Plant Circular RNA Database

Detail information of AT1G04120_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT1G04120_circ_g.2
					
						ID in PlantcircBase
						ath_circ_000549
					
						Alias
						1:1066607-1067849
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 1066607-1067849  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G04120						
					
						Parent gene annotation
						
							MRP5
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G03910_circ_g.1 AT1G03910_circ_g.2 AT1G03910_circ_g.3 AT1G03910_circ_g.4 AT1G03910_circ_g.5 AT1G03910_circ_g.6 AT1G03910_circ_g.7 AT1G03910_circ_g.8 1_circ_ag.9 AT1G03910_circ_g.10 AT1G03930_circ_g.1 AT1G03930_circ_g.2 AT1G03930_circ_g.3 AT1G03960_circ_g.1 AT1G03960_circ_g.2 AT1G03960_circ_g.3 AT1G03970_circ_g.1 AT1G03980_circ_g.1 AT1G04010_circ_g.1 AT1G04010_circ_g.2 AT1G04010_circ_g.3 AT1G04020_circ_g.1 AT1G04020_circ_g.2 AT1G04020_circ_g.3 AT1G04020_circ_g.4 AT1G04020_circ_g.5 AT1G04020_circ_g.6 AT1G04020_circ_g.7 AT1G04040_circ_g.1 AT1G04040_circ_g.2 AT1G04050_circ_g.1 AT1G04080_circ_g.1 AT1G04080_circ_g.2 AT1G04080_circ_g.3 AT1G04080_circ_g.4 AT1G04080_circ_g.5 AT1G04080_circ_g.6 AT1G04080_circ_g.7 AT1G04080_circ_g.8 AT1G04080_circ_g.9 AT1G04080_circ_g.10 AT1G04080_circ_g.11 AT1G04080_circ_g.12 AT1G04120_circ_g.1 AT1G04120_circ_g.3 AT1G04120_circ_g.4 AT1G04120_circ_g.5 AT1G04120_circ_g.6 AT1G04120_circ_g.7 AT1G04130_circ_g.1 AT1G04130_circ_g.2 AT1G04140_circ_g.1 AT1G04140_circ_g.2 AT1G04140_circ_g.3 AT1G04140_circ_g.4 AT1G04140_circ_g.5 AT1G04140_circ_g.6 						
					
						Support reads
						2
					
						Tissues
						seedling
					
						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
						AT1G04120.2:3
AT1G04120.1:3
AT1G04120.3:3

General Information
CircRNA Name	AT1G04120_circ_g.2
ID in PlantcircBase	ath_circ_000549
Alias	1:1066607-1067849
Organism	Arabidpsis thaliana
Position	chr1: 1066607-1067849 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G04120
Parent gene annotation	MRP5
Parent gene strand	-
Alternative splicing	AT1G03910_circ_g.1 AT1G03910_circ_g.2 AT1G03910_circ_g.3 AT1G03910_circ_g.4 AT1G03910_circ_g.5 AT1G03910_circ_g.6 AT1G03910_circ_g.7 AT1G03910_circ_g.8 1_circ_ag.9 AT1G03910_circ_g.10 AT1G03930_circ_g.1 AT1G03930_circ_g.2 AT1G03930_circ_g.3 AT1G03960_circ_g.1 AT1G03960_circ_g.2 AT1G03960_circ_g.3 AT1G03970_circ_g.1 AT1G03980_circ_g.1 AT1G04010_circ_g.1 AT1G04010_circ_g.2 AT1G04010_circ_g.3 AT1G04020_circ_g.1 AT1G04020_circ_g.2 AT1G04020_circ_g.3 AT1G04020_circ_g.4 AT1G04020_circ_g.5 AT1G04020_circ_g.6 AT1G04020_circ_g.7 AT1G04040_circ_g.1 AT1G04040_circ_g.2 AT1G04050_circ_g.1 AT1G04080_circ_g.1 AT1G04080_circ_g.2 AT1G04080_circ_g.3 AT1G04080_circ_g.4 AT1G04080_circ_g.5 AT1G04080_circ_g.6 AT1G04080_circ_g.7 AT1G04080_circ_g.8 AT1G04080_circ_g.9 AT1G04080_circ_g.10 AT1G04080_circ_g.11 AT1G04080_circ_g.12 AT1G04120_circ_g.1 AT1G04120_circ_g.3 AT1G04120_circ_g.4 AT1G04120_circ_g.5 AT1G04120_circ_g.6 AT1G04120_circ_g.7 AT1G04130_circ_g.1 AT1G04130_circ_g.2 AT1G04140_circ_g.1 AT1G04140_circ_g.2 AT1G04140_circ_g.3 AT1G04140_circ_g.4 AT1G04140_circ_g.5 AT1G04140_circ_g.6
Support reads	2
Tissues	seedling
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	AT1G04120.2:3 AT1G04120.1:3 AT1G04120.3:3

			
						 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  
						
							AAGAGTTTCTTACCAATATTAGATCAGCTGCAGGGAGAAACTCAACTTGATGCGTTACAAAAAC
CACAGTTTTCTCAGCCAATGCAGATAGAATATAATCctgcatccaaaagcaagcaacagctacc
ggaacaacaagaaggaaaacttgccaggtaacattggtcattacagcgacaatgccacagagtt
gtattgtt

									
								

					

						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: 951
Transcript exons: 1066607-1066771,1066852-1067550,1067763-1067849
CTGCATCCAAAAGCAAGCAACAGCTACCGGAACAACAAGAAGGAAAACTTGCCAGGTAACATTG
GTCATTACAGCGACAATGCCACAGAGTTGTATTGTTGTTGAAGCAAACCCACCGAGTCTAAAAG
GAATGTCAAGATCTACAACACTTTGATCAATAGAAACCCGATTCAAAATTCTTCCTGCAGGAGT
GGAATCAAAGAATGACATTGGCGCTCGGAACACACTTCTGAGCATATTTAAGAACAGTTTCTGT
GCAGCTGCAAGACCAAAAGTTGCAACCAGAGCAGCTCGAACAAATATGAACACAGAGCTCCCGA
AAGCTAAAGCCGTATAAACGATGAGAAGCAGAGTAGGATCCACTTTAGATTCGTCACCTTCAGT
TTGAGGATTTGCCCAAGCCATCCACCAATTACTAGCAATCTGAAGAAATTGGAAAGCAGCTTGT
GCGAGTATAATAAGAGGAATCAGAGCCCCTTTATATGCAGCACCCATGTATGACAAGTACACCT
TCATGCTGACTTTTCCCTTTACTCGTTCCTCTTCTTGAACAAGCTGCTTTTTGCGGGAACGCTT
AGCTTTCTTCTTCTTCTCTTTGATTGCCTTTAGATCTGAAGCAGATCCTCCCTCTTGTACTTCC
TTTGCCAAAGTCTCGATGTCATTTTCAAAAACATCAGACTTTGGATTATGCAAGACCAAACTAT
CGCGAATAGGATTTTCATCAGAGTCTTCTGAGGAGGGACTTGGGATGTCCATTGCCTCGATTGC
TTCATGGTGGGCAGACACTAAGGCCTTAAAATCAGTACCTGCTTGCAGCAGATCATCATATTTA
CCCGATTGAATAATCCTGCCTTCCTTCAGAACCAATATTAGATCAGCTGCAGGGAGAAACTCAA
CTTGATGCGTTACAAAAACCACAGTTTTCTCAGCCAATGCAGATAGAATATAATC
						
					

						Genomic sequence
						
							CTGCATCCAAAAGCAAGCAACAGCTACCGGAACAACAAGAAGGAAAACTTGCCAGGTAACATTG
GTCATTACAGCGACAATGCCACAGAGTTGTATTGTTGTTGAAGCAAACCCACCGAGTCTAAAAG
GAATGTCAAGATCTACAACACTTTGATCAATAGAAACCTGCACATCAATAAAATCCCCAAAATC
AGAAAAGTAACACAGAAACTGTGGAATTTGGTTATAATACCACATCTACATACCCGATTCAAAA
TTCTTCCTGCAGGAGTGGAATCAAAGAATGACATTGGCGCTCGGAACACACTTCTGAGCATATT
TAAGAACAGTTTCTGTGCAGCTGCAAGACCAAAAGTTGCAACCAGAGCAGCTCGAACAAATATG
AACACAGAGCTCCCGAAAGCTAAAGCCGTATAAACGATGAGAAGCAGAGTAGGATCCACTTTAG
ATTCGTCACCTTCAGTTTGAGGATTTGCCCAAGCCATCCACCAATTACTAGCAATCTGAAGAAA
TTGGAAAGCAGCTTGTGCGAGTATAATAAGAGGAATCAGAGCCCCTTTATATGCAGCACCCATG
TATGACAAGTACACCTTCATGCTGACTTTTCCCTTTACTCGTTCCTCTTCTTGAACAAGCTGCT
TTTTGCGGGAACGCTTAGCTTTCTTCTTCTTCTCTTTGATTGCCTTTAGATCTGAAGCAGATCC
TCCCTCTTGTACTTCCTTTGCCAAAGTCTCGATGTCATTTTCAAAAACATCAGACTTTGGATTA
TGCAAGACCAAACTATCGCGAATAGGATTTTCATCAGAGTCTTCTGAGGAGGGACTTGGGATGT
CCATTGCCTCGATTGCTTCATGGTGGGCAGACACTAAGGCCTTAAAATCAGTACCTGCTTGCAG
CAGATCATCATATTTACCCGATTGAATAATCCTGCCTTCCTTCAGAACCTTTGAAACAACACAA
ATAAATATTTCAGAGCTTATCATAACGGAAACAGTTTGGAAACTCCTTCAACAATTTTACCTTT
CTGCAACAATAGAGATAAGTTCATCACAGGCTGGTAAGCTAAACACCTAAAAGAGACCCTTTAG
CAATTCTAAAAGGACCAACAGTAGCCAGAATTAATGTGTAGTAAAACCGAGAAAAAAGAGTTTC
TTACCAATATTAGATCAGCTGCAGGGAGAAACTCAACTTGATGCGTTACAAAAACCACAGTTTT
CTCAGCCAATGCAGATAGAATATAATC
						
					

			
		

Sequences
Splice junction sequence	AAGAGTTTCTTACCAATATTAGATCAGCTGCAGGGAGAAACTCAACTTGATGCGTTACAAAAAC CACAGTTTTCTCAGCCAATGCAGATAGAATATAATCctgcatccaaaagcaagcaacagctacc ggaacaacaagaaggaaaacttgccaggtaacattggtcattacagcgacaatgccacagagtt gtattgtt
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: 951 Transcript exons: 1066607-1066771,1066852-1067550,1067763-1067849 CTGCATCCAAAAGCAAGCAACAGCTACCGGAACAACAAGAAGGAAAACTTGCCAGGTAACATTG GTCATTACAGCGACAATGCCACAGAGTTGTATTGTTGTTGAAGCAAACCCACCGAGTCTAAAAG GAATGTCAAGATCTACAACACTTTGATCAATAGAAACCCGATTCAAAATTCTTCCTGCAGGAGT GGAATCAAAGAATGACATTGGCGCTCGGAACACACTTCTGAGCATATTTAAGAACAGTTTCTGT GCAGCTGCAAGACCAAAAGTTGCAACCAGAGCAGCTCGAACAAATATGAACACAGAGCTCCCGA AAGCTAAAGCCGTATAAACGATGAGAAGCAGAGTAGGATCCACTTTAGATTCGTCACCTTCAGT TTGAGGATTTGCCCAAGCCATCCACCAATTACTAGCAATCTGAAGAAATTGGAAAGCAGCTTGT GCGAGTATAATAAGAGGAATCAGAGCCCCTTTATATGCAGCACCCATGTATGACAAGTACACCT TCATGCTGACTTTTCCCTTTACTCGTTCCTCTTCTTGAACAAGCTGCTTTTTGCGGGAACGCTT AGCTTTCTTCTTCTTCTCTTTGATTGCCTTTAGATCTGAAGCAGATCCTCCCTCTTGTACTTCC TTTGCCAAAGTCTCGATGTCATTTTCAAAAACATCAGACTTTGGATTATGCAAGACCAAACTAT CGCGAATAGGATTTTCATCAGAGTCTTCTGAGGAGGGACTTGGGATGTCCATTGCCTCGATTGC TTCATGGTGGGCAGACACTAAGGCCTTAAAATCAGTACCTGCTTGCAGCAGATCATCATATTTA CCCGATTGAATAATCCTGCCTTCCTTCAGAACCAATATTAGATCAGCTGCAGGGAGAAACTCAA CTTGATGCGTTACAAAAACCACAGTTTTCTCAGCCAATGCAGATAGAATATAATC
Genomic sequence	CTGCATCCAAAAGCAAGCAACAGCTACCGGAACAACAAGAAGGAAAACTTGCCAGGTAACATTG GTCATTACAGCGACAATGCCACAGAGTTGTATTGTTGTTGAAGCAAACCCACCGAGTCTAAAAG GAATGTCAAGATCTACAACACTTTGATCAATAGAAACCTGCACATCAATAAAATCCCCAAAATC AGAAAAGTAACACAGAAACTGTGGAATTTGGTTATAATACCACATCTACATACCCGATTCAAAA TTCTTCCTGCAGGAGTGGAATCAAAGAATGACATTGGCGCTCGGAACACACTTCTGAGCATATT TAAGAACAGTTTCTGTGCAGCTGCAAGACCAAAAGTTGCAACCAGAGCAGCTCGAACAAATATG AACACAGAGCTCCCGAAAGCTAAAGCCGTATAAACGATGAGAAGCAGAGTAGGATCCACTTTAG ATTCGTCACCTTCAGTTTGAGGATTTGCCCAAGCCATCCACCAATTACTAGCAATCTGAAGAAA TTGGAAAGCAGCTTGTGCGAGTATAATAAGAGGAATCAGAGCCCCTTTATATGCAGCACCCATG TATGACAAGTACACCTTCATGCTGACTTTTCCCTTTACTCGTTCCTCTTCTTGAACAAGCTGCT TTTTGCGGGAACGCTTAGCTTTCTTCTTCTTCTCTTTGATTGCCTTTAGATCTGAAGCAGATCC TCCCTCTTGTACTTCCTTTGCCAAAGTCTCGATGTCATTTTCAAAAACATCAGACTTTGGATTA TGCAAGACCAAACTATCGCGAATAGGATTTTCATCAGAGTCTTCTGAGGAGGGACTTGGGATGT CCATTGCCTCGATTGCTTCATGGTGGGCAGACACTAAGGCCTTAAAATCAGTACCTGCTTGCAG CAGATCATCATATTTACCCGATTGAATAATCCTGCCTTCCTTCAGAACCTTTGAAACAACACAA ATAAATATTTCAGAGCTTATCATAACGGAAACAGTTTGGAAACTCCTTCAACAATTTTACCTTT CTGCAACAATAGAGATAAGTTCATCACAGGCTGGTAAGCTAAACACCTAAAAGAGACCCTTTAG CAATTCTAAAAGGACCAACAGTAGCCAGAATTAATGTGTAGTAAAACCGAGAAAAAAGAGTTTC TTACCAATATTAGATCAGCTGCAGGGAGAAACTCAACTTGATGCGTTACAAAAACCACAGTTTT CTCAGCCAATGCAGATAGAATATAATC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.36625137

Conservation Information
Conserved circRNAs	NA
PMCS	0.36625137

			
						 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 AT1G04120_circ_g.2

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