Plant Circular RNA Database

Detail information of AT5G48880_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT5G48880_circ_g.3
					
						ID in PlantcircBase
						ath_circ_043160
					
						Alias
						Ath_circ_FC3723, Ath_circ_FC3724
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 19815301-19816283  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							AT5G48880						
					
						Parent gene annotation
						
							PKT2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G48880_circ_g.1 AT5G48880_circ_g.2 AT5G48880_circ_g.4 AT5G48880_circ_g.5 AT5G48880_circ_g.6 AT5G48880_circ_g.7 AT5G48880_circ_g.8 AT5G48880_circ_g.9 AT5G48880_circ_g.10 AT5G48880_circ_g.11 AT5G48880_circ_g.12 AT5G48880_circ_g.13 AT5G48880_circ_g.14 AT5G48880_circ_g.15 						
					
						Support reads
						23
					
						Tissues
						seed
					
						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
						AT5G48880.2:6
AT5G48880.1:6
AT5G48880.3:6
AT5G48880.4:6

General Information
CircRNA Name	AT5G48880_circ_g.3
ID in PlantcircBase	ath_circ_043160
Alias	Ath_circ_FC3723, Ath_circ_FC3724
Organism	Arabidpsis thaliana
Position	chr5: 19815301-19816283 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	AT5G48880
Parent gene annotation	PKT2
Parent gene strand	-
Alternative splicing	AT5G48880_circ_g.1 AT5G48880_circ_g.2 AT5G48880_circ_g.4 AT5G48880_circ_g.5 AT5G48880_circ_g.6 AT5G48880_circ_g.7 AT5G48880_circ_g.8 AT5G48880_circ_g.9 AT5G48880_circ_g.10 AT5G48880_circ_g.11 AT5G48880_circ_g.12 AT5G48880_circ_g.13 AT5G48880_circ_g.14 AT5G48880_circ_g.15
Support reads	23
Tissues	seed
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	AT5G48880.2:6 AT5G48880.1:6 AT5G48880.3:6 AT5G48880.4:6

			
						 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  
						
							CCAATGTCGTAATAACCAGCTCTAATGGAAGCAGCAACATCAGCAACTGCTTGTAGTCCTGATG
AGCATTGTCTATTGACAGTTCTAACTGGCACGGAGTctgaatactccaagaatgggaagtccct
tcttcatagccaaacttctcttcattagcagtactgctccagcaccatcactgatctgactagc
attgccta

									
								

					

						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: 589
Transcript exons: 19815301-19815397,19815478-19815610,19815689-19815766,19
815835-19815942,19816023-19816096,19816185-19816283
CTGAATACTCCAAGAATGGGAAGTCCCTTCTTCATAGCCAAACTTCTCTTCATTAGCAGTACTG
CTCCAGCACCATCACTGATCTGACTAGCATTGCCAGCTGTGGTGGAACCGTTCTGTTTAAAGAC
AGTCTTCAGCTTTGCCAAATCTGCCATGTTTGAGTTTGGACGTACACCGTCATCAACAGATACG
ACGATTGCCTTCTCTGCTTTAGTCTCAGGGTCCACAATCTTAGTAGCAACAGGAATGATTTCAT
CCTTGAGTTTACCAGACGCGATTGCAGCTGCAGCGCGTTTGTGAGACTCCACCGCAGCCATATC
TTGCTCTTCTCTTGTGACACCGAACCTTTCTGCAACGTTTTCAGAAGTAATTCCCATTGGAAGC
AAACAATCACGGGCTTTTGGGAAATCCTGTGCTCTTGGATTAGAGCCATGAAAGCCGCCTCCAG
GAATATGATCAGTTGACATTGATTCCACTCCAGCACCAATACCAATGTCGTAATAACCAGCTCT
AATGGAAGCAGCAACATCAGCAACTGCTTGTAGTCCTGATGAGCATTGTCTATTGACAGTTCTA
ACTGGCACGGAGT
						
					

						Genomic sequence
						
							CTGAATACTCCAAGAATGGGAAGTCCCTTCTTCATAGCCAAACTTCTCTTCATTAGCAGTACTG
CTCCAGCACCATCACTGATCTGACTAGCATTGCCTACACAAAACACATATACTTAAATGCTTCA
ATCTATGATCTCACTTATGCCAGTGATAGTTAAGAGAGTTGTTTCTAACCAGCTGTGGTGGAAC
CGTTCTGTTTAAAGACAGTCTTCAGCTTTGCCAAATCTGCCATGTTTGAGTTTGGACGTACACC
GTCATCAACAGATACGACGATTGCCTTCTCTGCTTTAGTCTCAGGGTCCACAATCTGTCAAGAA
CAATATCATTTACTGAGAAAGCTCTACCAAAAGGGCTTTAAAGGAAGTTTGGGAGGTTCTTGTT
TTACCTTAGTAGCAACAGGAATGATTTCATCCTTGAGTTTACCAGACGCGATTGCAGCTGCAGC
GCGTTTGTGAGACTCCACCTGATTATTACTGAATCAGTACTTATATGAACTAGAGAGGAAAAAA
GTGAAGAGAATAACTAACTAACCGCAGCCATATCTTGCTCTTCTCTTGTGACACCGAACCTTTC
TGCAACGTTTTCAGAAGTAATTCCCATTGGAAGCAAACAATCACGGGCTTTTGGGAAATCCTGT
GCCTATTCCCATGTAGAGTTTACAAGATCATCACAAAACTCTTCTTGTTGAGTAAATTTATACA
CTCATTGTGATAGCTTACTCTTGGATTAGAGCCATGAAAGCCGCCTCCAGGAATATGATCAGTT
GACATTGATTCCACTCCAGCACCAATACCTATGCAATTCACAAAGTTGAGAGAATCAATCCCAT
GGCCTATACAAGCAGCTAGAGACTACAAAAAACTGATGCAGCAGCATCTTACCAATGTCGTAAT
AACCAGCTCTAATGGAAGCAGCAACATCAGCAACTGCTTGTAGTCCTGATGAGCATTGTCTATT
GACAGTTCTAACTGGCACGGAGT
						
					

			
		

Sequences
Splice junction sequence	CCAATGTCGTAATAACCAGCTCTAATGGAAGCAGCAACATCAGCAACTGCTTGTAGTCCTGATG AGCATTGTCTATTGACAGTTCTAACTGGCACGGAGTctgaatactccaagaatgggaagtccct tcttcatagccaaacttctcttcattagcagtactgctccagcaccatcactgatctgactagc attgccta
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: 589 Transcript exons: 19815301-19815397,19815478-19815610,19815689-19815766,19 815835-19815942,19816023-19816096,19816185-19816283 CTGAATACTCCAAGAATGGGAAGTCCCTTCTTCATAGCCAAACTTCTCTTCATTAGCAGTACTG CTCCAGCACCATCACTGATCTGACTAGCATTGCCAGCTGTGGTGGAACCGTTCTGTTTAAAGAC AGTCTTCAGCTTTGCCAAATCTGCCATGTTTGAGTTTGGACGTACACCGTCATCAACAGATACG ACGATTGCCTTCTCTGCTTTAGTCTCAGGGTCCACAATCTTAGTAGCAACAGGAATGATTTCAT CCTTGAGTTTACCAGACGCGATTGCAGCTGCAGCGCGTTTGTGAGACTCCACCGCAGCCATATC TTGCTCTTCTCTTGTGACACCGAACCTTTCTGCAACGTTTTCAGAAGTAATTCCCATTGGAAGC AAACAATCACGGGCTTTTGGGAAATCCTGTGCTCTTGGATTAGAGCCATGAAAGCCGCCTCCAG GAATATGATCAGTTGACATTGATTCCACTCCAGCACCAATACCAATGTCGTAATAACCAGCTCT AATGGAAGCAGCAACATCAGCAACTGCTTGTAGTCCTGATGAGCATTGTCTATTGACAGTTCTA ACTGGCACGGAGT
Genomic sequence	CTGAATACTCCAAGAATGGGAAGTCCCTTCTTCATAGCCAAACTTCTCTTCATTAGCAGTACTG CTCCAGCACCATCACTGATCTGACTAGCATTGCCTACACAAAACACATATACTTAAATGCTTCA ATCTATGATCTCACTTATGCCAGTGATAGTTAAGAGAGTTGTTTCTAACCAGCTGTGGTGGAAC CGTTCTGTTTAAAGACAGTCTTCAGCTTTGCCAAATCTGCCATGTTTGAGTTTGGACGTACACC GTCATCAACAGATACGACGATTGCCTTCTCTGCTTTAGTCTCAGGGTCCACAATCTGTCAAGAA CAATATCATTTACTGAGAAAGCTCTACCAAAAGGGCTTTAAAGGAAGTTTGGGAGGTTCTTGTT TTACCTTAGTAGCAACAGGAATGATTTCATCCTTGAGTTTACCAGACGCGATTGCAGCTGCAGC GCGTTTGTGAGACTCCACCTGATTATTACTGAATCAGTACTTATATGAACTAGAGAGGAAAAAA GTGAAGAGAATAACTAACTAACCGCAGCCATATCTTGCTCTTCTCTTGTGACACCGAACCTTTC TGCAACGTTTTCAGAAGTAATTCCCATTGGAAGCAAACAATCACGGGCTTTTGGGAAATCCTGT GCCTATTCCCATGTAGAGTTTACAAGATCATCACAAAACTCTTCTTGTTGAGTAAATTTATACA CTCATTGTGATAGCTTACTCTTGGATTAGAGCCATGAAAGCCGCCTCCAGGAATATGATCAGTT GACATTGATTCCACTCCAGCACCAATACCTATGCAATTCACAAAGTTGAGAGAATCAATCCCAT GGCCTATACAAGCAGCTAGAGACTACAAAAAACTGATGCAGCAGCATCTTACCAATGTCGTAAT AACCAGCTCTAATGGAAGCAGCAACATCAGCAACTGCTTGTAGTCCTGATGAGCATTGTCTATT GACAGTTCTAACTGGCACGGAGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.242075107

Conservation Information
Conserved circRNAs	NA
PMCS	0.242075107

			
						 Functional Information
					
						Coding potential
						N
					
						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	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of AT5G48880_circ_g.3

Address

Any questions?

Supported by