Plant Circular RNA Database

Detail information of AT5G21060_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT5G21060_circ_g.2
					
						ID in PlantcircBase
						ath_circ_039611
					
						Alias
						5:7150584-7152382
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 7150584-7152382  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G21060						
					
						Parent gene annotation
						
							Homoserine dehydrogenase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G21060_circ_g.1 AT5G21060_circ_g.3 AT5G21060_circ_g.4 						
					
						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  
						
							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
						AT5G21060.2:7
AT5G21060.3:7
AT5G21060.1:7

General Information
CircRNA Name	AT5G21060_circ_g.2
ID in PlantcircBase	ath_circ_039611
Alias	5:7150584-7152382
Organism	Arabidpsis thaliana
Position	chr5: 7150584-7152382 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G21060
Parent gene annotation	Homoserine dehydrogenase
Parent gene strand	-
Alternative splicing	AT5G21060_circ_g.1 AT5G21060_circ_g.3 AT5G21060_circ_g.4
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	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	AT5G21060.2:7 AT5G21060.3:7 AT5G21060.1:7

			
						 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  
						
							CTTCTGACAAGAGTTCATCATTCAGTTCCTCTTTGAGCACATCCATTGGAGCAACTAAGGATTT
ACTATCACATACTCCAATCACCCGTATATGAACTCCctttctagcaacatccatgccaccgagg
tcgtcacgtggatctgtgaagaaaacaaaagaacatgtcaatcaaacatcatattaagaatatt
caaagatg

									
								

					

						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
						
							CTTTCTAGCAACATCCATGCCACCGAGGTCGTCACGTGGATCTGTGAAGAAAACAAAAGAACAT
GTCAATCAAACATCATATTAAGAATATTCAAAGATGATCTTTCTTTTCATCTATTACATGTAGT
TTTTCCCAAGGCTAAACCAACTATGATGCACTATCAGGTCAAAGCAAGTTGGAGTATATTGTCG
AGCTACAAAACAGCTAATGGAGTGTAGAAAAGCAGACAAAGCAATATCTATTTGAAGATAGTGT
TGCTAAAATAGTAGTAGATAAAGCAGATGTGAGATGACTATCAATCAGAAAACAAGATATGTGC
TATGATGACTAAAATAAAACTGGACGGACCTGGTTCAGTGTACCCCAGCTTTTTGGCAGCTTGA
ACAACTTGGCTTAGAGGCTTGCCATCTTCAAGCTCACTCATTACATATCCCAAGGTACCTATCA
TTAATCGAGAACGGATACAAAGATACGTAAATAAATAATACATGCATATATTGGGATAAGAAAA
ACGATAAACATCTGAAGTCTGCTTACCGCTCAAACTACCGACAATCCTATGAACAGGATCTCCA
GACGAAATTATGCGGTTCAAGGATGCGATGACAGGAAGACCAGCACCAACCTATAAATAAACAT
ATGTCAGGCGCAAAAGCTTTTCACTACCTACTGTATAGAGCCAACAATACCACCACATGTTTAC
AACTAGTTTCATTTTCAAATGAGTACTAAAATGTGATATAATAGTGTTATACTCTATACACAAG
CTGTGTTTCACCTACAGTAGATTCATGGCGGATGAATCGCGGATGCAAAGCCAATTTGTCGTAA
TGTTCCTGCGCAGAAGACAAGATGAGAGAAAATATGAGTAATTTCCAACTACTTGAAAAATTAG
ATTAGCACAGATGTACTGAGAAACTTTTTTTGTAGTTCTCGCCTACTATCTAGGGTATGTCCGG
TTGTTAAAAAAACAAGATGGATTTGCAGATAGAGAATTTGGAGAACTAGATTAACTTCTTATTC
TTGAAACAATTTGCAGAAAGGGTATTTTTAATTCAAAGAGAACCTAAGGCAACTTCTTATTCTT
GAAAACAACATAAAGTAAAAGTTCAAGATTCTATGATGTCCCTGAATATACCTGTTCAAGCTAA
TGATACACAACAATAAAACCAAAAGGGAAGAGAAACAGCTTCAGGGAACAATCCGATGCGTATG
CTTTCACATTAATAACATAAGCAGAACATGCACTAGTGACAAGAAGTTACCAGCGTTGAAGTAA
CAGGCTTCTTATTTGCCAGGACAATACAGCAACCCAAGTCAACTGCCTTCATCAATATTTCAAT
CGTCTCCATGCTGGCTGAGCAATCCACCACAGCTAAGCCTATAGCAAGTACATAGATTTTATCT
ATCAGAAGCTATTGAGGCCCAACACCAGATTTCAAACGTTACAAAATGTTGACCACAACAGTTG
TAATTCAACCTTATATTTGGTACAAACCTGTAGATTTACCAAGAAGTTTTGCAATCTCTTCTGT
TTCCGTGCTTAACTCGGAATCATGGACGACTCGATATCCACCTTTTTCTGGGATTAAGAACATA
TGATCATTCGGCTTATGATCCATAAAGAGACTCATGGTAAATACTTACCCAAAGCACCCAACTT
CGATAATGCAGAACCAGTTGATTTGATAAGGCAAACTTCTGACAAGAGTTCATCATTCAGTTCC
TCTTTGAGCACATCCATTGGAGCAACTAAGGATTTACTATCACATACTCCAATCACCCGTATAT
GAACTCC
						
					

			
		

Sequences
Splice junction sequence	CTTCTGACAAGAGTTCATCATTCAGTTCCTCTTTGAGCACATCCATTGGAGCAACTAAGGATTT ACTATCACATACTCCAATCACCCGTATATGAACTCCctttctagcaacatccatgccaccgagg tcgtcacgtggatctgtgaagaaaacaaaagaacatgtcaatcaaacatcatattaagaatatt caaagatg
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	CTTTCTAGCAACATCCATGCCACCGAGGTCGTCACGTGGATCTGTGAAGAAAACAAAAGAACAT GTCAATCAAACATCATATTAAGAATATTCAAAGATGATCTTTCTTTTCATCTATTACATGTAGT TTTTCCCAAGGCTAAACCAACTATGATGCACTATCAGGTCAAAGCAAGTTGGAGTATATTGTCG AGCTACAAAACAGCTAATGGAGTGTAGAAAAGCAGACAAAGCAATATCTATTTGAAGATAGTGT TGCTAAAATAGTAGTAGATAAAGCAGATGTGAGATGACTATCAATCAGAAAACAAGATATGTGC TATGATGACTAAAATAAAACTGGACGGACCTGGTTCAGTGTACCCCAGCTTTTTGGCAGCTTGA ACAACTTGGCTTAGAGGCTTGCCATCTTCAAGCTCACTCATTACATATCCCAAGGTACCTATCA TTAATCGAGAACGGATACAAAGATACGTAAATAAATAATACATGCATATATTGGGATAAGAAAA ACGATAAACATCTGAAGTCTGCTTACCGCTCAAACTACCGACAATCCTATGAACAGGATCTCCA GACGAAATTATGCGGTTCAAGGATGCGATGACAGGAAGACCAGCACCAACCTATAAATAAACAT ATGTCAGGCGCAAAAGCTTTTCACTACCTACTGTATAGAGCCAACAATACCACCACATGTTTAC AACTAGTTTCATTTTCAAATGAGTACTAAAATGTGATATAATAGTGTTATACTCTATACACAAG CTGTGTTTCACCTACAGTAGATTCATGGCGGATGAATCGCGGATGCAAAGCCAATTTGTCGTAA TGTTCCTGCGCAGAAGACAAGATGAGAGAAAATATGAGTAATTTCCAACTACTTGAAAAATTAG ATTAGCACAGATGTACTGAGAAACTTTTTTTGTAGTTCTCGCCTACTATCTAGGGTATGTCCGG TTGTTAAAAAAACAAGATGGATTTGCAGATAGAGAATTTGGAGAACTAGATTAACTTCTTATTC TTGAAACAATTTGCAGAAAGGGTATTTTTAATTCAAAGAGAACCTAAGGCAACTTCTTATTCTT GAAAACAACATAAAGTAAAAGTTCAAGATTCTATGATGTCCCTGAATATACCTGTTCAAGCTAA TGATACACAACAATAAAACCAAAAGGGAAGAGAAACAGCTTCAGGGAACAATCCGATGCGTATG CTTTCACATTAATAACATAAGCAGAACATGCACTAGTGACAAGAAGTTACCAGCGTTGAAGTAA CAGGCTTCTTATTTGCCAGGACAATACAGCAACCCAAGTCAACTGCCTTCATCAATATTTCAAT CGTCTCCATGCTGGCTGAGCAATCCACCACAGCTAAGCCTATAGCAAGTACATAGATTTTATCT ATCAGAAGCTATTGAGGCCCAACACCAGATTTCAAACGTTACAAAATGTTGACCACAACAGTTG TAATTCAACCTTATATTTGGTACAAACCTGTAGATTTACCAAGAAGTTTTGCAATCTCTTCTGT TTCCGTGCTTAACTCGGAATCATGGACGACTCGATATCCACCTTTTTCTGGGATTAAGAACATA TGATCATTCGGCTTATGATCCATAAAGAGACTCATGGTAAATACTTACCCAAAGCACCCAACTT CGATAATGCAGAACCAGTTGATTTGATAAGGCAAACTTCTGACAAGAGTTCATCATTCAGTTCC TCTTTGAGCACATCCATTGGAGCAACTAAGGATTTACTATCACATACTCCAATCACCCGTATAT GAACTCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.11161045

Conservation Information
Conserved circRNAs	NA
PMCS	0.11161045

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							ath-miR158a-5p 						
					
						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	ath-miR158a-5p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT5G21060_circ_g.2

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