Plant Circular RNA Database

Detail information of Csa6G139140_circ_g.4

			
						 General Information
					
						CircRNA Name
						Csa6G139140_circ_g.4
					
						ID in PlantcircBase
						csa_circ_003768
					
						Alias
						Chr6:9768353_9770627
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr6: 9768353-9770627  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Csa6G139140						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							Csa6G139140_circ_g.1 Csa6G139140_circ_g.2 Csa6G139140_circ_g.3 Chr6_circ_ig.56 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,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
						Csa6G139140.1:3

General Information
CircRNA Name	Csa6G139140_circ_g.4
ID in PlantcircBase	csa_circ_003768
Alias	Chr6:9768353_9770627
Organism	Cucumis sativus
Position	chrChr6: 9768353-9770627 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	CIRI2
Parent gene	Csa6G139140
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	Csa6G139140_circ_g.1 Csa6G139140_circ_g.2 Csa6G139140_circ_g.3 Chr6_circ_ig.56 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,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	Csa6G139140.1:3

			
						 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  
						
							CTTCAGAGTGCAATTTCTCTGGTTCGAAATTTTGCCTTGAATTGGTGAAGATTGTTAAAGAAGA
TTTGATTAGATACTCTGATGGCTCACCATCTCTTAAgtccttgactatctcaaagcatctccga
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: 440
Transcript exons: 9768353-9768513,9768907-9769058,9770501-9770627
GTCCTTGACTATCTCAAAGCATCTCCGAAAGACTACAAATGCATATTTACTTCTGGTGCAACAG
CAGCACTAAAATTAGTTGGTGAAGCTTTCCCATGGAGTCACCAGAGCAGCTTTGTGTACACAAT
GGAGAATCACAACAGTGTTCTTGGAATCAGGGAATATGCTCTTGAACAAGGCGCTCAAGCCTAT
GCTGTAGATATTGAAGAAGCAGAACATGATGCATTCACAGGAAATGTTGCATCAGTGCAAGCAA
CAAAGCACCAAATACTAACGAGAAATGAAGCCAAGTTTCTTGATAAAGATCATACAGGCAGTGC
GTATAACTTGTTTGCCTTCCCTTCAGAGTGCAATTTCTCTGGTTCGAAATTTTGCCTTGAATTG
GTGAAGATTGTTAAAGAAGATTTGATTAGATACTCTGATGGCTCACCATCTCTTAA
						
					

						Genomic sequence
						
							GTCCTTGACTATCTCAAAGCATCTCCGAAAGACTACAAATGCATATTTACTTCTGGTGCAACAG
CAGCACTAAAATTAGTTGGTGAAGCTTTCCCATGGAGTCACCAGAGCAGCTTTGTGTACACAAT
GGAGAATCACAACAGTGTTCTTGGAATCAGGGAGTATCCTTCAAGTTCAGCGTGATTTCTGTTT
GTTATTACTTTCATGTGAACAGCTTTGGCTACCTTTATTTGTATGTTTTTGTTCTTTTCAGGGG
ATTTACTTGATGATGCCAAGCTTGAACATTATTGTGATACAGTGATTATTGGCCATTTTATTGA
TTGTTCAATGTACTCTTATGTAATTAGTTGCATTTTGACATTTTCTGTGCCTGTATTTAACTTA
TTTAGTAGATTCATAGGCCAAATCTCTGTAAGATACAAATATGTTATTTGTGTTCTTTTCTGTT
TGCTGTTGCTTCTTAGAGTCTTTGTTTTTCTTTTCTGTCTTTCACTTGAGGAGATTCTCATTTT
TTGTTGTTTATAATCCATGTCAAATTTCTTAATTGCTATAAGATATGCTCTTGAACAAGGCGCT
CAAGCCTATGCTGTAGATATTGAAGAAGCAGAACATGATGCATTCACAGGAAATGTTGCATCAG
TGCAAGCAACAAAGCACCAAATACTAACGAGAAATGAAGCCAAGTTTCTTGATAAAGATCATAC
AGGTTTGTCTTTGGCTGTAGTGGGATAACTCATGTTATCATGTTCTATGTGTGCAAGTTGAGAG
TGTTGGTTTCTAGCCCATTTATAATTTATTTGAAATTTTCTGGTCTCAAAAGTTGGATCGTTTG
ATGGCATTATATGGGGATTACCGGGCTTCCCCTTGGTTTAATAATTCAATGAAAACTTATTCTT
CCTTTTTAAGTTAGGACAATCTTATCAAGTCCTAACAGTAACATTTAGTATAAGAACATACTGT
TGCTTTTCCTAAAAGTTATCCTCCTATAGGATGTTTCCCAAATCTGCTATTATCTGTGTCTGTG
ATGACTGAAATATTTTTCTATTTTATCTGTTCATTTGCTATAATCACTTGGACTTTGGGAAATG
GCTTACCTAGTATGCTTTCACAGTTTCTGCTCACTCTTAAAGTTGTAAAACTGCAAAATATTTT
ATGTGAGTGTTGGAATTAGTGGGCTTGGCCTTAGGGTATTTATTGGAAAGATTATGGAAATATT
TATCCTAATTCCTATATTTTATTTTTTTATTCCCTTGTGTATTCTATTTATTCTCCCTCATTGT
ACCTATTGTAAAATTTATCAGAAAATAAGAAGAAGAAAAATATAGTGGTTTTTCTCTTGGTACT
CGGGTTTCCACGTAAATTTGTGTTCTTTGTCTTTAATTTCAATAGTGAGCAACAACTGTTTGTG
GATTATTTCTATTATTTTCGAAAGTATATGTACTTCATCTCACCATAGAGCATATTAAACCAGA
ATTTATTCAAATTTAAAAATATATCAATAACTTCATAATCATTCCAAATATTTGTACACGAGGC
ACCTGTCTTGATTTATAATCTTTCAAACGTCTATATGGGGCAGATTTCAGGTGTTATGATTAAC
CTTCAGAAGGATTAATATTAACTGTTGAGGCTATGGGTTTGATTTGGGATGGCTAGTCATGCCT
CCATGTCCTAACTTTGCTATGATTGTTATATGACTTGGTTCCTTTGTGATGTCCTCATACAAAT
TGGTTTGTTTAACTTCTTGATATCTGAGTTTCTATCTGTAAAGAATTTTTTATAACTTCCCGAT
TCCTGAATTTCTACGTGTAAAGAAATTTAACTTCCTGAGTCTTGGGACTCATGGCCTGCATGCA
TGACTGCATCCATAATGCTTTCTTCTGGTTTATTTTGTGCTATTCACTTGACTCATATTTTTCT
CCAATAAAGAAAATGCATATGAACTACTTGTTTTCTGTTAACAAGATCATTGTATTGTGCAATT
TTAATCTTGATCCATCTTGTTTGCATTTAAGAGGTATGGAAAAATCCATGCTCATTGTACATTT
TGTCAAAGAATTTGACTTATGTTATGACTTCGATGCTGATAGCATCAATTTTGAAGTAGTTTCC
ATAACTTCATCTTTATCTTATGTCCAACTTGTGCAGGCAGTGCGTATAACTTGTTTGCCTTCCC
TTCAGAGTGCAATTTCTCTGGTTCGAAATTTTGCCTTGAATTGGTGAAGATTGTTAAAGAAGAT
TTGATTAGATACTCTGATGGCTCACCATCTCTTAA
						
					

			
		

Sequences
Splice junction sequence	CTTCAGAGTGCAATTTCTCTGGTTCGAAATTTTGCCTTGAATTGGTGAAGATTGTTAAAGAAGA TTTGATTAGATACTCTGATGGCTCACCATCTCTTAAgtccttgactatctcaaagcatctccga 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: 440 Transcript exons: 9768353-9768513,9768907-9769058,9770501-9770627 GTCCTTGACTATCTCAAAGCATCTCCGAAAGACTACAAATGCATATTTACTTCTGGTGCAACAG CAGCACTAAAATTAGTTGGTGAAGCTTTCCCATGGAGTCACCAGAGCAGCTTTGTGTACACAAT GGAGAATCACAACAGTGTTCTTGGAATCAGGGAATATGCTCTTGAACAAGGCGCTCAAGCCTAT GCTGTAGATATTGAAGAAGCAGAACATGATGCATTCACAGGAAATGTTGCATCAGTGCAAGCAA CAAAGCACCAAATACTAACGAGAAATGAAGCCAAGTTTCTTGATAAAGATCATACAGGCAGTGC GTATAACTTGTTTGCCTTCCCTTCAGAGTGCAATTTCTCTGGTTCGAAATTTTGCCTTGAATTG GTGAAGATTGTTAAAGAAGATTTGATTAGATACTCTGATGGCTCACCATCTCTTAA
Genomic sequence	GTCCTTGACTATCTCAAAGCATCTCCGAAAGACTACAAATGCATATTTACTTCTGGTGCAACAG CAGCACTAAAATTAGTTGGTGAAGCTTTCCCATGGAGTCACCAGAGCAGCTTTGTGTACACAAT GGAGAATCACAACAGTGTTCTTGGAATCAGGGAGTATCCTTCAAGTTCAGCGTGATTTCTGTTT GTTATTACTTTCATGTGAACAGCTTTGGCTACCTTTATTTGTATGTTTTTGTTCTTTTCAGGGG ATTTACTTGATGATGCCAAGCTTGAACATTATTGTGATACAGTGATTATTGGCCATTTTATTGA TTGTTCAATGTACTCTTATGTAATTAGTTGCATTTTGACATTTTCTGTGCCTGTATTTAACTTA TTTAGTAGATTCATAGGCCAAATCTCTGTAAGATACAAATATGTTATTTGTGTTCTTTTCTGTT TGCTGTTGCTTCTTAGAGTCTTTGTTTTTCTTTTCTGTCTTTCACTTGAGGAGATTCTCATTTT TTGTTGTTTATAATCCATGTCAAATTTCTTAATTGCTATAAGATATGCTCTTGAACAAGGCGCT CAAGCCTATGCTGTAGATATTGAAGAAGCAGAACATGATGCATTCACAGGAAATGTTGCATCAG TGCAAGCAACAAAGCACCAAATACTAACGAGAAATGAAGCCAAGTTTCTTGATAAAGATCATAC AGGTTTGTCTTTGGCTGTAGTGGGATAACTCATGTTATCATGTTCTATGTGTGCAAGTTGAGAG TGTTGGTTTCTAGCCCATTTATAATTTATTTGAAATTTTCTGGTCTCAAAAGTTGGATCGTTTG ATGGCATTATATGGGGATTACCGGGCTTCCCCTTGGTTTAATAATTCAATGAAAACTTATTCTT CCTTTTTAAGTTAGGACAATCTTATCAAGTCCTAACAGTAACATTTAGTATAAGAACATACTGT TGCTTTTCCTAAAAGTTATCCTCCTATAGGATGTTTCCCAAATCTGCTATTATCTGTGTCTGTG ATGACTGAAATATTTTTCTATTTTATCTGTTCATTTGCTATAATCACTTGGACTTTGGGAAATG GCTTACCTAGTATGCTTTCACAGTTTCTGCTCACTCTTAAAGTTGTAAAACTGCAAAATATTTT ATGTGAGTGTTGGAATTAGTGGGCTTGGCCTTAGGGTATTTATTGGAAAGATTATGGAAATATT TATCCTAATTCCTATATTTTATTTTTTTATTCCCTTGTGTATTCTATTTATTCTCCCTCATTGT ACCTATTGTAAAATTTATCAGAAAATAAGAAGAAGAAAAATATAGTGGTTTTTCTCTTGGTACT CGGGTTTCCACGTAAATTTGTGTTCTTTGTCTTTAATTTCAATAGTGAGCAACAACTGTTTGTG GATTATTTCTATTATTTTCGAAAGTATATGTACTTCATCTCACCATAGAGCATATTAAACCAGA ATTTATTCAAATTTAAAAATATATCAATAACTTCATAATCATTCCAAATATTTGTACACGAGGC ACCTGTCTTGATTTATAATCTTTCAAACGTCTATATGGGGCAGATTTCAGGTGTTATGATTAAC CTTCAGAAGGATTAATATTAACTGTTGAGGCTATGGGTTTGATTTGGGATGGCTAGTCATGCCT CCATGTCCTAACTTTGCTATGATTGTTATATGACTTGGTTCCTTTGTGATGTCCTCATACAAAT TGGTTTGTTTAACTTCTTGATATCTGAGTTTCTATCTGTAAAGAATTTTTTATAACTTCCCGAT TCCTGAATTTCTACGTGTAAAGAAATTTAACTTCCTGAGTCTTGGGACTCATGGCCTGCATGCA TGACTGCATCCATAATGCTTTCTTCTGGTTTATTTTGTGCTATTCACTTGACTCATATTTTTCT CCAATAAAGAAAATGCATATGAACTACTTGTTTTCTGTTAACAAGATCATTGTATTGTGCAATT TTAATCTTGATCCATCTTGTTTGCATTTAAGAGGTATGGAAAAATCCATGCTCATTGTACATTT TGTCAAAGAATTTGACTTATGTTATGACTTCGATGCTGATAGCATCAATTTTGAAGTAGTTTCC ATAACTTCATCTTTATCTTATGTCCAACTTGTGCAGGCAGTGCGTATAACTTGTTTGCCTTCCC TTCAGAGTGCAATTTCTCTGGTTCGAAATTTTGCCTTGAATTGGTGAAGATTGTTAAAGAAGAT TTGATTAGATACTCTGATGGCTCACCATCTCTTAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.475230359

Conservation Information
Conserved circRNAs	NA
PMCS	0.475230359

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9768480-9768422(+)
						
						Potential amino acid sequence
						
							MENHNSVLGIREYALEQGAQAYAVDIEEAEHDAFTGNVASVQATKHQILTRNEAKFLDKDHTGS
AYNLFAFPSECNFSGSKFCLELVKIVKEDLIRYSDGSPSLKSLTISKHLRKTTNAYLLLVQQQH
*
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	9768480-9768422(+)
Potential amino acid sequence	MENHNSVLGIREYALEQGAQAYAVDIEEAEHDAFTGNVASVQATKHQILTRNEAKFLDKDHTGS AYNLFAFPSECNFSGSKFCLELVKIVKEDLIRYSDGSPSLKSLTISKHLRKTTNAYLLLVQQQH *
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhu et al., 2019

circRNA

Detail information of Csa6G139140_circ_g.4

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