Plant Circular RNA Database

Detail information of Csa1G560800_circ_g.1

			
						 General Information
					
						CircRNA Name
						Csa1G560800_circ_g.1
					
						ID in PlantcircBase
						csa_circ_000461
					
						Alias
						Chr1:20454568_20464986
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr1: 20454568-20464986  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Csa1G560800						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							Csa1G560800_circ_g.2 Csa1G560800_circ_g.3 Csa1G560800_circ_g.4 Csa1G560800_circ_g.5 						
					
						Support reads
						NA
					
						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
						Csa1G560800.2:8
Csa1G560800.1:8

General Information
CircRNA Name	Csa1G560800_circ_g.1
ID in PlantcircBase	csa_circ_000461
Alias	Chr1:20454568_20464986
Organism	Cucumis sativus
Position	chrChr1: 20454568-20464986 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	ue-circRNA
Identification method	CIRI2
Parent gene	Csa1G560800
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	Csa1G560800_circ_g.2 Csa1G560800_circ_g.3 Csa1G560800_circ_g.4 Csa1G560800_circ_g.5
Support reads	NA
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	Csa1G560800.2:8 Csa1G560800.1:8

			
						 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  
						
							CTTTATATATTTTTTTTATTATTATCCTCCTCATTCTTGATATTTTAAACAGATGCAACGGAGG
GAAAACAATGTGCAATCTTTTGAAAAGCTTCGCCAGcggcctagatatatagtgcttcatcgtg
ttgatcactacgaggatttcaattgttaaccgtcagccgtagagggttggtgcatcacaaagga
ttgaaaag

						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	CTTTATATATTTTTTTTATTATTATCCTCCTCATTCTTGATATTTTAAACAGATGCAACGGAGG GAAAACAATGTGCAATCTTTTGAAAAGCTTCGCCAGcggcctagatatatagtgcttcatcgtg ttgatcactacgaggatttcaattgttaaccgtcagccgtagagggttggtgcatcacaaagga ttgaaaag
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
						
							NA						
					
						PMCS
						0.087665013

Conservation Information
Conserved circRNAs	NA
PMCS	0.087665013

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							20454686-20454621(+)
20458773-20454580(+)
						
						Potential amino acid sequence
						
							MSRLSFRPRPLDIHKKLPIVKSVKELEDEETPTSTRNSQLLRVAAEVDNEVHQVPCKKLAPDIP
TPQFVVVDTYEIDYSRTFSQPTSYLRGRGARTELGEFVEYDLDNEDEDWLHDLNKERKILAPER
FESFLFKLEVLDHKARERAGIITTTLGSPVPVLLQHDNAIEALQTQAIKYSVIESVYTYWKEKR
ERWQKPILRRLQPPPPVNDTNPYNVFRPREKAHRLHTRRMQRRENNVQSFEKLRQRPRYIVLHR
VDHYEDFNC*
MIMLLRLYKHKQSNIQLLNLFTLIGRKSVNGGKSLYCGVCSRLHLSMTQIHIMSLGQGRKPIDF
TQEGCNGGKTMCNLLKSFASGLDI*
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to salt stress in root

Functional Information
Coding potential	Y
Potential coding position	20454686-20454621(+) 20458773-20454580(+)
Potential amino acid sequence	MSRLSFRPRPLDIHKKLPIVKSVKELEDEETPTSTRNSQLLRVAAEVDNEVHQVPCKKLAPDIP TPQFVVVDTYEIDYSRTFSQPTSYLRGRGARTELGEFVEYDLDNEDEDWLHDLNKERKILAPER FESFLFKLEVLDHKARERAGIITTTLGSPVPVLLQHDNAIEALQTQAIKYSVIESVYTYWKEKR ERWQKPILRRLQPPPPVNDTNPYNVFRPREKAHRLHTRRMQRRENNVQSFEKLRQRPRYIVLHR VDHYEDFNC* MIMLLRLYKHKQSNIQLLNLFTLIGRKSVNGGKSLYCGVCSRLHLSMTQIHIMSLGQGRKPIDF TQEGCNGGKTMCNLLKSFASGLDI*
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to salt stress in root

			
						 Other Information
					
						References
						Zhu et al., 2019

circRNA

Detail information of Csa1G560800_circ_g.1

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