Plant Circular RNA Database

Detail information of Csa3G134840_circ_g.2

			
						 General Information
					
						CircRNA Name
						Csa3G134840_circ_g.2
					
						ID in PlantcircBase
						csa_circ_001558
					
						Alias
						Chr3:9053736_9055364
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr3: 9053736-9055364  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Csa3G134840						
					
						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
						Csa3G134840.2:4
Csa3G134840.1:4

General Information
CircRNA Name	Csa3G134840_circ_g.2
ID in PlantcircBase	csa_circ_001558
Alias	Chr3:9053736_9055364
Organism	Cucumis sativus
Position	chrChr3: 9053736-9055364 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	ue-circRNA
Identification method	CIRI2
Parent gene	Csa3G134840
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	Csa3G134840.2:4 Csa3G134840.1:4

			
						 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  
						
							ATATTCACAAAGCACTTCGCCAACAGTGACAGGAAAAAGGCTATGAAATATTTGAGGCCTCAGC
AGCCTAAAGATTCCCACATGACCACCTTCTTTGTTGagaggtcggaattaaacgaaacgtcggc
cgaagtatcggagacggatgaagcaatagcggcattggagaggcacggggttacgttcataaat
gcggccgt

									
								

					

						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: 594
Transcript exons: 9053736-9054078,9054740-9054788,9054899-9054970,9055235-
9055364
AGAGGTCGGAATTAAACGAAACGTCGGCCGAAGTATCGGAGACGGATGAAGCAATAGCGGCATT
GGAGAGGCACGGGGTTACGTTCATAAATGCGGCCGTGAGAGGGAAGACAAAGAAAGGGAATAAG
CCCAAAATGGCACTAAGAGTGGATATTCCAGCCACCACTCCGTCGAGGACAATCTCTGCCGTGA
TGGGAATGCTGTGGGAGGATCTGATCAACAACCCCAAGAAAGATGTCTCCGGCGACTCCATTAG
CCGGAAGAAAATACAGTGGGCGGAGAAGATGATCCGAGGCGCCTTTGTTGAACTTTACAAAGGC
CTTGGCCTACTCAAAACCTTCAGTTCACTGAACATGAAGGCATTCGTAAAGATTCTGAAAAAAT
TCGACAAGGTGGCGAACCAAAAATCGTCGGTGAGTTATCTTCAAGAGGTGAAACAGTCACCCTT
TATCAGCTCCGATAAGGTGGTAAGATTAATGGACGAAGTGGAATCCATATTCACAAAGCACTTC
GCCAACAGTGACAGGAAAAAGGCTATGAAATATTTGAGGCCTCAGCAGCCTAAAGATTCCCACA
TGACCACCTTCTTTGTTG
						
					

						Genomic sequence
						
							AGAGGTCGGAATTAAACGAAACGTCGGCCGAAGTATCGGAGACGGATGAAGCAATAGCGGCATT
GGAGAGGCACGGGGTTACGTTCATAAATGCGGCCGTGAGAGGGAAGACAAAGAAAGGGAATAAG
CCCAAAATGGCACTAAGAGTGGATATTCCAGCCACCACTCCGTCGAGGACAATCTCTGCCGTGA
TGGGAATGCTGTGGGAGGATCTGATCAACAACCCCAAGAAAGATGTCTCCGGCGACTCCATTAG
CCGGAAGAAAATACAGTGGGCGGAGAAGATGATCCGAGGCGCCTTTGTTGAACTTTACAAAGGC
CTTGGCCTACTCAAAACCTTCAGGTTCTCACTACTTTTTTTTCAAATATGAAATTATGTCTATT
TACTTTATAATATATATTTTTTGAAGTACACAAAGAATATAAAAGTTTGCAATATTTGATATAT
CTAAAATTGTCCTTTTCATCATATAATTTACTATGTTTTTCTTTAAAATCAATGATTGTATTGT
GTAAGGACTAATTAAGCTCAAATTGGATGGTCAAATAATCCTTAAATAAGACACAATTGTTTTT
CTTGAAGGAAAAGGAAAAAAACTGTTTTTTTCCTCCCTTTTTACACTTTATTAAGGAAATAAAA
GTTTAAAATTAATTGAAATTTGAATTTTTTTATTATTAAATGATAAATGAATAGTGAAAAAAGC
TAATTAATTACAGTTATTTTAATTCTCTTAATTTTCATTACTGGCATTAAAACCAAATGACTAA
AAATGTGTATTTAGTGAAACCTACACCTAAAATCTAGGGACAAAACAGTATTTTTTTTTCCTAA
GTAGAAAATAATACTTATGTTTCTTAAAGATTAAAACTAAAAGTTAAACAGCAAGTAAATGTTG
AAATGAATGAAGACTCATAACCACAGATGAAACTTATATTAATTAGGTAATTATGTTATTAATG
CATATTAACAGCAAAGCTTATGGGTTTGATTTCTTTATGAGCAGTTCACTGAACATGAAGGCAT
TCGTAAAGATTCTGAAAAAATTCGACAAGGTGATGAAAACATTAAATTATTAGTTAAATAACAA
TGTTAATTTTGTAAGATTAAAGCAAAAACAATGTTTGATAGTAACTAATATGGTTGTTTTTGGT
GAATTAAATAGGTGGCGAACCAAAAATCGTCGGTGAGTTATCTTCAAGAGGTGAAACAGTCACC
CTTTATCAGCTCCGATAAGGTACGCATTAGTTAAAGAATTAATTAATTAAAAGATTAACTTAAG
CCATTTAATTAAGTAATTCAAATTTCTTCAAATATTAGAAAATATTTTATGAGACAACGATTTC
CTGGCTGGCATGCATAAACACAATAAGAAGAATAAAATGAAGAAATTTAGTGGATTTTGAACTT
TTGTAGAAAATGGGTGAAAATTAGAAAAGGAATGAATGAATGAATTAATATTAAATTTTTAAAT
TTGGGAAAAATGGTTTGTGTAATGAAGGTGGTAAGATTAATGGACGAAGTGGAATCCATATTCA
CAAAGCACTTCGCCAACAGTGACAGGAAAAAGGCTATGAAATATTTGAGGCCTCAGCAGCCTAA
AGATTCCCACATGACCACCTTCTTTGTTG
						
					

			
		

Sequences
Splice junction sequence	ATATTCACAAAGCACTTCGCCAACAGTGACAGGAAAAAGGCTATGAAATATTTGAGGCCTCAGC AGCCTAAAGATTCCCACATGACCACCTTCTTTGTTGagaggtcggaattaaacgaaacgtcggc cgaagtatcggagacggatgaagcaatagcggcattggagaggcacggggttacgttcataaat gcggccgt
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: 594 Transcript exons: 9053736-9054078,9054740-9054788,9054899-9054970,9055235- 9055364 AGAGGTCGGAATTAAACGAAACGTCGGCCGAAGTATCGGAGACGGATGAAGCAATAGCGGCATT GGAGAGGCACGGGGTTACGTTCATAAATGCGGCCGTGAGAGGGAAGACAAAGAAAGGGAATAAG CCCAAAATGGCACTAAGAGTGGATATTCCAGCCACCACTCCGTCGAGGACAATCTCTGCCGTGA TGGGAATGCTGTGGGAGGATCTGATCAACAACCCCAAGAAAGATGTCTCCGGCGACTCCATTAG CCGGAAGAAAATACAGTGGGCGGAGAAGATGATCCGAGGCGCCTTTGTTGAACTTTACAAAGGC CTTGGCCTACTCAAAACCTTCAGTTCACTGAACATGAAGGCATTCGTAAAGATTCTGAAAAAAT TCGACAAGGTGGCGAACCAAAAATCGTCGGTGAGTTATCTTCAAGAGGTGAAACAGTCACCCTT TATCAGCTCCGATAAGGTGGTAAGATTAATGGACGAAGTGGAATCCATATTCACAAAGCACTTC GCCAACAGTGACAGGAAAAAGGCTATGAAATATTTGAGGCCTCAGCAGCCTAAAGATTCCCACA TGACCACCTTCTTTGTTG
Genomic sequence	AGAGGTCGGAATTAAACGAAACGTCGGCCGAAGTATCGGAGACGGATGAAGCAATAGCGGCATT GGAGAGGCACGGGGTTACGTTCATAAATGCGGCCGTGAGAGGGAAGACAAAGAAAGGGAATAAG CCCAAAATGGCACTAAGAGTGGATATTCCAGCCACCACTCCGTCGAGGACAATCTCTGCCGTGA TGGGAATGCTGTGGGAGGATCTGATCAACAACCCCAAGAAAGATGTCTCCGGCGACTCCATTAG CCGGAAGAAAATACAGTGGGCGGAGAAGATGATCCGAGGCGCCTTTGTTGAACTTTACAAAGGC CTTGGCCTACTCAAAACCTTCAGGTTCTCACTACTTTTTTTTCAAATATGAAATTATGTCTATT TACTTTATAATATATATTTTTTGAAGTACACAAAGAATATAAAAGTTTGCAATATTTGATATAT CTAAAATTGTCCTTTTCATCATATAATTTACTATGTTTTTCTTTAAAATCAATGATTGTATTGT GTAAGGACTAATTAAGCTCAAATTGGATGGTCAAATAATCCTTAAATAAGACACAATTGTTTTT CTTGAAGGAAAAGGAAAAAAACTGTTTTTTTCCTCCCTTTTTACACTTTATTAAGGAAATAAAA GTTTAAAATTAATTGAAATTTGAATTTTTTTATTATTAAATGATAAATGAATAGTGAAAAAAGC TAATTAATTACAGTTATTTTAATTCTCTTAATTTTCATTACTGGCATTAAAACCAAATGACTAA AAATGTGTATTTAGTGAAACCTACACCTAAAATCTAGGGACAAAACAGTATTTTTTTTTCCTAA GTAGAAAATAATACTTATGTTTCTTAAAGATTAAAACTAAAAGTTAAACAGCAAGTAAATGTTG AAATGAATGAAGACTCATAACCACAGATGAAACTTATATTAATTAGGTAATTATGTTATTAATG CATATTAACAGCAAAGCTTATGGGTTTGATTTCTTTATGAGCAGTTCACTGAACATGAAGGCAT TCGTAAAGATTCTGAAAAAATTCGACAAGGTGATGAAAACATTAAATTATTAGTTAAATAACAA TGTTAATTTTGTAAGATTAAAGCAAAAACAATGTTTGATAGTAACTAATATGGTTGTTTTTGGT GAATTAAATAGGTGGCGAACCAAAAATCGTCGGTGAGTTATCTTCAAGAGGTGAAACAGTCACC CTTTATCAGCTCCGATAAGGTACGCATTAGTTAAAGAATTAATTAATTAAAAGATTAACTTAAG CCATTTAATTAAGTAATTCAAATTTCTTCAAATATTAGAAAATATTTTATGAGACAACGATTTC CTGGCTGGCATGCATAAACACAATAAGAAGAATAAAATGAAGAAATTTAGTGGATTTTGAACTT TTGTAGAAAATGGGTGAAAATTAGAAAAGGAATGAATGAATGAATTAATATTAAATTTTTAAAT TTGGGAAAAATGGTTTGTGTAATGAAGGTGGTAAGATTAATGGACGAAGTGGAATCCATATTCA CAAAGCACTTCGCCAACAGTGACAGGAAAAAGGCTATGAAATATTTGAGGCCTCAGCAGCCTAA AGATTCCCACATGACCACCTTCTTTGTTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.500807269

Conservation Information
Conserved circRNAs	NA
PMCS	0.500807269

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9053871-9055361(+)
						
						Potential amino acid sequence
						
							MALRVDIPATTPSRTISAVMGMLWEDLINNPKKDVSGDSISRKKIQWAEKMIRGAFVELYKGLG
LLKTFSSLNMKAFVKILKKFDKVANQKSSVSYLQEVKQSPFISSDKVVRLMDEVESIFTKHFAN
SDRKKAMKYLRPQQPKDSHMTTFFVERSELNETSAEVSETDEAIAALERHGVTFINAAVRGKTK
KGNKPKMALRVDIPATTPSRTISAVMGMLWEDLINNPKKDVSGDSISRKKIQWAEKMIRGAFVE
LYKGLGLLKTFSSLNMKAFVKILKKFDKVANQKSSVSYLQEVKQSPFISSDKVVRLMDEVESIF
TKHFANSDRKKAMKYLRPQQPKDSHMTTFFVERSELNETSAEVSETDEAIAALERHGVTFINAA
VRGKTKKGNKPKMALRVDIPATTPSRTISAVMGMLWEDLINNPKKDVSGDSISRKKIQWAEKMI
RGAFVELYKGLGLLKTFSSLNMKAFVKILKKFDKVANQKSSVSYLQEVKQSPFISSDKVVRLMD
EVESIFTKHFANSDRKKAMKYLRPQQPKDSHMTTFFVERSELNETSAEVSETDEAIAALERHGV
TFINAAVRGKTKKGNKPKMALRVDIPATTPSRTISAVMGMLWEDLINNPKKDVSGDSISRKKIQ
WAEKMIRGAFVELYKGLGLLKTFSSLNMKAFVKILKKFDKVANQKSSVSYLQEVKQSPFISSDK
VVRLMDEVESIFTKHFANSDRKKAMKYLRPQQPKDSHMTTFFV
						
						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	9053871-9055361(+)
Potential amino acid sequence	MALRVDIPATTPSRTISAVMGMLWEDLINNPKKDVSGDSISRKKIQWAEKMIRGAFVELYKGLG LLKTFSSLNMKAFVKILKKFDKVANQKSSVSYLQEVKQSPFISSDKVVRLMDEVESIFTKHFAN SDRKKAMKYLRPQQPKDSHMTTFFVERSELNETSAEVSETDEAIAALERHGVTFINAAVRGKTK KGNKPKMALRVDIPATTPSRTISAVMGMLWEDLINNPKKDVSGDSISRKKIQWAEKMIRGAFVE LYKGLGLLKTFSSLNMKAFVKILKKFDKVANQKSSVSYLQEVKQSPFISSDKVVRLMDEVESIF TKHFANSDRKKAMKYLRPQQPKDSHMTTFFVERSELNETSAEVSETDEAIAALERHGVTFINAA VRGKTKKGNKPKMALRVDIPATTPSRTISAVMGMLWEDLINNPKKDVSGDSISRKKIQWAEKMI RGAFVELYKGLGLLKTFSSLNMKAFVKILKKFDKVANQKSSVSYLQEVKQSPFISSDKVVRLMD EVESIFTKHFANSDRKKAMKYLRPQQPKDSHMTTFFVERSELNETSAEVSETDEAIAALERHGV TFINAAVRGKTKKGNKPKMALRVDIPATTPSRTISAVMGMLWEDLINNPKKDVSGDSISRKKIQ WAEKMIRGAFVELYKGLGLLKTFSSLNMKAFVKILKKFDKVANQKSSVSYLQEVKQSPFISSDK VVRLMDEVESIFTKHFANSDRKKAMKYLRPQQPKDSHMTTFFV
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 Csa3G134840_circ_g.2

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