Plant Circular RNA Database

Detail information of Csa2G169730_circ_g.1

			
						 General Information
					
						CircRNA Name
						Csa2G169730_circ_g.1
					
						ID in PlantcircBase
						csa_circ_000990
					
						Alias
						Chr2:9567963_9570258
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr2: 9567963-9570258  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2;Find_circ
					
						Parent gene
						
							Csa2G169730						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							Csa2G169730_circ_g.2 Csa2G169730_circ_g.3 Csa2G169730_circ_g.4 						
					
						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
						Csa2G169730.1:5

General Information
CircRNA Name	Csa2G169730_circ_g.1
ID in PlantcircBase	csa_circ_000990
Alias	Chr2:9567963_9570258
Organism	Cucumis sativus
Position	chrChr2: 9567963-9570258 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	CIRI2;Find_circ
Parent gene	Csa2G169730
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	Csa2G169730_circ_g.2 Csa2G169730_circ_g.3 Csa2G169730_circ_g.4
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	Csa2G169730.1:5

			
						 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  
						
							CTGATCGGAAGAGATTATTCAGCATACTGGTGCAAGGTAGAGATAAAGTGGAGACACGAATTCT
CCTCTGACCAAATACTGTAGTGTAGAGTAGCGCACAcgtaggtaggaacatctttgacgtcgta
tctcattcatcaagtcattgagtttctttgatagaggattgtcgtactgctgcagcacagactg
agcaagtg

									
								

					

						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: 716
Transcript exons: 9567963-9568051,9568697-9568873,9568965-9569110,9569509-
9569673,9570120-9570258
CGTAGGTAGGAACATCTTTGACGTCGTATCTCATTCATCAAGTCATTGAGTTTCTTTGATAGAG
GATTGTCGTACTGCTGCAGCACAGACTGAGCCGGAATTTCGTCAACTGAGGAAATACCAAATAA
CTGCTGCAGTATGTCTCTATCAACCAAGTTCCCAACATATACTAAACAATCTTCACCATTCTCA
AGAAGATAAATTCCCTCTTCGCTCACATGCTCACTGGAAAGAGGAATTGGAGTACCGGGAGTTG
AATCACCATCCTCCGTATCAAGGTTATGTATAGCCAACATTCTAGGATAGACCAAGGGAACAGC
CAGAGGAATTGGGAGGGAAGAAACATGGTTGACCCAAAAAGATCGATCATCAATTCTCCCTTCA
GTTCTCAAACCTGTACTTTTTATTAACGCAATGGTATAAAGTGGCAGTAGCTTTAGAGCCTCTG
GCAGGATGAGTTGTCCAGATGATGATACTGTTGCACAATACTTGCGGTATGAAAGCAAAACGTT
GACACAAAGATTTGTAATACGTTCTCGAATTTGCAGGAGTGGAGATGAAGGAACTTCATTTGCC
GCTTGCTTCAGAAAACATGCGAACTGAGTGTCCAAGTCAGCTGATCGGAAGAGATTATTCAGCA
TACTGGTGCAAGGTAGAGATAAAGTGGAGACACGAATTCTCCTCTGACCAAATACTGTAGTGTA
GAGTAGCGCACA
						
					

						Genomic sequence
						
							CGTAGGTAGGAACATCTTTGACGTCGTATCTCATTCATCAAGTCATTGAGTTTCTTTGATAGAG
GATTGTCGTACTGCTGCAGCACAGACTGAGCAAGTGGCAGATTTAAAAGACATTAGATTCCATC
CAACATATGAATCCAATTAAGACATCACATGCATACACAATTTATTAAGTTCGCAGCAATTTTA
TATACCAAACCATGATAAGAAAAAAAAATAACAGCAGTTCTCTTTTCCCTCTATCATCATCTCC
TTTCTAGAGTCAATGGCCAGATATTGTTTTCCTTCATCTATATATATACATATAGATAGGAAAC
AATAACTTCATTGATGCGATGAAAGAGCACCTATCCAATGGATTACAGAAAACCTCTCCAATTG
GTCATAAGATTAGTTAAACTATAGTTACAAAAAGAGGAGATCAATTTAATTTTACACCAACTCA
GATATAAGAAAGTTAAAGAAGTGAGAAATGTTATATTTTTTTGTAAAACCAAGTGAATTTGTGT
TCTACATGATCTTTCCTGGCTACGTGATTTAAAATGAAAAACTCTGTGAGCAGTACTAACAATA
ATACCCATGCCTAGGTGCGCGCCCGAGTGTGCCTTTCCAAACACTGGGCTTACCTCCCCTTTTA
TAATCCCATTCAATCAATAAAATTGTTTCTCATCCCATAAATAAATAATATGCATATTTAACAT
GCTTGGCAAGTCTGCATAGTAGAGTAATACCTGAGCCGGAATTTCGTCAACTGAGGAAATACCA
AATAACTGCTGCAGTATGTCTCTATCAACCAAGTTCCCAACATATACTAAACAATCTTCACCAT
TCTCAAGAAGATAAATTCCCTCTTCGCTCACATGCTCACTGGAAAGAGGAATTGGAGTACCGGG
AGTTGAATCACCATCCTGTCAACAAAGAGGAATTAACACCAACCGAGAACAGTGCACCACTGAG
AAAGAAAACAAACAAAATATATGAACAAAGTGAAAGTCATACCTCCGTATCAAGGTTATGTATA
GCCAACATTCTAGGATAGACCAAGGGAACAGCCAGAGGAATTGGGAGGGAAGAAACATGGTTGA
CCCAAAAAGATCGATCATCAATTCTCCCTTCAGTTCTCAAACCTGTACTTTTTATTAACGCTGA
AAGAATCCAATAGAATAATATCATTGATCCCCATCCATGTACCAAAATTTATCAGCACAAATAT
GCTTATACTTTATTCTTATGCTTATGAACAGATAACTGAATTCTCTCCATTCAACAAATTCAAC
TAAATATCTTAGTTAAATCCCATATTCTCCAATTTCCCAAGATGATCCAAAGATTATTAACTAC
CAAGTCTTTATCAAGATGCTCCTGTGTGTTCTCCAGATAGTATTATTTATTGGTGTACGAGTTC
AGAATTAATGCACAAAAAAAATATAGTTTGTAAAACCTAATAAGGAGAAAATGGATTTTAAAGC
AAAGAAACTTTCTGATATATGTGCAGAAAACCGTGGGTCAATTAGATACATTATTGTATGGATA
AAATACACACCAATGGTATAAAGTGGCAGTAGCTTTAGAGCCTCTGGCAGGATGAGTTGTCCAG
ATGATGATACTGTTGCACAATACTTGCGGTATGAAAGCAAAACGTTGACACAAAGATTTGTAAT
ACGTTCTCGAATTTGCAGGAGTGGAGATGAAGGAACTTCATTTGCCGCTACAAAAATTAGACAA
AAAAGTAAAAACATAACGCTGATGCAACTAGAGAACTCATATTGAAACAAATATTAAAGGTTGC
ATATAGCATTGAAAGGGCAAAGTATGAAATCGATTCCAGTGACATTAAAGTTTGTTCATGCGAA
GATTATATGTCATCTGACGACAATCAATCAACTATGAGGAAGTGTAGATGTGAGACCTTTTCTT
TTTTTGAAAAGGAAGGAAACAAGAACTTCTATTGAAAATAAATGTAAATGTGAGACCAATGATA
ATGGCAGCAAGTAGCAACAGTTTCTTATTCCCAAAAGAAAAGAAGAAAAAGAAGAAAACTTTTT
TTTAGAAGGAAATGAGAGAAAAAAAAGATAATTACAGCAACAAACTGCAAAAGAGATTTATTAA
AACAAAATTGAAAAAAAAAAAAAAAACCCAAGAAAGTGAAGATACCTTGCTTCAGAAAACATGC
GAACTGAGTGTCCAAGTCAGCTGATCGGAAGAGATTATTCAGCATACTGGTGCAAGGTAGAGAT
AAAGTGGAGACACGAATTCTCCTCTGACCAAATACTGTAGTGTAGAGTAGCGCACA
						
					

			
		

Sequences
Splice junction sequence	CTGATCGGAAGAGATTATTCAGCATACTGGTGCAAGGTAGAGATAAAGTGGAGACACGAATTCT CCTCTGACCAAATACTGTAGTGTAGAGTAGCGCACAcgtaggtaggaacatctttgacgtcgta tctcattcatcaagtcattgagtttctttgatagaggattgtcgtactgctgcagcacagactg agcaagtg
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: 716 Transcript exons: 9567963-9568051,9568697-9568873,9568965-9569110,9569509- 9569673,9570120-9570258 CGTAGGTAGGAACATCTTTGACGTCGTATCTCATTCATCAAGTCATTGAGTTTCTTTGATAGAG GATTGTCGTACTGCTGCAGCACAGACTGAGCCGGAATTTCGTCAACTGAGGAAATACCAAATAA CTGCTGCAGTATGTCTCTATCAACCAAGTTCCCAACATATACTAAACAATCTTCACCATTCTCA AGAAGATAAATTCCCTCTTCGCTCACATGCTCACTGGAAAGAGGAATTGGAGTACCGGGAGTTG AATCACCATCCTCCGTATCAAGGTTATGTATAGCCAACATTCTAGGATAGACCAAGGGAACAGC CAGAGGAATTGGGAGGGAAGAAACATGGTTGACCCAAAAAGATCGATCATCAATTCTCCCTTCA GTTCTCAAACCTGTACTTTTTATTAACGCAATGGTATAAAGTGGCAGTAGCTTTAGAGCCTCTG GCAGGATGAGTTGTCCAGATGATGATACTGTTGCACAATACTTGCGGTATGAAAGCAAAACGTT GACACAAAGATTTGTAATACGTTCTCGAATTTGCAGGAGTGGAGATGAAGGAACTTCATTTGCC GCTTGCTTCAGAAAACATGCGAACTGAGTGTCCAAGTCAGCTGATCGGAAGAGATTATTCAGCA TACTGGTGCAAGGTAGAGATAAAGTGGAGACACGAATTCTCCTCTGACCAAATACTGTAGTGTA GAGTAGCGCACA
Genomic sequence	CGTAGGTAGGAACATCTTTGACGTCGTATCTCATTCATCAAGTCATTGAGTTTCTTTGATAGAG GATTGTCGTACTGCTGCAGCACAGACTGAGCAAGTGGCAGATTTAAAAGACATTAGATTCCATC CAACATATGAATCCAATTAAGACATCACATGCATACACAATTTATTAAGTTCGCAGCAATTTTA TATACCAAACCATGATAAGAAAAAAAAATAACAGCAGTTCTCTTTTCCCTCTATCATCATCTCC TTTCTAGAGTCAATGGCCAGATATTGTTTTCCTTCATCTATATATATACATATAGATAGGAAAC AATAACTTCATTGATGCGATGAAAGAGCACCTATCCAATGGATTACAGAAAACCTCTCCAATTG GTCATAAGATTAGTTAAACTATAGTTACAAAAAGAGGAGATCAATTTAATTTTACACCAACTCA GATATAAGAAAGTTAAAGAAGTGAGAAATGTTATATTTTTTTGTAAAACCAAGTGAATTTGTGT TCTACATGATCTTTCCTGGCTACGTGATTTAAAATGAAAAACTCTGTGAGCAGTACTAACAATA ATACCCATGCCTAGGTGCGCGCCCGAGTGTGCCTTTCCAAACACTGGGCTTACCTCCCCTTTTA TAATCCCATTCAATCAATAAAATTGTTTCTCATCCCATAAATAAATAATATGCATATTTAACAT GCTTGGCAAGTCTGCATAGTAGAGTAATACCTGAGCCGGAATTTCGTCAACTGAGGAAATACCA AATAACTGCTGCAGTATGTCTCTATCAACCAAGTTCCCAACATATACTAAACAATCTTCACCAT TCTCAAGAAGATAAATTCCCTCTTCGCTCACATGCTCACTGGAAAGAGGAATTGGAGTACCGGG AGTTGAATCACCATCCTGTCAACAAAGAGGAATTAACACCAACCGAGAACAGTGCACCACTGAG AAAGAAAACAAACAAAATATATGAACAAAGTGAAAGTCATACCTCCGTATCAAGGTTATGTATA GCCAACATTCTAGGATAGACCAAGGGAACAGCCAGAGGAATTGGGAGGGAAGAAACATGGTTGA CCCAAAAAGATCGATCATCAATTCTCCCTTCAGTTCTCAAACCTGTACTTTTTATTAACGCTGA AAGAATCCAATAGAATAATATCATTGATCCCCATCCATGTACCAAAATTTATCAGCACAAATAT GCTTATACTTTATTCTTATGCTTATGAACAGATAACTGAATTCTCTCCATTCAACAAATTCAAC TAAATATCTTAGTTAAATCCCATATTCTCCAATTTCCCAAGATGATCCAAAGATTATTAACTAC CAAGTCTTTATCAAGATGCTCCTGTGTGTTCTCCAGATAGTATTATTTATTGGTGTACGAGTTC AGAATTAATGCACAAAAAAAATATAGTTTGTAAAACCTAATAAGGAGAAAATGGATTTTAAAGC AAAGAAACTTTCTGATATATGTGCAGAAAACCGTGGGTCAATTAGATACATTATTGTATGGATA AAATACACACCAATGGTATAAAGTGGCAGTAGCTTTAGAGCCTCTGGCAGGATGAGTTGTCCAG ATGATGATACTGTTGCACAATACTTGCGGTATGAAAGCAAAACGTTGACACAAAGATTTGTAAT ACGTTCTCGAATTTGCAGGAGTGGAGATGAAGGAACTTCATTTGCCGCTACAAAAATTAGACAA AAAAGTAAAAACATAACGCTGATGCAACTAGAGAACTCATATTGAAACAAATATTAAAGGTTGC ATATAGCATTGAAAGGGCAAAGTATGAAATCGATTCCAGTGACATTAAAGTTTGTTCATGCGAA GATTATATGTCATCTGACGACAATCAATCAACTATGAGGAAGTGTAGATGTGAGACCTTTTCTT TTTTTGAAAAGGAAGGAAACAAGAACTTCTATTGAAAATAAATGTAAATGTGAGACCAATGATA ATGGCAGCAAGTAGCAACAGTTTCTTATTCCCAAAAGAAAAGAAGAAAAAGAAGAAAACTTTTT TTTAGAAGGAAATGAGAGAAAAAAAAGATAATTACAGCAACAAACTGCAAAAGAGATTTATTAA AACAAAATTGAAAAAAAAAAAAAAAACCCAAGAAAGTGAAGATACCTTGCTTCAGAAAACATGC GAACTGAGTGTCCAAGTCAGCTGATCGGAAGAGATTATTCAGCATACTGGTGCAAGGTAGAGAT AAAGTGGAGACACGAATTCTCCTCTGACCAAATACTGTAGTGTAGAGTAGCGCACA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						1.10350948

Conservation Information
Conserved circRNAs	NA
PMCS	1.10350948

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9570185-9570179(-)
9567998-9570175(-)
9567979-9570179(-)
						
						Potential amino acid sequence
						
							MLNNLFRSADLDTQFACFLKQAANEVPSSPLLQIRERITNLCVNVLLSYRKYCATVSSSGQLIL
PEALKLLPLYTIALIKSTGLRTEGRIDDRSFWVNHVSSLPIPLAVPLVYPRMLAIHNLDTEDGD
STPGTPIPLSSEHVSEEGIYLLENGEDCLVYVGNLVDRDILQQLFGISSVDEIPAQSVLQQYDN
PLSKKLNDLMNEIRRQRCSYLRVRYSTLQYLVRGEFVSPLYLYLAPVC*
MRYDVKDVPTYVCATLHYSIWSEENSCLHFISTLHQYAE*
MFLPTCALLYTTVFGQRRIRVSTLSLPCTSMLNNLFRSADLDTQFACFLKQAANEVPSSPLLQI
RERITNLCVNVLLSYRKYCATVSSSGQLILPEALKLLPLYTIALIKSTGLRTEGRIDDRSFWVN
HVSSLPIPLAVPLVYPRMLAIHNLDTEDGDSTPGTPIPLSSEHVSEEGIYLLENGEDCLVYVGN
LVDRDILQQLFGISSVDEIPAQSVLQQYDNPLSKKLNDLMNEIRRQRCSYLRVRYSTLQYLVRG
EFVSPLYLYLAPVC*
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	9570185-9570179(-) 9567998-9570175(-) 9567979-9570179(-)
Potential amino acid sequence	MLNNLFRSADLDTQFACFLKQAANEVPSSPLLQIRERITNLCVNVLLSYRKYCATVSSSGQLIL PEALKLLPLYTIALIKSTGLRTEGRIDDRSFWVNHVSSLPIPLAVPLVYPRMLAIHNLDTEDGD STPGTPIPLSSEHVSEEGIYLLENGEDCLVYVGNLVDRDILQQLFGISSVDEIPAQSVLQQYDN PLSKKLNDLMNEIRRQRCSYLRVRYSTLQYLVRGEFVSPLYLYLAPVC* MRYDVKDVPTYVCATLHYSIWSEENSCLHFISTLHQYAE* MFLPTCALLYTTVFGQRRIRVSTLSLPCTSMLNNLFRSADLDTQFACFLKQAANEVPSSPLLQI RERITNLCVNVLLSYRKYCATVSSSGQLILPEALKLLPLYTIALIKSTGLRTEGRIDDRSFWVN HVSSLPIPLAVPLVYPRMLAIHNLDTEDGDSTPGTPIPLSSEHVSEEGIYLLENGEDCLVYVGN LVDRDILQQLFGISSVDEIPAQSVLQQYDNPLSKKLNDLMNEIRRQRCSYLRVRYSTLQYLVRG EFVSPLYLYLAPVC*
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 Csa2G169730_circ_g.1

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