Plant Circular RNA Database

Detail information of Csa1G574770_circ_g.3

			
						 General Information
					
						CircRNA Name
						Csa1G574770_circ_g.3
					
						ID in PlantcircBase
						csa_circ_000504
					
						Alias
						Chr1:21549571_21554885
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr1: 21549571-21554885  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Csa1G574770						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							Chr5_circ_ig.118 Chr5_circ_ig.119 						
					
						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
						Csa1G574770.1:8

General Information
CircRNA Name	Csa1G574770_circ_g.3
ID in PlantcircBase	csa_circ_000504
Alias	Chr1:21549571_21554885
Organism	Cucumis sativus
Position	chrChr1: 21549571-21554885 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	CIRI2
Parent gene	Csa1G574770
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	Chr5_circ_ig.118 Chr5_circ_ig.119
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	Csa1G574770.1:8

			
						 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  
						
							GTAATTAGATAAACATTATGATAATAAGTGTTAATTTTAGGTCTTGGATACTCTTGCGGCTCTA
GATCGAGCAATTCATTCGCCACATGCCATGACTCAGgtccatgagacgagtgaagaaagcttgg
cagctgtcgcagggatgtttagtagcaaggccaaaggtagctatgttctttatttaacttgtgt
tattaaat

						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	GTAATTAGATAAACATTATGATAATAAGTGTTAATTTTAGGTCTTGGATACTCTTGCGGCTCTA GATCGAGCAATTCATTCGCCACATGCCATGACTCAGgtccatgagacgagtgaagaaagcttgg cagctgtcgcagggatgtttagtagcaaggccaaaggtagctatgttctttatttaacttgtgt tattaaat
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
						0.0905265

Conservation Information
Conserved circRNAs	NA
PMCS	0.0905265

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							21549614-21554882(+)
						
						Potential amino acid sequence
						
							MFSSKAKGVEWSLDGDASNATVLVASEAHAITLAVEGLLGVVFTVATLTDEAVDLGELESPRFD
YEPPGKCNGRIASVCISMVDSLWLTILDALSLILTRSQGEAIILEILKGYQAFTQACGVLHAVE
PLNSFLASLCKFTINFPSEVEKKSILQSPNSKRLEPFTDQRDTVVLTPKNVQALRTLFNIAHRL
HNVLGPSWVLVLDTLAALDRAIHSPHAMTQVHETSEESLAAVAGMFSSKAKGVEWSLDGDASNA
TVLVASEAHAITLAVEGLLGVVFTVATLTDEAVDLGELESPRFDYEPPGKCNGRIASVCISMVD
SLWLTILDALSLILTRSQGEAIILEILKGYQAFTQACGVLHAVEPLNSFLASLCKFTINFPSEV
EKKSILQSPNSKRLEPFTDQRDTVVLTPKNVQALRTLFNIAHRLHNVLGPSWVLVLDTLAALDR
AIHSPHAMTQVHETSEESLAAVAGMFSSKAKGVEWSLDGDASNATVLVASEAHAITLAVEGLLG
VVFTVATLTDEAVDLGELESPRFDYEPPGKCNGRIASVCISMVDSLWLTILDALSLILTRSQGE
AIILEILKGYQAFTQACGVLHAVEPLNSFLASLCKFTINFPSEVEKKSILQSPNSKRLEPFTDQ
RDTVVLTPKNVQALRTLFNIAHRLHNVLGPSWVLVLDTLAALDRAIHSPHAMTQVHETSEESLA
AVAGMFSSKAKGVEWSLDGDASNATVLVASEAHAITLAVEGLLGVVFTVATLTDEAVDLGELES
PRFDYEPPGKCNGRIASVCISMVDSLWLTILDALSLILTRSQGEAIILEILKGYQAFTQACGVL
HAVEPLNSFLASLCKFTINFPSEVEKKSILQSPNSKRLEPFTDQRDTVVLTPKNVQALRTLFNI
AHRLHNVLGPSWVLVLDTLAALDRAIHSPHAMTQ
						
						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	21549614-21554882(+)
Potential amino acid sequence	MFSSKAKGVEWSLDGDASNATVLVASEAHAITLAVEGLLGVVFTVATLTDEAVDLGELESPRFD YEPPGKCNGRIASVCISMVDSLWLTILDALSLILTRSQGEAIILEILKGYQAFTQACGVLHAVE PLNSFLASLCKFTINFPSEVEKKSILQSPNSKRLEPFTDQRDTVVLTPKNVQALRTLFNIAHRL HNVLGPSWVLVLDTLAALDRAIHSPHAMTQVHETSEESLAAVAGMFSSKAKGVEWSLDGDASNA TVLVASEAHAITLAVEGLLGVVFTVATLTDEAVDLGELESPRFDYEPPGKCNGRIASVCISMVD SLWLTILDALSLILTRSQGEAIILEILKGYQAFTQACGVLHAVEPLNSFLASLCKFTINFPSEV EKKSILQSPNSKRLEPFTDQRDTVVLTPKNVQALRTLFNIAHRLHNVLGPSWVLVLDTLAALDR AIHSPHAMTQVHETSEESLAAVAGMFSSKAKGVEWSLDGDASNATVLVASEAHAITLAVEGLLG VVFTVATLTDEAVDLGELESPRFDYEPPGKCNGRIASVCISMVDSLWLTILDALSLILTRSQGE AIILEILKGYQAFTQACGVLHAVEPLNSFLASLCKFTINFPSEVEKKSILQSPNSKRLEPFTDQ RDTVVLTPKNVQALRTLFNIAHRLHNVLGPSWVLVLDTLAALDRAIHSPHAMTQVHETSEESLA AVAGMFSSKAKGVEWSLDGDASNATVLVASEAHAITLAVEGLLGVVFTVATLTDEAVDLGELES PRFDYEPPGKCNGRIASVCISMVDSLWLTILDALSLILTRSQGEAIILEILKGYQAFTQACGVL HAVEPLNSFLASLCKFTINFPSEVEKKSILQSPNSKRLEPFTDQRDTVVLTPKNVQALRTLFNI AHRLHNVLGPSWVLVLDTLAALDRAIHSPHAMTQ
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 Csa1G574770_circ_g.3

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