Plant Circular RNA Database

Detail information of AT5G16715_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT5G16715_circ_g.1
					
						ID in PlantcircBase
						ath_circ_038640
					
						Alias
						Chr5:5486230|5489798
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 5486230-5489798  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ei-circRNA							
									
						Identification method
						CIRCexplorer; CIRI
					
						Parent gene
						
							AT5G16715						
					
						Parent gene annotation
						
							Valine--tRNA ligase, chloroplastic/mitochondrial 2
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G16715_circ_g.2 AT5G16715_circ_g.3 AT5G16715_circ_g.4 AT5G16715_circ_g.5 AT5G16715_circ_g.6 AT5G16715_circ_g.7 AT5G16715_circ_g.8 AT5G16715_circ_g.9 AT5G16715_circ_g.10 AT5G16715_circ_g.11 						
					
						Support reads
						3
					
						Tissues
						seedling
					
						Exon boundary  
						
							No-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-CA							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
						AT5G16715.1:12

General Information
CircRNA Name	AT5G16715_circ_g.1
ID in PlantcircBase	ath_circ_038640
Alias	Chr5:5486230\|5489798
Organism	Arabidpsis thaliana
Position	chr5: 5486230-5489798 JBrowse»
Reference genome	TAIR10.38
Type	ei-circRNA
Identification method	CIRCexplorer; CIRI
Parent gene	AT5G16715
Parent gene annotation	Valine--tRNA ligase, chloroplastic/mitochondrial 2
Parent gene strand	+
Alternative splicing	AT5G16715_circ_g.2 AT5G16715_circ_g.3 AT5G16715_circ_g.4 AT5G16715_circ_g.5 AT5G16715_circ_g.6 AT5G16715_circ_g.7 AT5G16715_circ_g.8 AT5G16715_circ_g.9 AT5G16715_circ_g.10 AT5G16715_circ_g.11
Support reads	3
Tissues	seedling
Exon boundary	No-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-CA 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	AT5G16715.1:12

			
						 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  
						
							CTAAAAGTGCTGAAGAAGCCCTTGAGAAAGCCCTTGAGAAGTATGGAAAAGATGTTGAAATATA
TCAGGATCCAGATGTTCTTGACACCTGGTTTTCCAGggatattatggttcgatacaataggatg
aatgggagaccaacactttggcttcccgggactgatcatgctggtattgccactcaggttcatt
tcctcgtt

									
								

					

						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
						
							GGATATTATGGTTCGATACAATAGGATGAATGGGAGACCAACACTTTGGCTTCCCGGGACTGAT
CATGCTGGTATTGCCACTCAGGTTCATTTCCTCGTTCAAATTTCAAGCTTTTTTGCATGGTATT
TCTACTAGTGTTTGCGTGTTTGTTTTGTGCTCACTATGATTCTTACATCTTCTTCTTCACAATC
CATTGCTCTTGTTCCTATACCAATCTACCACATTTACTTTGTCAAAAAGTTCTTTTCTTGTAGA
GTATAATTTGTATAGATAATATTTGCATTGTTTGGTGAATGTTTCTGAAATATTCTACTGAAGC
TGCAATATTTCTTTCAGTTGGTCGTGGAAAAGATGCTAGCGTCAGAAGGCATTAAGAGAGTGGA
CTTAGGTAGAGATGAGTTTACCAAAAGAGTCTGGGAATGGAAGGAAAAGTATGCTGTCTAATCA
CTGCAATGAATAAATTCAAAATATCTATTTCAAAAGTATCTGTATGATACTCTGGCGGTGTTTC
CATTCTTCGAACGAGTCATAAGTTATTGATCTTCTGGAAAACTATGAAGTATTTTAAGCAGGAG
ATGATTCCTGTACATTTCTTATAATTGAGTAATCTGATGTTCCTGAACCATTCCAAAGGCCAAT
GCTTTCATTAAAAGATAAAATCCACTGTACTTGTATCTGATGTGTTAAGGGTAAGGCTGGAATT
ATAGTTTGTGTGGTTTTTCTCAGGTATGGCGGAACCATCACAAATCAGATTAAAAGACTGGGTG
CTTCTTGTGATTGGAGTAGAGAGCGCTTTACTCTTGACGAGCAATTGAGTCGTAAGGCATCTTT
CATAGTTTCCATATCTTCTAGATGGTGATTCTTAAAGCAGACCATAGGTGGTGCTCAAAGTTGA
CTTTATATGATTTTGAGTGGTATTTTGGAATTCAAAAACTTCGGCAAGTAAAATATTATTCAGT
TGTTAGGTGGTTCAAAAAGTTTCTCGTTGCTCTTAATTTCAAATTGTATGTACTTTCACCTTGA
ATTTATTCCTTGATTCTCTTTTACCTTGAATTTGTAGGAGCTGTGGTCGAAGCTTTTGTGAAGC
TTCATGACAAGGGGTTGATATATCAAGGTAAGCTATTATGAATTTATGTATTTTGGTTTCTGTT
GTCGTAGCTGTAAGTAGAGCTGTGCTGTACTCATACGACTATTGGTGATTTTGGCATAATGTTT
TTCCAGGATCTTACATGGTCAACTGGTCCCCAAATTTACAGACTGCTGTTTCAGACTTGGTGTG
TGATGTATTTTTATCTAACACTCTGTTGTTTGATTACTTTTTTTTTCTTTCTAAAAGTGACTGC
CTTGTTCTTACCAGGAAGTAGAATATTCGGAGGAACCTGGGTTTCTATACCATATTAAATACCG
TGTAGCTGGAAGGTACTGTCCAACTACCAGTACTACCTTCGCCTTTCCTTATACTTTGTATTTT
ATGGACCCTTATATGTAGCAAAATTATGTGAAAAGATAATTTTTTCTCACATCAATTTGATTAT
GCTCTGCTATTAGAGAGTTCAAAGAAGCATTATAGTGTTTGAAAAACGTATCTTATGGAGGCTT
TAGATTATGTCGTATGATCATTAAAACTTGTGAAACACAGCGTTGGGTCTGTAAGAGTTGCTTC
GGCAGTAGTTAACCTTAAATTTTGCTAGCAAATTATTCTTGGAAGATCAGTGACTACTTTTGTT
CTGTTTATGGAAATGGCTAATCTGATCTTTCCTCGTACAGTCCTGATTTTCTTACTATAGCAAC
GACTCGTCCAGAGACATTGTTTGGTGACGTGGCCCTTGCCGTGCATCCTGAGGTAGGTGGTGAT
ATTTTTTTGGTTTCGTTGATAATAGGACATCGGGAATGACAGATGGCATTATCAAAGTCTGTTT
GACGTGTTTATAATTTTTGAATACACACAGAGCTCAGTTAACAAACTTAGAAGCAAGTTTTTTT
TTTTGATAAAAACTTAGAAGCAAATTTAATATTAGGGAGGAAAAGTATATAATGTGTAACACAT
TTTATTTTCTTCTTCCTTTTGTGGTTTTCATTTATATTTCTATTATGTAAAATTTAAATGAAAT
TGAAAATGTAGTCCAGGTAGTTTGTCAGGTTGCTGGTCCAATTTAATGTAAGCAGATGTAATCT
ACAAAGTAGATGCTGATTTTTTTGGATCTCATGTGAATGTAGATCGTCTTCTAGTCGTTTCCTG
GAATAGGTGCTCTTTTTTGGGTATCGTTTGAGGATTAATGTTGTGAAATGTATTTGGCATCTGG
CAGGATGATCGTTACTCAAAATATGTTGGTCAGACAGCAATTGTACCTATGACATATGGTCGTC
ATGTCCCAATTATTGCTGATAAGGTGAACTCCGATCTACTGCCTATGCACTCTTTATGATGTCT
TTTAGGATCAAATATCTTTTTCAAGTCCAACAAGGAAAACGCTGCAGTTGTTTTTCTTTGCCAT
TTTTCGTGCTTTAAGTATCAGTATTTTGCTGGGAAACTTCTAAGTTCTAGTTACTCAGAACCAA
GAAACTGAGTACCTCATAGTATTTCCTCTGCTGCTCTTCAGGCATTTCTCATCAGTTTTTTTGT
GTACCATGGCAGTATGTTGATAAGGATTTTGGGACTGGTGTTCTGAAGATAAGTCCTGGGCATG
ATCACAACGATTACCTTCTTGCAAGAAAGCTAGGTCTCCCCATTCTGAATGTGATGAACAAGGA
TGCAACACTTAATGACGTCGCTGGCTTGTTTTGGTAACATTTTGTTTAAAACTTATATTTTAGC
TGAATGGAATACCCTTTGGTTACATCTTAACGTCCATGGCGCCTTAACATACATCGTATTTTCA
GTGGCCTTGACAGGTTTGAGGTGAGGGAGAAACTATGGGCAGATCTTGAGGAGATAGGTTTAGC
TGTTAAGAAGGAGCCTCACACTTTACGAGTTCCAAGATCTCAGCGTGGTGGAGAAGTATCTTTC
TACTGACCCAGCATTAATTTTTCAGTTCGTTTGAAGTTCATAATTTTCTCATGCATGGTTTAAC
TGGTGTTAGGTTATTGAGCCACTTGTAAGCAAACAATGGTTTGTCCACATGGATCCTTTAGCTG
AGAAGGCTCTTCTTGCTGTTGAAAACAAAGAACTTACTATCATACCTGAGAGATTTGAGAAGGT
ATGCAAGCGACTGGTTGGTGTTATTAGTTACTGAGCTGGTATCTGTCTTTTTCTCCTCAGTTTG
GCAAATTCTCTGAAAGGTTTTGATTTTTGATTGTTTACACTGCATACTTCTGCTTTTGCTTTTA
TTTCCTGTCACCACTTGCAGATATACAATCACTGGCTGACAAATATTAAGGATTGGTGCATAAG
CCGGCAGCTGTGGTGGGGACATCGCATACCAGTTTGGTATGTGGTTGGAAAGGATTGCGAGGAG
GACTACATAGTTGCTAAAAGTGCTGAAGAAGCCCTTGAGAAAGCCCTTGAGAAGTATGGAAAAG
ATGTTGAAATATATCAGGATCCAGATGTTCTTGACACCTGGTTTTCCAG
						
					

			
		

Sequences
Splice junction sequence	CTAAAAGTGCTGAAGAAGCCCTTGAGAAAGCCCTTGAGAAGTATGGAAAAGATGTTGAAATATA TCAGGATCCAGATGTTCTTGACACCTGGTTTTCCAGggatattatggttcgatacaataggatg aatgggagaccaacactttggcttcccgggactgatcatgctggtattgccactcaggttcatt tcctcgtt
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	GGATATTATGGTTCGATACAATAGGATGAATGGGAGACCAACACTTTGGCTTCCCGGGACTGAT CATGCTGGTATTGCCACTCAGGTTCATTTCCTCGTTCAAATTTCAAGCTTTTTTGCATGGTATT TCTACTAGTGTTTGCGTGTTTGTTTTGTGCTCACTATGATTCTTACATCTTCTTCTTCACAATC CATTGCTCTTGTTCCTATACCAATCTACCACATTTACTTTGTCAAAAAGTTCTTTTCTTGTAGA GTATAATTTGTATAGATAATATTTGCATTGTTTGGTGAATGTTTCTGAAATATTCTACTGAAGC TGCAATATTTCTTTCAGTTGGTCGTGGAAAAGATGCTAGCGTCAGAAGGCATTAAGAGAGTGGA CTTAGGTAGAGATGAGTTTACCAAAAGAGTCTGGGAATGGAAGGAAAAGTATGCTGTCTAATCA CTGCAATGAATAAATTCAAAATATCTATTTCAAAAGTATCTGTATGATACTCTGGCGGTGTTTC CATTCTTCGAACGAGTCATAAGTTATTGATCTTCTGGAAAACTATGAAGTATTTTAAGCAGGAG ATGATTCCTGTACATTTCTTATAATTGAGTAATCTGATGTTCCTGAACCATTCCAAAGGCCAAT GCTTTCATTAAAAGATAAAATCCACTGTACTTGTATCTGATGTGTTAAGGGTAAGGCTGGAATT ATAGTTTGTGTGGTTTTTCTCAGGTATGGCGGAACCATCACAAATCAGATTAAAAGACTGGGTG CTTCTTGTGATTGGAGTAGAGAGCGCTTTACTCTTGACGAGCAATTGAGTCGTAAGGCATCTTT CATAGTTTCCATATCTTCTAGATGGTGATTCTTAAAGCAGACCATAGGTGGTGCTCAAAGTTGA CTTTATATGATTTTGAGTGGTATTTTGGAATTCAAAAACTTCGGCAAGTAAAATATTATTCAGT TGTTAGGTGGTTCAAAAAGTTTCTCGTTGCTCTTAATTTCAAATTGTATGTACTTTCACCTTGA ATTTATTCCTTGATTCTCTTTTACCTTGAATTTGTAGGAGCTGTGGTCGAAGCTTTTGTGAAGC TTCATGACAAGGGGTTGATATATCAAGGTAAGCTATTATGAATTTATGTATTTTGGTTTCTGTT GTCGTAGCTGTAAGTAGAGCTGTGCTGTACTCATACGACTATTGGTGATTTTGGCATAATGTTT TTCCAGGATCTTACATGGTCAACTGGTCCCCAAATTTACAGACTGCTGTTTCAGACTTGGTGTG TGATGTATTTTTATCTAACACTCTGTTGTTTGATTACTTTTTTTTTCTTTCTAAAAGTGACTGC CTTGTTCTTACCAGGAAGTAGAATATTCGGAGGAACCTGGGTTTCTATACCATATTAAATACCG TGTAGCTGGAAGGTACTGTCCAACTACCAGTACTACCTTCGCCTTTCCTTATACTTTGTATTTT ATGGACCCTTATATGTAGCAAAATTATGTGAAAAGATAATTTTTTCTCACATCAATTTGATTAT GCTCTGCTATTAGAGAGTTCAAAGAAGCATTATAGTGTTTGAAAAACGTATCTTATGGAGGCTT TAGATTATGTCGTATGATCATTAAAACTTGTGAAACACAGCGTTGGGTCTGTAAGAGTTGCTTC GGCAGTAGTTAACCTTAAATTTTGCTAGCAAATTATTCTTGGAAGATCAGTGACTACTTTTGTT CTGTTTATGGAAATGGCTAATCTGATCTTTCCTCGTACAGTCCTGATTTTCTTACTATAGCAAC GACTCGTCCAGAGACATTGTTTGGTGACGTGGCCCTTGCCGTGCATCCTGAGGTAGGTGGTGAT ATTTTTTTGGTTTCGTTGATAATAGGACATCGGGAATGACAGATGGCATTATCAAAGTCTGTTT GACGTGTTTATAATTTTTGAATACACACAGAGCTCAGTTAACAAACTTAGAAGCAAGTTTTTTT TTTTGATAAAAACTTAGAAGCAAATTTAATATTAGGGAGGAAAAGTATATAATGTGTAACACAT TTTATTTTCTTCTTCCTTTTGTGGTTTTCATTTATATTTCTATTATGTAAAATTTAAATGAAAT TGAAAATGTAGTCCAGGTAGTTTGTCAGGTTGCTGGTCCAATTTAATGTAAGCAGATGTAATCT ACAAAGTAGATGCTGATTTTTTTGGATCTCATGTGAATGTAGATCGTCTTCTAGTCGTTTCCTG GAATAGGTGCTCTTTTTTGGGTATCGTTTGAGGATTAATGTTGTGAAATGTATTTGGCATCTGG CAGGATGATCGTTACTCAAAATATGTTGGTCAGACAGCAATTGTACCTATGACATATGGTCGTC ATGTCCCAATTATTGCTGATAAGGTGAACTCCGATCTACTGCCTATGCACTCTTTATGATGTCT TTTAGGATCAAATATCTTTTTCAAGTCCAACAAGGAAAACGCTGCAGTTGTTTTTCTTTGCCAT TTTTCGTGCTTTAAGTATCAGTATTTTGCTGGGAAACTTCTAAGTTCTAGTTACTCAGAACCAA GAAACTGAGTACCTCATAGTATTTCCTCTGCTGCTCTTCAGGCATTTCTCATCAGTTTTTTTGT GTACCATGGCAGTATGTTGATAAGGATTTTGGGACTGGTGTTCTGAAGATAAGTCCTGGGCATG ATCACAACGATTACCTTCTTGCAAGAAAGCTAGGTCTCCCCATTCTGAATGTGATGAACAAGGA TGCAACACTTAATGACGTCGCTGGCTTGTTTTGGTAACATTTTGTTTAAAACTTATATTTTAGC TGAATGGAATACCCTTTGGTTACATCTTAACGTCCATGGCGCCTTAACATACATCGTATTTTCA GTGGCCTTGACAGGTTTGAGGTGAGGGAGAAACTATGGGCAGATCTTGAGGAGATAGGTTTAGC TGTTAAGAAGGAGCCTCACACTTTACGAGTTCCAAGATCTCAGCGTGGTGGAGAAGTATCTTTC TACTGACCCAGCATTAATTTTTCAGTTCGTTTGAAGTTCATAATTTTCTCATGCATGGTTTAAC TGGTGTTAGGTTATTGAGCCACTTGTAAGCAAACAATGGTTTGTCCACATGGATCCTTTAGCTG AGAAGGCTCTTCTTGCTGTTGAAAACAAAGAACTTACTATCATACCTGAGAGATTTGAGAAGGT ATGCAAGCGACTGGTTGGTGTTATTAGTTACTGAGCTGGTATCTGTCTTTTTCTCCTCAGTTTG GCAAATTCTCTGAAAGGTTTTGATTTTTGATTGTTTACACTGCATACTTCTGCTTTTGCTTTTA TTTCCTGTCACCACTTGCAGATATACAATCACTGGCTGACAAATATTAAGGATTGGTGCATAAG CCGGCAGCTGTGGTGGGGACATCGCATACCAGTTTGGTATGTGGTTGGAAAGGATTGCGAGGAG GACTACATAGTTGCTAAAAGTGCTGAAGAAGCCCTTGAGAAAGCCCTTGAGAAGTATGGAAAAG ATGTTGAAATATATCAGGATCCAGATGTTCTTGACACCTGGTTTTCCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.132144053

Conservation Information
Conserved circRNAs	NA
PMCS	0.132144053

			
						 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
						responsive to methyl jasmonate

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	responsive to methyl jasmonate

			
						 Other Information
					
						References
						Zhang et al., 2020

circRNA

Detail information of AT5G16715_circ_g.1

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