Plant Circular RNA Database

Detail information of AT5G01460_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT5G01460_circ_g.2
					
						ID in PlantcircBase
						ath_circ_035878
					
						Alias
						5:187542-188413
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 187542-188413  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G01460						
					
						Parent gene annotation
						
							LIMR family protein At5g01460
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G01460_circ_g.1 AT5G01460_circ_g.3 AT5G01460_circ_g.4 AT5G01460_circ_g.5 AT5G01460_circ_g.6 AT5G01460_circ_g.7 						
					
						Support reads
						1/1
					
						Tissues
						seedling;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
						AT5G01460.1:4

General Information
CircRNA Name	AT5G01460_circ_g.2
ID in PlantcircBase	ath_circ_035878
Alias	5:187542-188413
Organism	Arabidpsis thaliana
Position	chr5: 187542-188413 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G01460
Parent gene annotation	LIMR family protein At5g01460
Parent gene strand	+
Alternative splicing	AT5G01460_circ_g.1 AT5G01460_circ_g.3 AT5G01460_circ_g.4 AT5G01460_circ_g.5 AT5G01460_circ_g.6 AT5G01460_circ_g.7
Support reads	1/1
Tissues	seedling;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	AT5G01460.1:4

			
						 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  
						
							GGCAAGAGATCTAAAGAAAGCAGCTGATGCACTTCACCAGGAAGAACGAAGTGGTGCTAAGGGA
AGGAAGTGGAGGAAAAATGTGAAAGCAGTTGAAAAGgagtcattgggaaggtggacttctctgt
aaggcacttgtcttctgccacgactactttccctacttcatggcagttttcaaataatcaacct
tgcattgg

						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: 449
Transcript exons: 187542-187657,187775-187885,188070-188168,188291-188413
GAGTCATTGGGAAGGTGGACTTCTCTGTAAGGCACTTGTCTTCTGCCACGACTACTTTCCCTAC
TTCATGGCAGTTTTCAAATAATCAACCTTGCATTGGTAACACTGCTCGTCAGTGCTCAGCATAT
ACAGCTAATGCTGCGTCTGAAAAGACATGGTCCATGCGTACTACGTTTCCAGAATATGTTGTTG
CTCTTGCTACAATCGTTGGGTCAGTGCTCTTCACGATATTTGGTGGTGTTGGTATTGCTTGCCT
ACCCTTGGGCCTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGGTCACAGTAT
ATAAAGGAAGCAACTGAACTAGGTAAAAAGGCAAGAGATCTAAAGAAAGCAGCTGATGCACTTC
ACCAGGAAGAACGAAGTGGTGCTAAGGGAAGGAAGTGGAGGAAAAATGTGAAAGCAGTTGAAAA
G
						
						Genomic sequence
						
							GAGTCATTGGGAAGGTGGACTTCTCTGTAAGGCACTTGTCTTCTGCCACGACTACTTTCCCTAC
TTCATGGCAGTTTTCAAATAATCAACCTTGCATTGGTAACACTGCTCGTCAGGTAATACTTTAA
ATTTTCTTGCATTCTTGTTATGAGTTTTTCTTTCGTTAGTCTCTATGCAAAATATATTTCAGTA
TGTAAAATATCTTCTCTTCTCCTTGGTATATTGATCGGCAGTGCTCAGCATATACAGCTAATGC
TGCGTCTGAAAAGACATGGTCCATGCGTACTACGTTTCCAGAATATGTTGTTGCTCTTGCTACA
ATCGTTGGGTCAGTGCTCTTCACGGTATGTACATCTCTCTATTAGGTGTTTTGTGTTAAAAGTT
TCACCTCATTGTCTTGGAAGGCATATAATCTTTCTCATATTAAGGCTTGGTTGTGTTCTCTTGC
AGTTAAAAGACTTTTGGTAGCTGTGATTTTTTGCTTTCCTCTAAAGATTCTGAGAAACTCTTTT
ATCTCAAATGTTGTAGATATTTGGTGGTGTTGGTATTGCTTGCCTACCCTTGGGCCTTATCACT
GCATTCATCAGGCGACCAAAGGCTGTTATCACTCGGTCACAGTATATAAAGGTTCATTTGTGCT
GGTTATTGTTGTCTACTTGTCTTCATGCAAAGCTTTTCTAAAGAATACATGTACACTTCGGGTA
GTTGGCAGTGTTAGTGGCCTGACAAGTCATCTAATTGTTTTTCAGGAAGCAACTGAACTAGGTA
AAAAGGCAAGAGATCTAAAGAAAGCAGCTGATGCACTTCACCAGGAAGAACGAAGTGGTGCTAA
GGGAAGGAAGTGGAGGAAAAATGTGAAAGCAGTTGAAAAG

Sequences
Splice junction sequence	GGCAAGAGATCTAAAGAAAGCAGCTGATGCACTTCACCAGGAAGAACGAAGTGGTGCTAAGGGA AGGAAGTGGAGGAAAAATGTGAAAGCAGTTGAAAAGgagtcattgggaaggtggacttctctgt aaggcacttgtcttctgccacgactactttccctacttcatggcagttttcaaataatcaacct tgcattgg
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: 449 Transcript exons: 187542-187657,187775-187885,188070-188168,188291-188413 GAGTCATTGGGAAGGTGGACTTCTCTGTAAGGCACTTGTCTTCTGCCACGACTACTTTCCCTAC TTCATGGCAGTTTTCAAATAATCAACCTTGCATTGGTAACACTGCTCGTCAGTGCTCAGCATAT ACAGCTAATGCTGCGTCTGAAAAGACATGGTCCATGCGTACTACGTTTCCAGAATATGTTGTTG CTCTTGCTACAATCGTTGGGTCAGTGCTCTTCACGATATTTGGTGGTGTTGGTATTGCTTGCCT ACCCTTGGGCCTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGGTCACAGTAT ATAAAGGAAGCAACTGAACTAGGTAAAAAGGCAAGAGATCTAAAGAAAGCAGCTGATGCACTTC ACCAGGAAGAACGAAGTGGTGCTAAGGGAAGGAAGTGGAGGAAAAATGTGAAAGCAGTTGAAAA G
Genomic sequence	GAGTCATTGGGAAGGTGGACTTCTCTGTAAGGCACTTGTCTTCTGCCACGACTACTTTCCCTAC TTCATGGCAGTTTTCAAATAATCAACCTTGCATTGGTAACACTGCTCGTCAGGTAATACTTTAA ATTTTCTTGCATTCTTGTTATGAGTTTTTCTTTCGTTAGTCTCTATGCAAAATATATTTCAGTA TGTAAAATATCTTCTCTTCTCCTTGGTATATTGATCGGCAGTGCTCAGCATATACAGCTAATGC TGCGTCTGAAAAGACATGGTCCATGCGTACTACGTTTCCAGAATATGTTGTTGCTCTTGCTACA ATCGTTGGGTCAGTGCTCTTCACGGTATGTACATCTCTCTATTAGGTGTTTTGTGTTAAAAGTT TCACCTCATTGTCTTGGAAGGCATATAATCTTTCTCATATTAAGGCTTGGTTGTGTTCTCTTGC AGTTAAAAGACTTTTGGTAGCTGTGATTTTTTGCTTTCCTCTAAAGATTCTGAGAAACTCTTTT ATCTCAAATGTTGTAGATATTTGGTGGTGTTGGTATTGCTTGCCTACCCTTGGGCCTTATCACT GCATTCATCAGGCGACCAAAGGCTGTTATCACTCGGTCACAGTATATAAAGGTTCATTTGTGCT GGTTATTGTTGTCTACTTGTCTTCATGCAAAGCTTTTCTAAAGAATACATGTACACTTCGGGTA GTTGGCAGTGTTAGTGGCCTGACAAGTCATCTAATTGTTTTTCAGGAAGCAACTGAACTAGGTA AAAAGGCAAGAGATCTAAAGAAAGCAGCTGATGCACTTCACCAGGAAGAACGAAGTGGTGCTAA GGGAAGGAAGTGGAGGAAAAATGTGAAAGCAGTTGAAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.227820859

Conservation Information
Conserved circRNAs	NA
PMCS	0.227820859

			
						 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 AT5G01460_circ_g.2

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