Plant Circular RNA Database

Detail information of Csa1G109350_circ_g.1

			
						 General Information
					
						CircRNA Name
						Csa1G109350_circ_g.1
					
						ID in PlantcircBase
						csa_circ_000275
					
						Alias
						Chr1:8834920_8836475
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr1: 8834920-8836475  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Csa1G109350						
					
						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  
						
							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
						Csa1G109350.1:2

General Information
CircRNA Name	Csa1G109350_circ_g.1
ID in PlantcircBase	csa_circ_000275
Alias	Chr1:8834920_8836475
Organism	Cucumis sativus
Position	chrChr1: 8834920-8836475 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	CIRI2
Parent gene	Csa1G109350
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	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	Csa1G109350.1:2

			
						 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  
						
							CTCTCCCCAACATAGGCATCTGGAAATTTCTTCCCTGTCCTTTATTGTTCATGAGGTTCTGAGA
TGTCTGAGAAATGTGATTGTGCATATTCCAATTATCcccttcatcttggtcaaaactttcagag
ggaaccacattagtttcggtcctgcatttagcatgcactatgggccctaactgagaaatatcca
tgccggct

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							CCCTTCATCTTGGTCAAAACTTTCAGAGGGAACCACATTAGTTTCGGTCCTGCATTTAGCATGC
ACTATGGGCCCTAACTGAGAAATATCCATGCCGGCTGTTTGTCCATCAGGTGCATTCATGTAGA
CAGCACCCCGATACATCCACTCCTCTGTTTCATCACTGTAAAAATCCTCGAAAGGTTCTCCACA
TAATGCACATGTCTTCTGATCCTCGTCAGCAGGAACAGCCAGTTCTTCATCATCTTTTTTCTCT
ACAACAACCTCAGCAGGCAAAAATCCTGGAACTGCCTCCGTTCCTAAAGCCTCTGCACCGCTAA
GCCACATGCTAATACTTACAAACCATTTGCGAGAAGGCTTTTGCTTCCTACTTTTCGACATACG
ATTTTTAGTGACATGCCAATCCATATGATTACTATGCTCTTCCTGGGTCTTGAATCGAAGACCA
CAGGTCATGCATTGTCGAGGAAGATCAGCATATAGAGCAGTGATTGCAGATTCATGTCGCACCT
TGAGTACATCTGGATTGAATTCTAACCCAACAGAATCCTAACATTTAACTCTCTTAGTGGATAA
AATATAACAGTAGAAAAAATTAAATGCCCAAACTAAAGTTAGTAAGAGGGGTACTACCCAGATG
TATATACCTGTACAGAAGCTTGATTGTTTAATGAGATTAAACCCCGGGCCATGAGAGAACTTAT
TAGCCCAGAAATTGCAGTTCCCGGTTGCTGTCCAGGAACCTTTTGAGAGATAGGTATAGTCGGA
CCAGAAGTAGGATGAGGCCCAGGTGGAAGAGGTGGCAGCGGCCCTCCTTGTAAATGCAAAGGGT
TACTGGAGCTATTATGAACAGACAAATTCCATTGTCCAATAGGGGCAGAACTTGACAAACCCTC
ACTAATAGCAGGGCGATGTCCTTGTGAAATGTATCCTTGACTCAAAGATGGTGCCATTAAATGT
GGTAACACTGGAGGTACTGCTGATCCACTAAAATTATCTTGCATGTCCTGAGATGGTAGAAATT
GCGGTTTTAAAGGCATGCCCTGCAATTGGTTTCCCCGAGTTAAAGGAATATGCCCAGTATGTTG
GTTGCCAACTTGTGGCGACTTAGTTGTAAGACTTAGCTCCTTATTTCTCAAGTTATTCATCTGC
TGCTCAGGCAAAAAAGTCCTATTTGCACAATTCATGAAAGAATTGCTACCATTTAAAGACTCAA
ACTGACTTGCATTGTGTCTTGGTACAGGAAAAATTGGAGGTCTAGAGGGTGGGCAAGAGTTAGA
AAGATTCAGAGGATGCCTTGGGCCCATAGATTGTACAATTGATTGCGACTCCATGCTAGAGTCG
AGACCAGAAGAACCCAATCTCGAAGCAATGTTAGTGGGCCTATGTAAAGCATCATTGGTCAAAA
GCTTGTCACCATAAGGAGACATCTTCTCACCAACAGAGGAAGTTATGCCTCTCCCCAACATAGG
CATCTGGAAATTTCTTCCCTGTCCTTTATTGTTCATGAGGTTCTGAGATGTCTGAGAAATGTGA
TTGTGCATATTCCAATTATC
						
					

			
		

Sequences
Splice junction sequence	CTCTCCCCAACATAGGCATCTGGAAATTTCTTCCCTGTCCTTTATTGTTCATGAGGTTCTGAGA TGTCTGAGAAATGTGATTGTGCATATTCCAATTATCcccttcatcttggtcaaaactttcagag ggaaccacattagtttcggtcctgcatttagcatgcactatgggccctaactgagaaatatcca tgccggct
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CCCTTCATCTTGGTCAAAACTTTCAGAGGGAACCACATTAGTTTCGGTCCTGCATTTAGCATGC ACTATGGGCCCTAACTGAGAAATATCCATGCCGGCTGTTTGTCCATCAGGTGCATTCATGTAGA CAGCACCCCGATACATCCACTCCTCTGTTTCATCACTGTAAAAATCCTCGAAAGGTTCTCCACA TAATGCACATGTCTTCTGATCCTCGTCAGCAGGAACAGCCAGTTCTTCATCATCTTTTTTCTCT ACAACAACCTCAGCAGGCAAAAATCCTGGAACTGCCTCCGTTCCTAAAGCCTCTGCACCGCTAA GCCACATGCTAATACTTACAAACCATTTGCGAGAAGGCTTTTGCTTCCTACTTTTCGACATACG ATTTTTAGTGACATGCCAATCCATATGATTACTATGCTCTTCCTGGGTCTTGAATCGAAGACCA CAGGTCATGCATTGTCGAGGAAGATCAGCATATAGAGCAGTGATTGCAGATTCATGTCGCACCT TGAGTACATCTGGATTGAATTCTAACCCAACAGAATCCTAACATTTAACTCTCTTAGTGGATAA AATATAACAGTAGAAAAAATTAAATGCCCAAACTAAAGTTAGTAAGAGGGGTACTACCCAGATG TATATACCTGTACAGAAGCTTGATTGTTTAATGAGATTAAACCCCGGGCCATGAGAGAACTTAT TAGCCCAGAAATTGCAGTTCCCGGTTGCTGTCCAGGAACCTTTTGAGAGATAGGTATAGTCGGA CCAGAAGTAGGATGAGGCCCAGGTGGAAGAGGTGGCAGCGGCCCTCCTTGTAAATGCAAAGGGT TACTGGAGCTATTATGAACAGACAAATTCCATTGTCCAATAGGGGCAGAACTTGACAAACCCTC ACTAATAGCAGGGCGATGTCCTTGTGAAATGTATCCTTGACTCAAAGATGGTGCCATTAAATGT GGTAACACTGGAGGTACTGCTGATCCACTAAAATTATCTTGCATGTCCTGAGATGGTAGAAATT GCGGTTTTAAAGGCATGCCCTGCAATTGGTTTCCCCGAGTTAAAGGAATATGCCCAGTATGTTG GTTGCCAACTTGTGGCGACTTAGTTGTAAGACTTAGCTCCTTATTTCTCAAGTTATTCATCTGC TGCTCAGGCAAAAAAGTCCTATTTGCACAATTCATGAAAGAATTGCTACCATTTAAAGACTCAA ACTGACTTGCATTGTGTCTTGGTACAGGAAAAATTGGAGGTCTAGAGGGTGGGCAAGAGTTAGA AAGATTCAGAGGATGCCTTGGGCCCATAGATTGTACAATTGATTGCGACTCCATGCTAGAGTCG AGACCAGAAGAACCCAATCTCGAAGCAATGTTAGTGGGCCTATGTAAAGCATCATTGGTCAAAA GCTTGTCACCATAAGGAGACATCTTCTCACCAACAGAGGAAGTTATGCCTCTCCCCAACATAGG CATCTGGAAATTTCTTCCCTGTCCTTTATTGTTCATGAGGTTCTGAGATGTCTGAGAAATGTGA TTGTGCATATTCCAATTATC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.556125134

Conservation Information
Conserved circRNAs	NA
PMCS	0.556125134

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							8836465-8834922(-)
8834983-8836426(-)
						
					

						Potential amino acid sequence
						
							MHNHISQTSQNLMNNKGQGRNFQMPMLGRGITSSVGEKMSPYGDKLLTNDALHRPTNIASRLGS
SGLDSSMESQSIVQSMGPRHPLNLSNSCPPSRPPIFPVPRHNASQFESLNGSNSFMNCANRTFL
PEQQMNNLRNKELSLTTKSPQVGNQHTGHIPLTRGNQLQGMPLKPQFLPSQDMQDNFSGSAVPP
VLPHLMAPSLSQGYISQGHRPAISEGLSSSAPIGQWNLSVHNSSSNPLHLQGGPLPPLPPGPHP
TSGPTIPISQKVPGQQPGTAISGLISSLMARGLISLNNQASVQDSVGLEFNPDVLKVRHESAIT
ALYADLPRQCMTCGLRFKTQEEHSNHMDWHVTKNRMSKSRKQKPSRKWFVSISMWLSGAEALGT
EAVPGFLPAEVVVEKKDDEELAVPADEDQKTCALCGEPFEDFYSDETEEWMYRGAVYMNAPDGQ
TAGMDISQLGPIVHAKCRTETNVVPSESFDQDEGDNWNMHNHISQTSQNLMNNKGQGRNFQMPM
LGRGITSSVGEKMSPYGDKLLTNDALHRPTNIASRLGSSGLDSSMESQSIVQSMGPRHPLNLSN
SCPPSRPPIFPVPRHNASQFESLNGSNSFMNCANRTFLPEQQMNNLRNKELSLTTKSPQVGNQH
TGHIPLTRGNQLQGMPLKPQFLPSQDMQDNFSGSAVPPVLPHLMAPSLSQGYISQGHRPAISEG
LSSSAPIGQWNLSVHNSSSNPLHLQGGPLPPLPPGPHPTSGPTIPISQKVPGQQPGTAISGLIS
SLMARGLISLNNQASVQDSVGLEFNPDVLKVRHESAITALYADLPRQCMTCGLRFKTQEEHSNH
MDWHVTKNRMSKSRKQKPSRKWFVSISMWLSGAEALGTEAVPGFLPAEVVVEKKDDEELAVPAD
EDQKTCALCGEPFEDFYSDETEEWMYRGAVYMNAPDGQTAGMDISQLGPIVHAKCRTETNVVPS
ESFDQDEGDNWNMHNHISQTSQNLMNNKGQGRNFQMPMLGRGITSSVGEKMSPYGDKLLTNDAL
HRPTNIASRLGSSGLDSSMESQSIVQSMGPRHPLNLSNSCPPSRPPIFPVPRHNASQFESLNGS
NSFMNCANRTFLPEQQMNNLRNKELSLTTKSPQVGNQHTGHIPLTRGNQLQGMPLKPQFLPSQD
MQDNFSGSAVPPVLPHLMAPSLSQGYISQGHRPAISEGLSSSAPIGQWNLSVHNSSSNPLHLQG
GPLPPLPPGPHPTSGPTIPISQKVPGQQPGTAISGLISSLMARGLISLNNQASVQDSVGLEFNP
DVLKVRHESAITALYADLPRQCMTCGLRFKTQEEHSNHMDWHVTKNRMSKSRKQKPSRKWFVSI
SMWLSGAEALGTEAVPGFLPAEVVVEKKDDEELAVPADEDQKTCALCGEPFEDFYSDETEEWMY
RGAVYMNAPDGQTAGMDISQLGPIVHAKCRTETNVVPSESFDQDEGDNWNMHNHISQTSQNLMN
NKGQGRNFQMPMLGRGITSSVGEKMSPYGDKLLTNDALHRPTNIASRLGSSGLDSSMESQSIVQ
SMGPRHPLNLSNSCPPSRPPIFPVPRHNASQFESLNGSNSFMNCANRTFLPEQQMNNLRNKELS
LTTKSPQVGNQHTGHIPLTRGNQLQGMPLKPQFLPSQDMQDNFSGSAVPPVLPHLMAPSLSQGY
ISQGHRPAISEGLSSSAPIGQWNLSVHNSSSNPLHLQGGPLPPLPPGPHPTSGPTIPISQKVPG
QQPGTAISGLISSLMARGLISLNNQASVQDSVGLEFNPDVLKVRHESAITALYADLPRQCMTCG
LRFKTQEEHSNHMDWHVTKNRMSKSRKQKPSRKWFVSISMWLSGAEALGTEAVPGFLPAEVVVE
KKDDEELAVPADEDQKTCALCGEPFEDFYSDETEEWMYRGAVYMNAPDGQTAGMDISQLGPIVH
AKCRTETNVVPSESFDQDEG
MLNAGPKLMWFPLKVLTKMKGIIGICTITFLRHLRTS*
						
					

						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	8836465-8834922(-) 8834983-8836426(-)
Potential amino acid sequence	MHNHISQTSQNLMNNKGQGRNFQMPMLGRGITSSVGEKMSPYGDKLLTNDALHRPTNIASRLGS SGLDSSMESQSIVQSMGPRHPLNLSNSCPPSRPPIFPVPRHNASQFESLNGSNSFMNCANRTFL PEQQMNNLRNKELSLTTKSPQVGNQHTGHIPLTRGNQLQGMPLKPQFLPSQDMQDNFSGSAVPP VLPHLMAPSLSQGYISQGHRPAISEGLSSSAPIGQWNLSVHNSSSNPLHLQGGPLPPLPPGPHP TSGPTIPISQKVPGQQPGTAISGLISSLMARGLISLNNQASVQDSVGLEFNPDVLKVRHESAIT ALYADLPRQCMTCGLRFKTQEEHSNHMDWHVTKNRMSKSRKQKPSRKWFVSISMWLSGAEALGT EAVPGFLPAEVVVEKKDDEELAVPADEDQKTCALCGEPFEDFYSDETEEWMYRGAVYMNAPDGQ TAGMDISQLGPIVHAKCRTETNVVPSESFDQDEGDNWNMHNHISQTSQNLMNNKGQGRNFQMPM LGRGITSSVGEKMSPYGDKLLTNDALHRPTNIASRLGSSGLDSSMESQSIVQSMGPRHPLNLSN SCPPSRPPIFPVPRHNASQFESLNGSNSFMNCANRTFLPEQQMNNLRNKELSLTTKSPQVGNQH TGHIPLTRGNQLQGMPLKPQFLPSQDMQDNFSGSAVPPVLPHLMAPSLSQGYISQGHRPAISEG LSSSAPIGQWNLSVHNSSSNPLHLQGGPLPPLPPGPHPTSGPTIPISQKVPGQQPGTAISGLIS SLMARGLISLNNQASVQDSVGLEFNPDVLKVRHESAITALYADLPRQCMTCGLRFKTQEEHSNH MDWHVTKNRMSKSRKQKPSRKWFVSISMWLSGAEALGTEAVPGFLPAEVVVEKKDDEELAVPAD EDQKTCALCGEPFEDFYSDETEEWMYRGAVYMNAPDGQTAGMDISQLGPIVHAKCRTETNVVPS ESFDQDEGDNWNMHNHISQTSQNLMNNKGQGRNFQMPMLGRGITSSVGEKMSPYGDKLLTNDAL HRPTNIASRLGSSGLDSSMESQSIVQSMGPRHPLNLSNSCPPSRPPIFPVPRHNASQFESLNGS NSFMNCANRTFLPEQQMNNLRNKELSLTTKSPQVGNQHTGHIPLTRGNQLQGMPLKPQFLPSQD MQDNFSGSAVPPVLPHLMAPSLSQGYISQGHRPAISEGLSSSAPIGQWNLSVHNSSSNPLHLQG GPLPPLPPGPHPTSGPTIPISQKVPGQQPGTAISGLISSLMARGLISLNNQASVQDSVGLEFNP DVLKVRHESAITALYADLPRQCMTCGLRFKTQEEHSNHMDWHVTKNRMSKSRKQKPSRKWFVSI SMWLSGAEALGTEAVPGFLPAEVVVEKKDDEELAVPADEDQKTCALCGEPFEDFYSDETEEWMY RGAVYMNAPDGQTAGMDISQLGPIVHAKCRTETNVVPSESFDQDEGDNWNMHNHISQTSQNLMN NKGQGRNFQMPMLGRGITSSVGEKMSPYGDKLLTNDALHRPTNIASRLGSSGLDSSMESQSIVQ SMGPRHPLNLSNSCPPSRPPIFPVPRHNASQFESLNGSNSFMNCANRTFLPEQQMNNLRNKELS LTTKSPQVGNQHTGHIPLTRGNQLQGMPLKPQFLPSQDMQDNFSGSAVPPVLPHLMAPSLSQGY ISQGHRPAISEGLSSSAPIGQWNLSVHNSSSNPLHLQGGPLPPLPPGPHPTSGPTIPISQKVPG QQPGTAISGLISSLMARGLISLNNQASVQDSVGLEFNPDVLKVRHESAITALYADLPRQCMTCG LRFKTQEEHSNHMDWHVTKNRMSKSRKQKPSRKWFVSISMWLSGAEALGTEAVPGFLPAEVVVE KKDDEELAVPADEDQKTCALCGEPFEDFYSDETEEWMYRGAVYMNAPDGQTAGMDISQLGPIVH AKCRTETNVVPSESFDQDEG MLNAGPKLMWFPLKVLTKMKGIIGICTITFLRHLRTS*
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 Csa1G109350_circ_g.1

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