGCTGGTGGGACCGAAAGTTATGATGTTTCGTGCT
TGTGTTCGCATAGCTTTTGCTGGAAT
						
					

			
		

Sequences
Splice junction sequence	GTGGTGTCCTGCCCCAGGATGTGAACATGCAATTGATTTTGCTGGTGGGACCGAAAGTTATGAT GTTTCGTGCTTGTGTTCGCATAGCTTTTGCTGGAATagtaattatgttgttctcaaggaagaag atattcgcaggcatcagaacgatgatgttgggcgagtttccgcggtcctctccataaccgatgt cgaagcaa
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	AGTAATTATGTTGTTCTCAAGGAAGAAGATATTCGCAGGCATCAGAACGATGATGTTGGGCGAG TTTCCGCGGTCCTCTCCATAACCGATGTCGAAGCAAGTACTTTGCTTCTTCACTATCACTGGTA AAATCCCTTTTACATTTACTGTGTGATTTTGTTATAAATCTTTCTGTTTCCTTTGTTTTCGATG ATATATCCACGACATTGTTTATCCTCTAGTTGTTTCAAAACGACTTTTCTCTTCCATGGGATTG TTTTGATCTGCTACATTTAATGGACTCTATATTGATGTCCAAACTAGTGTCTTTCTCTAGTTTC CTAATGCTCCTGAGAAATGTTTCTTTTTTTAGGAGTGTCAGTAAAGTTAATGATGAATGGTTTG CGGATGAGGAGAGAGTTCGCAGAACTGTTGGCATATTAGAGGGACCTGTTGTTACAACACCTGA TGGCAGAGAAGTAATTCCTTTAATTCTCGACTCGGAATTGTTTTCTATAATTCTCGCTTGGTAA ATCATGTTTCACTGACGCATGATTTGATGTTTAGTTTACATGTGGAATATGCTTTGATTCCTAC ACTCTTGAGGAAATTGTATCGGTTTCTTGTGGTCATCCTTTCTGCGCTACATGTTGGACAGGTA TGTTTTTTCCCTCCATTATCGTTAGATGCTTACATCTGTAGCTTCTTCAGAAACAGCGATTGTT GATTTATTACTTTCCTTGGATTTATCTGAGTGTTTATTTAGTTAGCATTTCGGTTTACACATTT TAAAAGATATTTGCCTATGAATTTAATTGTTAAGCTTTAGTTTCCTTCATGTCTGGAATGCGTA GATCTAAGTTTTATATACTGTTTTTCCTACTAAAACATCTCTTTTCTGATACCTTTCGTTTTAT ACTGTGCACTTTTGTAGGTTATATAAGCACAACCATCAATGATGGCCCAGGCTGTTTGATGCTA AAATGTCCCGACCCTTCTTGTCCTGCTGCTATTGGTCGAGATATGATCGATAAGTTGGCTTCTA AGGAAGACAAGGAGAAGTATTATAGATATTTTCTTAGATCTTATGTCGAAGTCAACAGAGAGGT AAGCTTCCAAGATAATATATATTCAGACTGCATATCTTCATGCAAGAAGCATAAACTACTTGAT GCTCTTGCGAGTTCTTTCGATCCGTCTATATAGTTTAAACTTTAAAATTCAGTTTATCCGCGTG TCCTCCCTATGATGCTTTAATTGACTCCAATTTCCAGGAAGCTTTTACTTCTCTATACTGGCTA TTACAATTTTTAGCATATACTAGTATTGGTCGAAGATTTTCTCTGTCTCCAGATTTACCTAATT TTTCCTCTTCTTAATCTTGTATGGAATGGCGTCCAGCTTTTCTTCTTGAATTACATCACAATAA TCCCAACGTATTTCAATGCATTTGCTTTGAGCAAAGTACTACTTTGTCATCAGTTTTTGTGTCT TTGTGTGTCTAGTTTGAAATATTGCTCGTATTTGTTTTTTCTGTTTCAGATGAAGTGGTGTCCT GCCCCAGGATGTGAACATGCAATTGATTTTGCTGGTGGGACCGAAAGTTATGATGTTTCGTGCT TGTGTTCGCATAGCTTTTGCTGGAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.17420512

Conservation Information
Conserved circRNAs	NA
PMCS	0.17420512

			
						 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 AT1G05890_circ_g.4

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