Plant Circular RNA Database

Detail information of AT3G21820_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT3G21820_circ_g.4
					
						ID in PlantcircBase
						ath_circ_023142
					
						Alias
						3:7689815-7690600
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 7689815-7690600  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G21820						
					
						Parent gene annotation
						
							Histone-lysine N-methyltransferase ATXR2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G21820_circ_g.5 AT3G21820_circ_g.6 AT3G21820_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  
						
							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
						AT3G21820.1:4

General Information
CircRNA Name	AT3G21820_circ_g.4
ID in PlantcircBase	ath_circ_023142
Alias	3:7689815-7690600
Organism	Arabidpsis thaliana
Position	chr3: 7689815-7690600 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G21820
Parent gene annotation	Histone-lysine N-methyltransferase ATXR2
Parent gene strand	-
Alternative splicing	AT3G21820_circ_g.5 AT3G21820_circ_g.6 AT3G21820_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	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	AT3G21820.1:4

			
						 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  
						
							AATAAACTCTCCAAGCGCCTCTCTAGATATTGATTCAGACCTCTCACCAGTACAAAGTAAGGAA
TGAGAACTCTCCCAATCTGCCGCTGCGCATGATTCAcgtacacgcaaggttctttatttgcatc
ctgaaggctccttcatcagtaggatcaacatcatctggcaatgcaatgcagtcccaccacctac
caaagagt

						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: 367
Transcript exons: 7689815-7689902,7690087-7690220,7690373-7690404,7690488-
7690600
CGTACACGCAAGGTTCTTTATTTGCATCCTGAAGGCTCCTTCATCAGTAGGATCAACATCATCT
GGCAATGCAATGCAGTCCCACCACCTTCTTTTGTATCCAATCGATACTGGTTTCCATGCTTCCA
AGAGAAGCGACTGCTTTGGCTCACTCTGTTTCGCTTTTTTGTCCACATGTTCTGCTTTCAGTTT
CCTGTACCTTAGAATGGTAAAGGCGATTGCCTTCGCAGCCAGGAGAAAAATATCATTGGTATCA
TTAGCATGTTTAATAAACTCTCCAAGCGCCTCTCTAGATATTGATTCAGACCTCTCACCAGTAC
AAAGTAAGGAATGAGAACTCTCCCAATCTGCCGCTGCGCATGATTCA
						
						Genomic sequence
						
							CGTACACGCAAGGTTCTTTATTTGCATCCTGAAGGCTCCTTCATCAGTAGGATCAACATCATCT
GGCAATGCAATGCAGTCCCACCACCTACCAAAGAGTTTTAGATAATTTATATGTGGCGTAGGTA
TATCACCGAAAAGCTTATTAAGTATGATCATGAGGTACCATATGTAATTTGGATCACATTCAGA
AACACATAGAAAAAAAAAGCAAGTGATTCATTTTCTTCTTCAACAGTCAAGAAATATCTAATGG
CAACATCAATGTATACCTTCTTTTGTATCCAATCGATACTGGTTTCCATGCTTCCAAGAGAAGC
GACTGCTTTGGCTCACTCTGTTTCGCTTTTTTGTCCACATGTTCTGCTTTCAGTTTCCTGTACC
TTAGAATGGTAAAGGCGATTGCCTAGCCATAATACATTTTCCAGAACAGGTTAGTTTATTTTAT
TTATATAGTATGCGAAAGGGTCATTCCCCGTAAACTAATATGTCGAAAGTTCCATGGCATTTTA
TATACGATATTCAAAAAGTAGACATAACAACTTATACAAGATATACCTTCGCAGCCAGGAGAAA
AATATCATTGGTATCTGAAAATAAAAAAACGAAAGATATAAATATAGTTATCGCAAGACAAAAC
ATTCAAGTCCAAAGAGACTAATAATAATTTTACCATTAGCATGTTTAATAAACTCTCCAAGCGC
CTCTCTAGATATTGATTCAGACCTCTCACCAGTACAAAGTAAGGAATGAGAACTCTCCCAATCT
GCCGCTGCGCATGATTCA

Sequences
Splice junction sequence	AATAAACTCTCCAAGCGCCTCTCTAGATATTGATTCAGACCTCTCACCAGTACAAAGTAAGGAA TGAGAACTCTCCCAATCTGCCGCTGCGCATGATTCAcgtacacgcaaggttctttatttgcatc ctgaaggctccttcatcagtaggatcaacatcatctggcaatgcaatgcagtcccaccacctac caaagagt
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: 367 Transcript exons: 7689815-7689902,7690087-7690220,7690373-7690404,7690488- 7690600 CGTACACGCAAGGTTCTTTATTTGCATCCTGAAGGCTCCTTCATCAGTAGGATCAACATCATCT GGCAATGCAATGCAGTCCCACCACCTTCTTTTGTATCCAATCGATACTGGTTTCCATGCTTCCA AGAGAAGCGACTGCTTTGGCTCACTCTGTTTCGCTTTTTTGTCCACATGTTCTGCTTTCAGTTT CCTGTACCTTAGAATGGTAAAGGCGATTGCCTTCGCAGCCAGGAGAAAAATATCATTGGTATCA TTAGCATGTTTAATAAACTCTCCAAGCGCCTCTCTAGATATTGATTCAGACCTCTCACCAGTAC AAAGTAAGGAATGAGAACTCTCCCAATCTGCCGCTGCGCATGATTCA
Genomic sequence	CGTACACGCAAGGTTCTTTATTTGCATCCTGAAGGCTCCTTCATCAGTAGGATCAACATCATCT GGCAATGCAATGCAGTCCCACCACCTACCAAAGAGTTTTAGATAATTTATATGTGGCGTAGGTA TATCACCGAAAAGCTTATTAAGTATGATCATGAGGTACCATATGTAATTTGGATCACATTCAGA AACACATAGAAAAAAAAAGCAAGTGATTCATTTTCTTCTTCAACAGTCAAGAAATATCTAATGG CAACATCAATGTATACCTTCTTTTGTATCCAATCGATACTGGTTTCCATGCTTCCAAGAGAAGC GACTGCTTTGGCTCACTCTGTTTCGCTTTTTTGTCCACATGTTCTGCTTTCAGTTTCCTGTACC TTAGAATGGTAAAGGCGATTGCCTAGCCATAATACATTTTCCAGAACAGGTTAGTTTATTTTAT TTATATAGTATGCGAAAGGGTCATTCCCCGTAAACTAATATGTCGAAAGTTCCATGGCATTTTA TATACGATATTCAAAAAGTAGACATAACAACTTATACAAGATATACCTTCGCAGCCAGGAGAAA AATATCATTGGTATCTGAAAATAAAAAAACGAAAGATATAAATATAGTTATCGCAAGACAAAAC ATTCAAGTCCAAAGAGACTAATAATAATTTTACCATTAGCATGTTTAATAAACTCTCCAAGCGC CTCTCTAGATATTGATTCAGACCTCTCACCAGTACAAAGTAAGGAATGAGAACTCTCCCAATCT GCCGCTGCGCATGATTCA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.182237754

Conservation Information
Conserved circRNAs	NA
PMCS	0.182237754

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							ath-miR408-5p 						
					
						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-miR408-5p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT3G21820_circ_g.4

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