Plant Circular RNA Database

Detail information of AT4G39540_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT4G39540_circ_g.4
					
						ID in PlantcircBase
						ath_circ_035712
					
						Alias
						At_ciR2706
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 18379334-18379582  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							AT4G39540						
					
						Parent gene annotation
						
							Shikimate kinase 2
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G39540_circ_g.3 AT4G39540_circ_g.5 AT4G39540_circ_g.6 AT4G39540_circ_g.7 AT4G39540_circ_g.8 						
					
						Support reads
						3
					
						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  
						
							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
						AT4G39540.3:2
AT4G39540.2:2
AT4G39540.1:2

General Information
CircRNA Name	AT4G39540_circ_g.4
ID in PlantcircBase	ath_circ_035712
Alias	At_ciR2706
Organism	Arabidpsis thaliana
Position	chr4: 18379334-18379582 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ
Parent gene	AT4G39540
Parent gene annotation	Shikimate kinase 2
Parent gene strand	+
Alternative splicing	AT4G39540_circ_g.3 AT4G39540_circ_g.5 AT4G39540_circ_g.6 AT4G39540_circ_g.7 AT4G39540_circ_g.8
Support reads	3
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	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	AT4G39540.3:2 AT4G39540.2:2 AT4G39540.1:2

			
						 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  
						
							TGCTTTATTCCTAGACTGAAGCGTTAAAGAAACTCTCTTTGATGTACCACCAAGTTGTTGTTTC
AACCGGGGGAGGGGCAGTTATAAGACCCATCAATTGtgacactttgatcgagcaggctatgaag
ggaacttctgtagctgagatatttgagcatttcggtgagagtgtcttcagagaaaaagaggttg
gttttatg

						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: 174
Transcript exons: 18379334-18379421,18379497-18379582
TGACACTTTGATCGAGCAGGCTATGAAGGGAACTTCTGTAGCTGAGATATTTGAGCATTTCGGT
GAGAGTGTCTTCAGAGAAAAAGAGACTGAAGCGTTAAAGAAACTCTCTTTGATGTACCACCAAG
TTGTTGTTTCAACCGGGGGAGGGGCAGTTATAAGACCCATCAATTG
						
						Genomic sequence
						
							TGACACTTTGATCGAGCAGGCTATGAAGGGAACTTCTGTAGCTGAGATATTTGAGCATTTCGGT
GAGAGTGTCTTCAGAGAAAAAGAGGTTGGTTTTATGCACTTCTTCCCCTAAGTCTTATTGTAGT
CTAGCTGCTAATTTCACCACATGCTTTATTCCTAGACTGAAGCGTTAAAGAAACTCTCTTTGAT
GTACCACCAAGTTGTTGTTTCAACCGGGGGAGGGGCAGTTATAAGACCCATCAATTG

Sequences
Splice junction sequence	TGCTTTATTCCTAGACTGAAGCGTTAAAGAAACTCTCTTTGATGTACCACCAAGTTGTTGTTTC AACCGGGGGAGGGGCAGTTATAAGACCCATCAATTGtgacactttgatcgagcaggctatgaag ggaacttctgtagctgagatatttgagcatttcggtgagagtgtcttcagagaaaaagaggttg gttttatg
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: 174 Transcript exons: 18379334-18379421,18379497-18379582 TGACACTTTGATCGAGCAGGCTATGAAGGGAACTTCTGTAGCTGAGATATTTGAGCATTTCGGT GAGAGTGTCTTCAGAGAAAAAGAGACTGAAGCGTTAAAGAAACTCTCTTTGATGTACCACCAAG TTGTTGTTTCAACCGGGGGAGGGGCAGTTATAAGACCCATCAATTG
Genomic sequence	TGACACTTTGATCGAGCAGGCTATGAAGGGAACTTCTGTAGCTGAGATATTTGAGCATTTCGGT GAGAGTGTCTTCAGAGAAAAAGAGGTTGGTTTTATGCACTTCTTCCCCTAAGTCTTATTGTAGT CTAGCTGCTAATTTCACCACATGCTTTATTCCTAGACTGAAGCGTTAAAGAAACTCTCTTTGAT GTACCACCAAGTTGTTGTTTCAACCGGGGGAGGGGCAGTTATAAGACCCATCAATTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.242953816

Conservation Information
Conserved circRNAs	NA
PMCS	0.242953816

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							18379356-18379579(+)
18379577-18379336(-)
						
						Potential amino acid sequence
						
							MKGTSVAEIFEHFGESVFREKETEALKKLSLMYHQVVVSTGGGAVIRPINCDTLIEQAMKGTSV
AEIFEHFGESVFREKETEALKKLSLMYHQVVVSTGGGAVIRPINCDTLIEQAMKGTSVAEIFEH
FGESVFREKETEALKKLSLMYHQVVVSTGGGAVIRPINCDTLIEQAMKGTSVAEIFEHFGESVF
REKETEALKKLSLMYHQVVVSTGGGAVIRPIN(+)
MGLITAPPPVETTTWWYIKESFFNASVSFSLKTLSPKCSNISATEVPFIACSIKVSQLMGLITA
PPPVETTTWWYIKESFFNASVSFSLKTLSPKCSNISATEVPFIACSIKVSQLMGLITAPPPVET
TTWWYIKESFFNASVSFSLKTLSPKCSNISATEVPFIACSIKVSQLMGLITAPPPVETTTWWYI
KESFFNASVSFSLKTLSPKCSNISATEVPFIACSIKVS(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	18379356-18379579(+) 18379577-18379336(-)
Potential amino acid sequence	MKGTSVAEIFEHFGESVFREKETEALKKLSLMYHQVVVSTGGGAVIRPINCDTLIEQAMKGTSV AEIFEHFGESVFREKETEALKKLSLMYHQVVVSTGGGAVIRPINCDTLIEQAMKGTSVAEIFEH FGESVFREKETEALKKLSLMYHQVVVSTGGGAVIRPINCDTLIEQAMKGTSVAEIFEHFGESVF REKETEALKKLSLMYHQVVVSTGGGAVIRPIN(+) MGLITAPPPVETTTWWYIKESFFNASVSFSLKTLSPKCSNISATEVPFIACSIKVSQLMGLITA PPPVETTTWWYIKESFFNASVSFSLKTLSPKCSNISATEVPFIACSIKVSQLMGLITAPPPVET TTWWYIKESFFNASVSFSLKTLSPKCSNISATEVPFIACSIKVSQLMGLITAPPPVETTTWWYI KESFFNASVSFSLKTLSPKCSNISATEVPFIACSIKVS(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of AT4G39540_circ_g.4

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