Plant Circular RNA Database

Detail information of Csa6G139140_circ_g.2

			
						 General Information
					
						CircRNA Name
						Csa6G139140_circ_g.2
					
						ID in PlantcircBase
						csa_circ_003765
					
						Alias
						Chr6:9768353_9778012
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr6: 9768353-9778012  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Find_circ
					
						Parent gene
						
							Csa6G139140						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							Csa6G139140_circ_g.1 Csa6G139140_circ_g.3 Chr6_circ_ig.56 Csa6G139140_circ_g.4 Csa6G139140_circ_g.5 Csa6G139140_circ_g.6 Csa6G139140_circ_g.7 Csa6G139140_circ_g.8 Csa6G139140_circ_g.9 Csa6G139140_circ_g.10 Csa6G139140_circ_g.11 						
					
						Support reads
						NA
					
						Tissues
						leaf
					
						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
						Csa6G139140.1:7

General Information
CircRNA Name	Csa6G139140_circ_g.2
ID in PlantcircBase	csa_circ_003765
Alias	Chr6:9768353_9778012
Organism	Cucumis sativus
Position	chrChr6: 9768353-9778012 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	Find_circ
Parent gene	Csa6G139140
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	Csa6G139140_circ_g.1 Csa6G139140_circ_g.3 Chr6_circ_ig.56 Csa6G139140_circ_g.4 Csa6G139140_circ_g.5 Csa6G139140_circ_g.6 Csa6G139140_circ_g.7 Csa6G139140_circ_g.8 Csa6G139140_circ_g.9 Csa6G139140_circ_g.10 Csa6G139140_circ_g.11
Support reads	NA
Tissues	leaf
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	Csa6G139140.1:7

			
						 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  
						
							AGGAGCTCTTTGAAGATGGTACAATCCCATTCCTGAGCATAGCCTCTCTATGCCATGGGTTCAA
AGTTTTAAATTCTCTAACTATACCTGCAATATCTCGgtccttgactatctcaaagcatctccga
aagactacaaatgcatatttacttctggtgcaacagcagcactaaaattagttggtgaagcttt
cccatgga

						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: 785
Transcript exons: 9768353-9768513,9768907-9769058,9770501-9770627,9776305-
9776407,9776499-9776544,9777084-9777122,9777856-9778012
GTCCTTGACTATCTCAAAGCATCTCCGAAAGACTACAAATGCATATTTACTTCTGGTGCAACAG
CAGCACTAAAATTAGTTGGTGAAGCTTTCCCATGGAGTCACCAGAGCAGCTTTGTGTACACAAT
GGAGAATCACAACAGTGTTCTTGGAATCAGGGAATATGCTCTTGAACAAGGCGCTCAAGCCTAT
GCTGTAGATATTGAAGAAGCAGAACATGATGCATTCACAGGAAATGTTGCATCAGTGCAAGCAA
CAAAGCACCAAATACTAACGAGAAATGAAGCCAAGTTTCTTGATAAAGATCATACAGGCAGTGC
GTATAACTTGTTTGCCTTCCCTTCAGAGTGCAATTTCTCTGGTTCGAAATTTTGCCTTGAATTG
GTGAAGATTGTTAAAGAAGATTTGATTAGATACTCTGATGGCTCACCATCTCTTAAGGGACGCT
GGAAGGTTTTGATCGATGCTGCAAAAGGATGTGCCACAGAACCCCCAGATTTATCCAAGTATCC
TGCTGATTTTGTTGTTATCTCTTTCTATAAGCTGTTTGGGTATCCAACTGGACTTGGAGCTCTC
ATAGTGCATACTGATGCTGCCAAGCTATTGAAGAGAACATACTTCAGTGGAGGCACTGTTGCTG
CTTCAATTGCTGATATTAACTATGTTAAACGAAGAGAGGGCATCGAGGAGCTCTTTGAAGATGG
TACAATCCCATTCCTGAGCATAGCCTCTCTATGCCATGGGTTCAAAGTTTTAAATTCTCTAACT
ATACCTGCAATATCTCG
						
						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	AGGAGCTCTTTGAAGATGGTACAATCCCATTCCTGAGCATAGCCTCTCTATGCCATGGGTTCAA AGTTTTAAATTCTCTAACTATACCTGCAATATCTCGgtccttgactatctcaaagcatctccga aagactacaaatgcatatttacttctggtgcaacagcagcactaaaattagttggtgaagcttt cccatgga
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: 785 Transcript exons: 9768353-9768513,9768907-9769058,9770501-9770627,9776305- 9776407,9776499-9776544,9777084-9777122,9777856-9778012 GTCCTTGACTATCTCAAAGCATCTCCGAAAGACTACAAATGCATATTTACTTCTGGTGCAACAG CAGCACTAAAATTAGTTGGTGAAGCTTTCCCATGGAGTCACCAGAGCAGCTTTGTGTACACAAT GGAGAATCACAACAGTGTTCTTGGAATCAGGGAATATGCTCTTGAACAAGGCGCTCAAGCCTAT GCTGTAGATATTGAAGAAGCAGAACATGATGCATTCACAGGAAATGTTGCATCAGTGCAAGCAA CAAAGCACCAAATACTAACGAGAAATGAAGCCAAGTTTCTTGATAAAGATCATACAGGCAGTGC GTATAACTTGTTTGCCTTCCCTTCAGAGTGCAATTTCTCTGGTTCGAAATTTTGCCTTGAATTG GTGAAGATTGTTAAAGAAGATTTGATTAGATACTCTGATGGCTCACCATCTCTTAAGGGACGCT GGAAGGTTTTGATCGATGCTGCAAAAGGATGTGCCACAGAACCCCCAGATTTATCCAAGTATCC TGCTGATTTTGTTGTTATCTCTTTCTATAAGCTGTTTGGGTATCCAACTGGACTTGGAGCTCTC ATAGTGCATACTGATGCTGCCAAGCTATTGAAGAGAACATACTTCAGTGGAGGCACTGTTGCTG CTTCAATTGCTGATATTAACTATGTTAAACGAAGAGAGGGCATCGAGGAGCTCTTTGAAGATGG TACAATCCCATTCCTGAGCATAGCCTCTCTATGCCATGGGTTCAAAGTTTTAAATTCTCTAACT ATACCTGCAATATCTCG
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
						0.465481674

Conservation Information
Conserved circRNAs	NA
PMCS	0.465481674

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9768480-9768422(+)
9777963-9768422(+)
						
						Potential amino acid sequence
						
							MENHNSVLGIREYALEQGAQAYAVDIEEAEHDAFTGNVASVQATKHQILTRNEAKFLDKDHTGS
AYNLFAFPSECNFSGSKFCLELVKIVKEDLIRYSDGSPSLKGRWKVLIDAAKGCATEPPDLSKY
PADFVVISFYKLFGYPTGLGALIVHTDAAKLLKRTYFSGGTVAASIADINYVKRREGIEELFED
GTIPFLSIASLCHGFKVLNSLTIPAISRSLTISKHLRKTTNAYLLLVQQQH*
MPWVQSFKFSNYTCNISVLDYLKASPKDYKCIFTSGATAALKLVGEAFPWSHQSSFVYTMENHN
SVLGIREYALEQGAQAYAVDIEEAEHDAFTGNVASVQATKHQILTRNEAKFLDKDHTGSAYNLF
AFPSECNFSGSKFCLELVKIVKEDLIRYSDGSPSLKGRWKVLIDAAKGCATEPPDLSKYPADFV
VISFYKLFGYPTGLGALIVHTDAAKLLKRTYFSGGTVAASIADINYVKRREGIEELFEDGTIPF
LSIASLCHGFKVLNSLTIPAISRSLTISKHLRKTTNAYLLLVQQQH*
						
						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	9768480-9768422(+) 9777963-9768422(+)
Potential amino acid sequence	MENHNSVLGIREYALEQGAQAYAVDIEEAEHDAFTGNVASVQATKHQILTRNEAKFLDKDHTGS AYNLFAFPSECNFSGSKFCLELVKIVKEDLIRYSDGSPSLKGRWKVLIDAAKGCATEPPDLSKY PADFVVISFYKLFGYPTGLGALIVHTDAAKLLKRTYFSGGTVAASIADINYVKRREGIEELFED GTIPFLSIASLCHGFKVLNSLTIPAISRSLTISKHLRKTTNAYLLLVQQQH* MPWVQSFKFSNYTCNISVLDYLKASPKDYKCIFTSGATAALKLVGEAFPWSHQSSFVYTMENHN SVLGIREYALEQGAQAYAVDIEEAEHDAFTGNVASVQATKHQILTRNEAKFLDKDHTGSAYNLF AFPSECNFSGSKFCLELVKIVKEDLIRYSDGSPSLKGRWKVLIDAAKGCATEPPDLSKYPADFV VISFYKLFGYPTGLGALIVHTDAAKLLKRTYFSGGTVAASIADINYVKRREGIEELFEDGTIPF LSIASLCHGFKVLNSLTIPAISRSLTISKHLRKTTNAYLLLVQQQH*
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to salt stress in root

			
						 Other Information
					
						References
						He et al., 2020

circRNA

Detail information of Csa6G139140_circ_g.2

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