Plant Circular RNA Database

Detail information of AT5G42950_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT5G42950_circ_g.3
					
						ID in PlantcircBase
						ath_circ_042134
					
						Alias
						5:17225028-17226447
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 17225028-17226447  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G42950						
					
						Parent gene annotation
						
							GYF domain-containing protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G42950_circ_g.4 AT5G42950_circ_g.5 						
					
						Support reads
						1/2
					
						Tissues
						seedling;root
					
						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
						AT5G42950.1:4

General Information
CircRNA Name	AT5G42950_circ_g.3
ID in PlantcircBase	ath_circ_042134
Alias	5:17225028-17226447
Organism	Arabidpsis thaliana
Position	chr5: 17225028-17226447 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G42950
Parent gene annotation	GYF domain-containing protein
Parent gene strand	+
Alternative splicing	AT5G42950_circ_g.4 AT5G42950_circ_g.5
Support reads	1/2
Tissues	seedling;root
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	AT5G42950.1:4

			
						 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  
						
							GCAGCTGGAAGCAGAGAAGATATGACATTCGGTGCTGAGGAGTCTAAAGATGAAAGTGGAGAAA
CAAGGAACTATCCAGATGATAAGTTTAGGCCTGAAGatatccaaggttctgacaatgcgattcc
tctttcaccacagtggcttctctccaaaccaggggagaacaagactgggatgggaactggggta
tgtttcta

									
								

					

						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: 1176
Transcript exons: 17225028-17225116,17225194-17226063,17226146-17226266,17
226352-17226447
ATATCCAAGGTTCTGACAATGCGATTCCTCTTTCACCACAGTGGCTTCTCTCCAAACCAGGGGA
GAACAAGACTGGGATGGGAACTGGGGATCCTAATCAGTATGGAAACCATTCGGATGTTGTGAGA
ACAACAGGGAATGGGGAGGAGACACTGGATAATCTGAAGAAAAAAGATGTTTTCCGGCCATCCT
TGCTTGATGCAGAAAGTGGTCGTCGTGATCGTTGGCGTGATGAGGAAAGGGACACCTTGTCCTC
AGTCCGAAATGACCGCTGGCGGAATGGCGACAAAGACTCTGGTGATAATAAGAAGGTTGACCGG
TGGGATAATGTGGCTCCTAAATTTGGGGAACAACGACGTGGTCCGAATGACCGGTGGACTGATT
CAGGAAACAAGGATGCTGCGCCAGAGCAGAGGCGTGAGAGCAAGTGGAACTCTCGCTGGGGTCC
TGATGACAAGGAAGCTGAGATTCCGCGTAATAAGTGGGATGAACCTGGTAAGGACGGTGAAATC
ATTCGTGAGAAGGGTCCATCTCTTCCTACTAGCGATGGAGACCATTACCGGCCCTGGAGACCCT
CTCAAGGTCGAGGAAGAGGAGAAGCTCTTCACAACCAATCAACACCAAACAAACAGGTTACTTC
CTTCTCCCACAGCAGGGGGCGTGGAGAGAACACTGCTATCTTTTCAGCTGGACGTGGAAGGATG
AGTCCTGGTGGAAGCATTTTTACTAGCGCACCAAACCAGTCTCATCCCCCTGGATCTGCCTCTG
ACAAGGGGGAAAGTGGTCCTGGAGAACCTCCCCATCTGAGATATAGCAGAATGAAACTGTTGGA
TGTGTACAGGATGGCTGACACAGAGTGTTATGAAAAGTTTCCGGATGGGTTTATTGAGGTGCCT
TCCCTAACGTCTGAGGAGCCAACGGATCCTCTGGCTCTTTGTGCTCCAAGTTCCGATGAAGTGA
ATGTTCTGGATGCGATTGAGAAAGGAAAAATAGTGAGCAGTGGTGCCCCTCAGACGTCCAAGGA
TGGCCCTACTGGACGAAATCCGGTCGAGTTTTCACAACCTAGACGGATCAGGCCTGCTGGAAGC
AGAGAAGATATGACATTCGGTGCTGAGGAGTCTAAAGATGAAAGTGGAGAAACAAGGAACTATC
CAGATGATAAGTTTAGGCCTGAAG
						
					

						Genomic sequence
						
							ATATCCAAGGTTCTGACAATGCGATTCCTCTTTCACCACAGTGGCTTCTCTCCAAACCAGGGGA
GAACAAGACTGGGATGGGAACTGGGGTATGTTTCTATTGTTTGTGTATGCGTGCAGTTTGTTTT
TGATTTCTTAACATGTGAGCTGGTTTAATGTTTTACAGGATCCTAATCAGTATGGAAACCATTC
GGATGTTGTGAGAACAACAGGGAATGGGGAGGAGACACTGGATAATCTGAAGAAAAAAGATGTT
TTCCGGCCATCCTTGCTTGATGCAGAAAGTGGTCGTCGTGATCGTTGGCGTGATGAGGAAAGGG
ACACCTTGTCCTCAGTCCGAAATGACCGCTGGCGGAATGGCGACAAAGACTCTGGTGATAATAA
GAAGGTTGACCGGTGGGATAATGTGGCTCCTAAATTTGGGGAACAACGACGTGGTCCGAATGAC
CGGTGGACTGATTCAGGAAACAAGGATGCTGCGCCAGAGCAGAGGCGTGAGAGCAAGTGGAACT
CTCGCTGGGGTCCTGATGACAAGGAAGCTGAGATTCCGCGTAATAAGTGGGATGAACCTGGTAA
GGACGGTGAAATCATTCGTGAGAAGGGTCCATCTCTTCCTACTAGCGATGGAGACCATTACCGG
CCCTGGAGACCCTCTCAAGGTCGAGGAAGAGGAGAAGCTCTTCACAACCAATCAACACCAAACA
AACAGGTTACTTCCTTCTCCCACAGCAGGGGGCGTGGAGAGAACACTGCTATCTTTTCAGCTGG
ACGTGGAAGGATGAGTCCTGGTGGAAGCATTTTTACTAGCGCACCAAACCAGTCTCATCCCCCT
GGATCTGCCTCTGACAAGGGGGAAAGTGGTCCTGGAGAACCTCCCCATCTGAGATATAGCAGAA
TGAAACTGTTGGATGTGTACAGGATGGCTGACACAGAGTGTTATGAAAAGTTTCCGGATGGGTT
TATTGAGGTGCCTTCCCTAACGTCTGAGGAGCCAACGGATCCTCTGGCTCTTTGTGCTCCAAGT
TCCGATGAAGTGGTTTGTAGTCATAATTTAGTTGATGTTTTTCTTTTTCCTCTGGTATCTCAGT
TCTGATCCTTATACCCACTTTTACTCACAGAATGTTCTGGATGCGATTGAGAAAGGAAAAATAG
TGAGCAGTGGTGCCCCTCAGACGTCCAAGGATGGCCCTACTGGACGAAATCCGGTCGAGTTTTC
ACAACCTAGACGGATCAGGCCTGGTAAGAATTCTGTAAAAGACATCCAGGCTTCTAGTCTTTTG
TGTTTATGAAATAAATGGTAAATTTTGTGAATACCTTGTTGCAGCTGGAAGCAGAGAAGATATG
ACATTCGGTGCTGAGGAGTCTAAAGATGAAAGTGGAGAAACAAGGAACTATCCAGATGATAAGT
TTAGGCCTGAAG
						
					

			
		

Sequences
Splice junction sequence	GCAGCTGGAAGCAGAGAAGATATGACATTCGGTGCTGAGGAGTCTAAAGATGAAAGTGGAGAAA CAAGGAACTATCCAGATGATAAGTTTAGGCCTGAAGatatccaaggttctgacaatgcgattcc tctttcaccacagtggcttctctccaaaccaggggagaacaagactgggatgggaactggggta tgtttcta
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: 1176 Transcript exons: 17225028-17225116,17225194-17226063,17226146-17226266,17 226352-17226447 ATATCCAAGGTTCTGACAATGCGATTCCTCTTTCACCACAGTGGCTTCTCTCCAAACCAGGGGA GAACAAGACTGGGATGGGAACTGGGGATCCTAATCAGTATGGAAACCATTCGGATGTTGTGAGA ACAACAGGGAATGGGGAGGAGACACTGGATAATCTGAAGAAAAAAGATGTTTTCCGGCCATCCT TGCTTGATGCAGAAAGTGGTCGTCGTGATCGTTGGCGTGATGAGGAAAGGGACACCTTGTCCTC AGTCCGAAATGACCGCTGGCGGAATGGCGACAAAGACTCTGGTGATAATAAGAAGGTTGACCGG TGGGATAATGTGGCTCCTAAATTTGGGGAACAACGACGTGGTCCGAATGACCGGTGGACTGATT CAGGAAACAAGGATGCTGCGCCAGAGCAGAGGCGTGAGAGCAAGTGGAACTCTCGCTGGGGTCC TGATGACAAGGAAGCTGAGATTCCGCGTAATAAGTGGGATGAACCTGGTAAGGACGGTGAAATC ATTCGTGAGAAGGGTCCATCTCTTCCTACTAGCGATGGAGACCATTACCGGCCCTGGAGACCCT CTCAAGGTCGAGGAAGAGGAGAAGCTCTTCACAACCAATCAACACCAAACAAACAGGTTACTTC CTTCTCCCACAGCAGGGGGCGTGGAGAGAACACTGCTATCTTTTCAGCTGGACGTGGAAGGATG AGTCCTGGTGGAAGCATTTTTACTAGCGCACCAAACCAGTCTCATCCCCCTGGATCTGCCTCTG ACAAGGGGGAAAGTGGTCCTGGAGAACCTCCCCATCTGAGATATAGCAGAATGAAACTGTTGGA TGTGTACAGGATGGCTGACACAGAGTGTTATGAAAAGTTTCCGGATGGGTTTATTGAGGTGCCT TCCCTAACGTCTGAGGAGCCAACGGATCCTCTGGCTCTTTGTGCTCCAAGTTCCGATGAAGTGA ATGTTCTGGATGCGATTGAGAAAGGAAAAATAGTGAGCAGTGGTGCCCCTCAGACGTCCAAGGA TGGCCCTACTGGACGAAATCCGGTCGAGTTTTCACAACCTAGACGGATCAGGCCTGCTGGAAGC AGAGAAGATATGACATTCGGTGCTGAGGAGTCTAAAGATGAAAGTGGAGAAACAAGGAACTATC CAGATGATAAGTTTAGGCCTGAAG
Genomic sequence	ATATCCAAGGTTCTGACAATGCGATTCCTCTTTCACCACAGTGGCTTCTCTCCAAACCAGGGGA GAACAAGACTGGGATGGGAACTGGGGTATGTTTCTATTGTTTGTGTATGCGTGCAGTTTGTTTT TGATTTCTTAACATGTGAGCTGGTTTAATGTTTTACAGGATCCTAATCAGTATGGAAACCATTC GGATGTTGTGAGAACAACAGGGAATGGGGAGGAGACACTGGATAATCTGAAGAAAAAAGATGTT TTCCGGCCATCCTTGCTTGATGCAGAAAGTGGTCGTCGTGATCGTTGGCGTGATGAGGAAAGGG ACACCTTGTCCTCAGTCCGAAATGACCGCTGGCGGAATGGCGACAAAGACTCTGGTGATAATAA GAAGGTTGACCGGTGGGATAATGTGGCTCCTAAATTTGGGGAACAACGACGTGGTCCGAATGAC CGGTGGACTGATTCAGGAAACAAGGATGCTGCGCCAGAGCAGAGGCGTGAGAGCAAGTGGAACT CTCGCTGGGGTCCTGATGACAAGGAAGCTGAGATTCCGCGTAATAAGTGGGATGAACCTGGTAA GGACGGTGAAATCATTCGTGAGAAGGGTCCATCTCTTCCTACTAGCGATGGAGACCATTACCGG CCCTGGAGACCCTCTCAAGGTCGAGGAAGAGGAGAAGCTCTTCACAACCAATCAACACCAAACA AACAGGTTACTTCCTTCTCCCACAGCAGGGGGCGTGGAGAGAACACTGCTATCTTTTCAGCTGG ACGTGGAAGGATGAGTCCTGGTGGAAGCATTTTTACTAGCGCACCAAACCAGTCTCATCCCCCT GGATCTGCCTCTGACAAGGGGGAAAGTGGTCCTGGAGAACCTCCCCATCTGAGATATAGCAGAA TGAAACTGTTGGATGTGTACAGGATGGCTGACACAGAGTGTTATGAAAAGTTTCCGGATGGGTT TATTGAGGTGCCTTCCCTAACGTCTGAGGAGCCAACGGATCCTCTGGCTCTTTGTGCTCCAAGT TCCGATGAAGTGGTTTGTAGTCATAATTTAGTTGATGTTTTTCTTTTTCCTCTGGTATCTCAGT TCTGATCCTTATACCCACTTTTACTCACAGAATGTTCTGGATGCGATTGAGAAAGGAAAAATAG TGAGCAGTGGTGCCCCTCAGACGTCCAAGGATGGCCCTACTGGACGAAATCCGGTCGAGTTTTC ACAACCTAGACGGATCAGGCCTGGTAAGAATTCTGTAAAAGACATCCAGGCTTCTAGTCTTTTG TGTTTATGAAATAAATGGTAAATTTTGTGAATACCTTGTTGCAGCTGGAAGCAGAGAAGATATG ACATTCGGTGCTGAGGAGTCTAAAGATGAAAGTGGAGAAACAAGGAACTATCCAGATGATAAGT TTAGGCCTGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.286552419

Conservation Information
Conserved circRNAs	NA
PMCS	0.286552419

			
						 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 AT5G42950_circ_g.3

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