Plant Circular RNA Database

Detail information of AT2G16950_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT2G16950_circ_g.1
					
						ID in PlantcircBase
						ath_circ_013490
					
						Alias
						Ath_circ_FC1217
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 7354907-7355456  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT2G16950						
					
						Parent gene annotation
						
							transportin 1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT2G16950_circ_g.2 AT2G16950_circ_g.3 AT2G16950_circ_g.4 AT2G16950_circ_g.5 AT2G16950_circ_g.6 AT2G16950_circ_g.7 AT2G16950_circ_g.8 AT2G16950_circ_g.9 AT2G16950_circ_g.10 AT2G16950_circ_g.11 AT2G16950_circ_g.12 AT2G16950_circ_g.13 AT2G16950_circ_g.14 AT2G16950_circ_g.15 AT2G16950_circ_g.16 AT2G16950_circ_g.17 AT2G16950_circ_g.18 AT2G16950_circ_g.19 2_circ_ag.20 AT2G16950_circ_g.21 AT2G16950_circ_g.22 2_circ_ag.23 AT2G16950_circ_g.24 AT2G16950_circ_g.25 2_circ_ag.26 AT2G16950_circ_g.27 AT2G16950_circ_g.28 AT2G16950_circ_g.29 						
					
						Support reads
						7/3
					
						Tissues
						aerial, whole_plant/seedlings
					
						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
						AT2G16950.1:2
AT2G16950.2:2

General Information
CircRNA Name	AT2G16950_circ_g.1
ID in PlantcircBase	ath_circ_013490
Alias	Ath_circ_FC1217
Organism	Arabidpsis thaliana
Position	chr2: 7354907-7355456 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
Parent gene	AT2G16950
Parent gene annotation	transportin 1
Parent gene strand	+
Alternative splicing	AT2G16950_circ_g.2 AT2G16950_circ_g.3 AT2G16950_circ_g.4 AT2G16950_circ_g.5 AT2G16950_circ_g.6 AT2G16950_circ_g.7 AT2G16950_circ_g.8 AT2G16950_circ_g.9 AT2G16950_circ_g.10 AT2G16950_circ_g.11 AT2G16950_circ_g.12 AT2G16950_circ_g.13 AT2G16950_circ_g.14 AT2G16950_circ_g.15 AT2G16950_circ_g.16 AT2G16950_circ_g.17 AT2G16950_circ_g.18 AT2G16950_circ_g.19 2_circ_ag.20 AT2G16950_circ_g.21 AT2G16950_circ_g.22 2_circ_ag.23 AT2G16950_circ_g.24 AT2G16950_circ_g.25 2_circ_ag.26 AT2G16950_circ_g.27 AT2G16950_circ_g.28 AT2G16950_circ_g.29
Support reads	7/3
Tissues	aerial, whole_plant/seedlings
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	AT2G16950.1:2 AT2G16950.2:2

			
						 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  
						
							TATCAATCAGATTTGTGAGGATATTCCGCATGTCTTGGATACAGAAGTGCCTGGCTTAGCAGAA
CGCCCTATCAACATTTTCCTGCCTAGGCTATTACAGggaaagtctgttgaggttcgtcaagctg
ctggattgcttttgaaaaataatttgaggggtgcttatccatccatgactcaagaaaaccaaaa
atatatca

						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: 378
Transcript exons: 7354907-7355194,7355367-7355456
GGAAAGTCTGTTGAGGTTCGTCAAGCTGCTGGATTGCTTTTGAAAAATAATTTGAGGGGTGCTT
ATCCATCCATGACTCAAGAAAACCAAAAATATATCAAGTCAGAGTTACTGCCTTGTCTGGGAGC
AGCGGACAGGAATATACGGACTACAGTTGGAACTATCATCAGTGTTATTGTTAATATTGAGGGA
GTTTCTGGATGGCATGAGCTTTTGCCAGCTCTTGTTACTTGTTTAGACAGTAATGACCTTAATC
ACATGGATGGTGCTATGGATGCATTGTCAAAGATTTGTGAGGATATTCCGCATGTCTTGGATAC
AGAAGTGCCTGGCTTAGCAGAACGCCCTATCAACATTTTCCTGCCTAGGCTATTACAG
						
						Genomic sequence
						
							GGAAAGTCTGTTGAGGTTCGTCAAGCTGCTGGATTGCTTTTGAAAAATAATTTGAGGGGTGCTT
ATCCATCCATGACTCAAGAAAACCAAAAATATATCAAGTCAGAGTTACTGCCTTGTCTGGGAGC
AGCGGACAGGAATATACGGACTACAGTTGGAACTATCATCAGTGTTATTGTTAATATTGAGGGA
GTTTCTGGATGGCATGAGCTTTTGCCAGCTCTTGTTACTTGTTTAGACAGTAATGACCTTAATC
ACATGGATGGTGCTATGGATGCATTGTCAAAGGTATGTAGCAGCTATGTGTTCTCTTTTCTGTT
TCTTGCTCTTTTCGTTGAACCTTTGATTTATGAACCATAAGCTTGTGTAATCCAAAGTTGTGAT
TGTTGGTTTTGATGATATATTTGGAGTTTTTTTCAAAGTTTTTCTAATATCTACATGTCGTATT
CTTATCAATCAGATTTGTGAGGATATTCCGCATGTCTTGGATACAGAAGTGCCTGGCTTAGCAG
AACGCCCTATCAACATTTTCCTGCCTAGGCTATTACAG

Sequences
Splice junction sequence	TATCAATCAGATTTGTGAGGATATTCCGCATGTCTTGGATACAGAAGTGCCTGGCTTAGCAGAA CGCCCTATCAACATTTTCCTGCCTAGGCTATTACAGggaaagtctgttgaggttcgtcaagctg ctggattgcttttgaaaaataatttgaggggtgcttatccatccatgactcaagaaaaccaaaa atatatca
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: 378 Transcript exons: 7354907-7355194,7355367-7355456 GGAAAGTCTGTTGAGGTTCGTCAAGCTGCTGGATTGCTTTTGAAAAATAATTTGAGGGGTGCTT ATCCATCCATGACTCAAGAAAACCAAAAATATATCAAGTCAGAGTTACTGCCTTGTCTGGGAGC AGCGGACAGGAATATACGGACTACAGTTGGAACTATCATCAGTGTTATTGTTAATATTGAGGGA GTTTCTGGATGGCATGAGCTTTTGCCAGCTCTTGTTACTTGTTTAGACAGTAATGACCTTAATC ACATGGATGGTGCTATGGATGCATTGTCAAAGATTTGTGAGGATATTCCGCATGTCTTGGATAC AGAAGTGCCTGGCTTAGCAGAACGCCCTATCAACATTTTCCTGCCTAGGCTATTACAG
Genomic sequence	GGAAAGTCTGTTGAGGTTCGTCAAGCTGCTGGATTGCTTTTGAAAAATAATTTGAGGGGTGCTT ATCCATCCATGACTCAAGAAAACCAAAAATATATCAAGTCAGAGTTACTGCCTTGTCTGGGAGC AGCGGACAGGAATATACGGACTACAGTTGGAACTATCATCAGTGTTATTGTTAATATTGAGGGA GTTTCTGGATGGCATGAGCTTTTGCCAGCTCTTGTTACTTGTTTAGACAGTAATGACCTTAATC ACATGGATGGTGCTATGGATGCATTGTCAAAGGTATGTAGCAGCTATGTGTTCTCTTTTCTGTT TCTTGCTCTTTTCGTTGAACCTTTGATTTATGAACCATAAGCTTGTGTAATCCAAAGTTGTGAT TGTTGGTTTTGATGATATATTTGGAGTTTTTTTCAAAGTTTTTCTAATATCTACATGTCGTATT CTTATCAATCAGATTTGTGAGGATATTCCGCATGTCTTGGATACAGAAGTGCCTGGCTTAGCAG AACGCCCTATCAACATTTTCCTGCCTAGGCTATTACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.367637627

Conservation Information
Conserved circRNAs	NA
PMCS	0.367637627

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							7354979-7355453(+)
						
						Potential amino acid sequence
						
							MTQENQKYIKSELLPCLGAADRNIRTTVGTIISVIVNIEGVSGWHELLPALVTCLDSNDLNHMD
GAMDALSKICEDIPHVLDTEVPGLAERPINIFLPRLLQGKSVEVRQAAGLLLKNNLRGAYPSMT
QENQKYIKSELLPCLGAADRNIRTTVGTIISVIVNIEGVSGWHELLPALVTCLDSNDLNHMDGA
MDALSKICEDIPHVLDTEVPGLAERPINIFLPRLLQGKSVEVRQAAGLLLKNNLRGAYPSMTQE
NQKYIKSELLPCLGAADRNIRTTVGTIISVIVNIEGVSGWHELLPALVTCLDSNDLNHMDGAMD
ALSKICEDIPHVLDTEVPGLAERPINIFLPRLLQGKSVEVRQAAGLLLKNNLRGAYPSMTQENQ
KYIKSELLPCLGAADRNIRTTVGTIISVIVNIEGVSGWHELLPALVTCLDSNDLNHMDGAMDAL
SKICEDIPHVLDTEVPGLAERPINIFLPRLLQ(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	7354979-7355453(+)
Potential amino acid sequence	MTQENQKYIKSELLPCLGAADRNIRTTVGTIISVIVNIEGVSGWHELLPALVTCLDSNDLNHMD GAMDALSKICEDIPHVLDTEVPGLAERPINIFLPRLLQGKSVEVRQAAGLLLKNNLRGAYPSMT QENQKYIKSELLPCLGAADRNIRTTVGTIISVIVNIEGVSGWHELLPALVTCLDSNDLNHMDGA MDALSKICEDIPHVLDTEVPGLAERPINIFLPRLLQGKSVEVRQAAGLLLKNNLRGAYPSMTQE NQKYIKSELLPCLGAADRNIRTTVGTIISVIVNIEGVSGWHELLPALVTCLDSNDLNHMDGAMD ALSKICEDIPHVLDTEVPGLAERPINIFLPRLLQGKSVEVRQAAGLLLKNNLRGAYPSMTQENQ KYIKSELLPCLGAADRNIRTTVGTIISVIVNIEGVSGWHELLPALVTCLDSNDLNHMDGAMDAL SKICEDIPHVLDTEVPGLAERPINIFLPRLLQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of AT2G16950_circ_g.1

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