Plant Circular RNA Database

Detail information of Csa4G023010_circ_g.1

			
						 General Information
					
						CircRNA Name
						Csa4G023010_circ_g.1
					
						ID in PlantcircBase
						csa_circ_002329
					
						Alias
						Chr4:2578243_2583378
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr4: 2578243-2583378  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2;Find_circ
					
						Parent gene
						
							Csa4G023010						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						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
						Csa4G023010.1:8

General Information
CircRNA Name	Csa4G023010_circ_g.1
ID in PlantcircBase	csa_circ_002329
Alias	Chr4:2578243_2583378
Organism	Cucumis sativus
Position	chrChr4: 2578243-2583378 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	CIRI2;Find_circ
Parent gene	Csa4G023010
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	NA
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	Csa4G023010.1:8

			
						 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  
						
							CACTCTTCTTGCTCAGAGTGCTGTCCACGGTGCCATGGCTGGATACACTGGCTTTACTGTTGGA
CCTGTAAATAGCAGACATGCTTATATTCCAATTGCTggaggatacagagggttttactccaaga
atacactaacattgacaccaaaagttgtcaacaatatccacaaacacggtggtacgtttcttcg
tacttcac

						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: 882
Transcript exons: 2578243-2578401,2578532-2578585,2578670-2578738,2579949-
2580078,2580181-2580221,2581710-2581934,2582336-2582384,
2583224-2583378
GGAGGATACAGAGGGTTTTACTCCAAGAATACACTAACATTGACACCAAAAGTTGTCAACAATA
TCCACAAACACGGTGGTACGTTTCTTCGTACTTCACGAGGAGGCCATGATACAAATAAGATTGT
TGATAACATTCAGGATCGTGGAATAAATCAGGTGTATATCATTGGCGGTGATGGTACTCAAAGA
GGAGCAGCTTTAATTTATCAGGAAATTGCAAAACGTGGTCTTCAAGTTTCTGTTGCTGGGATCC
CCAAGACGATTGATAATGACATTGCTGTAATAGACAAATCTTTTGGGTTTGATACTGCGGTTGA
AGAAGCTCAGAGGGCCATTAACGCTGCTCATGTTGAGGTTGGAAGTGTAGACAATGGAGTTGGA
ATAGTTAAACTTATGGGTCGATATAGCGGTTTTATTGCCACAATTGCAACTTTGGCTAGTAGAG
ACGTGGATTGTTGCTTGATTCCCGAATCACCATTCTACTTGGAAGGGACCGGAGGGCTCTTTGA
ATTTATAGAACAGCGGCTTAAAGAGAATGGGCATATTGTTATTGTGTTAGCAGAAGGAGCAGGA
CAAGATTTTATAGCTCGAGACATGCATGCAGCTGAAGAGAAAGATGCGTCAGGAAATAGATTAC
TACTCGATGTTGGTCCGTGGTTATCTCAGAAGATTAAGGATCATTTTACGAAGGTTCAGAAGAT
GGCAGTTAATATGAAATACATAGATCCTACATATATGATTCGAGCTATTCCTAGTAATGCCTCA
GATAATGTTTACTGCACTCTTCTTGCTCAGAGTGCTGTCCACGGTGCCATGGCTGGATACACTG
GCTTTACTGTTGGACCTGTAAATAGCAGACATGCTTATATTCCAATTGCT
						
						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	CACTCTTCTTGCTCAGAGTGCTGTCCACGGTGCCATGGCTGGATACACTGGCTTTACTGTTGGA CCTGTAAATAGCAGACATGCTTATATTCCAATTGCTggaggatacagagggttttactccaaga atacactaacattgacaccaaaagttgtcaacaatatccacaaacacggtggtacgtttcttcg tacttcac
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: 882 Transcript exons: 2578243-2578401,2578532-2578585,2578670-2578738,2579949- 2580078,2580181-2580221,2581710-2581934,2582336-2582384, 2583224-2583378 GGAGGATACAGAGGGTTTTACTCCAAGAATACACTAACATTGACACCAAAAGTTGTCAACAATA TCCACAAACACGGTGGTACGTTTCTTCGTACTTCACGAGGAGGCCATGATACAAATAAGATTGT TGATAACATTCAGGATCGTGGAATAAATCAGGTGTATATCATTGGCGGTGATGGTACTCAAAGA GGAGCAGCTTTAATTTATCAGGAAATTGCAAAACGTGGTCTTCAAGTTTCTGTTGCTGGGATCC CCAAGACGATTGATAATGACATTGCTGTAATAGACAAATCTTTTGGGTTTGATACTGCGGTTGA AGAAGCTCAGAGGGCCATTAACGCTGCTCATGTTGAGGTTGGAAGTGTAGACAATGGAGTTGGA ATAGTTAAACTTATGGGTCGATATAGCGGTTTTATTGCCACAATTGCAACTTTGGCTAGTAGAG ACGTGGATTGTTGCTTGATTCCCGAATCACCATTCTACTTGGAAGGGACCGGAGGGCTCTTTGA ATTTATAGAACAGCGGCTTAAAGAGAATGGGCATATTGTTATTGTGTTAGCAGAAGGAGCAGGA CAAGATTTTATAGCTCGAGACATGCATGCAGCTGAAGAGAAAGATGCGTCAGGAAATAGATTAC TACTCGATGTTGGTCCGTGGTTATCTCAGAAGATTAAGGATCATTTTACGAAGGTTCAGAAGAT GGCAGTTAATATGAAATACATAGATCCTACATATATGATTCGAGCTATTCCTAGTAATGCCTCA GATAATGTTTACTGCACTCTTCTTGCTCAGAGTGCTGTCCACGGTGCCATGGCTGGATACACTG GCTTTACTGTTGGACCTGTAAATAGCAGACATGCTTATATTCCAATTGCT
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
						0.856888154

Conservation Information
Conserved circRNAs	NA
PMCS	0.856888154

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2580064-2583375(+)
						
						Potential amino acid sequence
						
							MGRYSGFIATIATLASRDVDCCLIPESPFYLEGTGGLFEFIEQRLKENGHIVIVLAEGAGQDFI
ARDMHAAEEKDASGNRLLLDVGPWLSQKIKDHFTKVQKMAVNMKYIDPTYMIRAIPSNASDNVY
CTLLAQSAVHGAMAGYTGFTVGPVNSRHAYIPIAGGYRGFYSKNTLTLTPKVVNNIHKHGGTFL
RTSRGGHDTNKIVDNIQDRGINQVYIIGGDGTQRGAALIYQEIAKRGLQVSVAGIPKTIDNDIA
VIDKSFGFDTAVEEAQRAINAAHVEVGSVDNGVGIVKLMGRYSGFIATIATLASRDVDCCLIPE
SPFYLEGTGGLFEFIEQRLKENGHIVIVLAEGAGQDFIARDMHAAEEKDASGNRLLLDVGPWLS
QKIKDHFTKVQKMAVNMKYIDPTYMIRAIPSNASDNVYCTLLAQSAVHGAMAGYTGFTVGPVNS
RHAYIPIAGGYRGFYSKNTLTLTPKVVNNIHKHGGTFLRTSRGGHDTNKIVDNIQDRGINQVYI
IGGDGTQRGAALIYQEIAKRGLQVSVAGIPKTIDNDIAVIDKSFGFDTAVEEAQRAINAAHVEV
GSVDNGVGIVKLMGRYSGFIATIATLASRDVDCCLIPESPFYLEGTGGLFEFIEQRLKENGHIV
IVLAEGAGQDFIARDMHAAEEKDASGNRLLLDVGPWLSQKIKDHFTKVQKMAVNMKYIDPTYMI
RAIPSNASDNVYCTLLAQSAVHGAMAGYTGFTVGPVNSRHAYIPIAGGYRGFYSKNTLTLTPKV
VNNIHKHGGTFLRTSRGGHDTNKIVDNIQDRGINQVYIIGGDGTQRGAALIYQEIAKRGLQVSV
AGIPKTIDNDIAVIDKSFGFDTAVEEAQRAINAAHVEVGSVDNGVGIVKLMGRYSGFIATIATL
ASRDVDCCLIPESPFYLEGTGGLFEFIEQRLKENGHIVIVLAEGAGQDFIARDMHAAEEKDASG
NRLLLDVGPWLSQKIKDHFTKVQKMAVNMKYIDPTYMIRAIPSNASDNVYCTLLAQSAVHGAMA
GYTGFTVGPVNSRHAYIPIA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	2580064-2583375(+)
Potential amino acid sequence	MGRYSGFIATIATLASRDVDCCLIPESPFYLEGTGGLFEFIEQRLKENGHIVIVLAEGAGQDFI ARDMHAAEEKDASGNRLLLDVGPWLSQKIKDHFTKVQKMAVNMKYIDPTYMIRAIPSNASDNVY CTLLAQSAVHGAMAGYTGFTVGPVNSRHAYIPIAGGYRGFYSKNTLTLTPKVVNNIHKHGGTFL RTSRGGHDTNKIVDNIQDRGINQVYIIGGDGTQRGAALIYQEIAKRGLQVSVAGIPKTIDNDIA VIDKSFGFDTAVEEAQRAINAAHVEVGSVDNGVGIVKLMGRYSGFIATIATLASRDVDCCLIPE SPFYLEGTGGLFEFIEQRLKENGHIVIVLAEGAGQDFIARDMHAAEEKDASGNRLLLDVGPWLS QKIKDHFTKVQKMAVNMKYIDPTYMIRAIPSNASDNVYCTLLAQSAVHGAMAGYTGFTVGPVNS RHAYIPIAGGYRGFYSKNTLTLTPKVVNNIHKHGGTFLRTSRGGHDTNKIVDNIQDRGINQVYI IGGDGTQRGAALIYQEIAKRGLQVSVAGIPKTIDNDIAVIDKSFGFDTAVEEAQRAINAAHVEV GSVDNGVGIVKLMGRYSGFIATIATLASRDVDCCLIPESPFYLEGTGGLFEFIEQRLKENGHIV IVLAEGAGQDFIARDMHAAEEKDASGNRLLLDVGPWLSQKIKDHFTKVQKMAVNMKYIDPTYMI RAIPSNASDNVYCTLLAQSAVHGAMAGYTGFTVGPVNSRHAYIPIAGGYRGFYSKNTLTLTPKV VNNIHKHGGTFLRTSRGGHDTNKIVDNIQDRGINQVYIIGGDGTQRGAALIYQEIAKRGLQVSV AGIPKTIDNDIAVIDKSFGFDTAVEEAQRAINAAHVEVGSVDNGVGIVKLMGRYSGFIATIATL ASRDVDCCLIPESPFYLEGTGGLFEFIEQRLKENGHIVIVLAEGAGQDFIARDMHAAEEKDASG NRLLLDVGPWLSQKIKDHFTKVQKMAVNMKYIDPTYMIRAIPSNASDNVYCTLLAQSAVHGAMA GYTGFTVGPVNSRHAYIPIA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhu et al., 2019;He et al., 2020

circRNA

Detail information of Csa4G023010_circ_g.1

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