Plant Circular RNA Database

Detail information of AT5G40550_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT5G40550_circ_g.1
					
						ID in PlantcircBase
						ath_circ_041750
					
						Alias
						At_ciR5457
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 16241877-16242312  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							AT5G40550						
					
						Parent gene annotation
						
							SGF29 tudor-like domain
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G40450_circ_g.1 AT5G40450_circ_g.2 AT5G40450_circ_g.3 5_circ_ag.4 AT5G40450_circ_g.5 AT5G40450_circ_g.6 AT5G40450_circ_g.7 AT5G40450_circ_g.8 AT5G40450_circ_g.9 AT5G40450_circ_g.10 AT5G40450_circ_g.11 AT5G40450_circ_g.12 AT5G40450_circ_g.13 AT5G40450_circ_g.14 AT5G40450_circ_g.15 AT5G40450_circ_g.16 AT5G40450_circ_g.17 AT5G40450_circ_g.18 AT5G40450_circ_g.19 AT5G40450_circ_g.20 AT5G40450_circ_g.21 AT5G40450_circ_g.22 AT5G40450_circ_g.23 AT5G40450_circ_g.24 AT5G40450_circ_g.25 AT5G40450_circ_g.26 AT5G40480_circ_g.1 AT5G40480_circ_g.2 AT5G40480_circ_g.3 AT5G40480_circ_g.4 AT5G40480_circ_g.5 AT5G40480_circ_g.6 AT5G40480_circ_g.7 AT5G40480_circ_g.8 AT5G40490_circ_g.1 AT5G40530_circ_g.1 AT5G40530_circ_g.2 AT5G40530_circ_g.3 AT5G40530_circ_g.4 AT5G40530_circ_g.5 AT5G40580_circ_g.1 AT5G40580_circ_g.2 AT5G40600_circ_g.1 AT5G40610_circ_g.1 AT5G40630_circ_g.1 AT5G40640_circ_g.1 AT5G40645_circ_g.1 AT5G40670_circ_g.1 AT5G40670_circ_g.2 AT5G40690_circ_g.1 AT5G40710_circ_g.1 AT5G40740_circ_g.1 AT5G40740_circ_g.2 						
					
						Support reads
						2
					
						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
						AT5G40550.3:3
AT5G40550.1:3
AT5G40550.4:3
AT5G40550.2:3

General Information
CircRNA Name	AT5G40550_circ_g.1
ID in PlantcircBase	ath_circ_041750
Alias	At_ciR5457
Organism	Arabidpsis thaliana
Position	chr5: 16241877-16242312 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ
Parent gene	AT5G40550
Parent gene annotation	SGF29 tudor-like domain
Parent gene strand	+
Alternative splicing	AT5G40450_circ_g.1 AT5G40450_circ_g.2 AT5G40450_circ_g.3 5_circ_ag.4 AT5G40450_circ_g.5 AT5G40450_circ_g.6 AT5G40450_circ_g.7 AT5G40450_circ_g.8 AT5G40450_circ_g.9 AT5G40450_circ_g.10 AT5G40450_circ_g.11 AT5G40450_circ_g.12 AT5G40450_circ_g.13 AT5G40450_circ_g.14 AT5G40450_circ_g.15 AT5G40450_circ_g.16 AT5G40450_circ_g.17 AT5G40450_circ_g.18 AT5G40450_circ_g.19 AT5G40450_circ_g.20 AT5G40450_circ_g.21 AT5G40450_circ_g.22 AT5G40450_circ_g.23 AT5G40450_circ_g.24 AT5G40450_circ_g.25 AT5G40450_circ_g.26 AT5G40480_circ_g.1 AT5G40480_circ_g.2 AT5G40480_circ_g.3 AT5G40480_circ_g.4 AT5G40480_circ_g.5 AT5G40480_circ_g.6 AT5G40480_circ_g.7 AT5G40480_circ_g.8 AT5G40490_circ_g.1 AT5G40530_circ_g.1 AT5G40530_circ_g.2 AT5G40530_circ_g.3 AT5G40530_circ_g.4 AT5G40530_circ_g.5 AT5G40580_circ_g.1 AT5G40580_circ_g.2 AT5G40600_circ_g.1 AT5G40610_circ_g.1 AT5G40630_circ_g.1 AT5G40640_circ_g.1 AT5G40645_circ_g.1 AT5G40670_circ_g.1 AT5G40670_circ_g.2 AT5G40690_circ_g.1 AT5G40710_circ_g.1 AT5G40740_circ_g.1 AT5G40740_circ_g.2
Support reads	2
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	AT5G40550.3:3 AT5G40550.1:3 AT5G40550.4:3 AT5G40550.2:3

			
						 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  
						
							TCTGATTTATGCAGGTTGCTGCAAGAGTTACTGCAGAGAGTGCTGATAAGGATGAATGGTTTGT
GGTTAAAGTTATTCACTTCGATAGAGAAACAAAAGAcgtatcgaacattttgcttactcagttg
gatttgctgcttccatatggaccaacagggcagcaaagaagaaagttaggcggtacacacaagt
tactttaa

						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: 276
Transcript exons: 16241877-16241956,16242044-16242153,16242227-16242312
CGTATCGAACATTTTGCTTACTCAGTTGGATTTGCTGCTTCCATATGGACCAACAGGGCAGCAA
AGAAGAAAGTTAGGCGAAGGTAATGATCAGAAGAGGAAGAGGATGAAAGTTGATTCAGATGTAA
TAAGACTTTCTCCTTCCATGAGAAATCAAATCGAAGCATATGCAAGTCTTAAGGGTGAACAGGT
TGCTGCAAGAGTTACTGCAGAGAGTGCTGATAAGGATGAATGGTTTGTGGTTAAAGTTATTCAC
TTCGATAGAGAAACAAAAGA
						
						Genomic sequence
						
							CGTATCGAACATTTTGCTTACTCAGTTGGATTTGCTGCTTCCATATGGACCAACAGGGCAGCAA
AGAAGAAAGTTAGGCGGTACACACAAGTTACTTTAATTGAACTGTAATGTTATTCTCTGGCAAA
GACTTATGCTTGTAATGTTAATCACATAAGTGGTGGCAGAAGGTAATGATCAGAAGAGGAAGAG
GATGAAAGTTGATTCAGATGTAATAAGACTTTCTCCTTCCATGAGAAATCAAATCGAAGCATAT
GCAAGTCTTAAGGGTGAACAGGTAATCTTTCTTATAATGCACCTGCTTTCGATATTGCGATCAG
TTCCATTCTCACAATGTCTGATTTATGCAGGTTGCTGCAAGAGTTACTGCAGAGAGTGCTGATA
AGGATGAATGGTTTGTGGTTAAAGTTATTCACTTCGATAGAGAAACAAAAGA

Sequences
Splice junction sequence	TCTGATTTATGCAGGTTGCTGCAAGAGTTACTGCAGAGAGTGCTGATAAGGATGAATGGTTTGT GGTTAAAGTTATTCACTTCGATAGAGAAACAAAAGAcgtatcgaacattttgcttactcagttg gatttgctgcttccatatggaccaacagggcagcaaagaagaaagttaggcggtacacacaagt tactttaa
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: 276 Transcript exons: 16241877-16241956,16242044-16242153,16242227-16242312 CGTATCGAACATTTTGCTTACTCAGTTGGATTTGCTGCTTCCATATGGACCAACAGGGCAGCAA AGAAGAAAGTTAGGCGAAGGTAATGATCAGAAGAGGAAGAGGATGAAAGTTGATTCAGATGTAA TAAGACTTTCTCCTTCCATGAGAAATCAAATCGAAGCATATGCAAGTCTTAAGGGTGAACAGGT TGCTGCAAGAGTTACTGCAGAGAGTGCTGATAAGGATGAATGGTTTGTGGTTAAAGTTATTCAC TTCGATAGAGAAACAAAAGA
Genomic sequence	CGTATCGAACATTTTGCTTACTCAGTTGGATTTGCTGCTTCCATATGGACCAACAGGGCAGCAA AGAAGAAAGTTAGGCGGTACACACAAGTTACTTTAATTGAACTGTAATGTTATTCTCTGGCAAA GACTTATGCTTGTAATGTTAATCACATAAGTGGTGGCAGAAGGTAATGATCAGAAGAGGAAGAG GATGAAAGTTGATTCAGATGTAATAAGACTTTCTCCTTCCATGAGAAATCAAATCGAAGCATAT GCAAGTCTTAAGGGTGAACAGGTAATCTTTCTTATAATGCACCTGCTTTCGATATTGCGATCAG TTCCATTCTCACAATGTCTGATTTATGCAGGTTGCTGCAAGAGTTACTGCAGAGAGTGCTGATA AGGATGAATGGTTTGTGGTTAAAGTTATTCACTTCGATAGAGAAACAAAAGA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.21112604

Conservation Information
Conserved circRNAs	NA
PMCS	0.21112604

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							16242070-16242309(+)
						
						Potential amino acid sequence
						
							MKVDSDVIRLSPSMRNQIEAYASLKGEQVAARVTAESADKDEWFVVKVIHFDRETKDVSNILLT
QLDLLLPYGPTGQQRRKLGVVAEGNDQKRKRMKVDSDVIRLSPSMRNQIEAYASLKGEQVAARV
TAESADKDEWFVVKVIHFDRETKDVSNILLTQLDLLLPYGPTGQQRRKLGVVAEGNDQKRKRMK
VDSDVIRLSPSMRNQIEAYASLKGEQVAARVTAESADKDEWFVVKVIHFDRETKDVSNILLTQL
DLLLPYGPTGQQRRKLGVVAEGNDQKRKRMKVDSDVIRLSPSMRNQIEAYASLKGEQVAARVTA
ESADKDEWFVVKVIHFDRETK(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	16242070-16242309(+)
Potential amino acid sequence	MKVDSDVIRLSPSMRNQIEAYASLKGEQVAARVTAESADKDEWFVVKVIHFDRETKDVSNILLT QLDLLLPYGPTGQQRRKLGVVAEGNDQKRKRMKVDSDVIRLSPSMRNQIEAYASLKGEQVAARV TAESADKDEWFVVKVIHFDRETKDVSNILLTQLDLLLPYGPTGQQRRKLGVVAEGNDQKRKRMK VDSDVIRLSPSMRNQIEAYASLKGEQVAARVTAESADKDEWFVVKVIHFDRETKDVSNILLTQL DLLLPYGPTGQQRRKLGVVAEGNDQKRKRMKVDSDVIRLSPSMRNQIEAYASLKGEQVAARVTA ESADKDEWFVVKVIHFDRETK(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of AT5G40550_circ_g.1

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