Plant Circular RNA Database

Detail information of AT1G71860_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT1G71860_circ_g.2
					
						ID in PlantcircBase
						ath_circ_009678
					
						Alias
						1:27027336-27028677
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 27027336-27028677  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G71860						
					
						Parent gene annotation
						
							Protein-tyrosine-phosphatase PTP1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G71860_circ_g.1 AT1G71860_circ_g.3 AT1G71860_circ_g.4 AT1G71860_circ_g.5 AT1G71860_circ_g.6 AT1G71860_circ_g.7 						
					
						Support reads
						1/1
					
						Tissues
						seedling;root
					
						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  
						
							GT-AG							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
						AT1G71860.2:6
AT1G71860.1:6
AT1G71860.3:6

General Information
CircRNA Name	AT1G71860_circ_g.2
ID in PlantcircBase	ath_circ_009678
Alias	1:27027336-27028677
Organism	Arabidpsis thaliana
Position	chr1: 27027336-27028677 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G71860
Parent gene annotation	Protein-tyrosine-phosphatase PTP1
Parent gene strand	+
Alternative splicing	AT1G71860_circ_g.1 AT1G71860_circ_g.3 AT1G71860_circ_g.4 AT1G71860_circ_g.5 AT1G71860_circ_g.6 AT1G71860_circ_g.7
Support reads	1/1
Tissues	seedling;root
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	GT-AG 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	AT1G71860.2:6 AT1G71860.1:6 AT1G71860.3:6

			
						 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  
						
							ACTCTTTTTTGAAGGATCAATACTTCTTTTGCTACAATGCTATTGTTGATGAATTAGAAGATCT
AACCGCGGGGACAAATGCTGGAACGAGTTCCTAAAGttgacaagaacaggattgttctgaatcc
atgtaaagactcatctgcaaaaggatatgtgaatgcaagcttaattaaggtacacttcttatta
gtctgttt

									
								

					

						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: 730
Transcript exons: 27027336-27027412,27027497-27027637,27027897-27028031,27
028132-27028280,27028354-27028495,27028592-27028677
TTGACAAGAACAGGATTGTTCTGAATCCATGTAAAGACTCATCTGCAAAAGGATATGTGAATGC
AAGCTTAATTAAGACGTCGGAGTCTGAGAGTATTTCTCAGTTCATAGCTACGCAAGGTCCTTTA
CCACACACGATGGAGGACTTCTGGGAGATGGTTATTCAGCAGCATTGCCCAATCATAGTGATGC
TCACTCGATTGGTTGATAATAATAGGACTGTTAAATGCGGGGACTATTTTCAAGACGAAGATGG
ACCTAGAGAATTTGGCAACATATCTCTTACAACAAAGTGGATAAAGACTACTGACACTTCATTG
ATGTTACGGAATCTTGAGGTTAACTACAAGGAGACAGAGGATCAGCCCATGTCCGTTTTGCATA
TTCAGTATCCAGAATGGCCTGATCATGGAGTTCCCAAGGATACAGTGGCTGTCCGTGAAATTCT
AAAAAGACTATATCAAGTACCACCTAGTCTCGGCCCAATCATTGTGCACTGCAGTGCAGGTATA
GGAAGAACTGGAACATACTGTGCGATACATAACACAATCCAAAGAATTCTTGCTGGCGATATGT
CTGCGTTGGATCTTGCTAAAACCGTGGCACTATTTCGCAAGCAACGCATTGGCATGGTTCAAAC
CATGGATCAATACTTCTTTTGCTACAATGCTATTGTTGATGAATTAGAAGATCTAACCGCGGGG
ACAAATGCTGGAACGAGTTCCTAAAG
						
					

						Genomic sequence
						
							TTGACAAGAACAGGATTGTTCTGAATCCATGTAAAGACTCATCTGCAAAAGGATATGTGAATGC
AAGCTTAATTAAGGTACACTTCTTATTAGTCTGTTTATCTGTATCTTTTTGTGGTGATAGATTT
TTGAAGGTTTTACAATGTGTTAATGTTATGTAGACGTCGGAGTCTGAGAGTATTTCTCAGTTCA
TAGCTACGCAAGGTCCTTTACCACACACGATGGAGGACTTCTGGGAGATGGTTATTCAGCAGCA
TTGCCCAATCATAGTGATGCTCACTCGATTGGTTGATAATAATAGGGTAAACTTCCTTGTCTTG
CTTGTGTATATGAGTCTCTTTTTAGACGATTGGATATTAATATGATCTGTTGCAAATATACTAG
TACAAGCGAAGTTGTTGTGAGCATTTGTTTCTCAAGTTAAATTTCTTCGTATTAAATTTTAGCA
AGTTTTAAATGTTCCATAAACAGTGATGAAGATAGAAACTATCTCGTTGATATTGATTGTTGAA
CTTATCTTGTTTGTTTTTTCATGCTAACTTATCTAATTACTTGTTACAGACTGTTAAATGCGGG
GACTATTTTCAAGACGAAGATGGACCTAGAGAATTTGGCAACATATCTCTTACAACAAAGTGGA
TAAAGACTACTGACACTTCATTGATGTTACGGAATCTTGAGGTTAACTACAAGGAGGTAAGAAT
CTTGTATCAGTTTTCTTCTGTTTATTTTTACCAGATCAAGTTATTTCTTCGAGGGTTAAGCATG
TTTCAATTATTGATATTGTGTTTTACAGACAGAGGATCAGCCCATGTCCGTTTTGCATATTCAG
TATCCAGAATGGCCTGATCATGGAGTTCCCAAGGATACAGTGGCTGTCCGTGAAATTCTAAAAA
GACTATATCAAGTACCACCTAGTCTCGGCCCAATCATTGTGCACTGCAGGTACGATGCATGTCA
ATGAGGGATACAAGTGTTGTTCAACGTCTCCTGAGAGAATTGTTTTTTTCTCTCTCAGTGCAGG
TATAGGAAGAACTGGAACATACTGTGCGATACATAACACAATCCAAAGAATTCTTGCTGGCGAT
ATGTCTGCGTTGGATCTTGCTAAAACCGTGGCACTATTTCGCAAGCAACGCATTGGCATGGTTC
AAACCATGGTAAATCTTTCAGCGTTACAATTTTTAGCTACCAAATTTCTGTATCTCACCACATA
ATTTGTTCTGAATTGTTCAATTCCTTACTCTTTTTTGAAGGATCAATACTTCTTTTGCTACAAT
GCTATTGTTGATGAATTAGAAGATCTAACCGCGGGGACAAATGCTGGAACGAGTTCCTAAAG
						
					

			
		

Sequences
Splice junction sequence	ACTCTTTTTTGAAGGATCAATACTTCTTTTGCTACAATGCTATTGTTGATGAATTAGAAGATCT AACCGCGGGGACAAATGCTGGAACGAGTTCCTAAAGttgacaagaacaggattgttctgaatcc atgtaaagactcatctgcaaaaggatatgtgaatgcaagcttaattaaggtacacttcttatta gtctgttt
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: 730 Transcript exons: 27027336-27027412,27027497-27027637,27027897-27028031,27 028132-27028280,27028354-27028495,27028592-27028677 TTGACAAGAACAGGATTGTTCTGAATCCATGTAAAGACTCATCTGCAAAAGGATATGTGAATGC AAGCTTAATTAAGACGTCGGAGTCTGAGAGTATTTCTCAGTTCATAGCTACGCAAGGTCCTTTA CCACACACGATGGAGGACTTCTGGGAGATGGTTATTCAGCAGCATTGCCCAATCATAGTGATGC TCACTCGATTGGTTGATAATAATAGGACTGTTAAATGCGGGGACTATTTTCAAGACGAAGATGG ACCTAGAGAATTTGGCAACATATCTCTTACAACAAAGTGGATAAAGACTACTGACACTTCATTG ATGTTACGGAATCTTGAGGTTAACTACAAGGAGACAGAGGATCAGCCCATGTCCGTTTTGCATA TTCAGTATCCAGAATGGCCTGATCATGGAGTTCCCAAGGATACAGTGGCTGTCCGTGAAATTCT AAAAAGACTATATCAAGTACCACCTAGTCTCGGCCCAATCATTGTGCACTGCAGTGCAGGTATA GGAAGAACTGGAACATACTGTGCGATACATAACACAATCCAAAGAATTCTTGCTGGCGATATGT CTGCGTTGGATCTTGCTAAAACCGTGGCACTATTTCGCAAGCAACGCATTGGCATGGTTCAAAC CATGGATCAATACTTCTTTTGCTACAATGCTATTGTTGATGAATTAGAAGATCTAACCGCGGGG ACAAATGCTGGAACGAGTTCCTAAAG
Genomic sequence	TTGACAAGAACAGGATTGTTCTGAATCCATGTAAAGACTCATCTGCAAAAGGATATGTGAATGC AAGCTTAATTAAGGTACACTTCTTATTAGTCTGTTTATCTGTATCTTTTTGTGGTGATAGATTT TTGAAGGTTTTACAATGTGTTAATGTTATGTAGACGTCGGAGTCTGAGAGTATTTCTCAGTTCA TAGCTACGCAAGGTCCTTTACCACACACGATGGAGGACTTCTGGGAGATGGTTATTCAGCAGCA TTGCCCAATCATAGTGATGCTCACTCGATTGGTTGATAATAATAGGGTAAACTTCCTTGTCTTG CTTGTGTATATGAGTCTCTTTTTAGACGATTGGATATTAATATGATCTGTTGCAAATATACTAG TACAAGCGAAGTTGTTGTGAGCATTTGTTTCTCAAGTTAAATTTCTTCGTATTAAATTTTAGCA AGTTTTAAATGTTCCATAAACAGTGATGAAGATAGAAACTATCTCGTTGATATTGATTGTTGAA CTTATCTTGTTTGTTTTTTCATGCTAACTTATCTAATTACTTGTTACAGACTGTTAAATGCGGG GACTATTTTCAAGACGAAGATGGACCTAGAGAATTTGGCAACATATCTCTTACAACAAAGTGGA TAAAGACTACTGACACTTCATTGATGTTACGGAATCTTGAGGTTAACTACAAGGAGGTAAGAAT CTTGTATCAGTTTTCTTCTGTTTATTTTTACCAGATCAAGTTATTTCTTCGAGGGTTAAGCATG TTTCAATTATTGATATTGTGTTTTACAGACAGAGGATCAGCCCATGTCCGTTTTGCATATTCAG TATCCAGAATGGCCTGATCATGGAGTTCCCAAGGATACAGTGGCTGTCCGTGAAATTCTAAAAA GACTATATCAAGTACCACCTAGTCTCGGCCCAATCATTGTGCACTGCAGGTACGATGCATGTCA ATGAGGGATACAAGTGTTGTTCAACGTCTCCTGAGAGAATTGTTTTTTTCTCTCTCAGTGCAGG TATAGGAAGAACTGGAACATACTGTGCGATACATAACACAATCCAAAGAATTCTTGCTGGCGAT ATGTCTGCGTTGGATCTTGCTAAAACCGTGGCACTATTTCGCAAGCAACGCATTGGCATGGTTC AAACCATGGTAAATCTTTCAGCGTTACAATTTTTAGCTACCAAATTTCTGTATCTCACCACATA ATTTGTTCTGAATTGTTCAATTCCTTACTCTTTTTTGAAGGATCAATACTTCTTTTGCTACAAT GCTATTGTTGATGAATTAGAAGATCTAACCGCGGGGACAAATGCTGGAACGAGTTCCTAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.209241297

Conservation Information
Conserved circRNAs	NA
PMCS	0.209241297

			
						 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 AT1G71860_circ_g.2

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