Plant Circular RNA Database

Detail information of Csa3G608160_circ_g.1

			
						 General Information
					
						CircRNA Name
						Csa3G608160_circ_g.1
					
						ID in PlantcircBase
						csa_circ_001831
					
						Alias
						Chr3:23563394_23565172
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr3: 23563394-23565172  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Csa3G608160						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						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
						Csa3G608160.1:5
Csa3G608160.2:5

General Information
CircRNA Name	Csa3G608160_circ_g.1
ID in PlantcircBase	csa_circ_001831
Alias	Chr3:23563394_23565172
Organism	Cucumis sativus
Position	chrChr3: 23563394-23565172 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	CIRI2
Parent gene	Csa3G608160
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	NA
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	Csa3G608160.1:5 Csa3G608160.2:5

			
						 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  
						
							TTCTTCCAGGAACCAGAAGGATTTGAGCAATTGGGCATCTGCATCAGATGGGGTAAACAAATGG
ACGTTTTGTGGGTCAGCTCTGTCTGCTGAAGAAAGGggatctaaaaacacttcagattggatat
ctgttataactagtgctgatgacaaaaagttgcaattgtcgaagtgtacaagttctgcttctga
agaggaag

									
								

					

						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: 822
Transcript exons: 23563394-23563732,23563855-23563955,23564274-23564460,23
564598-23564701,23565082-23565172
GGATCTAAAAACACTTCAGATTGGATATCTGTTATAACTAGTGCTGATGACAAAAAGTTGCAAT
TGTCGAAGTGTACAAGTTCTGCTTCTGAAGAGGAAGGTCACCTGAGGGACCTCAAGAGACAAAA
GTTGAATTATGGTCAGTTAAAGTTTCGCATAAGCAGTGCTGATCAAACTCATCCTCCAGTTTCA
GAGCCTGGAAATTCAGAGACTTCGAATTCTGGGATGGAACACAAATCTCAAGTAACTAATGCTA
GCAGCATGCCTCTTGCCGATGCAGATGACACCATTGTGAGGAATGTCAAATGTGCGTTTTGCCA
GTCATCTAAAGTTACAGAGGATACTGGAGCTGTCCTGCATTATATGAATGGCAGATTGGTTGAT
GGAGTTGAGGCAGCAAGTCCAAATGTCATACATGTTCACAAACTTTGTGTTGAATGGGCACCGC
AGGCATACTTTCAGGGTGATGATGTCCATAATTTGAAGGCTGAAGTGGCAAGGGGTTCAAAGCT
TAAGTGCAGTAAATGTGGGCTAAAAGGAGCAGCCCTAGGTTGTTATTTGAGGTCTTGCCAGAAA
AGCTATCACGTTCCTTGTGCACTTGAAATAGACGAGTGCCGTTGGGACATGGACAATTTTCTTG
TTCTGTGCCCCTCACATACGTCAGCAAGATTTCCAGATGAAAGGTCAAAGCCTAGGAAGATGCC
TAGAGATCAGGCTTCTCTATTTCAAATGAACCAGAAGGATTTGAGCAATTGGGCATCTGCATCA
GATGGGGTAAACAAATGGACGTTTTGTGGGTCAGCTCTGTCTGCTGAAGAAAGG
						
					

						Genomic sequence
						
							GGATCTAAAAACACTTCAGATTGGATATCTGTTATAACTAGTGCTGATGACAAAAAGTTGCAAT
TGTCGAAGTGTACAAGTTCTGCTTCTGAAGAGGAAGGTCACCTGAGGGACCTCAAGAGACAAAA
GTTGAATTATGGTCAGTTAAAGTTTCGCATAAGCAGTGCTGATCAAACTCATCCTCCAGTTTCA
GAGCCTGGAAATTCAGAGACTTCGAATTCTGGGATGGAACACAAATCTCAAGTAACTAATGCTA
GCAGCATGCCTCTTGCCGATGCAGATGACACCATTGTGAGGAATGTCAAATGTGCGTTTTGCCA
GTCATCTAAAGTTACAGAGGTATTAATATTAAAGATCATATATTTGTTATCTGCATCTCTGTTT
GCTTTATATCACGTAATGGATAAATGGTGATTTGATATATAATTTGTTTCTTTATGTTAATTTT
CTATTAATTCTAGGATACTGGAGCTGTCCTGCATTATATGAATGGCAGATTGGTTGATGGAGTT
GAGGCAGCAAGTCCAAATGTCATACATGTTCACAAACTTTGTGTTGAATGGTATTCAATCTCCA
TCCCATGTACCCTGCATTTTAATGGGAAGCCAATTTAAACAATTTGCAAGTTTGTAGGGTTGAA
GATTAGCATTTTTTTTCTTGTTTTGTAATTCTTGTTTTTTTCTTTTTTTAAATTTAACTTTTAA
TGCTGTTATTTATTTATTTTTACTTTAATAAAAGAGAGTGCACGTTAGCAATTGTAATTTGTTC
GTGTGCTTGGTCATTTTTTTATGATGACTTTTTCAATTGTGCTGTGCTGTGCTGTCTTGTCTTT
TTTCTTTATGGTATTGGTGATGATATAACATGCTGATTTGAAATGCAGGGCACCGCAGGCATAC
TTTCAGGGTGATGATGTCCATAATTTGAAGGCTGAAGTGGCAAGGGGTTCAAAGCTTAAGTGCA
GTAAATGTGGGCTAAAAGGAGCAGCCCTAGGTTGTTATTTGAGGTCTTGCCAGAAAAGCTATCA
CGTTCCTTGTGCACTTGAAATAGACGAGTGCCGTTGGGACATGGTAAATGCACTATCCTCGAGA
ATTGTAGACTTGCCATTGCCATTGTCTTTGTTTTTCTTAGTTTTCTTTGGTGACATATTTATTA
TTCTTTCTTAAAGTAGTACATATGCTTATTATTATCTTTCTAAATTTTACAGGACAATTTTCTT
GTTCTGTGCCCCTCACATACGTCAGCAAGATTTCCAGATGAAAGGTCAAAGCCTAGGAAGATGC
CTAGAGATCAGGCTTCTCTATTTCAAATGTAAAATATTTTATCTTTTCAGTCGCTTTGAAATGT
TCAACTTGTATTTATTTAATTTGGCTTGGCACTTCGGAATCTTGGTTGATTCTAATATCTAAAT
TAATTACTTCATGTCGGCCAGGCTTCATTATGCTTTAATATTGCTACTAGTTCTTAAAATATAT
GGGTTATATTCGTTTGTCCTATTTGTGATGTGAGGTGCAAACACAAATCTAAAGCAAAACAATA
GATGTTTTACTCTAAATCTCACAGAATAATTATGAAACATGTCAATGCAATACTCATTTTATAT
TTCACGATGGATATATTTTTTTTTTTTGGAAGAACAGAGATTTGCTTCGTGACAATAATTTTGA
TGTGTTTAATATTGTTTCTTCCAGGAACCAGAAGGATTTGAGCAATTGGGCATCTGCATCAGAT
GGGGTAAACAAATGGACGTTTTGTGGGTCAGCTCTGTCTGCTGAAGAAAGG
						
					

			
		

Sequences
Splice junction sequence	TTCTTCCAGGAACCAGAAGGATTTGAGCAATTGGGCATCTGCATCAGATGGGGTAAACAAATGG ACGTTTTGTGGGTCAGCTCTGTCTGCTGAAGAAAGGggatctaaaaacacttcagattggatat ctgttataactagtgctgatgacaaaaagttgcaattgtcgaagtgtacaagttctgcttctga agaggaag
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: 822 Transcript exons: 23563394-23563732,23563855-23563955,23564274-23564460,23 564598-23564701,23565082-23565172 GGATCTAAAAACACTTCAGATTGGATATCTGTTATAACTAGTGCTGATGACAAAAAGTTGCAAT TGTCGAAGTGTACAAGTTCTGCTTCTGAAGAGGAAGGTCACCTGAGGGACCTCAAGAGACAAAA GTTGAATTATGGTCAGTTAAAGTTTCGCATAAGCAGTGCTGATCAAACTCATCCTCCAGTTTCA GAGCCTGGAAATTCAGAGACTTCGAATTCTGGGATGGAACACAAATCTCAAGTAACTAATGCTA GCAGCATGCCTCTTGCCGATGCAGATGACACCATTGTGAGGAATGTCAAATGTGCGTTTTGCCA GTCATCTAAAGTTACAGAGGATACTGGAGCTGTCCTGCATTATATGAATGGCAGATTGGTTGAT GGAGTTGAGGCAGCAAGTCCAAATGTCATACATGTTCACAAACTTTGTGTTGAATGGGCACCGC AGGCATACTTTCAGGGTGATGATGTCCATAATTTGAAGGCTGAAGTGGCAAGGGGTTCAAAGCT TAAGTGCAGTAAATGTGGGCTAAAAGGAGCAGCCCTAGGTTGTTATTTGAGGTCTTGCCAGAAA AGCTATCACGTTCCTTGTGCACTTGAAATAGACGAGTGCCGTTGGGACATGGACAATTTTCTTG TTCTGTGCCCCTCACATACGTCAGCAAGATTTCCAGATGAAAGGTCAAAGCCTAGGAAGATGCC TAGAGATCAGGCTTCTCTATTTCAAATGAACCAGAAGGATTTGAGCAATTGGGCATCTGCATCA GATGGGGTAAACAAATGGACGTTTTGTGGGTCAGCTCTGTCTGCTGAAGAAAGG
Genomic sequence	GGATCTAAAAACACTTCAGATTGGATATCTGTTATAACTAGTGCTGATGACAAAAAGTTGCAAT TGTCGAAGTGTACAAGTTCTGCTTCTGAAGAGGAAGGTCACCTGAGGGACCTCAAGAGACAAAA GTTGAATTATGGTCAGTTAAAGTTTCGCATAAGCAGTGCTGATCAAACTCATCCTCCAGTTTCA GAGCCTGGAAATTCAGAGACTTCGAATTCTGGGATGGAACACAAATCTCAAGTAACTAATGCTA GCAGCATGCCTCTTGCCGATGCAGATGACACCATTGTGAGGAATGTCAAATGTGCGTTTTGCCA GTCATCTAAAGTTACAGAGGTATTAATATTAAAGATCATATATTTGTTATCTGCATCTCTGTTT GCTTTATATCACGTAATGGATAAATGGTGATTTGATATATAATTTGTTTCTTTATGTTAATTTT CTATTAATTCTAGGATACTGGAGCTGTCCTGCATTATATGAATGGCAGATTGGTTGATGGAGTT GAGGCAGCAAGTCCAAATGTCATACATGTTCACAAACTTTGTGTTGAATGGTATTCAATCTCCA TCCCATGTACCCTGCATTTTAATGGGAAGCCAATTTAAACAATTTGCAAGTTTGTAGGGTTGAA GATTAGCATTTTTTTTCTTGTTTTGTAATTCTTGTTTTTTTCTTTTTTTAAATTTAACTTTTAA TGCTGTTATTTATTTATTTTTACTTTAATAAAAGAGAGTGCACGTTAGCAATTGTAATTTGTTC GTGTGCTTGGTCATTTTTTTATGATGACTTTTTCAATTGTGCTGTGCTGTGCTGTCTTGTCTTT TTTCTTTATGGTATTGGTGATGATATAACATGCTGATTTGAAATGCAGGGCACCGCAGGCATAC TTTCAGGGTGATGATGTCCATAATTTGAAGGCTGAAGTGGCAAGGGGTTCAAAGCTTAAGTGCA GTAAATGTGGGCTAAAAGGAGCAGCCCTAGGTTGTTATTTGAGGTCTTGCCAGAAAAGCTATCA CGTTCCTTGTGCACTTGAAATAGACGAGTGCCGTTGGGACATGGTAAATGCACTATCCTCGAGA ATTGTAGACTTGCCATTGCCATTGTCTTTGTTTTTCTTAGTTTTCTTTGGTGACATATTTATTA TTCTTTCTTAAAGTAGTACATATGCTTATTATTATCTTTCTAAATTTTACAGGACAATTTTCTT GTTCTGTGCCCCTCACATACGTCAGCAAGATTTCCAGATGAAAGGTCAAAGCCTAGGAAGATGC CTAGAGATCAGGCTTCTCTATTTCAAATGTAAAATATTTTATCTTTTCAGTCGCTTTGAAATGT TCAACTTGTATTTATTTAATTTGGCTTGGCACTTCGGAATCTTGGTTGATTCTAATATCTAAAT TAATTACTTCATGTCGGCCAGGCTTCATTATGCTTTAATATTGCTACTAGTTCTTAAAATATAT GGGTTATATTCGTTTGTCCTATTTGTGATGTGAGGTGCAAACACAAATCTAAAGCAAAACAATA GATGTTTTACTCTAAATCTCACAGAATAATTATGAAACATGTCAATGCAATACTCATTTTATAT TTCACGATGGATATATTTTTTTTTTTTGGAAGAACAGAGATTTGCTTCGTGACAATAATTTTGA TGTGTTTAATATTGTTTCTTCCAGGAACCAGAAGGATTTGAGCAATTGGGCATCTGCATCAGAT GGGGTAAACAAATGGACGTTTTGTGGGTCAGCTCTGTCTGCTGAAGAAAGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.473779961

Conservation Information
Conserved circRNAs	NA
PMCS	0.473779961

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							23563620-23565169(+)
						
						Potential amino acid sequence
						
							MEHKSQVTNASSMPLADADDTIVRNVKCAFCQSSKVTEDTGAVLHYMNGRLVDGVEAASPNVIH
VHKLCVEWAPQAYFQGDDVHNLKAEVARGSKLKCSKCGLKGAALGCYLRSCQKSYHVPCALEID
ECRWDMDNFLVLCPSHTSARFPDERSKPRKMPRDQASLFQMNQKDLSNWASASDGVNKWTFCGS
ALSAEERGSKNTSDWISVITSADDKKLQLSKCTSSASEEEGHLRDLKRQKLNYGQLKFRISSAD
QTHPPVSEPGNSETSNSGMEHKSQVTNASSMPLADADDTIVRNVKCAFCQSSKVTEDTGAVLHY
MNGRLVDGVEAASPNVIHVHKLCVEWAPQAYFQGDDVHNLKAEVARGSKLKCSKCGLKGAALGC
YLRSCQKSYHVPCALEIDECRWDMDNFLVLCPSHTSARFPDERSKPRKMPRDQASLFQMNQKDL
SNWASASDGVNKWTFCGSALSAEERGSKNTSDWISVITSADDKKLQLSKCTSSASEEEGHLRDL
KRQKLNYGQLKFRISSADQTHPPVSEPGNSETSNSGMEHKSQVTNASSMPLADADDTIVRNVKC
AFCQSSKVTEDTGAVLHYMNGRLVDGVEAASPNVIHVHKLCVEWAPQAYFQGDDVHNLKAEVAR
GSKLKCSKCGLKGAALGCYLRSCQKSYHVPCALEIDECRWDMDNFLVLCPSHTSARFPDERSKP
RKMPRDQASLFQMNQKDLSNWASASDGVNKWTFCGSALSAEERGSKNTSDWISVITSADDKKLQ
LSKCTSSASEEEGHLRDLKRQKLNYGQLKFRISSADQTHPPVSEPGNSETSNSGMEHKSQVTNA
SSMPLADADDTIVRNVKCAFCQSSKVTEDTGAVLHYMNGRLVDGVEAASPNVIHVHKLCVEWAP
QAYFQGDDVHNLKAEVARGSKLKCSKCGLKGAALGCYLRSCQKSYHVPCALEIDECRWDMDNFL
VLCPSHTSARFPDERSKPRKMPRDQASLFQMNQKDLSNWASASDGVNKWTFCGSALSAEER
						
						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	23563620-23565169(+)
Potential amino acid sequence	MEHKSQVTNASSMPLADADDTIVRNVKCAFCQSSKVTEDTGAVLHYMNGRLVDGVEAASPNVIH VHKLCVEWAPQAYFQGDDVHNLKAEVARGSKLKCSKCGLKGAALGCYLRSCQKSYHVPCALEID ECRWDMDNFLVLCPSHTSARFPDERSKPRKMPRDQASLFQMNQKDLSNWASASDGVNKWTFCGS ALSAEERGSKNTSDWISVITSADDKKLQLSKCTSSASEEEGHLRDLKRQKLNYGQLKFRISSAD QTHPPVSEPGNSETSNSGMEHKSQVTNASSMPLADADDTIVRNVKCAFCQSSKVTEDTGAVLHY MNGRLVDGVEAASPNVIHVHKLCVEWAPQAYFQGDDVHNLKAEVARGSKLKCSKCGLKGAALGC YLRSCQKSYHVPCALEIDECRWDMDNFLVLCPSHTSARFPDERSKPRKMPRDQASLFQMNQKDL SNWASASDGVNKWTFCGSALSAEERGSKNTSDWISVITSADDKKLQLSKCTSSASEEEGHLRDL KRQKLNYGQLKFRISSADQTHPPVSEPGNSETSNSGMEHKSQVTNASSMPLADADDTIVRNVKC AFCQSSKVTEDTGAVLHYMNGRLVDGVEAASPNVIHVHKLCVEWAPQAYFQGDDVHNLKAEVAR GSKLKCSKCGLKGAALGCYLRSCQKSYHVPCALEIDECRWDMDNFLVLCPSHTSARFPDERSKP RKMPRDQASLFQMNQKDLSNWASASDGVNKWTFCGSALSAEERGSKNTSDWISVITSADDKKLQ LSKCTSSASEEEGHLRDLKRQKLNYGQLKFRISSADQTHPPVSEPGNSETSNSGMEHKSQVTNA SSMPLADADDTIVRNVKCAFCQSSKVTEDTGAVLHYMNGRLVDGVEAASPNVIHVHKLCVEWAP QAYFQGDDVHNLKAEVARGSKLKCSKCGLKGAALGCYLRSCQKSYHVPCALEIDECRWDMDNFL VLCPSHTSARFPDERSKPRKMPRDQASLFQMNQKDLSNWASASDGVNKWTFCGSALSAEER
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to salt stress in root

			
						 Other Information
					
						References
						Zhu et al., 2019

circRNA

Detail information of Csa3G608160_circ_g.1

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