Plant Circular RNA Database

Detail information of Csa3G822420_circ_g.1

			
						 General Information
					
						CircRNA Name
						Csa3G822420_circ_g.1
					
						ID in PlantcircBase
						csa_circ_002068
					
						Alias
						Chr3:32301511_32307157
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr3: 32301511-32307157  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2;Find_circ
					
						Parent gene
						
							Csa3G822420						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							Csa3G822420_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  
						
							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
						Csa3G822420.1:8

General Information
CircRNA Name	Csa3G822420_circ_g.1
ID in PlantcircBase	csa_circ_002068
Alias	Chr3:32301511_32307157
Organism	Cucumis sativus
Position	chrChr3: 32301511-32307157 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	CIRI2;Find_circ
Parent gene	Csa3G822420
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	Csa3G822420_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	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	Csa3G822420.1:8

			
						 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  
						
							GTCTTCCTTGCAAGCTAAGCATCTTCAGAGCATCATTTCTGATATTCTTACGGCGGCTTTACCT
TGGTCGTCTGTCTCAAGGCATCATTTTAGATCCAAGgatgccattggatgcttggcttctatca
tggactccagggtgaccaaaaaggtttttatgtcacttcttgagaggtttcagtttctaaatac
taaggatg

						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: 930
Transcript exons: 32301511-32301683,32302726-32302819,32303342-32303398,32
304101-32304235,32305314-32305382,32306008-32306118,3230
6787-32306948,32307029-32307157
GATGCCATTGGATGCTTGGCTTCTATCATGGACTCCAGGGTGACCAAAAAGGTTTTTATGTCAC
TTCTTGAGAGGTTTCAGTTTCTAAATACTAAGGATGAGTTTGAGGAGCGAGAAGCCAATGCTGA
TGAATCAGCTCAGAATGCTGAAGGAAAGTCTAGGACCAGAGAGAGATGTGTAATGCTGGAGCTA
GCTGCAGCTATCGTCAGGGGAGCTGATGAGGATTTAATTGATCTAATTTATAAATTTGTTAAGT
TTTCTTTTCAGGGATCTTTAGGGTCGGACCATCATGAAGTGTATCAAACTCTGAGCAGAATTTT
GGAGGAACATGCTTGGTTTGCTTCTTCTAGATTTCCTGAACTGGTAGATATGTTAATTGATCTG
CAATCCCCTGTTGATACTTCTTCTCAAAGAAGTCGGTTTGGTTGCTTCCACATTCTTCTGGTTC
ATTCATTGAAGGTTAGCTCGGCAGAGGAGAGCAACAAGGCTTTTCTTATGCTCAACGAGATCAT
CATCACATTAAAAAGTGCAGAGGAAGACAGCAGGAAAGCAGCTTATGACATTCTTCATTGTATC
AGTTGCAGCCTAAAAGATTTGTCGCATACAAATTCTGATGCACATAAAAAATTTGTGGCCATGA
TAATGGGCTATCTGTCTGGTGCATCTCCTCATGTAAAAAGTGGAGCAATCTCTGCAGTCTCAGT
GTTGATTTATGAAGACGCAGATATATGTCTTTCAATACCTGATCTTGTGCCCTCCATCTTATCT
TTGCTACGAGGAAAGGCTATAGAAGTTATAAAAGCAGTGCTGGGGTTCGTGAAAGTTTTAGTGT
CTTCCTTGCAAGCTAAGCATCTTCAGAGCATCATTTCTGATATTCTTACGGCGGCTTTACCTTG
GTCGTCTGTCTCAAGGCATCATTTTAGATCCAAG
						
						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	GTCTTCCTTGCAAGCTAAGCATCTTCAGAGCATCATTTCTGATATTCTTACGGCGGCTTTACCT TGGTCGTCTGTCTCAAGGCATCATTTTAGATCCAAGgatgccattggatgcttggcttctatca tggactccagggtgaccaaaaaggtttttatgtcacttcttgagaggtttcagtttctaaatac taaggatg
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: 930 Transcript exons: 32301511-32301683,32302726-32302819,32303342-32303398,32 304101-32304235,32305314-32305382,32306008-32306118,3230 6787-32306948,32307029-32307157 GATGCCATTGGATGCTTGGCTTCTATCATGGACTCCAGGGTGACCAAAAAGGTTTTTATGTCAC TTCTTGAGAGGTTTCAGTTTCTAAATACTAAGGATGAGTTTGAGGAGCGAGAAGCCAATGCTGA TGAATCAGCTCAGAATGCTGAAGGAAAGTCTAGGACCAGAGAGAGATGTGTAATGCTGGAGCTA GCTGCAGCTATCGTCAGGGGAGCTGATGAGGATTTAATTGATCTAATTTATAAATTTGTTAAGT TTTCTTTTCAGGGATCTTTAGGGTCGGACCATCATGAAGTGTATCAAACTCTGAGCAGAATTTT GGAGGAACATGCTTGGTTTGCTTCTTCTAGATTTCCTGAACTGGTAGATATGTTAATTGATCTG CAATCCCCTGTTGATACTTCTTCTCAAAGAAGTCGGTTTGGTTGCTTCCACATTCTTCTGGTTC ATTCATTGAAGGTTAGCTCGGCAGAGGAGAGCAACAAGGCTTTTCTTATGCTCAACGAGATCAT CATCACATTAAAAAGTGCAGAGGAAGACAGCAGGAAAGCAGCTTATGACATTCTTCATTGTATC AGTTGCAGCCTAAAAGATTTGTCGCATACAAATTCTGATGCACATAAAAAATTTGTGGCCATGA TAATGGGCTATCTGTCTGGTGCATCTCCTCATGTAAAAAGTGGAGCAATCTCTGCAGTCTCAGT GTTGATTTATGAAGACGCAGATATATGTCTTTCAATACCTGATCTTGTGCCCTCCATCTTATCT TTGCTACGAGGAAAGGCTATAGAAGTTATAAAAGCAGTGCTGGGGTTCGTGAAAGTTTTAGTGT CTTCCTTGCAAGCTAAGCATCTTCAGAGCATCATTTCTGATATTCTTACGGCGGCTTTACCTTG GTCGTCTGTCTCAAGGCATCATTTTAGATCCAAG
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
						0.464994491

Conservation Information
Conserved circRNAs	NA
PMCS	0.464994491

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							32301539-32307154(+)
						
						Potential amino acid sequence
						
							MDSRVTKKVFMSLLERFQFLNTKDEFEEREANADESAQNAEGKSRTRERCVMLELAAAIVRGAD
EDLIDLIYKFVKFSFQGSLGSDHHEVYQTLSRILEEHAWFASSRFPELVDMLIDLQSPVDTSSQ
RSRFGCFHILLVHSLKVSSAEESNKAFLMLNEIIITLKSAEEDSRKAAYDILHCISCSLKDLSH
TNSDAHKKFVAMIMGYLSGASPHVKSGAISAVSVLIYEDADICLSIPDLVPSILSLLRGKAIEV
IKAVLGFVKVLVSSLQAKHLQSIISDILTAALPWSSVSRHHFRSKDAIGCLASIMDSRVTKKVF
MSLLERFQFLNTKDEFEEREANADESAQNAEGKSRTRERCVMLELAAAIVRGADEDLIDLIYKF
VKFSFQGSLGSDHHEVYQTLSRILEEHAWFASSRFPELVDMLIDLQSPVDTSSQRSRFGCFHIL
LVHSLKVSSAEESNKAFLMLNEIIITLKSAEEDSRKAAYDILHCISCSLKDLSHTNSDAHKKFV
AMIMGYLSGASPHVKSGAISAVSVLIYEDADICLSIPDLVPSILSLLRGKAIEVIKAVLGFVKV
LVSSLQAKHLQSIISDILTAALPWSSVSRHHFRSKDAIGCLASIMDSRVTKKVFMSLLERFQFL
NTKDEFEEREANADESAQNAEGKSRTRERCVMLELAAAIVRGADEDLIDLIYKFVKFSFQGSLG
SDHHEVYQTLSRILEEHAWFASSRFPELVDMLIDLQSPVDTSSQRSRFGCFHILLVHSLKVSSA
EESNKAFLMLNEIIITLKSAEEDSRKAAYDILHCISCSLKDLSHTNSDAHKKFVAMIMGYLSGA
SPHVKSGAISAVSVLIYEDADICLSIPDLVPSILSLLRGKAIEVIKAVLGFVKVLVSSLQAKHL
QSIISDILTAALPWSSVSRHHFRSKDAIGCLASIMDSRVTKKVFMSLLERFQFLNTKDEFEERE
ANADESAQNAEGKSRTRERCVMLELAAAIVRGADEDLIDLIYKFVKFSFQGSLGSDHHEVYQTL
SRILEEHAWFASSRFPELVDMLIDLQSPVDTSSQRSRFGCFHILLVHSLKVSSAEESNKAFLML
NEIIITLKSAEEDSRKAAYDILHCISCSLKDLSHTNSDAHKKFVAMIMGYLSGASPHVKSGAIS
AVSVLIYEDADICLSIPDLVPSILSLLRGKAIEVIKAVLGFVKVLVSSLQAKHLQSIISDILTA
ALPWSSVSRHHFRSK
						
						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	32301539-32307154(+)
Potential amino acid sequence	MDSRVTKKVFMSLLERFQFLNTKDEFEEREANADESAQNAEGKSRTRERCVMLELAAAIVRGAD EDLIDLIYKFVKFSFQGSLGSDHHEVYQTLSRILEEHAWFASSRFPELVDMLIDLQSPVDTSSQ RSRFGCFHILLVHSLKVSSAEESNKAFLMLNEIIITLKSAEEDSRKAAYDILHCISCSLKDLSH TNSDAHKKFVAMIMGYLSGASPHVKSGAISAVSVLIYEDADICLSIPDLVPSILSLLRGKAIEV IKAVLGFVKVLVSSLQAKHLQSIISDILTAALPWSSVSRHHFRSKDAIGCLASIMDSRVTKKVF MSLLERFQFLNTKDEFEEREANADESAQNAEGKSRTRERCVMLELAAAIVRGADEDLIDLIYKF VKFSFQGSLGSDHHEVYQTLSRILEEHAWFASSRFPELVDMLIDLQSPVDTSSQRSRFGCFHIL LVHSLKVSSAEESNKAFLMLNEIIITLKSAEEDSRKAAYDILHCISCSLKDLSHTNSDAHKKFV AMIMGYLSGASPHVKSGAISAVSVLIYEDADICLSIPDLVPSILSLLRGKAIEVIKAVLGFVKV LVSSLQAKHLQSIISDILTAALPWSSVSRHHFRSKDAIGCLASIMDSRVTKKVFMSLLERFQFL NTKDEFEEREANADESAQNAEGKSRTRERCVMLELAAAIVRGADEDLIDLIYKFVKFSFQGSLG SDHHEVYQTLSRILEEHAWFASSRFPELVDMLIDLQSPVDTSSQRSRFGCFHILLVHSLKVSSA EESNKAFLMLNEIIITLKSAEEDSRKAAYDILHCISCSLKDLSHTNSDAHKKFVAMIMGYLSGA SPHVKSGAISAVSVLIYEDADICLSIPDLVPSILSLLRGKAIEVIKAVLGFVKVLVSSLQAKHL QSIISDILTAALPWSSVSRHHFRSKDAIGCLASIMDSRVTKKVFMSLLERFQFLNTKDEFEERE ANADESAQNAEGKSRTRERCVMLELAAAIVRGADEDLIDLIYKFVKFSFQGSLGSDHHEVYQTL SRILEEHAWFASSRFPELVDMLIDLQSPVDTSSQRSRFGCFHILLVHSLKVSSAEESNKAFLML NEIIITLKSAEEDSRKAAYDILHCISCSLKDLSHTNSDAHKKFVAMIMGYLSGASPHVKSGAIS AVSVLIYEDADICLSIPDLVPSILSLLRGKAIEVIKAVLGFVKVLVSSLQAKHLQSIISDILTA ALPWSSVSRHHFRSK
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 Csa3G822420_circ_g.1

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