Plant Circular RNA Database

Detail information of Csa3G790980_circ_g.1

			
						 General Information
					
						CircRNA Name
						Csa3G790980_circ_g.1
					
						ID in PlantcircBase
						csa_circ_001991
					
						Alias
						Chr3:30586393_30591466
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr3: 30586393-30591466  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Find_circ
					
						Parent gene
						
							Csa3G790980						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							Csa3G790980_circ_g.2 						
					
						Support reads
						NA
					
						Tissues
						leaf
					
						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
						Csa3G790980.1:11

General Information
CircRNA Name	Csa3G790980_circ_g.1
ID in PlantcircBase	csa_circ_001991
Alias	Chr3:30586393_30591466
Organism	Cucumis sativus
Position	chrChr3: 30586393-30591466 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	Find_circ
Parent gene	Csa3G790980
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	Csa3G790980_circ_g.2
Support reads	NA
Tissues	leaf
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	Csa3G790980.1:11

			
						 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  
						
							TTTACAAGGTACCCTCGACTAGGATCATAAAGATCACTGAGAGGCATGAATGATGTAAAACCCC
AATCACTTTCTCTAGCATTGAATTGGTGTTTTGTGTcttgaaaagattaaaaggtacttgtttc
tgaatacggaaactgcgaactttgtcatgatcaacaagatcgaagtatatatccttccctattt
gttcttga

									
								

					

						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: 1421
Transcript exons: 30586393-30586512,30586804-30586884,30586976-30587122,30
587236-30587314,30588664-30588738,30589742-30589851,3058
9958-30590056,30590445-30590560,30590649-30590757,305909
13-30591131,30591201-30591466
CTTGAAAAGATTAAAAGGTACTTGTTTCTGAATACGGAAACTGCGAACTTTGTCATGATCAACA
AGATCGAAGTATATATCCTTCCCTATTTGTTCTTGAAGGTCCACATCTCGTGCAACCTTGATAA
TTGCATAGAGATGGGCCTGAGCTTTATATTTTCTCTTGTCTTCCTTCTCCTCCTGCTCTTTCTT
TAACCTTATCCTAAGGTGTTCAGCTATGTCTTTCTCATCCACATTGCAAATTATTTTGTCCTTG
TCACTTTCACGGATGTACACAAGCATATATGCATTAGAATATTTGGTGAACTTGAAGGGAGTAT
TGTTGAAACCAGGGTTGGTCTGCGGCAACTCTTCCTCACCACCATATTGCTCTTCTAATGCTCT
CTTCGTATCTTCTTTTGTTACACGCTCGTCATCAAATTTGTACCACTGATCGGATAAGGTTGGT
CTGATAAAAGCATAATAATGCCCACCATGGACACCACCACTATGTACCAGCACACTATGAAGTG
TGTACAGGTTCCGAACGCTCCTATCTGCTTCTGGCGATAGATACTTGCCGTTCTCTCTATCAAG
GTCTAGTTGAAGAGGAAACTCATAGCGATCATTTATCTTCACCATTGTATCCCGCATAAAATCG
TACTCAAACCTCTTCAACTGAAGTTGGAGGACTGGAGGGAAGTCAATAAACAAGACGCCCTTCT
TAGCTTCCTGCAAGCCATGCTCTTCTGCATGATACTTATTATCACCCTCAAGACGTTCAACTTC
CACATACTTATCAAAAGATGCATACACATCATTACAACCCTTCACATCAAGCTGGAGATCATAA
AATGACTCCTTTCTTGTAGATTTGTAGTCAACATTAATGCATTCTATGTAATTCATGTGATGAC
CCTCAAATAACTGCTGTATTGTCCCCTCTACAACAGTTCCCTTCATTTTATCTTCAAGCTTTTC
ACACAAAACTCTATTGAGTTCTTGCACATCATGTTGCATAAAAGAATCATAAGTATCCCATCCA
AAGGACTTAGTAAGCTCTTTAGTTGCAACACTGCTGGCATTAAATTGAAGTTTATAGAACAAAC
TTTGAAGAGCCAAAGGGATGCTTCCTGAAGGCATGTCATTCTCGGTTGTCGGCATATGGTAAAC
AGCCTTTCTGAAGTAAGGTATATGATAAAGTGTCTGAAGAAGAGAATTCATGTAACAAGTTGCT
CCTTGATTCTTAAGACCCACATATCCAGTTTCTTTCTTTGAATCATATGACCAGTAATCAAGCA
CCTTACGAACCAGAACCTCAGCTTCAACAATACATGTGTCATTTACAAGGTACCCTCGACTAGG
ATCATAAAGATCACTGAGAGGCATGAATGATGTAAAACCCCAATCACTTTCTCTAGCATTGAAT
TGGTGTTTTGTGT
						
					

						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	TTTACAAGGTACCCTCGACTAGGATCATAAAGATCACTGAGAGGCATGAATGATGTAAAACCCC AATCACTTTCTCTAGCATTGAATTGGTGTTTTGTGTcttgaaaagattaaaaggtacttgtttc tgaatacggaaactgcgaactttgtcatgatcaacaagatcgaagtatatatccttccctattt gttcttga
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: 1421 Transcript exons: 30586393-30586512,30586804-30586884,30586976-30587122,30 587236-30587314,30588664-30588738,30589742-30589851,3058 9958-30590056,30590445-30590560,30590649-30590757,305909 13-30591131,30591201-30591466 CTTGAAAAGATTAAAAGGTACTTGTTTCTGAATACGGAAACTGCGAACTTTGTCATGATCAACA AGATCGAAGTATATATCCTTCCCTATTTGTTCTTGAAGGTCCACATCTCGTGCAACCTTGATAA TTGCATAGAGATGGGCCTGAGCTTTATATTTTCTCTTGTCTTCCTTCTCCTCCTGCTCTTTCTT TAACCTTATCCTAAGGTGTTCAGCTATGTCTTTCTCATCCACATTGCAAATTATTTTGTCCTTG TCACTTTCACGGATGTACACAAGCATATATGCATTAGAATATTTGGTGAACTTGAAGGGAGTAT TGTTGAAACCAGGGTTGGTCTGCGGCAACTCTTCCTCACCACCATATTGCTCTTCTAATGCTCT CTTCGTATCTTCTTTTGTTACACGCTCGTCATCAAATTTGTACCACTGATCGGATAAGGTTGGT CTGATAAAAGCATAATAATGCCCACCATGGACACCACCACTATGTACCAGCACACTATGAAGTG TGTACAGGTTCCGAACGCTCCTATCTGCTTCTGGCGATAGATACTTGCCGTTCTCTCTATCAAG GTCTAGTTGAAGAGGAAACTCATAGCGATCATTTATCTTCACCATTGTATCCCGCATAAAATCG TACTCAAACCTCTTCAACTGAAGTTGGAGGACTGGAGGGAAGTCAATAAACAAGACGCCCTTCT TAGCTTCCTGCAAGCCATGCTCTTCTGCATGATACTTATTATCACCCTCAAGACGTTCAACTTC CACATACTTATCAAAAGATGCATACACATCATTACAACCCTTCACATCAAGCTGGAGATCATAA AATGACTCCTTTCTTGTAGATTTGTAGTCAACATTAATGCATTCTATGTAATTCATGTGATGAC CCTCAAATAACTGCTGTATTGTCCCCTCTACAACAGTTCCCTTCATTTTATCTTCAAGCTTTTC ACACAAAACTCTATTGAGTTCTTGCACATCATGTTGCATAAAAGAATCATAAGTATCCCATCCA AAGGACTTAGTAAGCTCTTTAGTTGCAACACTGCTGGCATTAAATTGAAGTTTATAGAACAAAC TTTGAAGAGCCAAAGGGATGCTTCCTGAAGGCATGTCATTCTCGGTTGTCGGCATATGGTAAAC AGCCTTTCTGAAGTAAGGTATATGATAAAGTGTCTGAAGAAGAGAATTCATGTAACAAGTTGCT CCTTGATTCTTAAGACCCACATATCCAGTTTCTTTCTTTGAATCATATGACCAGTAATCAAGCA CCTTACGAACCAGAACCTCAGCTTCAACAATACATGTGTCATTTACAAGGTACCCTCGACTAGG ATCATAAAGATCACTGAGAGGCATGAATGATGTAAAACCCCAATCACTTTCTCTAGCATTGAAT TGGTGTTTTGTGT
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
						0.516684698

Conservation Information
Conserved circRNAs	NA
PMCS	0.516684698

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							30586450-30591444(-)
30591415-30591370(-)
						
						Potential amino acid sequence
						
							MTKFAVSVFRNKYLLIFSRHKTPIQC*
MPLSDLYDPSRGYLVNDTCIVEAEVLVRKVLDYWSYDSKKETGYVGLKNQGATCYMNSLLQTLY
HIPYFRKAVYHMPTTENDMPSGSIPLALQSLFYKLQFNASSVATKELTKSFGWDTYDSFMQHDV
QELNRVLCEKLEDKMKGTVVEGTIQQLFEGHHMNYIECINVDYKSTRKESFYDLQLDVKGCNDV
YASFDKYVEVERLEGDNKYHAEEHGLQEAKKGVLFIDFPPVLQLQLKRFEYDFMRDTMVKINDR
YEFPLQLDLDRENGKYLSPEADRSVRNLYTLHSVLVHSGGVHGGHYYAFIRPTLSDQWYKFDDE
RVTKEDTKRALEEQYGGEEELPQTNPGFNNTPFKFTKYSNAYMLVYIRESDKDKIICNVDEKDI
AEHLRIRLKKEQEEKEDKRKYKAQAHLYAIIKVARDVDLQEQIGKDIYFDLVDHDKVRSFRIQK
QVPFNLFKTQNTNSMLEKVIGVLHHSCLSVIFMILVEGTL*
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	30586450-30591444(-) 30591415-30591370(-)
Potential amino acid sequence	MTKFAVSVFRNKYLLIFSRHKTPIQC* MPLSDLYDPSRGYLVNDTCIVEAEVLVRKVLDYWSYDSKKETGYVGLKNQGATCYMNSLLQTLY HIPYFRKAVYHMPTTENDMPSGSIPLALQSLFYKLQFNASSVATKELTKSFGWDTYDSFMQHDV QELNRVLCEKLEDKMKGTVVEGTIQQLFEGHHMNYIECINVDYKSTRKESFYDLQLDVKGCNDV YASFDKYVEVERLEGDNKYHAEEHGLQEAKKGVLFIDFPPVLQLQLKRFEYDFMRDTMVKINDR YEFPLQLDLDRENGKYLSPEADRSVRNLYTLHSVLVHSGGVHGGHYYAFIRPTLSDQWYKFDDE RVTKEDTKRALEEQYGGEEELPQTNPGFNNTPFKFTKYSNAYMLVYIRESDKDKIICNVDEKDI AEHLRIRLKKEQEEKEDKRKYKAQAHLYAIIKVARDVDLQEQIGKDIYFDLVDHDKVRSFRIQK QVPFNLFKTQNTNSMLEKVIGVLHHSCLSVIFMILVEGTL*
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						He et al., 2020

circRNA

Detail information of Csa3G790980_circ_g.1

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