Plant Circular RNA Database

Detail information of AT5G35980_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT5G35980_circ_g.4
					
						ID in PlantcircBase
						ath_circ_041202
					
						Alias
						At_ciR3511
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 14131163-14131797  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, find_circ
					
						Parent gene
						
							AT5G35980						
					
						Parent gene annotation
						
							Dual specificity protein kinase YAK1 homolog
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G35980_circ_g.1 AT5G35980_circ_g.2 AT5G35980_circ_g.3 AT5G35980_circ_g.5 AT5G35980_circ_g.6 						
					
						Support reads
						2/2
					
						Tissues
						leaf/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
						AT5G35980.3:3
AT5G35980.2:3
AT5G35980.1:3

General Information
CircRNA Name	AT5G35980_circ_g.4
ID in PlantcircBase	ath_circ_041202
Alias	At_ciR3511
Organism	Arabidpsis thaliana
Position	chr5: 14131163-14131797 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, find_circ
Parent gene	AT5G35980
Parent gene annotation	Dual specificity protein kinase YAK1 homolog
Parent gene strand	+
Alternative splicing	AT5G35980_circ_g.1 AT5G35980_circ_g.2 AT5G35980_circ_g.3 AT5G35980_circ_g.5 AT5G35980_circ_g.6
Support reads	2/2
Tissues	leaf/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	AT5G35980.3:3 AT5G35980.2:3 AT5G35980.1:3

			
						 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  
						
							GGTCTTTTGGCTGCATTGTTGCCGAGCTGTTTCTTGGATTGCCACTATTTCCAGGAGGTTCAGA
ATTTGATATCTTGAGGCGTATGATTGAAATACTAGGtgtgaagccaactgaaattaagataatt
gactttggatcagcgtgcatggaagataaaactgtttattcatatattcaggtttcttcttgct
ttctgttt

						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: 243
Transcript exons: 14131163-14131241,14131327-14131367,14131675-14131797
TGTGAAGCCAACTGAAATTAAGATAATTGACTTTGGATCAGCGTGCATGGAAGATAAAACTGTT
TATTCATATATTCAGAGTCGTTACTACAGATCGCCGGAAGTCTTACTTGGTTACCAATACACTA
CAGCTATTGACATGTGGTCTTTTGGCTGCATTGTTGCCGAGCTGTTTCTTGGATTGCCACTATT
TCCAGGAGGTTCAGAATTTGATATCTTGAGGCGTATGATTGAAATACTAGG
						
						Genomic sequence
						
							TGTGAAGCCAACTGAAATTAAGATAATTGACTTTGGATCAGCGTGCATGGAAGATAAAACTGTT
TATTCATATATTCAGGTTTCTTCTTGCTTTCTGTTTATATATCTGCTAGATTATGTCATAACAA
AAAAATAACTAAGCTTGCTGGTCAATCTTTCTACAGAGTCGTTACTACAGATCGCCGGAAGTCT
TACTTGGTTACCAGTATCCTTTTGAGGTCCAAGATGATAACCGTTTTCTCACCTAAATTAATAT
GTTTTCTCTTAGTCCTTTGGCACTGAACTGTCATATGTCAATGGACATAGGCTTGTTTTAGCAC
TATGATCATGTGACTCTTATTGATCTATTTGGCCAACTTGCGTTAACTTTGTCGATATAGTTCC
AGCAAATTGTTAGTTTCCTATCAACATCAATTTGACTGCAGACTAAATTTCGTTGCTATTTTGT
TCCTATGGTAGATGCTATCTAAAATTATCTTGAAGTCGTATTTGGAGGCTTAACCACTGTATAG
ATACACTACAGCTATTGACATGTGGTCTTTTGGCTGCATTGTTGCCGAGCTGTTTCTTGGATTG
CCACTATTTCCAGGAGGTTCAGAATTTGATATCTTGAGGCGTATGATTGAAATACTAGG

Sequences
Splice junction sequence	GGTCTTTTGGCTGCATTGTTGCCGAGCTGTTTCTTGGATTGCCACTATTTCCAGGAGGTTCAGA ATTTGATATCTTGAGGCGTATGATTGAAATACTAGGtgtgaagccaactgaaattaagataatt gactttggatcagcgtgcatggaagataaaactgtttattcatatattcaggtttcttcttgct ttctgttt
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: 243 Transcript exons: 14131163-14131241,14131327-14131367,14131675-14131797 TGTGAAGCCAACTGAAATTAAGATAATTGACTTTGGATCAGCGTGCATGGAAGATAAAACTGTT TATTCATATATTCAGAGTCGTTACTACAGATCGCCGGAAGTCTTACTTGGTTACCAATACACTA CAGCTATTGACATGTGGTCTTTTGGCTGCATTGTTGCCGAGCTGTTTCTTGGATTGCCACTATT TCCAGGAGGTTCAGAATTTGATATCTTGAGGCGTATGATTGAAATACTAGG
Genomic sequence	TGTGAAGCCAACTGAAATTAAGATAATTGACTTTGGATCAGCGTGCATGGAAGATAAAACTGTT TATTCATATATTCAGGTTTCTTCTTGCTTTCTGTTTATATATCTGCTAGATTATGTCATAACAA AAAAATAACTAAGCTTGCTGGTCAATCTTTCTACAGAGTCGTTACTACAGATCGCCGGAAGTCT TACTTGGTTACCAGTATCCTTTTGAGGTCCAAGATGATAACCGTTTTCTCACCTAAATTAATAT GTTTTCTCTTAGTCCTTTGGCACTGAACTGTCATATGTCAATGGACATAGGCTTGTTTTAGCAC TATGATCATGTGACTCTTATTGATCTATTTGGCCAACTTGCGTTAACTTTGTCGATATAGTTCC AGCAAATTGTTAGTTTCCTATCAACATCAATTTGACTGCAGACTAAATTTCGTTGCTATTTTGT TCCTATGGTAGATGCTATCTAAAATTATCTTGAAGTCGTATTTGGAGGCTTAACCACTGTATAG ATACACTACAGCTATTGACATGTGGTCTTTTGGCTGCATTGTTGCCGAGCTGTTTCTTGGATTG CCACTATTTCCAGGAGGTTCAGAATTTGATATCTTGAGGCGTATGATTGAAATACTAGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.352043647

Conservation Information
Conserved circRNAs	NA
PMCS	0.352043647

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							14131209-14131794(+)
						
						Potential amino acid sequence
						
							MEDKTVYSYIQSRYYRSPEVLLGYQYTTAIDMWSFGCIVAELFLGLPLFPGGSEFDILRRMIEI
LGVKPTEIKIIDFGSACMEDKTVYSYIQSRYYRSPEVLLGYQYTTAIDMWSFGCIVAELFLGLP
LFPGGSEFDILRRMIEILGVKPTEIKIIDFGSACMEDKTVYSYIQSRYYRSPEVLLGYQYTTAI
DMWSFGCIVAELFLGLPLFPGGSEFDILRRMIEILGVKPTEIKIIDFGSACMEDKTVYSYIQSR
YYRSPEVLLGYQYTTAIDMWSFGCIVAELFLGLPLFPGGSEFDILRRMIEIL(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	14131209-14131794(+)
Potential amino acid sequence	MEDKTVYSYIQSRYYRSPEVLLGYQYTTAIDMWSFGCIVAELFLGLPLFPGGSEFDILRRMIEI LGVKPTEIKIIDFGSACMEDKTVYSYIQSRYYRSPEVLLGYQYTTAIDMWSFGCIVAELFLGLP LFPGGSEFDILRRMIEILGVKPTEIKIIDFGSACMEDKTVYSYIQSRYYRSPEVLLGYQYTTAI DMWSFGCIVAELFLGLPLFPGGSEFDILRRMIEILGVKPTEIKIIDFGSACMEDKTVYSYIQSR YYRSPEVLLGYQYTTAIDMWSFGCIVAELFLGLPLFPGGSEFDILRRMIEIL(+)
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 AT5G35980_circ_g.4

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