Plant Circular RNA Database

Detail information of Cotton_A_37876_circ_g.2

			
						 General Information
					
						CircRNA Name
						Cotton_A_37876_circ_g.2
					
						ID in PlantcircBase
						gar_circ_000009
					
						Alias
						CA_chr1_BGI-A2_v1.0:3717588|3723941
					
						Organism
						
							Gossypium arboreum						
					
						Position
						
							chrCA_chr1_BGI-A2_v1.0: 3717588-3723941  JBrowse»						
					
						Reference genome
						
							BGI-A2_v1.0						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Cotton_A_37876						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							Cotton_A_37876_circ_g.1 						
					
						Support reads
						5
					
						Tissues
						ovule
					
						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
						Cotton_A_37876:7

General Information
CircRNA Name	Cotton_A_37876_circ_g.2
ID in PlantcircBase	gar_circ_000009
Alias	CA_chr1_BGI-A2_v1.0:3717588\|3723941
Organism	Gossypium arboreum
Position	chrCA_chr1_BGI-A2_v1.0: 3717588-3723941 JBrowse»
Reference genome	BGI-A2_v1.0
Type	e-circRNA
Identification method	CIRI
Parent gene	Cotton_A_37876
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	Cotton_A_37876_circ_g.1
Support reads	5
Tissues	ovule
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	Cotton_A_37876:7

			
						 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  
						
							ACTTTGTTCTTCCTGTTTTCCTCAGCTTGGTTATGAGCTTGACGATGTTCAGCTTGGGAACATA
TTCTGGCGCTTCAAAGAAGTAGCTGAACAAAAGAAGatctgaccgagagtttctgtatgagatt
ttgggtgaagtgatcaaggctggagcgacaactctgaacatacctgatactgttggcataacta
tgccgagc

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	ACTTTGTTCTTCCTGTTTTCCTCAGCTTGGTTATGAGCTTGACGATGTTCAGCTTGGGAACATA TTCTGGCGCTTCAAAGAAGTAGCTGAACAAAAGAAGatctgaccgagagtttctgtatgagatt ttgggtgaagtgatcaaggctggagcgacaactctgaacatacctgatactgttggcataacta tgccgagc
Assembled circRNA sequence	NA 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	NA
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							gra_circ_000478* ghi_circ_000248* 						
					
						PMCS

Conservation Information
Conserved circRNAs	gra_circ_000478* ghi_circ_000248*
PMCS

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3717679-3717590(+)
3717937-3723312(-)
						
						Potential amino acid sequence
						
							MPSEFGQLIADIKANTPGIENVIISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGERAGNA
SMEEVVMALKCRGEHVLGGLHTGINTRHIVMASKMVEEYTGLHVQPHKAIVGANAFAHESGIHQ
DGMLKHKGTYEIISPEDIGLERSNEAGIVLGKLRFLTFTNSMVLCYLELDMNVGVGPMGYGSVS
PNCFSILRVLGYELDDVQLGNIFWRFKEVAEQKKI*(+)
MPLIVTSTCLAPAQAPAIVLAVESPRSFWQCVEIITFSIPGVLAFISAINCPNSLGIVMPTVSG
MFRVVAPALITSPKISYRNSRSDLLLFSYFFEAPEYVPKLNIVKLITKNPQYTETIRTN*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3717679-3717590(+) 3717937-3723312(-)
Potential amino acid sequence	MPSEFGQLIADIKANTPGIENVIISTHCQNDLGLSTANTIAGACAGARQVEVTINGIGERAGNA SMEEVVMALKCRGEHVLGGLHTGINTRHIVMASKMVEEYTGLHVQPHKAIVGANAFAHESGIHQ DGMLKHKGTYEIISPEDIGLERSNEAGIVLGKLRFLTFTNSMVLCYLELDMNVGVGPMGYGSVS PNCFSILRVLGYELDDVQLGNIFWRFKEVAEQKKI(+) MPLIVTSTCLAPAQAPAIVLAVESPRSFWQCVEIITFSIPGVLAFISAINCPNSLGIVMPTVSG MFRVVAPALITSPKISYRNSRSDLLLFSYFFEAPEYVPKLNIVKLITKNPQYTETIRTN(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of Cotton_A_37876_circ_g.2

Address

Any questions?

Supported by