Plant Circular RNA Database

Detail information of AT5G38660_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT5G38660_circ_g.1
					
						ID in PlantcircBase
						ath_circ_041529
					
						Alias
						5:15473336-15474941
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 15473336-15474941  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G38660						
					
						Parent gene annotation
						
							Acclimation of photosynthesis to environment
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G38660_circ_g.2 AT5G38660_circ_g.3 AT5G38660_circ_g.4 AT5G38660_circ_g.5 AT5G38660_circ_g.6 AT5G38660_circ_g.7 AT5G38660_circ_g.8 AT5G38660_circ_g.9 AT5G38660_circ_g.10 						
					
						Support reads
						2/2
					
						Tissues
						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  
						
							CT-AC							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
						AT5G38660.1:8
AT5G38660.2:8

General Information
CircRNA Name	AT5G38660_circ_g.1
ID in PlantcircBase	ath_circ_041529
Alias	5:15473336-15474941
Organism	Arabidpsis thaliana
Position	chr5: 15473336-15474941 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G38660
Parent gene annotation	Acclimation of photosynthesis to environment
Parent gene strand	-
Alternative splicing	AT5G38660_circ_g.2 AT5G38660_circ_g.3 AT5G38660_circ_g.4 AT5G38660_circ_g.5 AT5G38660_circ_g.6 AT5G38660_circ_g.7 AT5G38660_circ_g.8 AT5G38660_circ_g.9 AT5G38660_circ_g.10
Support reads	2/2
Tissues	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	CT-AC 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	AT5G38660.1:8 AT5G38660.2:8

			
						 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  
						
							ATGCTAAACCTCACATATACCCATAGCAACAAAGAAGGCAAGAGAAAACTCACGAGAGTAGCGA
AACCCCGAGACCTAGCCCAATAACACCAAATGAAATttcatagagattctcactttctccttta
ccttcaaagcaaaacaacaataataattttttaagaaccgagaacaagaaattcataaacatga
atggagaa

									
								

					

						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
						
							TTCATAGAGATTCTCACTTTCTCCTTTACCTTCAAAGCAAAACAACAATAATAATTTTTTAAGA
ACCGAGAACAAGAAATTCATAAACATGAATGGAGAATTGATTCACTACTTACCGACTTCTGCCG
TGATGTTTGGTCCAAAGAAGGAAGTGAATTTCGCCTATCAAAACAAAATTTTTATGCTTAGTTC
CAGCTTTATGTTTTGCTACTTCTTAAAAACTAGATTTGATAAAACCAACGCTACTTAAGCTATT
TTCTTATGCGCCAAGCTGATTTGTTAGTAGTATATGAATCTAACTCTTACCTGTCTTTTTTCAA
AATCTGACAACGTCAGAGCTTTGGCCTCAAATACAAGGACCACACAGTACCGACCATCGGTCAG
GACCTACAGACATGATGAGTTATCAAAAATGATCCGTTTAAGTTTAGTTTCACCAGTCAATATC
CATGTCATATGCAAGTAAAAATTGAGTTATATATTTTGATGATTCATGTAAATAATATGATGTA
AAGTCATGCGCGTGAAGAAATGTACCTCTTCCCTTATCAGCTGTAAGATAGGTGCACTACGTCT
CGGGATTCCTCCTCCCTTATGACCAAAACAGTCGAAAGAAAGAGAGGTTAAAGCGGAAGTACAA
GAAGCGTGTGTTGTGCTTCATTTTGTTTTCGTGCTTCATTTTGTTTCAACAAAATAGCTTACCA
GCCCATATTGAAAGATTCGTTTTAGTGCTTCTTCCAAATGTTGTTCATCTCCATAACGGTATCT
CGTGACATCATTTCTAACCTAATAAAAGAAAGAAGAAGGCACATTAACAATTCACGAGAAGTAA
ATTTAAAATCCTATGTGCACTGACAAAACTACGATGTGATGTCATATAGGGAAACTAAACTGAG
CAAGACTTTCTGCAAAAGAACCTATGATACTGAAATCAAGCTAGTGTTTAGATTGAATTTCGAA
ATACTAATGACGAAAACTACTAACACCCCTTCCTCTTATCAGAAACATAAATATGTTTTAGGAA
ATTAATGTAACAAAGACGAGCTGAAGAACAACTAAAATCAGATTGAAGGTACTCCGGTCAGTCG
AGAGTAACCAGAACCACTACGTACCTGCGTTAAAATAGGAGTAGCACAGCTTTCTCTAAGCTTC
ACCGCATCCGAATAGCTCAAGCAAGGAACTGGTTTGAGTTCTGCGTACTGCAAAGGAAGCAAAA
CCCATCCTCAGGGACTAAAACAATTAACCATTCCGAAAACTCAAAGAAAGAAATGAGTAACTCT
AATACAAAAGTCAATTTTCTCAGTAATTTTACAGTTATCCGAAACATTCCACTTTCTCAAGGAC
ATGATAGTGAGAAAGATAACTAAAGAGCATAAAGAGCATACCTTAAGAGCCATTCCGATAATAG
AAAGGGGAAATCCATATGTTAGCATTATAGCAGACCACTCAGTTCCAGGAAGGATAGTAAAATA
GGCCCCAAAACCATACCTGTTAAACAGATCCATAATGCTAAACCTCACATATACCCATAGCAAC
AAAGAAGGCAAGAGAAAACTCACGAGAGTAGCGAAACCCCGAGACCTAGCCCAATAACACCAAA
TGAAAT
						
					

			
		

Sequences
Splice junction sequence	ATGCTAAACCTCACATATACCCATAGCAACAAAGAAGGCAAGAGAAAACTCACGAGAGTAGCGA AACCCCGAGACCTAGCCCAATAACACCAAATGAAATttcatagagattctcactttctccttta ccttcaaagcaaaacaacaataataattttttaagaaccgagaacaagaaattcataaacatga atggagaa
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	TTCATAGAGATTCTCACTTTCTCCTTTACCTTCAAAGCAAAACAACAATAATAATTTTTTAAGA ACCGAGAACAAGAAATTCATAAACATGAATGGAGAATTGATTCACTACTTACCGACTTCTGCCG TGATGTTTGGTCCAAAGAAGGAAGTGAATTTCGCCTATCAAAACAAAATTTTTATGCTTAGTTC CAGCTTTATGTTTTGCTACTTCTTAAAAACTAGATTTGATAAAACCAACGCTACTTAAGCTATT TTCTTATGCGCCAAGCTGATTTGTTAGTAGTATATGAATCTAACTCTTACCTGTCTTTTTTCAA AATCTGACAACGTCAGAGCTTTGGCCTCAAATACAAGGACCACACAGTACCGACCATCGGTCAG GACCTACAGACATGATGAGTTATCAAAAATGATCCGTTTAAGTTTAGTTTCACCAGTCAATATC CATGTCATATGCAAGTAAAAATTGAGTTATATATTTTGATGATTCATGTAAATAATATGATGTA AAGTCATGCGCGTGAAGAAATGTACCTCTTCCCTTATCAGCTGTAAGATAGGTGCACTACGTCT CGGGATTCCTCCTCCCTTATGACCAAAACAGTCGAAAGAAAGAGAGGTTAAAGCGGAAGTACAA GAAGCGTGTGTTGTGCTTCATTTTGTTTTCGTGCTTCATTTTGTTTCAACAAAATAGCTTACCA GCCCATATTGAAAGATTCGTTTTAGTGCTTCTTCCAAATGTTGTTCATCTCCATAACGGTATCT CGTGACATCATTTCTAACCTAATAAAAGAAAGAAGAAGGCACATTAACAATTCACGAGAAGTAA ATTTAAAATCCTATGTGCACTGACAAAACTACGATGTGATGTCATATAGGGAAACTAAACTGAG CAAGACTTTCTGCAAAAGAACCTATGATACTGAAATCAAGCTAGTGTTTAGATTGAATTTCGAA ATACTAATGACGAAAACTACTAACACCCCTTCCTCTTATCAGAAACATAAATATGTTTTAGGAA ATTAATGTAACAAAGACGAGCTGAAGAACAACTAAAATCAGATTGAAGGTACTCCGGTCAGTCG AGAGTAACCAGAACCACTACGTACCTGCGTTAAAATAGGAGTAGCACAGCTTTCTCTAAGCTTC ACCGCATCCGAATAGCTCAAGCAAGGAACTGGTTTGAGTTCTGCGTACTGCAAAGGAAGCAAAA CCCATCCTCAGGGACTAAAACAATTAACCATTCCGAAAACTCAAAGAAAGAAATGAGTAACTCT AATACAAAAGTCAATTTTCTCAGTAATTTTACAGTTATCCGAAACATTCCACTTTCTCAAGGAC ATGATAGTGAGAAAGATAACTAAAGAGCATAAAGAGCATACCTTAAGAGCCATTCCGATAATAG AAAGGGGAAATCCATATGTTAGCATTATAGCAGACCACTCAGTTCCAGGAAGGATAGTAAAATA GGCCCCAAAACCATACCTGTTAAACAGATCCATAATGCTAAACCTCACATATACCCATAGCAAC AAAGAAGGCAAGAGAAAACTCACGAGAGTAGCGAAACCCCGAGACCTAGCCCAATAACACCAAA TGAAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.104832914

Conservation Information
Conserved circRNAs	NA
PMCS	0.104832914

			
						 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 AT5G38660_circ_g.1

Address

Any questions?

Supported by