Plant Circular RNA Database

Detail information of Csa1G629080_circ_g.1

			
						 General Information
					
						CircRNA Name
						Csa1G629080_circ_g.1
					
						ID in PlantcircBase
						csa_circ_000615
					
						Alias
						Chr1:24879318_24885707
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr1: 24879318-24885707  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2;Find_circ
					
						Parent gene
						
							Csa1G629080						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							Csa1G629080_circ_g.7 Csa1G629080_circ_g.8 Csa1G629080_circ_g.9 Csa1G629080_circ_g.10 						
					
						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  
						
							CT-AC							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
						Csa1G629080.1:7

General Information
CircRNA Name	Csa1G629080_circ_g.1
ID in PlantcircBase	csa_circ_000615
Alias	Chr1:24879318_24885707
Organism	Cucumis sativus
Position	chrChr1: 24879318-24885707 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	CIRI2;Find_circ
Parent gene	Csa1G629080
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	Csa1G629080_circ_g.7 Csa1G629080_circ_g.8 Csa1G629080_circ_g.9 Csa1G629080_circ_g.10
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	CT-AC 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	Csa1G629080.1:7

			
						 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  
						
							TCTCAGAGTTCTTATGATGATCAAGACACGAATTTGAACTCTGAGCTAAATCATGATTCTCTCT
TGGGGATCCAACATCCGAATCATCTCCTCCAAAAGCctcattcctttgtttcctttcatgatta
acaaaagcaagtgtcgagtcaaaatcttgctgaagaaatctcctgcgggaagtaagactatttg
agagaaac

						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: 879
Transcript exons: 24879318-24879387,24881078-24881247,24881336-24881449,24
882094-24882177,24882256-24882316,24883737-24883786,2488
5378-24885707
CTCATTCCTTTGTTTCCTTTCATGATTAACAAAAGCAAGTGTCGAGTCAAAATCTTGCTGAAGA
AATCTCAATTGGGAGCCATGATTCTGAACATGCTGATATCGGTCACATGCATCAGATAAAGAAC
CATAGTTGTGTTGGCGTTGCTGATTCAACTGGTGGTGGAGCTCAGCAACTTTCTGCTTTAACCG
AGCCACATCTGCTTCAGCAAGAGCAATCTCCTCAAGCTCAGCCCTTGTCTTCGAATCCATGCCC
CGTGAATTATTAAATTGTCCAGAAGACATGCTTAGGCCAACTTCCAGAGCAGCTCTAAGATCTC
TTTCTGCTTGCAATTGCTCTTGTAATCTTGAAACATCTTGTTCAAGTGCCAACCGTCGTTCATG
CAAAGCTTGTTTCCTTCTTTCCAAGCTGGCTTGTAAAATTGCATTGCCTCTAGCCTCCTTCGCA
ATCCTCTGTTGCAGGTCATTTTTTGTCATCTCAAGCCTCTGAATAGCAAGCTCTTCTTCTCCAG
AAGAATCTACCGACTCAATAGATGGCGTCTTTCTGGCACTGCTCCTTCCCCAGAAAGTTGATCT
CTTAGCATTAATATTAGAGCTTGAAACTTTACCAACTGGCTTCCCAGAACTTGACTCATTTCCA
GGATCCATTGAATTTAAAATTTCTCCCATTGATCGGTAAGATTCGCCAGCAAGTGAGATATTCG
GAGTTTCCACCTCAGTCAAAGAATTTGCATTTCCTTTCTTTTGTTTGGTTAGGTCCCCAATCGG
TTGAACATTGGTCTCAGAGTTCTTATGATGATCAAGACACGAATTTGAACTCTGAGCTAAATCA
TGATTCTCTCTTGGGGATCCAACATCCGAATCATCTCCTCCAAAAGC
						
						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	TCTCAGAGTTCTTATGATGATCAAGACACGAATTTGAACTCTGAGCTAAATCATGATTCTCTCT TGGGGATCCAACATCCGAATCATCTCCTCCAAAAGCctcattcctttgtttcctttcatgatta acaaaagcaagtgtcgagtcaaaatcttgctgaagaaatctcctgcgggaagtaagactatttg agagaaac
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: 879 Transcript exons: 24879318-24879387,24881078-24881247,24881336-24881449,24 882094-24882177,24882256-24882316,24883737-24883786,2488 5378-24885707 CTCATTCCTTTGTTTCCTTTCATGATTAACAAAAGCAAGTGTCGAGTCAAAATCTTGCTGAAGA AATCTCAATTGGGAGCCATGATTCTGAACATGCTGATATCGGTCACATGCATCAGATAAAGAAC CATAGTTGTGTTGGCGTTGCTGATTCAACTGGTGGTGGAGCTCAGCAACTTTCTGCTTTAACCG AGCCACATCTGCTTCAGCAAGAGCAATCTCCTCAAGCTCAGCCCTTGTCTTCGAATCCATGCCC CGTGAATTATTAAATTGTCCAGAAGACATGCTTAGGCCAACTTCCAGAGCAGCTCTAAGATCTC TTTCTGCTTGCAATTGCTCTTGTAATCTTGAAACATCTTGTTCAAGTGCCAACCGTCGTTCATG CAAAGCTTGTTTCCTTCTTTCCAAGCTGGCTTGTAAAATTGCATTGCCTCTAGCCTCCTTCGCA ATCCTCTGTTGCAGGTCATTTTTTGTCATCTCAAGCCTCTGAATAGCAAGCTCTTCTTCTCCAG AAGAATCTACCGACTCAATAGATGGCGTCTTTCTGGCACTGCTCCTTCCCCAGAAAGTTGATCT CTTAGCATTAATATTAGAGCTTGAAACTTTACCAACTGGCTTCCCAGAACTTGACTCATTTCCA GGATCCATTGAATTTAAAATTTCTCCCATTGATCGGTAAGATTCGCCAGCAAGTGAGATATTCG GAGTTTCCACCTCAGTCAAAGAATTTGCATTTCCTTTCTTTTGTTTGGTTAGGTCCCCAATCGG TTGAACATTGGTCTCAGAGTTCTTATGATGATCAAGACACGAATTTGAACTCTGAGCTAAATCA TGATTCTCTCTTGGGGATCCAACATCCGAATCATCTCCTCCAAAAGC
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
						0.85344267

Conservation Information
Conserved circRNAs	NA
PMCS	0.85344267

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							24885499-24879320(-)
24879342-24885655(-)
						
						Potential amino acid sequence
						
							MGEILNSMDPGNESSSGKPVGKVSSSNINAKRSTFWGRSSARKTPSIESVDSSGEEELAIQRLE
MTKNDLQQRIAKEARGNAILQASLERRKQALHERRLALEQDVSRLQEQLQAERDLRAALEVGLS
MSSGQFNNSRGMDSKTRAELEEIALAEADVARLKQKVAELHHQLNQQRQHNYGSLSDACDRYQH
VQNHGSQLRFLQQDFDSTLAFVNHERKQRNEAFGGDDSDVGSPRENHDLAQSSNSCLDHHKNSE
TNVQPIGDLTKQKKGNANSLTEVETPNISLAGESYRSMGEILNSMDPGNESSSGKPVGKVSSSN
INAKRSTFWGRSSARKTPSIESVDSSGEEELAIQRLEMTKNDLQQRIAKEARGNAILQASLERR
KQALHERRLALEQDVSRLQEQLQAERDLRAALEVGLSMSSGQFNNSRGMDSKTRAELEEIALAE
ADVARLKQKVAELHHQLNQQRQHNYGSLSDACDRYQHVQNHGSQLRFLQQDFDSTLAFVNHERK
QRNEAFGGDDSDVGSPRENHDLAQSSNSCLDHHKNSETNVQPIGDLTKQKKGNANSLTEVETPN
ISLAGESYRSMGEILNSMDPGNESSSGKPVGKVSSSNINAKRSTFWGRSSARKTPSIESVDSSG
EEELAIQRLEMTKNDLQQRIAKEARGNAILQASLERRKQALHERRLALEQDVSRLQEQLQAERD
LRAALEVGLSMSSGQFNNSRGMDSKTRAELEEIALAEADVARLKQKVAELHHQLNQQRQHNYGS
LSDACDRYQHVQNHGSQLRFLQQDFDSTLAFVNHERKQRNEAFGGDDSDVGSPRENHDLAQSSN
SCLDHHKNSETNVQPIGDLTKQKKGNANSLTEVETPNISLAGESYRSMGEILNSMDPGNESSSG
KPVGKVSSSNINAKRSTFWGRSSARKTPSIESVDSSGEEELAIQRLEMTKNDLQQRIAKEARGN
AILQASLERRKQALHERRLALEQDVSRLQEQLQAERDLRAALEVGLSMSSGQFNNSRGMDSKTR
AELEEIALAEADVARLKQKVAELHHQLNQQRQHNYGSLSDACDRYQHVQNHGSQLRFLQQDFDS
TLAFVNHERKQRNE
MKGNKGMRLLEEMIRMLDPQERIMI*
						
						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	24885499-24879320(-) 24879342-24885655(-)
Potential amino acid sequence	MGEILNSMDPGNESSSGKPVGKVSSSNINAKRSTFWGRSSARKTPSIESVDSSGEEELAIQRLE MTKNDLQQRIAKEARGNAILQASLERRKQALHERRLALEQDVSRLQEQLQAERDLRAALEVGLS MSSGQFNNSRGMDSKTRAELEEIALAEADVARLKQKVAELHHQLNQQRQHNYGSLSDACDRYQH VQNHGSQLRFLQQDFDSTLAFVNHERKQRNEAFGGDDSDVGSPRENHDLAQSSNSCLDHHKNSE TNVQPIGDLTKQKKGNANSLTEVETPNISLAGESYRSMGEILNSMDPGNESSSGKPVGKVSSSN INAKRSTFWGRSSARKTPSIESVDSSGEEELAIQRLEMTKNDLQQRIAKEARGNAILQASLERR KQALHERRLALEQDVSRLQEQLQAERDLRAALEVGLSMSSGQFNNSRGMDSKTRAELEEIALAE ADVARLKQKVAELHHQLNQQRQHNYGSLSDACDRYQHVQNHGSQLRFLQQDFDSTLAFVNHERK QRNEAFGGDDSDVGSPRENHDLAQSSNSCLDHHKNSETNVQPIGDLTKQKKGNANSLTEVETPN ISLAGESYRSMGEILNSMDPGNESSSGKPVGKVSSSNINAKRSTFWGRSSARKTPSIESVDSSG EEELAIQRLEMTKNDLQQRIAKEARGNAILQASLERRKQALHERRLALEQDVSRLQEQLQAERD LRAALEVGLSMSSGQFNNSRGMDSKTRAELEEIALAEADVARLKQKVAELHHQLNQQRQHNYGS LSDACDRYQHVQNHGSQLRFLQQDFDSTLAFVNHERKQRNEAFGGDDSDVGSPRENHDLAQSSN SCLDHHKNSETNVQPIGDLTKQKKGNANSLTEVETPNISLAGESYRSMGEILNSMDPGNESSSG KPVGKVSSSNINAKRSTFWGRSSARKTPSIESVDSSGEEELAIQRLEMTKNDLQQRIAKEARGN AILQASLERRKQALHERRLALEQDVSRLQEQLQAERDLRAALEVGLSMSSGQFNNSRGMDSKTR AELEEIALAEADVARLKQKVAELHHQLNQQRQHNYGSLSDACDRYQHVQNHGSQLRFLQQDFDS TLAFVNHERKQRNE MKGNKGMRLLEEMIRMLDPQERIMI*
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to salt stress in root

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

circRNA

Detail information of Csa1G629080_circ_g.1

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