Plant Circular RNA Database

Detail information of AT3G49410_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT3G49410_circ_g.4
					
						ID in PlantcircBase
						ath_circ_026697
					
						Alias
						Chr3:18326594|18328527
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 18326594-18328527  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer; CIRI
					
						Parent gene
						
							AT3G49410						
					
						Parent gene annotation
						
							Transcription factor IIIC, subunit 5
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G49410_circ_g.1 AT3G49410_circ_g.2 AT3G49410_circ_g.3 AT3G49410_circ_g.5 AT3G49410_circ_g.6 						
					
						Support reads
						4
					
						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
						AT3G49410.2:7
AT3G49410.4:7
AT3G49410.1:7
AT3G49410.3:7

General Information
CircRNA Name	AT3G49410_circ_g.4
ID in PlantcircBase	ath_circ_026697
Alias	Chr3:18326594\|18328527
Organism	Arabidpsis thaliana
Position	chr3: 18326594-18328527 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer; CIRI
Parent gene	AT3G49410
Parent gene annotation	Transcription factor IIIC, subunit 5
Parent gene strand	+
Alternative splicing	AT3G49410_circ_g.1 AT3G49410_circ_g.2 AT3G49410_circ_g.3 AT3G49410_circ_g.5 AT3G49410_circ_g.6
Support reads	4
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	AT3G49410.2:7 AT3G49410.4:7 AT3G49410.1:7 AT3G49410.3:7

			
						 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  
						
							TTTGTTGTTTTCTTCATTCGCTAGGATTCACACCGTTTCTCTGCTCCTCTTCTTTTGCAGGCTG
CAGGAGACAATGAGATATCTCTTGATTCCCATGGATgatcccaaagaaactgaagtgggaagac
tttgtttctcgcagctccaaccactggcaatggcaggtagcagtgtctgcattgtttgaggagc
ggcctata

									
								

					

						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
						
							GATCCCAAAGAAACTGAAGTGGGAAGACTTTGTTTCTCGCAGCTCCAACCACTGGCAATGGCAG
GTAGCAGTGTCTGCATTGTTTGAGGAGCGGCCTATATGGACAAGGGATTCTGTTGTTCAACGAC
TACTTGATAAAGGTCTTAAATGTACACATCATATGTTAAACAGGTGATATAGCTTTCTAATACG
GGGTTCTTATACTGAGGTGTTTTTAGTACTATATTGATCAATTTGGTCTCTCTGCAGGTTTCTG
CTCAGAGCTGCATATTATTTCTCCAGTGGTCCGTTTCTTAGGTTCTGGATTAAAAGAGGCTATG
ATCCACGGAATGATCCTGAGTCTCGTGTGTAAGTTCTCTTTTAAGACATTGATTTGTATATTCT
TATTGTATGGTTTGTGACATTTTTTAGGTGAAATGGTAATACACACAGATGGGTGCATAATGAC
TAGTTTTCACTTATATCTCCATTGAATAATTGTGTTTCAGATATCAGAGAATGGAATTCAGGGT
TCCTCCTGAATTACGAGGTTATTGTGATGCCAATGCAACTAACAAGTAAGTCTTTTTCTATTTC
TGTGGTTAACTCTTCCTGTATGACTGACACAGCCTCCTGGAGATTTAAGCCTGAATACTCTCTA
TAGCATTCTATGGTACTTGTTGTAGGATTGTATAATAGATTAAGCGTGATTTGTTTTGCAGCTG
AACCATTGGATTTATGCAGGAAAAAGTCCGATTTATATGTTTTTTCTTTTCTTTGCTACAGCTC
AAAGCCAAGCTGGAACGACATTTGTGCTTTTAAGTTATTTCCTTTTAAATGCCAAACGTTTCTG
CAGTTGTTTGAACTTGACGACGAGTACATCCAGCGAGAGATAAGAAAGCCTCCCAAGCAAACTA
CTTGTAGTGTGAGTTCTCAGCTTAGTTTTTCATGAAATCAATACCCATGAATCATGGTCTTTTG
CCTGTTGAATTAAAGCTTAAGCTCAGACAAAGTGTCGCATCTACGCCAATAAATAAACTTTGGC
AAGTACTCTTCAAGCTTATGATCTGATTCGTTTCTTGTTTGCAGCATAAATCAGGATGGTTTTC
AGAAGCCATGCTTGATACTTTGAGACTCCGTGTAGCTGTGAGGTTTGTGTCTGTGTTTCCTGAG
ACAGGTTTCGAAGATGTATTTAAATCCATCCAAGAAGAATTTGAGAGATCAGAAAAAGTACAAA
TTCAGAAAGAGACACTTAAACCATCTTTAGTGAAGCACCGGGAGGCAACTAAAGGTAAGATCAT
CAACAAAATTGTGTGTATATCTCTTTTAGCGTTTAGGAAGTCTAGTGAGTGCTTTTTGATGTGC
GTTCAGCATATTCCCTAATCTCTAGTGTGTTAGACCCTTATTCCTTTGCGTTTGTCGAGTATTT
TCCGGAGTCATCAAATCTTTAACAGAAACTTGAGCCTCAAAACCTAAGTGAAATTGACAGGAAA
AATTGGCTGCTTATACAGCATAAGTTATACTGCTCTACGAGATGTACATAAATATATATGAGAT
AAAAAAAATTGTGTAATAAATATTCTGCAATGAGCTAAACTAATTTTGATACGTATCATGTGTT
ATGCTTATTGTCATAAGTCAATGAACATGTTTCCTTGAATATTCTGAAGTAGCAGTTACTGAAC
AGTTCGTTTAATCTGCAGGCTCTGAAGATATGGAAACGTTTAAAAGCGTAAACGAAAATGTTGA
TGCTAATGTTAATGAGGATGGAGAAGATGAAAACCTGGATGACGAAGATGAAGATGAAGAAGAA
GAAGAAGAACTCGATATGGTAATATTACTGTTAAAGGAAAGTTTTGTTGTTTTCTTCATTCGCT
AGGATTCACACCGTTTCTCTGCTCCTCTTCTTTTGCAGGCTGCAGGAGACAATGAGATATCTCT
TGATTCCCATGGAT
						
					

			
		

Sequences
Splice junction sequence	TTTGTTGTTTTCTTCATTCGCTAGGATTCACACCGTTTCTCTGCTCCTCTTCTTTTGCAGGCTG CAGGAGACAATGAGATATCTCTTGATTCCCATGGATgatcccaaagaaactgaagtgggaagac tttgtttctcgcagctccaaccactggcaatggcaggtagcagtgtctgcattgtttgaggagc ggcctata
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	GATCCCAAAGAAACTGAAGTGGGAAGACTTTGTTTCTCGCAGCTCCAACCACTGGCAATGGCAG GTAGCAGTGTCTGCATTGTTTGAGGAGCGGCCTATATGGACAAGGGATTCTGTTGTTCAACGAC TACTTGATAAAGGTCTTAAATGTACACATCATATGTTAAACAGGTGATATAGCTTTCTAATACG GGGTTCTTATACTGAGGTGTTTTTAGTACTATATTGATCAATTTGGTCTCTCTGCAGGTTTCTG CTCAGAGCTGCATATTATTTCTCCAGTGGTCCGTTTCTTAGGTTCTGGATTAAAAGAGGCTATG ATCCACGGAATGATCCTGAGTCTCGTGTGTAAGTTCTCTTTTAAGACATTGATTTGTATATTCT TATTGTATGGTTTGTGACATTTTTTAGGTGAAATGGTAATACACACAGATGGGTGCATAATGAC TAGTTTTCACTTATATCTCCATTGAATAATTGTGTTTCAGATATCAGAGAATGGAATTCAGGGT TCCTCCTGAATTACGAGGTTATTGTGATGCCAATGCAACTAACAAGTAAGTCTTTTTCTATTTC TGTGGTTAACTCTTCCTGTATGACTGACACAGCCTCCTGGAGATTTAAGCCTGAATACTCTCTA TAGCATTCTATGGTACTTGTTGTAGGATTGTATAATAGATTAAGCGTGATTTGTTTTGCAGCTG AACCATTGGATTTATGCAGGAAAAAGTCCGATTTATATGTTTTTTCTTTTCTTTGCTACAGCTC AAAGCCAAGCTGGAACGACATTTGTGCTTTTAAGTTATTTCCTTTTAAATGCCAAACGTTTCTG CAGTTGTTTGAACTTGACGACGAGTACATCCAGCGAGAGATAAGAAAGCCTCCCAAGCAAACTA CTTGTAGTGTGAGTTCTCAGCTTAGTTTTTCATGAAATCAATACCCATGAATCATGGTCTTTTG CCTGTTGAATTAAAGCTTAAGCTCAGACAAAGTGTCGCATCTACGCCAATAAATAAACTTTGGC AAGTACTCTTCAAGCTTATGATCTGATTCGTTTCTTGTTTGCAGCATAAATCAGGATGGTTTTC AGAAGCCATGCTTGATACTTTGAGACTCCGTGTAGCTGTGAGGTTTGTGTCTGTGTTTCCTGAG ACAGGTTTCGAAGATGTATTTAAATCCATCCAAGAAGAATTTGAGAGATCAGAAAAAGTACAAA TTCAGAAAGAGACACTTAAACCATCTTTAGTGAAGCACCGGGAGGCAACTAAAGGTAAGATCAT CAACAAAATTGTGTGTATATCTCTTTTAGCGTTTAGGAAGTCTAGTGAGTGCTTTTTGATGTGC GTTCAGCATATTCCCTAATCTCTAGTGTGTTAGACCCTTATTCCTTTGCGTTTGTCGAGTATTT TCCGGAGTCATCAAATCTTTAACAGAAACTTGAGCCTCAAAACCTAAGTGAAATTGACAGGAAA AATTGGCTGCTTATACAGCATAAGTTATACTGCTCTACGAGATGTACATAAATATATATGAGAT AAAAAAAATTGTGTAATAAATATTCTGCAATGAGCTAAACTAATTTTGATACGTATCATGTGTT ATGCTTATTGTCATAAGTCAATGAACATGTTTCCTTGAATATTCTGAAGTAGCAGTTACTGAAC AGTTCGTTTAATCTGCAGGCTCTGAAGATATGGAAACGTTTAAAAGCGTAAACGAAAATGTTGA TGCTAATGTTAATGAGGATGGAGAAGATGAAAACCTGGATGACGAAGATGAAGATGAAGAAGAA GAAGAAGAACTCGATATGGTAATATTACTGTTAAAGGAAAGTTTTGTTGTTTTCTTCATTCGCT AGGATTCACACCGTTTCTCTGCTCCTCTTCTTTTGCAGGCTGCAGGAGACAATGAGATATCTCT TGATTCCCATGGAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.136055218

Conservation Information
Conserved circRNAs	NA
PMCS	0.136055218

			
						 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 AT3G49410_circ_g.4

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