Plant Circular RNA Database

Detail information of orai.004G034200_circ_g.1

			
						 General Information
					
						CircRNA Name
						orai.004G034200_circ_g.1
					
						ID in PlantcircBase
						gra_circ_000320
					
						Alias
						Chr04:2803529|2804379
					
						Organism
						
							Gossypium raimondii						
					
						Position
						
							chrChr04: 2803529-2804379  JBrowse»						
					
						Reference genome
						
							Graimondii_221						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gorai.004G034200						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						2
					
						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
						Gorai.004G034200.3:3
Gorai.004G034200.1:3
Gorai.004G034200.2:3

General Information
CircRNA Name	orai.004G034200_circ_g.1
ID in PlantcircBase	gra_circ_000320
Alias	Chr04:2803529\|2804379
Organism	Gossypium raimondii
Position	chrChr04: 2803529-2804379 JBrowse»
Reference genome	Graimondii_221
Type	e-circRNA
Identification method	CIRI
Parent gene	Gorai.004G034200
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	NA
Support reads	2
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	Gorai.004G034200.3:3 Gorai.004G034200.1:3 Gorai.004G034200.2:3

			
						 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  
						
							GCAAGTAGATTCTGCGTTTCAGAAAGGGATGGTTGAGCATACCAATGCTGCTCAGCAACAGTTA
GAGTCTGCAAGTTCTTCTTTGGCAATTACTTTAAGGctaattactacacaaaaggaaatgcaga
aacaaatgtcaagtattgtcaaccaaccagttacaaaagaaggaagaagactagaggctgctct
aggacgga

									
								

					

						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: 651
Transcript exons: 2803529-2803888,2803959-2804078,2804209-2804379
CTAATTACTACACAAAAGGAAATGCAGAAACAAATGTCAAGTATTGTCAACCAACCAGTTACAA
AAGAAGGAAGAAGACTAGAGGCTGCTCTAGGACGGAGTATTGAAAAAGCTCTTAAGGCCAATAC
TGATGCTCTATGGGCTCGTTTTCAGGAAGAAAATGCAAAAAATGAGAAGCTGCTTCGAGAACAT
ACACACCAGATAACTAGCTTGATCACTAATTTTATGAACAAGGATTTGGCAGTAATGTTGGACA
AAGTAGTCAAGAAGGAATTAGCTGGAGTTGGACCAGCTGTTATTCGTACCATTACTCCAGCAAT
AGAGAAAACCGTAACTTCAGTAATCAATGAGTCCTTCCAGAGAGGGGTCGGAGATAAAGCAGTG
AATCAACTAGAGAAGTCTGTTAATTCGAAACTCGAAGCTATAGTTGCCAGGCAAATTCAAGCCC
AGTTTCAAACTTCTGGCAAGCAAGCACTCCAGGAGGCTTTGAGGACTAGTGTGGAAGCTCTAGT
GGTCCCTGCTTTTGAGATTTCATGCAAAGCCCTGTTTGAGCAAGTAGATTCTGCGTTTCAGAAA
GGGATGGTTGAGCATACCAATGCTGCTCAGCAACAGTTAGAGTCTGCAAGTTCTTCTTTGGCAA
TTACTTTAAGG
						
					

						Genomic sequence
						
							CTAATTACTACACAAAAGGAAATGCAGAAACAAATGTCAAGTATTGTCAACCAACCAGTTACAA
AAGAAGGAAGAAGACTAGAGGCTGCTCTAGGACGGAGTATTGAAAAAGCTCTTAAGGCCAATAC
TGATGCTCTATGGGCTCGTTTTCAGGAAGAAAATGCAAAAAATGAGAAGCTGCTTCGAGAACAT
ACACACCAGATAACTAGCTTGATCACTAATTTTATGAACAAGGATTTGGCAGTAATGTTGGACA
AAGTAGTCAAGAAGGAATTAGCTGGAGTTGGACCAGCTGTTATTCGTACCATTACTCCAGCAAT
AGAGAAAACCGTAACTTCAGTAATCAATGAGTCCTTCCAGGTTAGACTTTTAAAATCTAGTTCT
TTTGCTGGAAAGCTTAATGGAATCTAACTAGTCCTTTGTATGACAGAGAGGGGTCGGAGATAAA
GCAGTGAATCAACTAGAGAAGTCTGTTAATTCGAAACTCGAAGCTATAGTTGCCAGGCAAATTC
AAGCCCAGTTTCAAACTTCTGGCAAGCAAGCACTCCAGGTATGCACAAGTTCACTGTATTTGGT
AATAGCTATAGGCGGATATTTTCTTTCTCTTGTTATGAGATCAAATTAGTGTCATTCGGTATGT
TCCAGGCAATTTCTGGTTATTAATTTATCATTTCTTTTAGGAGGCTTTGAGGACTAGTGTGGAA
GCTCTAGTGGTCCCTGCTTTTGAGATTTCATGCAAAGCCCTGTTTGAGCAAGTAGATTCTGCGT
TTCAGAAAGGGATGGTTGAGCATACCAATGCTGCTCAGCAACAGTTAGAGTCTGCAAGTTCTTC
TTTGGCAATTACTTTAAGG
						
					

			
		

Sequences
Splice junction sequence	GCAAGTAGATTCTGCGTTTCAGAAAGGGATGGTTGAGCATACCAATGCTGCTCAGCAACAGTTA GAGTCTGCAAGTTCTTCTTTGGCAATTACTTTAAGGctaattactacacaaaaggaaatgcaga aacaaatgtcaagtattgtcaaccaaccagttacaaaagaaggaagaagactagaggctgctct aggacgga
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: 651 Transcript exons: 2803529-2803888,2803959-2804078,2804209-2804379 CTAATTACTACACAAAAGGAAATGCAGAAACAAATGTCAAGTATTGTCAACCAACCAGTTACAA AAGAAGGAAGAAGACTAGAGGCTGCTCTAGGACGGAGTATTGAAAAAGCTCTTAAGGCCAATAC TGATGCTCTATGGGCTCGTTTTCAGGAAGAAAATGCAAAAAATGAGAAGCTGCTTCGAGAACAT ACACACCAGATAACTAGCTTGATCACTAATTTTATGAACAAGGATTTGGCAGTAATGTTGGACA AAGTAGTCAAGAAGGAATTAGCTGGAGTTGGACCAGCTGTTATTCGTACCATTACTCCAGCAAT AGAGAAAACCGTAACTTCAGTAATCAATGAGTCCTTCCAGAGAGGGGTCGGAGATAAAGCAGTG AATCAACTAGAGAAGTCTGTTAATTCGAAACTCGAAGCTATAGTTGCCAGGCAAATTCAAGCCC AGTTTCAAACTTCTGGCAAGCAAGCACTCCAGGAGGCTTTGAGGACTAGTGTGGAAGCTCTAGT GGTCCCTGCTTTTGAGATTTCATGCAAAGCCCTGTTTGAGCAAGTAGATTCTGCGTTTCAGAAA GGGATGGTTGAGCATACCAATGCTGCTCAGCAACAGTTAGAGTCTGCAAGTTCTTCTTTGGCAA TTACTTTAAGG
Genomic sequence	CTAATTACTACACAAAAGGAAATGCAGAAACAAATGTCAAGTATTGTCAACCAACCAGTTACAA AAGAAGGAAGAAGACTAGAGGCTGCTCTAGGACGGAGTATTGAAAAAGCTCTTAAGGCCAATAC TGATGCTCTATGGGCTCGTTTTCAGGAAGAAAATGCAAAAAATGAGAAGCTGCTTCGAGAACAT ACACACCAGATAACTAGCTTGATCACTAATTTTATGAACAAGGATTTGGCAGTAATGTTGGACA AAGTAGTCAAGAAGGAATTAGCTGGAGTTGGACCAGCTGTTATTCGTACCATTACTCCAGCAAT AGAGAAAACCGTAACTTCAGTAATCAATGAGTCCTTCCAGGTTAGACTTTTAAAATCTAGTTCT TTTGCTGGAAAGCTTAATGGAATCTAACTAGTCCTTTGTATGACAGAGAGGGGTCGGAGATAAA GCAGTGAATCAACTAGAGAAGTCTGTTAATTCGAAACTCGAAGCTATAGTTGCCAGGCAAATTC AAGCCCAGTTTCAAACTTCTGGCAAGCAAGCACTCCAGGTATGCACAAGTTCACTGTATTTGGT AATAGCTATAGGCGGATATTTTCTTTCTCTTGTTATGAGATCAAATTAGTGTCATTCGGTATGT TCCAGGCAATTTCTGGTTATTAATTTATCATTTCTTTTAGGAGGCTTTGAGGACTAGTGTGGAA GCTCTAGTGGTCCCTGCTTTTGAGATTTCATGCAAAGCCCTGTTTGAGCAAGTAGATTCTGCGT TTCAGAAAGGGATGGTTGAGCATACCAATGCTGCTCAGCAACAGTTAGAGTCTGCAAGTTCTTC TTTGGCAATTACTTTAAGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.798523208

Conservation Information
Conserved circRNAs	NA
PMCS	0.798523208

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2803550-2804376(+)
						
						Potential amino acid sequence
						
							MQKQMSSIVNQPVTKEGRRLEAALGRSIEKALKANTDALWARFQEENAKNEKLLREHTHQITSL
ITNFMNKDLAVMLDKVVKKELAGVGPAVIRTITPAIEKTVTSVINESFQRGVGDKAVNQLEKSV
NSKLEAIVARQIQAQFQTSGKQALQEALRTSVEALVVPAFEISCKALFEQVDSAFQKGMVEHTN
AAQQQLESASSSLAITLRLITTQKEMQKQMSSIVNQPVTKEGRRLEAALGRSIEKALKANTDAL
WARFQEENAKNEKLLREHTHQITSLITNFMNKDLAVMLDKVVKKELAGVGPAVIRTITPAIEKT
VTSVINESFQRGVGDKAVNQLEKSVNSKLEAIVARQIQAQFQTSGKQALQEALRTSVEALVVPA
FEISCKALFEQVDSAFQKGMVEHTNAAQQQLESASSSLAITLRLITTQKEMQKQMSSIVNQPVT
KEGRRLEAALGRSIEKALKANTDALWARFQEENAKNEKLLREHTHQITSLITNFMNKDLAVMLD
KVVKKELAGVGPAVIRTITPAIEKTVTSVINESFQRGVGDKAVNQLEKSVNSKLEAIVARQIQA
QFQTSGKQALQEALRTSVEALVVPAFEISCKALFEQVDSAFQKGMVEHTNAAQQQLESASSSLA
ITLRLITTQKEMQKQMSSIVNQPVTKEGRRLEAALGRSIEKALKANTDALWARFQEENAKNEKL
LREHTHQITSLITNFMNKDLAVMLDKVVKKELAGVGPAVIRTITPAIEKTVTSVINESFQRGVG
DKAVNQLEKSVNSKLEAIVARQIQAQFQTSGKQALQEALRTSVEALVVPAFEISCKALFEQVDS
AFQKGMVEHTNAAQQQLESASSSLAITLR(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	2803550-2804376(+)
Potential amino acid sequence	MQKQMSSIVNQPVTKEGRRLEAALGRSIEKALKANTDALWARFQEENAKNEKLLREHTHQITSL ITNFMNKDLAVMLDKVVKKELAGVGPAVIRTITPAIEKTVTSVINESFQRGVGDKAVNQLEKSV NSKLEAIVARQIQAQFQTSGKQALQEALRTSVEALVVPAFEISCKALFEQVDSAFQKGMVEHTN AAQQQLESASSSLAITLRLITTQKEMQKQMSSIVNQPVTKEGRRLEAALGRSIEKALKANTDAL WARFQEENAKNEKLLREHTHQITSLITNFMNKDLAVMLDKVVKKELAGVGPAVIRTITPAIEKT VTSVINESFQRGVGDKAVNQLEKSVNSKLEAIVARQIQAQFQTSGKQALQEALRTSVEALVVPA FEISCKALFEQVDSAFQKGMVEHTNAAQQQLESASSSLAITLRLITTQKEMQKQMSSIVNQPVT KEGRRLEAALGRSIEKALKANTDALWARFQEENAKNEKLLREHTHQITSLITNFMNKDLAVMLD KVVKKELAGVGPAVIRTITPAIEKTVTSVINESFQRGVGDKAVNQLEKSVNSKLEAIVARQIQA QFQTSGKQALQEALRTSVEALVVPAFEISCKALFEQVDSAFQKGMVEHTNAAQQQLESASSSLA ITLRLITTQKEMQKQMSSIVNQPVTKEGRRLEAALGRSIEKALKANTDALWARFQEENAKNEKL LREHTHQITSLITNFMNKDLAVMLDKVVKKELAGVGPAVIRTITPAIEKTVTSVINESFQRGVG DKAVNQLEKSVNSKLEAIVARQIQAQFQTSGKQALQEALRTSVEALVVPAFEISCKALFEQVDS AFQKGMVEHTNAAQQQLESASSSLAITLR(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of orai.004G034200_circ_g.1

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