Plant Circular RNA Database

Detail information of AT5G11030_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT5G11030_circ_g.4
					
						ID in PlantcircBase
						ath_circ_037515
					
						Alias
						5:3493310-3493633
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 3493310-3493633  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G11030						
					
						Parent gene annotation
						
							Aberrant root formation protein 4
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G11030_circ_g.3 						
					
						Support reads
						1/2/2
					
						Tissues
						leaf;flower
					
						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
						AT5G11030.6:2
AT5G11030.8:2
AT5G11030.1:2
AT5G11030.4:2
AT5G11030.9:2
AT5G11030.3:2
AT5G11030.7:2
AT5G11030.2:2
AT5G11030.5:2

General Information
CircRNA Name	AT5G11030_circ_g.4
ID in PlantcircBase	ath_circ_037515
Alias	5:3493310-3493633
Organism	Arabidpsis thaliana
Position	chr5: 3493310-3493633 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G11030
Parent gene annotation	Aberrant root formation protein 4
Parent gene strand	-
Alternative splicing	AT5G11030_circ_g.3
Support reads	1/2/2
Tissues	leaf;flower
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	AT5G11030.6:2 AT5G11030.8:2 AT5G11030.1:2 AT5G11030.4:2 AT5G11030.9:2 AT5G11030.3:2 AT5G11030.7:2 AT5G11030.2:2 AT5G11030.5:2

			
						 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  
						
							GTTCCATGATATCGAAACAAAGTTGGAATCAAGTACAAACCGTTATCTGTATCACATAGAGACA
AAGTAGACAACGGACTTTTGCTTCTTCTTCGTTATTctccagcaaccgtgctcattaatttttc
agtgtcattccccgtgattaaaccaagatgtgttaaaccacaggatgtcaagaacggttctaac
tgaatcac

						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: 211
Transcript exons: 3493310-3493460,3493574-3493633
CTCCAGCAACCGTGCTCATTAATTTTTCAGTGTCATTCCCCGTGATTAAACCAAGATGTGTTAA
ACCACAGGATGTCAAGAACGGTTCTAACTGAATCACCAGAGGAATACAAGAGGCCGCTTTGTCT
CTGATGCTAACTGAAATAATAGCCGTTATCTGTATCACATAGAGACAAAGTAGACAACGGACTT
TTGCTTCTTCTTCGTTATT
						
						Genomic sequence
						
							CTCCAGCAACCGTGCTCATTAATTTTTCAGTGTCATTCCCCGTGATTAAACCAAGATGTGTTAA
ACCACAGGATGTCAAGAACGGTTCTAACTGAATCACCAGAGGAATACAAGAGGCCGCTTTGTCT
CTGATGCTAACTGAAATAATAGCCTGCAAAACCAGACCAAATCTAAGGTATTGAAGAAAATCTA
TATGCTCATAATAAAAGAGAAAAGTCAGAAAAGTTCCATGATATCGAAACAAAGTTGGAATCAA
GTACAAACCGTTATCTGTATCACATAGAGACAAAGTAGACAACGGACTTTTGCTTCTTCTTCGT
TATT

Sequences
Splice junction sequence	GTTCCATGATATCGAAACAAAGTTGGAATCAAGTACAAACCGTTATCTGTATCACATAGAGACA AAGTAGACAACGGACTTTTGCTTCTTCTTCGTTATTctccagcaaccgtgctcattaatttttc agtgtcattccccgtgattaaaccaagatgtgttaaaccacaggatgtcaagaacggttctaac tgaatcac
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: 211 Transcript exons: 3493310-3493460,3493574-3493633 CTCCAGCAACCGTGCTCATTAATTTTTCAGTGTCATTCCCCGTGATTAAACCAAGATGTGTTAA ACCACAGGATGTCAAGAACGGTTCTAACTGAATCACCAGAGGAATACAAGAGGCCGCTTTGTCT CTGATGCTAACTGAAATAATAGCCGTTATCTGTATCACATAGAGACAAAGTAGACAACGGACTT TTGCTTCTTCTTCGTTATT
Genomic sequence	CTCCAGCAACCGTGCTCATTAATTTTTCAGTGTCATTCCCCGTGATTAAACCAAGATGTGTTAA ACCACAGGATGTCAAGAACGGTTCTAACTGAATCACCAGAGGAATACAAGAGGCCGCTTTGTCT CTGATGCTAACTGAAATAATAGCCTGCAAAACCAGACCAAATCTAAGGTATTGAAGAAAATCTA TATGCTCATAATAAAAGAGAAAAGTCAGAAAAGTTCCATGATATCGAAACAAAGTTGGAATCAA GTACAAACCGTTATCTGTATCACATAGAGACAAAGTAGACAACGGACTTTTGCTTCTTCTTCGT TATT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.282471528

Conservation Information
Conserved circRNAs	NA
PMCS	0.282471528

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

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT5G11030_circ_g.4

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