Plant Circular RNA Database

Detail information of Csa4G013540_circ_g.2

			
						 General Information
					
						CircRNA Name
						Csa4G013540_circ_g.2
					
						ID in PlantcircBase
						csa_circ_002309
					
						Alias
						Chr4:1953004_1954691
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr4: 1953004-1954691  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Csa4G013540						
					
						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
						Csa4G013540.1:4
Csa4G013540.2:4

General Information
CircRNA Name	Csa4G013540_circ_g.2
ID in PlantcircBase	csa_circ_002309
Alias	Chr4:1953004_1954691
Organism	Cucumis sativus
Position	chrChr4: 1953004-1954691 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	CIRI2
Parent gene	Csa4G013540
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	Csa4G013540.1:4 Csa4G013540.2:4

			
						 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  
						
							TCAAAAATCATTCAATGTGCTTGACCAATGGATAAACTCTGCCACCCAGAGTTTAGTATATTTT
GTCAGGAAAGAAATGGATGGCTATCGACTCTATACGgtgtttgattgctggtttgagagtgggt
ctatgccatatgcttacattcattatccatttgagaacgttgagctttttgagaagaattttcc
tgggcact

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							GTGTTTGATTGCTGGTTTGAGAGTGGGTCTATGCCATATGCTTACATTCATTATCCATTTGAGA
ACGTTGAGCTTTTTGAGAAGAATTTTCCTGGGCACTTTGTGGCAGAGGGGCTTGATCAAACTCG
TGGATGGTAAGTTTCTTGGTGTTTGTGTCTTTTATTTTTTTTTACCCTTCATAGTTCCAAAATA
TCAACTAGTCAAGTTGCAAAATTATTTTCCTGTTACTTTGGAGTTGTAAATCATTAGTGTTTTT
CTTACAATAATTGTAGGGGTAGTCGATCAAACCCCTCACCTTTAAGATGAAAGGTTATGCCAAT
TACCGTTGAGCTAAGCTCACTTTGGCAGTTGTAAATCACTAGTTGGATTGTATTTAGTGGTGAA
AAACTCAAATATATGCACGAGAGTGGAATGTTGATATAATTCTCTTTTAAATTGATGCTTCTTT
TTCTTTTTTGGTTGGACAATTGATAACTTATTTTATTGATATGAGGAAGCAGACACAATATGAG
CATGGTGTGAAACAATGACTTTTGGTGATTAATAATCTACTACATTATTTTTTCATGTTTTGAA
CACATTGAAAATCTACTACATATTTTTTTTCATTTTTTGAACACATTGAAAGGAACCAAAACTT
CATTAATATAATGAAAAGAGACTAATGTTCATTTTTGATGAGATATGGATTGTTTGCTCTTTAC
GTCTGCAGGTTCTACACTCTCATGGTTCTATCTACTGCTTTATTTGGGAAGCCTGCATTTAGGA
ACCTTATTTGTAATGGCCTTGTACTTGCTGAGGATGGTAAGAAGATGAGTAAAAGGTTGAAAAA
CTATCCTTCACCAATGGAAATCATAAATGATTATGGAGCTGTAAGTTCTGTATTATATCTATGT
TTTTCACTTATCTTGTATTTCTGACTTCACTTTTCATTATTCTGATGACAATGACATTGAAAAA
CAAGATTGGTGTAAATATACAAACTCCCTTAAAGACTATAGTTTCAAAAGCCTCATTGCTAGGT
GTTCTTGTATGATACCTTGGATGGTTGGAAGGCTCTTCCTTCCTTTGAGTACAATTTCGTTCAA
TCAATGAAATTATGTTTATTCTTCTTCCAAAAAGAGTTAATAATAATAATCATAAATAAAAAAG
CAAGCATCAAGATATTCATTGAGCTTTCTTTTCAATTAATCGTGGTTATTATTTTATGAAGGTT
GGTGTGTGTTTTTTTGTTGCAGGATGCTCTGAGATTATATCTTATAAATTCTCCAGTTGTACGT
GCAGAGACTTTGCGATTCAAGAAGGAGGGTGTCTTTGGTGTTGTAAGTCTTTACTGATATTTTA
CACTGTACCAAGTATTCTCGGTGCACCACTTGGGCACCATGTCTTCGTTAACTTTAACTTTACT
TCATAGTTCATGAACAGCTATACTGAGACCTGTTTTTCCTCACTTTGACTTTATGGACTGTTGA
CAGGTCAGGGATGTATTCCTGCCATGGTACAATGCATATAGATTCCTTGTTCAGAATGCCAAGA
GGCTCGAGATTGAGGGGTTTGCACCATTTTCTCCAGTGGATCAGGCCACCCTTCAAAAATCATT
CAATGTGCTTGACCAATGGATAAACTCTGCCACCCAGAGTTTAGTATATTTTGTCAGGAAAGAA
ATGGATGGCTATCGACTCTATACG
						
					

			
		

Sequences
Splice junction sequence	TCAAAAATCATTCAATGTGCTTGACCAATGGATAAACTCTGCCACCCAGAGTTTAGTATATTTT GTCAGGAAAGAAATGGATGGCTATCGACTCTATACGgtgtttgattgctggtttgagagtgggt ctatgccatatgcttacattcattatccatttgagaacgttgagctttttgagaagaattttcc tgggcact
Assembled circRNA sequence	NA 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	NA
Genomic sequence	GTGTTTGATTGCTGGTTTGAGAGTGGGTCTATGCCATATGCTTACATTCATTATCCATTTGAGA ACGTTGAGCTTTTTGAGAAGAATTTTCCTGGGCACTTTGTGGCAGAGGGGCTTGATCAAACTCG TGGATGGTAAGTTTCTTGGTGTTTGTGTCTTTTATTTTTTTTTACCCTTCATAGTTCCAAAATA TCAACTAGTCAAGTTGCAAAATTATTTTCCTGTTACTTTGGAGTTGTAAATCATTAGTGTTTTT CTTACAATAATTGTAGGGGTAGTCGATCAAACCCCTCACCTTTAAGATGAAAGGTTATGCCAAT TACCGTTGAGCTAAGCTCACTTTGGCAGTTGTAAATCACTAGTTGGATTGTATTTAGTGGTGAA AAACTCAAATATATGCACGAGAGTGGAATGTTGATATAATTCTCTTTTAAATTGATGCTTCTTT TTCTTTTTTGGTTGGACAATTGATAACTTATTTTATTGATATGAGGAAGCAGACACAATATGAG CATGGTGTGAAACAATGACTTTTGGTGATTAATAATCTACTACATTATTTTTTCATGTTTTGAA CACATTGAAAATCTACTACATATTTTTTTTCATTTTTTGAACACATTGAAAGGAACCAAAACTT CATTAATATAATGAAAAGAGACTAATGTTCATTTTTGATGAGATATGGATTGTTTGCTCTTTAC GTCTGCAGGTTCTACACTCTCATGGTTCTATCTACTGCTTTATTTGGGAAGCCTGCATTTAGGA ACCTTATTTGTAATGGCCTTGTACTTGCTGAGGATGGTAAGAAGATGAGTAAAAGGTTGAAAAA CTATCCTTCACCAATGGAAATCATAAATGATTATGGAGCTGTAAGTTCTGTATTATATCTATGT TTTTCACTTATCTTGTATTTCTGACTTCACTTTTCATTATTCTGATGACAATGACATTGAAAAA CAAGATTGGTGTAAATATACAAACTCCCTTAAAGACTATAGTTTCAAAAGCCTCATTGCTAGGT GTTCTTGTATGATACCTTGGATGGTTGGAAGGCTCTTCCTTCCTTTGAGTACAATTTCGTTCAA TCAATGAAATTATGTTTATTCTTCTTCCAAAAAGAGTTAATAATAATAATCATAAATAAAAAAG CAAGCATCAAGATATTCATTGAGCTTTCTTTTCAATTAATCGTGGTTATTATTTTATGAAGGTT GGTGTGTGTTTTTTTGTTGCAGGATGCTCTGAGATTATATCTTATAAATTCTCCAGTTGTACGT GCAGAGACTTTGCGATTCAAGAAGGAGGGTGTCTTTGGTGTTGTAAGTCTTTACTGATATTTTA CACTGTACCAAGTATTCTCGGTGCACCACTTGGGCACCATGTCTTCGTTAACTTTAACTTTACT TCATAGTTCATGAACAGCTATACTGAGACCTGTTTTTCCTCACTTTGACTTTATGGACTGTTGA CAGGTCAGGGATGTATTCCTGCCATGGTACAATGCATATAGATTCCTTGTTCAGAATGCCAAGA GGCTCGAGATTGAGGGGTTTGCACCATTTTCTCCAGTGGATCAGGCCACCCTTCAAAAATCATT CAATGTGCTTGACCAATGGATAAACTCTGCCACCCAGAGTTTAGTATATTTTGTCAGGAAAGAA ATGGATGGCTATCGACTCTATACG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.154881813

Conservation Information
Conserved circRNAs	NA
PMCS	0.154881813

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1953035-1954688(+)
1954673-1953816(+)
1954620-1953008(+)
						
						Potential amino acid sequence
						
							MPYAYIHYPFENVELFEKNFPGHFVAEGLDQTRGWFYTLMVLSTALFGKPAFRNLICNGLVLAE
DGKKMSKRLKNYPSPMEIINDYGADALRLYLINSPVVRAETLRFKKEGVFGVVRDVFLPWYNAY
RFLVQNAKRLEIEGFAPFSPVDQATLQKSFNVLDQWINSATQSLVYFVRKEMDGYRLYTVFDCW
FESGSMPYAYIHYPFENVELFEKNFPGHFVAEGLDQTRGWFYTLMVLSTALFGKPAFRNLICNG
LVLAEDGKKMSKRLKNYPSPMEIINDYGADALRLYLINSPVVRAETLRFKKEGVFGVVRDVFLP
WYNAYRFLVQNAKRLEIEGFAPFSPVDQATLQKSFNVLDQWINSATQSLVYFVRKEMDGYRLYT
VFDCWFESGSMPYAYIHYPFENVELFEKNFPGHFVAEGLDQTRGWFYTLMVLSTALFGKPAFRN
LICNGLVLAEDGKKMSKRLKNYPSPMEIINDYGADALRLYLINSPVVRAETLRFKKEGVFGVVR
DVFLPWYNAYRFLVQNAKRLEIEGFAPFSPVDQATLQKSFNVLDQWINSATQSLVYFVRKEMDG
YRLYTVFDCWFESGSMPYAYIHYPFENVELFEKNFPGHFVAEGLDQTRGWFYTLMVLSTALFGK
PAFRNLICNGLVLAEDGKKMSKRLKNYPSPMEIINDYGADALRLYLINSPVVRAETLRFKKEGV
FGVVRDVFLPWYNAYRFLVQNAKRLEIEGFAPFSPVDQATLQKSFNVLDQWINSATQSLVYFVR
KEMDGYRLYT
MAIDSIRCLIAGLRVGLCHMLTFIIHLRTLSFLRRIFLGTLWQRGLIKLVDGSTLSWFYLLLYL
GSLHLGTLFVMALYLLRMVRR*
MDKLCHPEFSIFCQERNGWLSTLYGV*
						
						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	1953035-1954688(+) 1954673-1953816(+) 1954620-1953008(+)
Potential amino acid sequence	MPYAYIHYPFENVELFEKNFPGHFVAEGLDQTRGWFYTLMVLSTALFGKPAFRNLICNGLVLAE DGKKMSKRLKNYPSPMEIINDYGADALRLYLINSPVVRAETLRFKKEGVFGVVRDVFLPWYNAY RFLVQNAKRLEIEGFAPFSPVDQATLQKSFNVLDQWINSATQSLVYFVRKEMDGYRLYTVFDCW FESGSMPYAYIHYPFENVELFEKNFPGHFVAEGLDQTRGWFYTLMVLSTALFGKPAFRNLICNG LVLAEDGKKMSKRLKNYPSPMEIINDYGADALRLYLINSPVVRAETLRFKKEGVFGVVRDVFLP WYNAYRFLVQNAKRLEIEGFAPFSPVDQATLQKSFNVLDQWINSATQSLVYFVRKEMDGYRLYT VFDCWFESGSMPYAYIHYPFENVELFEKNFPGHFVAEGLDQTRGWFYTLMVLSTALFGKPAFRN LICNGLVLAEDGKKMSKRLKNYPSPMEIINDYGADALRLYLINSPVVRAETLRFKKEGVFGVVR DVFLPWYNAYRFLVQNAKRLEIEGFAPFSPVDQATLQKSFNVLDQWINSATQSLVYFVRKEMDG YRLYTVFDCWFESGSMPYAYIHYPFENVELFEKNFPGHFVAEGLDQTRGWFYTLMVLSTALFGK PAFRNLICNGLVLAEDGKKMSKRLKNYPSPMEIINDYGADALRLYLINSPVVRAETLRFKKEGV FGVVRDVFLPWYNAYRFLVQNAKRLEIEGFAPFSPVDQATLQKSFNVLDQWINSATQSLVYFVR KEMDGYRLYT MAIDSIRCLIAGLRVGLCHMLTFIIHLRTLSFLRRIFLGTLWQRGLIKLVDGSTLSWFYLLLYL GSLHLGTLFVMALYLLRMVRR* MDKLCHPEFSIFCQERNGWLSTLYGV*
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 Csa4G013540_circ_g.2

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