Plant Circular RNA Database

Detail information of Csa3G253520_circ_g.3

			
						 General Information
					
						CircRNA Name
						Csa3G253520_circ_g.3
					
						ID in PlantcircBase
						csa_circ_001725
					
						Alias
						Chr3:15789793_15803075
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr3: 15789793-15803075  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Csa3G253520						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							Csa3G253520_circ_g.1 Csa3G253520_circ_g.2 Csa3G253520_circ_g.4 Csa3G253520_circ_g.5 Chr3_circ_ig.54 						
					
						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  
						
							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
						Csa3G253520.1:9

General Information
CircRNA Name	Csa3G253520_circ_g.3
ID in PlantcircBase	csa_circ_001725
Alias	Chr3:15789793_15803075
Organism	Cucumis sativus
Position	chrChr3: 15789793-15803075 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	CIRI2
Parent gene	Csa3G253520
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	Csa3G253520_circ_g.1 Csa3G253520_circ_g.2 Csa3G253520_circ_g.4 Csa3G253520_circ_g.5 Chr3_circ_ig.54
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	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	Csa3G253520.1:9

			
						 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  
						
							TGCTGGTATGTTCCCTCACCACATTAAGGGCAAATAATTTGCTCTCCACTTCCTTCCAAGGAAT
TGGTACATTACCATTGGTCCAACCACTGAAGAAGAGaagataggtatgacattgctgctaacgc
tgccccacgatgcatggcagtgcaacatatagcagccttctggaatgaaacctccaaaagagaa
ccagctgc

						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: 1135
Transcript exons: 15789793-15789904,15790025-15790212,15791045-15791232,15
795182-15795267,15797682-15797831,15798112-15798247,1580
1629-15801708,15801851-15801964,15802995-15803075
AAGATAGGTATGACATTGCTGCTAACGCTGCCCCACGATGCATGGCAGTGCAACATATAGCAGC
CTTCTGGAATGAAACCTCCAAAAGAGAACCAGCTGCAGCTAATATTTCCTTATGAGAGCATCGG
AGAAAAATTGATGCAAAATTTGTGTAAGCCTCCACTAGATCAGGTTCTTGGTCACATATGTAGG
AAGAATTAATAGCACTTACGGAAGCTGCATAAGTAAACCTTTCAAAAGTGGTGATAAACAAATG
TCCAAATTTTTCTTGATGGCCATATTCTTCAACAATAACTGAAGCTGAAGACTGAATGGCTAAA
GATAGAGCACGACAAGCAGCTGCAGAGAGATTACCATTCTCCATGTGTTCACACCTTAAAAGTT
TCTCTAGCATTGGCCAGAAAACTATCAGCAAAGAAAACATAGGATCATCGAGAGTAGGCTCAGT
TGATAAAGATGTGGCTAGATGGCTAAATACAGTTCCCATCCTATACAGGCCTCTCACAGCAGAG
GTTAAGATTTTTGTGTAAGTAGCCGGATTTTGTCTCAAAGATAGTGCATTATCTTCATCAACTA
GTTTCTCAATTGCTTCATAGCTTGACGAAAGCAATCTAGCCAACAAGTTGCTCTTCAGTTCTTT
ATTAGGAACTGAACCAAGAATCAAACTTACAGCACTCACTACTTCTTCCTCGTCCTCCAAAGGT
AAATGTAACTTCTCCAGACTCTCTCCAATCCAAATCAAAATTTCCAAATTTGGCAGTTCAAAGA
TTACAGCAGTTGCATCTTCACAAATTTTACGGAGGGCAAAGGCACAAGCATGTGAACAGACAGA
TTCTGTGATCCCAGTAGCAAGAAATAATAGCAAGGGTCTGGCATCTGTGTGAAAAGCAGAAATT
GACCTAAAGTAAGATCCAACAACTTCTGCCAGTGATCTATAAACAAGGCACATTAGGCCTTTGA
TCTCATTTGAAGGTCTAGCCGCCAACATGGTCACCAGTTGTGTTATTACAGAGAAATCAAAGCT
TTGACCCTCCTGTAGGACTACCTCAGCGACCACATTAAGGGCAAATAATTTGCTCTCCACTTCC
TTCCAAGGAATTGGTACATTACCATTGGTCCAACCACTGAAGAAGAG
						
						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	TGCTGGTATGTTCCCTCACCACATTAAGGGCAAATAATTTGCTCTCCACTTCCTTCCAAGGAAT TGGTACATTACCATTGGTCCAACCACTGAAGAAGAGaagataggtatgacattgctgctaacgc tgccccacgatgcatggcagtgcaacatatagcagccttctggaatgaaacctccaaaagagaa ccagctgc
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: 1135 Transcript exons: 15789793-15789904,15790025-15790212,15791045-15791232,15 795182-15795267,15797682-15797831,15798112-15798247,1580 1629-15801708,15801851-15801964,15802995-15803075 AAGATAGGTATGACATTGCTGCTAACGCTGCCCCACGATGCATGGCAGTGCAACATATAGCAGC CTTCTGGAATGAAACCTCCAAAAGAGAACCAGCTGCAGCTAATATTTCCTTATGAGAGCATCGG AGAAAAATTGATGCAAAATTTGTGTAAGCCTCCACTAGATCAGGTTCTTGGTCACATATGTAGG AAGAATTAATAGCACTTACGGAAGCTGCATAAGTAAACCTTTCAAAAGTGGTGATAAACAAATG TCCAAATTTTTCTTGATGGCCATATTCTTCAACAATAACTGAAGCTGAAGACTGAATGGCTAAA GATAGAGCACGACAAGCAGCTGCAGAGAGATTACCATTCTCCATGTGTTCACACCTTAAAAGTT TCTCTAGCATTGGCCAGAAAACTATCAGCAAAGAAAACATAGGATCATCGAGAGTAGGCTCAGT TGATAAAGATGTGGCTAGATGGCTAAATACAGTTCCCATCCTATACAGGCCTCTCACAGCAGAG GTTAAGATTTTTGTGTAAGTAGCCGGATTTTGTCTCAAAGATAGTGCATTATCTTCATCAACTA GTTTCTCAATTGCTTCATAGCTTGACGAAAGCAATCTAGCCAACAAGTTGCTCTTCAGTTCTTT ATTAGGAACTGAACCAAGAATCAAACTTACAGCACTCACTACTTCTTCCTCGTCCTCCAAAGGT AAATGTAACTTCTCCAGACTCTCTCCAATCCAAATCAAAATTTCCAAATTTGGCAGTTCAAAGA TTACAGCAGTTGCATCTTCACAAATTTTACGGAGGGCAAAGGCACAAGCATGTGAACAGACAGA TTCTGTGATCCCAGTAGCAAGAAATAATAGCAAGGGTCTGGCATCTGTGTGAAAAGCAGAAATT GACCTAAAGTAAGATCCAACAACTTCTGCCAGTGATCTATAAACAAGGCACATTAGGCCTTTGA TCTCATTTGAAGGTCTAGCCGCCAACATGGTCACCAGTTGTGTTATTACAGAGAAATCAAAGCT TTGACCCTCCTGTAGGACTACCTCAGCGACCACATTAAGGGCAAATAATTTGCTCTCCACTTCC TTCCAAGGAATTGGTACATTACCATTGGTCCAACCACTGAAGAAGAG
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
						0.46192102

Conservation Information
Conserved circRNAs	NA
PMCS	0.46192102

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							15801900-15803049(-)
15789850-15801954(-)
						
						Potential amino acid sequence
						
							MLAARPSNEIKGLMCLVYRSLAEVVGSYFRSISAFHTDARPLLLFLATGITESVCSHACAFALR
KICEDATAVIFELPNLEILIWIGESLEKLHLPLEDEEEVVSAVSLILGSVPNKELKSNLLARLL
SSSYEAIEKLVDEDNALSLRQNPATYTKILTSAVRGLYRMGTVFSHLATSLSTEPTLDDPMFSL
LIVFWPMLEKLLRCEHMENGNLSAAACRALSLAIQSSASVIVEEYGHQEKFGHLFITTFERFTY
AASVSAINSSYICDQEPDLVEAYTNFASIFLRCSHKEILAAAGSLLEVSFQKAAICCTAMHRGA
ALAAMSYLSSLLQWLDQW*
MLHCHASWGSVSSNVIPIFSSSVVGPMVMYQFLGRKWRANYLPLMWSLR*
						
						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	15801900-15803049(-) 15789850-15801954(-)
Potential amino acid sequence	MLAARPSNEIKGLMCLVYRSLAEVVGSYFRSISAFHTDARPLLLFLATGITESVCSHACAFALR KICEDATAVIFELPNLEILIWIGESLEKLHLPLEDEEEVVSAVSLILGSVPNKELKSNLLARLL SSSYEAIEKLVDEDNALSLRQNPATYTKILTSAVRGLYRMGTVFSHLATSLSTEPTLDDPMFSL LIVFWPMLEKLLRCEHMENGNLSAAACRALSLAIQSSASVIVEEYGHQEKFGHLFITTFERFTY AASVSAINSSYICDQEPDLVEAYTNFASIFLRCSHKEILAAAGSLLEVSFQKAAICCTAMHRGA ALAAMSYLSSLLQWLDQW* MLHCHASWGSVSSNVIPIFSSSVVGPMVMYQFLGRKWRANYLPLMWSLR*
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 Csa3G253520_circ_g.3

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