Plant Circular RNA Database

Detail information of AT1G67890_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT1G67890_circ_g.3
					
						ID in PlantcircBase
						ath_circ_009135
					
						Alias
						Ath_circ_FC0912
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 25459401-25461146  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						PcircRNA_finder
					
						Parent gene
						
							AT1G67890						
					
						Parent gene annotation
						
							PAS domain-containing protein tyrosine kinase family protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G67890_circ_g.1 AT1G67890_circ_g.2 						
					
						Support reads
						1
					
						Tissues
						whole_plant
					
						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
						AT1G67890.1:7
AT1G67890.4:7
AT1G67890.3:7
AT1G67890.2:7

General Information
CircRNA Name	AT1G67890_circ_g.3
ID in PlantcircBase	ath_circ_009135
Alias	Ath_circ_FC0912
Organism	Arabidpsis thaliana
Position	chr1: 25459401-25461146 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	PcircRNA_finder
Parent gene	AT1G67890
Parent gene annotation	PAS domain-containing protein tyrosine kinase family protein
Parent gene strand	+
Alternative splicing	AT1G67890_circ_g.1 AT1G67890_circ_g.2
Support reads	1
Tissues	whole_plant
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	AT1G67890.1:7 AT1G67890.4:7 AT1G67890.3:7 AT1G67890.2:7

			
						 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  
						
							CTACTCTTTAAATGGCAGGTCTGACGTTTACAGTTTTGGAGTAGTACTATGGGAGCTTGTGACA
GAGAAGATCCCATGGGAAAATCTAAATGCTATGCAGgatgtggctgtaaaggtgttttccaaac
aagaatattcagaagagatcataacatctttcaaacaagaggtattattgttttctgtcgcttc
tctaagca

									
								

					

						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
						
							GATGTGGCTGTAAAGGTGTTTTCCAAACAAGAATATTCAGAAGAGATCATAACATCTTTCAAAC
AAGAGGTATTATTGTTTTCTGTCGCTTCTCTAAGCATGTTTGGTAAAAGACTGTTAGAACTTGT
CTTTGTTTTAAGCGAATAATACCTGCCTTCTGTCTTCCATAATTTCGTATGAAAAAATGATTCT
GAAACTACCACAAATTTTCTGTACGAATCTTTTTCCAAACTGCATCTACCCCGAAAAATTACTC
ATTACAGAGATTAGCCTAGCTACTCATTCTAGTTTCGAAGTACCTATGCTGAAATTGTTTTATC
TTGAAGGTATCATTGATGAAAAGGCTTAGACATCCAAACGTTCTGCTGTTTATGGGAGCTGTGG
CATCACCTCAGCGTCTTTGTATAGTGACAGAGTTTCTACCACGGTTCGGCCTCTTCTCTTTTGC
TAATCCTACATTTCGAGATTTTTGTTCTCTGGGGTAAAAACTCTGACTCACATCTTAAGTCTAA
ATGTTTCGAAATAACATTTGCAGTGGAAGTCTCTTTCGTTTGCTGCAGAGGAACAAGTCAAAAC
TAGATTTGAGGCGACGTATCCATATGGCATCAGACATTGTGAGTATTAAACGTGATTTTCCAGT
TGTTGTCCAAGTTTTTCTAAAGTATAAGCTGCTCTATTTTGGTTCTTTGTTGCATTTTTTTGCA
TATCCTTCTTTTCCGCTCTTTGATTCAGTCTTTCATACAGGCTCGTGGCATGAATTATCTTCAC
CACTGTAGTCCTCCCATCATTCACCGTGATCTGAAGTCGTCAAATCTACTGGTTGATCGGAACT
GGACTGTGAAGGTATTGTTTTCATTGTTGAAATAGTTTCCACTTTCTGGACTACCAATAACCTT
ATGACGTTGGTAATTCTGATGGAGCTAAGAAGAAAATAATTATTTACCTACAAAATACCGTCCA
CTTTCATCAGATTTCGCAGATGACATGAGTTTGGTGGGTGAACTAGAAATGGATGTCCCCAGTT
TAAAAAATATTGCTTGATTGATTTCTTTGTGACACAAATGGAAAAATATTATTCTAGGTCAACA
AAATAATGTTATTAGGTCTAGTATTTCCCCTGTGTCAGGACTCAAGAGTTGTATCTTGTATGAG
AAAAAAATCGTTTGATAATTAAGTTACTACGACTTAGACTCTAAAGCAAAAGGGGAAATCATAT
ACACTATATTAATGAAGCTTTAGATAACGATTCGTCTTTTGTGTCTATATCAGAAAAGAATCAT
AGATTTTAATTTCAGGACAAACTATTATTGAAGTAAAAAGGGTGTTTGTCATGGTTAACTTACT
TTGTCAGCTCACAGGTTGCTGATTTTGGTCTTTCTCGCATCAAGCATGAGACGTACCTCACTAC
AAACGGAAGGGGAACGGTACTTTACATAGACTCTTACTGAATTGATTCCTCCTTTTTTTTTCTT
TTTTTTAATGAAATCAGATATCTCAGGATGAATTTCATTGCTTTTTTATGTTCTGTAGCCTCAA
TGGATGGCACCAGAAGTTCTTCGAAATGAGGCTGCTGATGAAAAGTATTTTCTCACTCTCTACT
TATTGGTTATTGTTTGTTGTAGCTTTCATCTATAACGATGCTCTTCCTACTCTTTAAATGGCAG
GTCTGACGTTTACAGTTTTGGAGTAGTACTATGGGAGCTTGTGACAGAGAAGATCCCATGGGAA
AATCTAAATGCTATGCAG
						
					

			
		

Sequences
Splice junction sequence	CTACTCTTTAAATGGCAGGTCTGACGTTTACAGTTTTGGAGTAGTACTATGGGAGCTTGTGACA GAGAAGATCCCATGGGAAAATCTAAATGCTATGCAGgatgtggctgtaaaggtgttttccaaac aagaatattcagaagagatcataacatctttcaaacaagaggtattattgttttctgtcgcttc tctaagca
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	GATGTGGCTGTAAAGGTGTTTTCCAAACAAGAATATTCAGAAGAGATCATAACATCTTTCAAAC AAGAGGTATTATTGTTTTCTGTCGCTTCTCTAAGCATGTTTGGTAAAAGACTGTTAGAACTTGT CTTTGTTTTAAGCGAATAATACCTGCCTTCTGTCTTCCATAATTTCGTATGAAAAAATGATTCT GAAACTACCACAAATTTTCTGTACGAATCTTTTTCCAAACTGCATCTACCCCGAAAAATTACTC ATTACAGAGATTAGCCTAGCTACTCATTCTAGTTTCGAAGTACCTATGCTGAAATTGTTTTATC TTGAAGGTATCATTGATGAAAAGGCTTAGACATCCAAACGTTCTGCTGTTTATGGGAGCTGTGG CATCACCTCAGCGTCTTTGTATAGTGACAGAGTTTCTACCACGGTTCGGCCTCTTCTCTTTTGC TAATCCTACATTTCGAGATTTTTGTTCTCTGGGGTAAAAACTCTGACTCACATCTTAAGTCTAA ATGTTTCGAAATAACATTTGCAGTGGAAGTCTCTTTCGTTTGCTGCAGAGGAACAAGTCAAAAC TAGATTTGAGGCGACGTATCCATATGGCATCAGACATTGTGAGTATTAAACGTGATTTTCCAGT TGTTGTCCAAGTTTTTCTAAAGTATAAGCTGCTCTATTTTGGTTCTTTGTTGCATTTTTTTGCA TATCCTTCTTTTCCGCTCTTTGATTCAGTCTTTCATACAGGCTCGTGGCATGAATTATCTTCAC CACTGTAGTCCTCCCATCATTCACCGTGATCTGAAGTCGTCAAATCTACTGGTTGATCGGAACT GGACTGTGAAGGTATTGTTTTCATTGTTGAAATAGTTTCCACTTTCTGGACTACCAATAACCTT ATGACGTTGGTAATTCTGATGGAGCTAAGAAGAAAATAATTATTTACCTACAAAATACCGTCCA CTTTCATCAGATTTCGCAGATGACATGAGTTTGGTGGGTGAACTAGAAATGGATGTCCCCAGTT TAAAAAATATTGCTTGATTGATTTCTTTGTGACACAAATGGAAAAATATTATTCTAGGTCAACA AAATAATGTTATTAGGTCTAGTATTTCCCCTGTGTCAGGACTCAAGAGTTGTATCTTGTATGAG AAAAAAATCGTTTGATAATTAAGTTACTACGACTTAGACTCTAAAGCAAAAGGGGAAATCATAT ACACTATATTAATGAAGCTTTAGATAACGATTCGTCTTTTGTGTCTATATCAGAAAAGAATCAT AGATTTTAATTTCAGGACAAACTATTATTGAAGTAAAAAGGGTGTTTGTCATGGTTAACTTACT TTGTCAGCTCACAGGTTGCTGATTTTGGTCTTTCTCGCATCAAGCATGAGACGTACCTCACTAC AAACGGAAGGGGAACGGTACTTTACATAGACTCTTACTGAATTGATTCCTCCTTTTTTTTTCTT TTTTTTAATGAAATCAGATATCTCAGGATGAATTTCATTGCTTTTTTATGTTCTGTAGCCTCAA TGGATGGCACCAGAAGTTCTTCGAAATGAGGCTGCTGATGAAAAGTATTTTCTCACTCTCTACT TATTGGTTATTGTTTGTTGTAGCTTTCATCTATAACGATGCTCTTCCTACTCTTTAAATGGCAG GTCTGACGTTTACAGTTTTGGAGTAGTACTATGGGAGCTTGTGACAGAGAAGATCCCATGGGAA AATCTAAATGCTATGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.123782498

Conservation Information
Conserved circRNAs	NA
PMCS	0.123782498

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							25459736-25461143(+)
						
						Potential amino acid sequence
						
							MKRLRHPNVLLFMGAVASPQRLCIVTEFLPRGSLFRLLQRNKSKLDLRRRIHMASDIARGMNYL
HHCSPPIIHRDLKSSNLLVDRNWTVKVADFGLSRIKHETYLTTNGRGTPQWMAPEVLRNEAADE
KSDVYSFGVVLWELVTEKIPWENLNAMQDVAVKVFSKQEYSEEIITSFKQEVSLMKRLRHPNVL
LFMGAVASPQRLCIVTEFLPRGSLFRLLQRNKSKLDLRRRIHMASDIARGMNYLHHCSPPIIHR
DLKSSNLLVDRNWTVKVADFGLSRIKHETYLTTNGRGTPQWMAPEVLRNEAADEKSDVYSFGVV
LWELVTEKIPWENLNAMQDVAVKVFSKQEYSEEIITSFKQEVSLMKRLRHPNVLLFMGAVASPQ
RLCIVTEFLPRGSLFRLLQRNKSKLDLRRRIHMASDIARGMNYLHHCSPPIIHRDLKSSNLLVD
RNWTVKVADFGLSRIKHETYLTTNGRGTPQWMAPEVLRNEAADEKSDVYSFGVVLWELVTEKIP
WENLNAMQDVAVKVFSKQEYSEEIITSFKQEVSLMKRLRHPNVLLFMGAVASPQRLCIVTEFLP
RGSLFRLLQRNKSKLDLRRRIHMASDIARGMNYLHHCSPPIIHRDLKSSNLLVDRNWTVKVADF
GLSRIKHETYLTTNGRGTPQWMAPEVLRNEAADEKSDVYSFGVVLWELVTEKIPWENLNAMQ(+
)
						
						Sponge-miRNAs
						
							ath-miR831-3p 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	25459736-25461143(+)
Potential amino acid sequence	MKRLRHPNVLLFMGAVASPQRLCIVTEFLPRGSLFRLLQRNKSKLDLRRRIHMASDIARGMNYL HHCSPPIIHRDLKSSNLLVDRNWTVKVADFGLSRIKHETYLTTNGRGTPQWMAPEVLRNEAADE KSDVYSFGVVLWELVTEKIPWENLNAMQDVAVKVFSKQEYSEEIITSFKQEVSLMKRLRHPNVL LFMGAVASPQRLCIVTEFLPRGSLFRLLQRNKSKLDLRRRIHMASDIARGMNYLHHCSPPIIHR DLKSSNLLVDRNWTVKVADFGLSRIKHETYLTTNGRGTPQWMAPEVLRNEAADEKSDVYSFGVV LWELVTEKIPWENLNAMQDVAVKVFSKQEYSEEIITSFKQEVSLMKRLRHPNVLLFMGAVASPQ RLCIVTEFLPRGSLFRLLQRNKSKLDLRRRIHMASDIARGMNYLHHCSPPIIHRDLKSSNLLVD RNWTVKVADFGLSRIKHETYLTTNGRGTPQWMAPEVLRNEAADEKSDVYSFGVVLWELVTEKIP WENLNAMQDVAVKVFSKQEYSEEIITSFKQEVSLMKRLRHPNVLLFMGAVASPQRLCIVTEFLP RGSLFRLLQRNKSKLDLRRRIHMASDIARGMNYLHHCSPPIIHRDLKSSNLLVDRNWTVKVADF GLSRIKHETYLTTNGRGTPQWMAPEVLRNEAADEKSDVYSFGVVLWELVTEKIPWENLNAMQ(+ )
Sponge-miRNAs	ath-miR831-3p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT1G67890_circ_g.3

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