Plant Circular RNA Database

Detail information of AT1G09932_circ_g.5

			
						 General Information
					
						CircRNA Name
						AT1G09932_circ_g.5
					
						ID in PlantcircBase
						ath_circ_001775
					
						Alias
						At_ciR1549
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 3232017-3232777  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						KNIFE, PcircRNA_finder, find_circ, CIRI-full
					
						Parent gene
						
							AT1G09932						
					
						Parent gene annotation
						
							Phosphoglycerate mutase family protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G09932_circ_g.2 AT1G09932_circ_g.3 AT1G09932_circ_g.4 						
					
						Support reads
						7/1
					
						Tissues
						leaf/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  
						
							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
						AT1G09932.2:3
AT1G09932.1:3
AT1G09932.3:3
AT1G09932.4:3

General Information
CircRNA Name	AT1G09932_circ_g.5
ID in PlantcircBase	ath_circ_001775
Alias	At_ciR1549
Organism	Arabidpsis thaliana
Position	chr1: 3232017-3232777 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	KNIFE, PcircRNA_finder, find_circ, CIRI-full
Parent gene	AT1G09932
Parent gene annotation	Phosphoglycerate mutase family protein
Parent gene strand	-
Alternative splicing	AT1G09932_circ_g.2 AT1G09932_circ_g.3 AT1G09932_circ_g.4
Support reads	7/1
Tissues	leaf/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	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	AT1G09932.2:3 AT1G09932.1:3 AT1G09932.3:3 AT1G09932.4:3

			
						 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  
						
							AACCCTTTGGAGAAAGGTGGGCGTCAAAAAGCTTTTCTGATTCAGGTTTCTCTCCCTTCTCTTC
TAATGCTATATTGTGGACTCCTTGTGCATGCCTCACcatgcgttctctacagatctcaagtgct
acaattggagggaagttgttagcttttgcaaagtcttcggatatatttacatatccttgtcccc
taaatatt

						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: 309
Transcript exons: 3232017-3232137,3232477-3232556,3232670-3232777
CATGCGTTCTCTACAGATCTCAAGTGCTACAATTGGAGGGAAGTTGTTAGCTTTTGCAAAGTCT
TCGGATATATTTACATATCCTTGTCCCCTAAATATTCCTATTGAAGTTTCCATTGCTCTGCACA
GCGGAGAGGTTATCACTAACTCGACAGTGTTAAGTAATCCTGATTCAAGGATTTGGTTGCGCCT
TTCCGAAACCTGTTGCAAACCCTTTGGAGAAAGGTGGGCGTCAAAAAGCTTTTCTGATTCAGGT
TTCTCTCCCTTCTCTTCTAATGCTATATTGTGGACTCCTTGTGCATGCCTCAC
						
						Genomic sequence
						
							CATGCGTTCTCTACAGATCTCAAGTGCTACAATTGGAGGGAAGTTGTTAGCTTTTGCAAAGTCT
TCGGATATATTTACATATCCTTGTCCCCTAAATATTCCTATTGAAGTTTCCATTGCTCTGAAAT
TAAATGGAACAGTGTTACTATTCGTGCTACCAAATTATGTATAACAATTCTAAATTCTTCACAT
TACATAATAATCAAGAATATTTGTGAACAAGGAACGACTTGCTCGATTGAGACTTGGGAACCAT
ATTAGAAAGAAAAAATGAAAAGAAAAAAAACTTCAAGGTTTGAATTATATGATATATCGAATAA
TTCAACTAATCATCGTTGAAAATATGAATGTTAGATATGCCTAGCCTTTAGGTCGATCATTTAT
TTTCATTGATATTGATGTTTACGACTTTACGATTTACCAATTCTTTAGCCTAAAATCCAAATTT
AGGTGGTAGTACCTGCACAGCGGAGAGGTTATCACTAACTCGACAGTGTTAAGTAATCCTGATT
CAAGGATTTGGTTGCGCCTTTCCGAAACCTGCAAAATTATCAAGAATGTTTCATAAATACAAGA
GTGCGTCTCAAGGTACTATATCAAACCCTAAAAATTTGGATTATGGTGGTAATAGTTAATAGAT
GTAGTTCCCACACCTGTTGCAAACCCTTTGGAGAAAGGTGGGCGTCAAAAAGCTTTTCTGATTC
AGGTTTCTCTCCCTTCTCTTCTAATGCTATATTGTGGACTCCTTGTGCATGCCTCAC

Sequences
Splice junction sequence	AACCCTTTGGAGAAAGGTGGGCGTCAAAAAGCTTTTCTGATTCAGGTTTCTCTCCCTTCTCTTC TAATGCTATATTGTGGACTCCTTGTGCATGCCTCACcatgcgttctctacagatctcaagtgct acaattggagggaagttgttagcttttgcaaagtcttcggatatatttacatatccttgtcccc taaatatt
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: 309 Transcript exons: 3232017-3232137,3232477-3232556,3232670-3232777 CATGCGTTCTCTACAGATCTCAAGTGCTACAATTGGAGGGAAGTTGTTAGCTTTTGCAAAGTCT TCGGATATATTTACATATCCTTGTCCCCTAAATATTCCTATTGAAGTTTCCATTGCTCTGCACA GCGGAGAGGTTATCACTAACTCGACAGTGTTAAGTAATCCTGATTCAAGGATTTGGTTGCGCCT TTCCGAAACCTGTTGCAAACCCTTTGGAGAAAGGTGGGCGTCAAAAAGCTTTTCTGATTCAGGT TTCTCTCCCTTCTCTTCTAATGCTATATTGTGGACTCCTTGTGCATGCCTCAC
Genomic sequence	CATGCGTTCTCTACAGATCTCAAGTGCTACAATTGGAGGGAAGTTGTTAGCTTTTGCAAAGTCT TCGGATATATTTACATATCCTTGTCCCCTAAATATTCCTATTGAAGTTTCCATTGCTCTGAAAT TAAATGGAACAGTGTTACTATTCGTGCTACCAAATTATGTATAACAATTCTAAATTCTTCACAT TACATAATAATCAAGAATATTTGTGAACAAGGAACGACTTGCTCGATTGAGACTTGGGAACCAT ATTAGAAAGAAAAAATGAAAAGAAAAAAAACTTCAAGGTTTGAATTATATGATATATCGAATAA TTCAACTAATCATCGTTGAAAATATGAATGTTAGATATGCCTAGCCTTTAGGTCGATCATTTAT TTTCATTGATATTGATGTTTACGACTTTACGATTTACCAATTCTTTAGCCTAAAATCCAAATTT AGGTGGTAGTACCTGCACAGCGGAGAGGTTATCACTAACTCGACAGTGTTAAGTAATCCTGATT CAAGGATTTGGTTGCGCCTTTCCGAAACCTGCAAAATTATCAAGAATGTTTCATAAATACAAGA GTGCGTCTCAAGGTACTATATCAAACCCTAAAAATTTGGATTATGGTGGTAATAGTTAATAGAT GTAGTTCCCACACCTGTTGCAAACCCTTTGGAGAAAGGTGGGCGTCAAAAAGCTTTTCTGATTC AGGTTTCTCTCCCTTCTCTTCTAATGCTATATTGTGGACTCCTTGTGCATGCCTCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.242226945

Conservation Information
Conserved circRNAs	NA
PMCS	0.242226945

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3232134-3232019(-)
						
						Potential amino acid sequence
						
							METSIGIFRGQGYVNISEDFAKANNFPPIVALEICRERMVRHAQGVHNIALEEKGEKPESEKLF
DAHLSPKGLQQVSERRNQILESGLLNTVELVITSPLCRAMETSIGIFRGQGYVNISEDFAKANN
FPPIVALEICRERMVRHAQGVHNIALEEKGEKPESEKLFDAHLSPKGLQQVSERRNQILESGLL
NTVELVITSPLCRAMETSIGIFRGQGYVNISEDFAKANNFPPIVALEICRERMVRHAQGVHNIA
LEEKGEKPESEKLFDAHLSPKGLQQVSERRNQILESGLLNTVELVITSPLCRAMETSIGIFRGQ
GYVNISEDFAKANNFPPIVALEICRERM(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3232134-3232019(-)
Potential amino acid sequence	METSIGIFRGQGYVNISEDFAKANNFPPIVALEICRERMVRHAQGVHNIALEEKGEKPESEKLF DAHLSPKGLQQVSERRNQILESGLLNTVELVITSPLCRAMETSIGIFRGQGYVNISEDFAKANN FPPIVALEICRERMVRHAQGVHNIALEEKGEKPESEKLFDAHLSPKGLQQVSERRNQILESGLL NTVELVITSPLCRAMETSIGIFRGQGYVNISEDFAKANNFPPIVALEICRERMVRHAQGVHNIA LEEKGEKPESEKLFDAHLSPKGLQQVSERRNQILESGLLNTVELVITSPLCRAMETSIGIFRGQ GYVNISEDFAKANNFPPIVALEICRERM(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of AT1G09932_circ_g.5

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