Plant Circular RNA Database

Detail information of AT5G13960_circ_g.5

			
						 General Information
					
						CircRNA Name
						AT5G13960_circ_g.5
					
						ID in PlantcircBase
						ath_circ_038142
					
						Alias
						5:4503400-4505065
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 4503400-4505065  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G13960						
					
						Parent gene annotation
						
							Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						3
					
						Tissues
						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
						AT5G13960.1:5
AT5G13960.2:5

General Information
CircRNA Name	AT5G13960_circ_g.5
ID in PlantcircBase	ath_circ_038142
Alias	5:4503400-4505065
Organism	Arabidpsis thaliana
Position	chr5: 4503400-4505065 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G13960
Parent gene annotation	Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4
Parent gene strand	+
Alternative splicing	NA
Support reads	3
Tissues	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	AT5G13960.1:5 AT5G13960.2:5

			
						 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  
						
							TGAGTCTCGAGATGTTGTATTTGAATGTGGTCCTCACTGTGGGTGTGGGCCAAAATGTGTCAAC
CGAACTTCTCAGAAGCGTCTAAGATTCAATCTTGAGgttgaaaagttctgggcacaaaagggcg
tttcaggatttacagtgtataagtaccgactgaaacgattggaggggcaaccagaactaactac
tgatcagg

									
								

					

						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: 507
Transcript exons: 4503400-4503498,4504263-4504312,4504394-4504485,4504570-
4504729,4504960-4505065
GTTGAAAAGTTCTGGGCACAAAAGGGCGTTTCAGGATTTACAGTGTATAAGTACCGACTGAAAC
GATTGGAGGGGCAACCAGAACTAACTACTGATCAGGTCAACTTTGTTGCTGGACGCATACCAAC
GAGTACTTCAGAAATTGAGGGTTTGGTATGTGAGGACATCTCCGGAGGGCTAGAATTTAAGGGT
ATCCCCGCCACTAATCGTGTTGATGATTCACCAGTTTCACCAACATCTGGTTTCACATACATCA
AATCTTTGATTATTGAGCCTAATGTCATAATTCCAAAGAGTTCAACTGGGTGTAACTGCCGAGG
CAGCTGCACTGACTCAAAGAAATGTGCATGTGCTAAGCTTAATGGGGGTAACTTTCCATATGTT
GACCTTAATGATGGCAGATTAATTGAGTCTCGAGATGTTGTATTTGAATGTGGTCCTCACTGTG
GGTGTGGGCCAAAATGTGTCAACCGAACTTCTCAGAAGCGTCTAAGATTCAATCTTGAG
						
					

						Genomic sequence
						
							GTTGAAAAGTTCTGGGCACAAAAGGGCGTTTCAGGATTTACAGTGTATAAGTACCGACTGAAAC
GATTGGAGGGGCAACCAGAACTAACTACTGATCAGGTCTGTATGTTCTCCTGTGTTATGGTTTA
TGATAGCTGATGTTTTTAATAAATCGTTCCATATACCAAAGTTCCATTTTCCTTGTGTGGATAT
CTGGTGCGACATTGTTTAGATAAGCTATTTCATTTCCACATAGTTACTCAATGTTCTGAACATA
TAACGTAGCTCATTCAAAAGACGCCTTTTAAACTAAATAAGTCCCTTCAAAACCAAGATTTGAT
ATTTTTTTCATCTGAACATGGTTTATCATTGAGGAAAGATATCTATGAAATCTTTTTAGTTTTG
CTATAAATTCACGGAGTAAATTGTTTACCATTATGTCTGTCACTCTTATTCTGTCATTGCTAAA
AAGCTGTCTTATTAATTATATATTCTTCCAGAGAAAATCTCTGATCTATCTCATAAGAGAATTT
TATTTATTCGAGCCAACATTTGCAAACCTCAAGAAATAAGTTTTTATCGCATTTCCTTTTTTCT
TAGACTTGCTGTATTCTTGGCTTTTTTTTACCATTTAGTTTCTGTACCGAACATGTGGTCAGCT
CACCTGTCATTTACATTTGACTATTAACTGAATCAATTATTTCTATTATTAATTTTCTAAATCT
TCTGGTGTTGTGAATGCTGTTTTGTAGAATTGTTTGTGTTTCTTTGGCAATATCAATTATGTTC
TGATTTCTAACCGGGATCAGAGAATGCATGTGGTTACTATGAATAGGTCTATATTTATGCATTT
TTTACTTGAGGTTTGTTTCTTGTCATTGCAGGTCAACTTTGTTGCTGGACGCATACCAACGAGT
ACTTCAGAAATTGAGGGGTACCTGTTCAATTGATTTCCATGTGGTATTGTACAATCAGTTGCAT
TTTAACATCCATTAATGTCATGTTTTTTGTGAAGTTTGGTATGTGAGGACATCTCCGGAGGGCT
AGAATTTAAGGGTATCCCCGCCACTAATCGTGTTGATGATTCACCAGTTTCACCAACATCTGGT
AAGTTGGAGCAGAACTAGAAAGTAATATTAGTATCCACTTTATGATATTATATGAGCTGAATTC
TCCTTTTTTGAGTATCAGGTTTCACATACATCAAATCTTTGATTATTGAGCCTAATGTCATAAT
TCCAAAGAGTTCAACTGGGTGTAACTGCCGAGGCAGCTGCACTGACTCAAAGAAATGTGCATGT
GCTAAGCTTAATGGGGGTAACTTTCCATATGTTGACCTTAATGATGGCAGGTGATATTCCTTGT
AGAGCCATTTACTCATGTTCCTTCATTTGTATAACCTTTGCGTATTATTTTGAACTGAAGTTTG
CATTGAGAGTACAAAATTAGTCTGCTTTACTGCTATTGTTCTTACCATTCTTTTTTCCATGAAA
TTTGACTATTAGAGTACTTGGTGTAATGTTGGAGTAATGTTTACAGTTGAACATTGTTTGGGTT
GATTTTCTGTTTTTTTCTTTTCAGATTAATTGAGTCTCGAGATGTTGTATTTGAATGTGGTCCT
CACTGTGGGTGTGGGCCAAAATGTGTCAACCGAACTTCTCAGAAGCGTCTAAGATTCAATCTTG
AG
						
					

			
		

Sequences
Splice junction sequence	TGAGTCTCGAGATGTTGTATTTGAATGTGGTCCTCACTGTGGGTGTGGGCCAAAATGTGTCAAC CGAACTTCTCAGAAGCGTCTAAGATTCAATCTTGAGgttgaaaagttctgggcacaaaagggcg tttcaggatttacagtgtataagtaccgactgaaacgattggaggggcaaccagaactaactac tgatcagg
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: 507 Transcript exons: 4503400-4503498,4504263-4504312,4504394-4504485,4504570- 4504729,4504960-4505065 GTTGAAAAGTTCTGGGCACAAAAGGGCGTTTCAGGATTTACAGTGTATAAGTACCGACTGAAAC GATTGGAGGGGCAACCAGAACTAACTACTGATCAGGTCAACTTTGTTGCTGGACGCATACCAAC GAGTACTTCAGAAATTGAGGGTTTGGTATGTGAGGACATCTCCGGAGGGCTAGAATTTAAGGGT ATCCCCGCCACTAATCGTGTTGATGATTCACCAGTTTCACCAACATCTGGTTTCACATACATCA AATCTTTGATTATTGAGCCTAATGTCATAATTCCAAAGAGTTCAACTGGGTGTAACTGCCGAGG CAGCTGCACTGACTCAAAGAAATGTGCATGTGCTAAGCTTAATGGGGGTAACTTTCCATATGTT GACCTTAATGATGGCAGATTAATTGAGTCTCGAGATGTTGTATTTGAATGTGGTCCTCACTGTG GGTGTGGGCCAAAATGTGTCAACCGAACTTCTCAGAAGCGTCTAAGATTCAATCTTGAG
Genomic sequence	GTTGAAAAGTTCTGGGCACAAAAGGGCGTTTCAGGATTTACAGTGTATAAGTACCGACTGAAAC GATTGGAGGGGCAACCAGAACTAACTACTGATCAGGTCTGTATGTTCTCCTGTGTTATGGTTTA TGATAGCTGATGTTTTTAATAAATCGTTCCATATACCAAAGTTCCATTTTCCTTGTGTGGATAT CTGGTGCGACATTGTTTAGATAAGCTATTTCATTTCCACATAGTTACTCAATGTTCTGAACATA TAACGTAGCTCATTCAAAAGACGCCTTTTAAACTAAATAAGTCCCTTCAAAACCAAGATTTGAT ATTTTTTTCATCTGAACATGGTTTATCATTGAGGAAAGATATCTATGAAATCTTTTTAGTTTTG CTATAAATTCACGGAGTAAATTGTTTACCATTATGTCTGTCACTCTTATTCTGTCATTGCTAAA AAGCTGTCTTATTAATTATATATTCTTCCAGAGAAAATCTCTGATCTATCTCATAAGAGAATTT TATTTATTCGAGCCAACATTTGCAAACCTCAAGAAATAAGTTTTTATCGCATTTCCTTTTTTCT TAGACTTGCTGTATTCTTGGCTTTTTTTTACCATTTAGTTTCTGTACCGAACATGTGGTCAGCT CACCTGTCATTTACATTTGACTATTAACTGAATCAATTATTTCTATTATTAATTTTCTAAATCT TCTGGTGTTGTGAATGCTGTTTTGTAGAATTGTTTGTGTTTCTTTGGCAATATCAATTATGTTC TGATTTCTAACCGGGATCAGAGAATGCATGTGGTTACTATGAATAGGTCTATATTTATGCATTT TTTACTTGAGGTTTGTTTCTTGTCATTGCAGGTCAACTTTGTTGCTGGACGCATACCAACGAGT ACTTCAGAAATTGAGGGGTACCTGTTCAATTGATTTCCATGTGGTATTGTACAATCAGTTGCAT TTTAACATCCATTAATGTCATGTTTTTTGTGAAGTTTGGTATGTGAGGACATCTCCGGAGGGCT AGAATTTAAGGGTATCCCCGCCACTAATCGTGTTGATGATTCACCAGTTTCACCAACATCTGGT AAGTTGGAGCAGAACTAGAAAGTAATATTAGTATCCACTTTATGATATTATATGAGCTGAATTC TCCTTTTTTGAGTATCAGGTTTCACATACATCAAATCTTTGATTATTGAGCCTAATGTCATAAT TCCAAAGAGTTCAACTGGGTGTAACTGCCGAGGCAGCTGCACTGACTCAAAGAAATGTGCATGT GCTAAGCTTAATGGGGGTAACTTTCCATATGTTGACCTTAATGATGGCAGGTGATATTCCTTGT AGAGCCATTTACTCATGTTCCTTCATTTGTATAACCTTTGCGTATTATTTTGAACTGAAGTTTG CATTGAGAGTACAAAATTAGTCTGCTTTACTGCTATTGTTCTTACCATTCTTTTTTCCATGAAA TTTGACTATTAGAGTACTTGGTGTAATGTTGGAGTAATGTTTACAGTTGAACATTGTTTGGGTT GATTTTCTGTTTTTTTCTTTTCAGATTAATTGAGTCTCGAGATGTTGTATTTGAATGTGGTCCT CACTGTGGGTGTGGGCCAAAATGTGTCAACCGAACTTCTCAGAAGCGTCTAAGATTCAATCTTG AG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.17994403

Conservation Information
Conserved circRNAs	NA
PMCS	0.17994403

			
						 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 AT5G13960_circ_g.5

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