Plant Circular RNA Database

Detail information of Csa7G336540_circ_g.3

			
						 General Information
					
						CircRNA Name
						Csa7G336540_circ_g.3
					
						ID in PlantcircBase
						csa_circ_004585
					
						Alias
						Chr7:12028409_12033765
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr7: 12028409-12033765  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Csa7G336540						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							Csa7G336540_circ_g.1 Csa7G336540_circ_g.2 						
					
						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
						Csa7G336540.2:7
Csa7G336540.1:7

General Information
CircRNA Name	Csa7G336540_circ_g.3
ID in PlantcircBase	csa_circ_004585
Alias	Chr7:12028409_12033765
Organism	Cucumis sativus
Position	chrChr7: 12028409-12033765 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	CIRI2
Parent gene	Csa7G336540
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	Csa7G336540_circ_g.1 Csa7G336540_circ_g.2
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	Csa7G336540.2:7 Csa7G336540.1:7

			
						 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  
						
							GATCTTTGAAGTCGGTGCTGAAATGATGTTGGTTCCAAGGTGTCTGAAGATAACTCTACGTGGA
GACTGTTACTTTTTGAAAACGATCGACCTGGAACACctttgggtttaggaacgatgtagggact
ccacaaataaacatgtggcacgtcagattcagagaattgtgaaccacttaaatatgttacaggt
cgtatctg

						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: 1008
Transcript exons: 12028409-12028586,12028867-12028924,12029086-12029149,12
029941-12030111,12030411-12030522,12032832-12033071,1203
3581-12033765
CTTTGGGTTTAGGAACGATGTAGGGACTCCACAAATAAACATGTGGCACGTCAGATTCAGAGAA
TTGTGAACCACTTAAATATGTTACAGGTCGTATCTGCAGCTTCTTCTTCCTAAAATCATTAATA
ATGTCTCGCAGTCCAAGCCAAATCAAGGAATCAACGATTTGATATGAAAGCCTATACCCTGCTT
GTTGCTTGACTCGGGATAGTGGATGTGGAAATTCACTAGTTGGCGTCCATGGCATTGTAAAAAA
TATATGAAGCGGTAGCTTAAGTCCCTCTGCCACATGTGTGTGCCCATATGCTGTGCGGTTGGCA
ATGATTGCATCTGCTTCAAAGGGAATCCCGGTATCCATATCGGGATCTTTGCAAGCTGGAAGAA
GGGAATAAATAATTTCCTTCATTTGATTTCTTTGAATAAGTATCTCAGAAGGCCAAGAAGGCAA
GAAGCCTTTATTTCTTACCATATAAGCTGCAAGCTCTTTAGGATCCCCCCCTAAAGGATAAAAT
TCCAATCCAGCCAGCAAGACAAATTCCTTGAAATTTGGATGAGTAGCTAATCTAACACGATGGC
CATAGTCCTGCAAACGCTTGCCAATTGGAATAAATGGCTGCACATCTCCCCGGGTTCCGACGAT
AAGTATTACTATTTGCATGGGCCTTATATACTGAAAGTCAGATGTATCAAGGGGTTCATCATCA
ACATTAGTGAAAATTTCTTCAGATTCAACGTTGATAGATAGAGATTCGATGTCTTCTGGAACTT
CAAACTCGACAGACCCATCATCTTTCACAGTAGTTACTCTGTGCAACAATTTAATCTTCTGATC
AATGGGAATTTTAATATCTAATATATGAGCTGCATCTTCTGCAAATATGGTTTCATGTCTCAGC
CTCTCAGTTTTTGATCTTTGAAGTCGGTGCTGAAATGATGTTGGTTCCAAGGTGTCTGAAGATA
ACTCTACGTGGAGACTGTTACTTTTTGAAAACGATCGACCTGGAACAC
						
						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	GATCTTTGAAGTCGGTGCTGAAATGATGTTGGTTCCAAGGTGTCTGAAGATAACTCTACGTGGA GACTGTTACTTTTTGAAAACGATCGACCTGGAACACctttgggtttaggaacgatgtagggact ccacaaataaacatgtggcacgtcagattcagagaattgtgaaccacttaaatatgttacaggt cgtatctg
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: 1008 Transcript exons: 12028409-12028586,12028867-12028924,12029086-12029149,12 029941-12030111,12030411-12030522,12032832-12033071,1203 3581-12033765 CTTTGGGTTTAGGAACGATGTAGGGACTCCACAAATAAACATGTGGCACGTCAGATTCAGAGAA TTGTGAACCACTTAAATATGTTACAGGTCGTATCTGCAGCTTCTTCTTCCTAAAATCATTAATA ATGTCTCGCAGTCCAAGCCAAATCAAGGAATCAACGATTTGATATGAAAGCCTATACCCTGCTT GTTGCTTGACTCGGGATAGTGGATGTGGAAATTCACTAGTTGGCGTCCATGGCATTGTAAAAAA TATATGAAGCGGTAGCTTAAGTCCCTCTGCCACATGTGTGTGCCCATATGCTGTGCGGTTGGCA ATGATTGCATCTGCTTCAAAGGGAATCCCGGTATCCATATCGGGATCTTTGCAAGCTGGAAGAA GGGAATAAATAATTTCCTTCATTTGATTTCTTTGAATAAGTATCTCAGAAGGCCAAGAAGGCAA GAAGCCTTTATTTCTTACCATATAAGCTGCAAGCTCTTTAGGATCCCCCCCTAAAGGATAAAAT TCCAATCCAGCCAGCAAGACAAATTCCTTGAAATTTGGATGAGTAGCTAATCTAACACGATGGC CATAGTCCTGCAAACGCTTGCCAATTGGAATAAATGGCTGCACATCTCCCCGGGTTCCGACGAT AAGTATTACTATTTGCATGGGCCTTATATACTGAAAGTCAGATGTATCAAGGGGTTCATCATCA ACATTAGTGAAAATTTCTTCAGATTCAACGTTGATAGATAGAGATTCGATGTCTTCTGGAACTT CAAACTCGACAGACCCATCATCTTTCACAGTAGTTACTCTGTGCAACAATTTAATCTTCTGATC AATGGGAATTTTAATATCTAATATATGAGCTGCATCTTCTGCAAATATGGTTTCATGTCTCAGC CTCTCAGTTTTTGATCTTTGAAGTCGGTGCTGAAATGATGTTGGTTCCAAGGTGTCTGAAGATA ACTCTACGTGGAGACTGTTACTTTTTGAAAACGATCGACCTGGAACAC
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
						0.470324368

Conservation Information
Conserved circRNAs	NA
PMCS	0.470324368

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							12028452-12033723(-)
12032908-12028411(-)
						
						Potential amino acid sequence
						
							MFICGVPTSFLNPKVFQVDRFQKVTVST*
MQIVILIVGTRGDVQPFIPIGKRLQDYGHRVRLATHPNFKEFVLLAGLEFYPLGGDPKELAAYM
VRNKGFLPSWPSEILIQRNQMKEIIYSLLPACKDPDMDTGIPFEADAIIANRTAYGHTHVAEGL
KLPLHIFFTMPWTPTSEFPHPLSRVKQQAGYRLSYQIVDSLIWLGLRDIINDFRKKKLQIRPVT
YLSGSQFSESDVPHVYLWSPYIVPKPKGVPGRSFSKSNSLHVELSSDTLEPTSFQHRLQRSKTE
RLRHETIFAEDAAHILDIKIPIDQKIKLLHRVTTVKDDGSVEFEVPEDIESLSINVESEEIFTN
VDDEPLDTSDFQYIRPMQIVILIVGTRGDVQPFIPIGKRLQDYGHRVRLATHPNFKEFVLLAGL
EFYPLGGDPKELAAYMVRNKGFLPSWPSEILIQRNQMKEIIYSLLPACKDPDMDTGIPFEADAI
IANRTAYGHTHVAEGLKLPLHIFFTMPWTPTSEFPHPLSRVKQQAGYRLSYQIVDSLIWLGLRD
IINDFRKKKLQIRPVTYLSGSQFSESDVPHVYLWSPYIVPKPKGVPGRSFSKSNSLHVELSSDT
LEPTSFQHRLQRSKTERLRHETIFAEDAAHILDIKIPIDQKIKLLHRVTTVKDDGSVEFEVPED
IESLSINVESEEIFTNVDDEPLDTSDFQYIRPMQIVILIVGTRGDVQPFIPIGKRLQDYGHRVR
LATHPNFKEFVLLAGLEFYPLGGDPKELAAYMVRNKGFLPSWPSEILIQRNQMKEIIYSLLPAC
KDPDMDTGIPFEADAIIANRTAYGHTHVAEGLKLPLHIFFTMPWTPTSEFPHPLSRVKQQAGYR
LSYQIVDSLIWLGLRDIINDFRKKKLQIRPVTYLSGSQFSESDVPHVYLWSPYIVPKPKGVPGR
SFSKSNSLHVELSSDTLEPTSFQHRLQRSKTERLRHETIFAEDAAHILDIKIPIDQKIKLLHRV
TTVKDDGSVEFEVPEDIESLSINVESEEIFTNVDDEPLDTSDFQYIRPMQIVILIVGTRGDVQP
FIPIGKRLQDYGHRVRLATHPNFKEFVLLAGLEFYPLGGDPKELAAYMVRNKGFLPSWPSEILI
QRNQMKEIIYSLLPACKDPDMDTGIPFEADAIIANRTAYGHTHVAEGLKLPLHIFFTMPWTPTS
EFPHPLSRVKQQAGYRLSYQIVDSLIWLGLRDIINDFRKKKLQIRPVTYLSGSQFSESDVPHVY
LWSPYIVPKPK
						
						Sponge-miRNAs
						
							PC-5p-22000 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to salt stress in root (acting as miRNA sponges)

Functional Information
Coding potential	Y
Potential coding position	12028452-12033723(-) 12032908-12028411(-)
Potential amino acid sequence	MFICGVPTSFLNPKVFQVDRFQKVTVST* MQIVILIVGTRGDVQPFIPIGKRLQDYGHRVRLATHPNFKEFVLLAGLEFYPLGGDPKELAAYM VRNKGFLPSWPSEILIQRNQMKEIIYSLLPACKDPDMDTGIPFEADAIIANRTAYGHTHVAEGL KLPLHIFFTMPWTPTSEFPHPLSRVKQQAGYRLSYQIVDSLIWLGLRDIINDFRKKKLQIRPVT YLSGSQFSESDVPHVYLWSPYIVPKPKGVPGRSFSKSNSLHVELSSDTLEPTSFQHRLQRSKTE RLRHETIFAEDAAHILDIKIPIDQKIKLLHRVTTVKDDGSVEFEVPEDIESLSINVESEEIFTN VDDEPLDTSDFQYIRPMQIVILIVGTRGDVQPFIPIGKRLQDYGHRVRLATHPNFKEFVLLAGL EFYPLGGDPKELAAYMVRNKGFLPSWPSEILIQRNQMKEIIYSLLPACKDPDMDTGIPFEADAI IANRTAYGHTHVAEGLKLPLHIFFTMPWTPTSEFPHPLSRVKQQAGYRLSYQIVDSLIWLGLRD IINDFRKKKLQIRPVTYLSGSQFSESDVPHVYLWSPYIVPKPKGVPGRSFSKSNSLHVELSSDT LEPTSFQHRLQRSKTERLRHETIFAEDAAHILDIKIPIDQKIKLLHRVTTVKDDGSVEFEVPED IESLSINVESEEIFTNVDDEPLDTSDFQYIRPMQIVILIVGTRGDVQPFIPIGKRLQDYGHRVR LATHPNFKEFVLLAGLEFYPLGGDPKELAAYMVRNKGFLPSWPSEILIQRNQMKEIIYSLLPAC KDPDMDTGIPFEADAIIANRTAYGHTHVAEGLKLPLHIFFTMPWTPTSEFPHPLSRVKQQAGYR LSYQIVDSLIWLGLRDIINDFRKKKLQIRPVTYLSGSQFSESDVPHVYLWSPYIVPKPKGVPGR SFSKSNSLHVELSSDTLEPTSFQHRLQRSKTERLRHETIFAEDAAHILDIKIPIDQKIKLLHRV TTVKDDGSVEFEVPEDIESLSINVESEEIFTNVDDEPLDTSDFQYIRPMQIVILIVGTRGDVQP FIPIGKRLQDYGHRVRLATHPNFKEFVLLAGLEFYPLGGDPKELAAYMVRNKGFLPSWPSEILI QRNQMKEIIYSLLPACKDPDMDTGIPFEADAIIANRTAYGHTHVAEGLKLPLHIFFTMPWTPTS EFPHPLSRVKQQAGYRLSYQIVDSLIWLGLRDIINDFRKKKLQIRPVTYLSGSQFSESDVPHVY LWSPYIVPKPK
Sponge-miRNAs	PC-5p-22000
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to salt stress in root (acting as miRNA sponges)

			
						 Other Information
					
						References
						Zhu et al., 2019

circRNA

Detail information of Csa7G336540_circ_g.3

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