Plant Circular RNA Database

Detail information of AT4G04910_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT4G04910_circ_g.3
					
						ID in PlantcircBase
						ath_circ_029726
					
						Alias
						Ath_circ_FC2550
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 2490232-2491221  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							AT4G04910						
					
						Parent gene annotation
						
							NSF
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G04910_circ_g.1 AT4G04910_circ_g.2 						
					
						Support reads
						2
					
						Tissues
						whole_plant
					
						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
						AT4G04910.1:6

General Information
CircRNA Name	AT4G04910_circ_g.3
ID in PlantcircBase	ath_circ_029726
Alias	Ath_circ_FC2550
Organism	Arabidpsis thaliana
Position	chr4: 2490232-2491221 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	AT4G04910
Parent gene annotation	NSF
Parent gene strand	-
Alternative splicing	AT4G04910_circ_g.1 AT4G04910_circ_g.2
Support reads	2
Tissues	whole_plant
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	AT4G04910.1:6

			
						 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  
						
							TAGAGGACTTCTAGTACTAACTTTAACTTGCTCGACTAGAAGCATAGCTCTTTTGTAAATGTGA
TTATGCCGATGACCACAATCTACCATCCCATTGAGTcttctttgcgtcctctttttgcagtgtc
ggaacagagtgagtgacagagaagcaatcagagataccaacagactctaagaaggttacttcac
ttgttgtc

									
								

					

						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: 523
Transcript exons: 2490232-2490354,2490468-2490555,2490662-2490720,2490800-
2490859,2490944-2491004,2491090-2491221
CTTCTTTGCGTCCTCTTTTTGCAGTGTCGGAACAGAGTGAGTGACAGAGAAGCAATCAGAGATA
CCAACAGACTCTAAGAAGGTTACTTCACTTGTTGTCCCAAAGACGAGAAGTTTCTTCCCCTTAG
GAGGAAGTCGTTTGAGAAGGACCATCAGCGTCTGTGAAATTATGTTTGAAAAGCGAGGACCGAT
TGCTATGAATTCCAACAATCTTTCAATATCGTCAAGGATAATGATGCTCATTGGAGATTTATAT
GCATCCTCAAAGACCTTGACAATGTGAGCACATTTTGTGCTCTCAGAAAGACCAATCATAGTTT
CCGCAGAAACTATCTTAACATATGGGAAGTCACTATCGATACCAATTGTTGCTGCTAAAGCAGT
TTTCCCACTTCCACTGGGCCCCTCCAGAAGGCAAGTGACTAGAGGACTTCTAGTACTAACTTTA
ACTTGCTCGACTAGAAGCATAGCTCTTTTGTAAATGTGATTATGCCGATGACCACAATCTACCA
TCCCATTGAGT
						
					

						Genomic sequence
						
							CTTCTTTGCGTCCTCTTTTTGCAGTGTCGGAACAGAGTGAGTGACAGAGAAGCAATCAGAGATA
CCAACAGACTCTAAGAAGGTTACTTCACTTGTTGTCCCAAAGACGAGAAGTTTCTTCCCCTGTG
AACAAAGATTTTACCAATTTAAAGATGTTCAACTGTAAGAAATTAACTTATGATGATCAAGCAT
ATATAAATATGGATAAGAAAATAACAAAACGGTAATGGAAGCACCTTAGGAGGAAGTCGTTTGA
GAAGGACCATCAGCGTCTGTGAAATTATGTTTGAAAAGCGAGGACCGATTGCTATGAATTCCAA
CAATCTGTAAATATCAGAAATTTAAGTACTTTCCAGAAGAAACTACAAACGTATGCTATAAGAT
ATTGAGCCAAGGTCTGAAACGTAGAATAAAAATAGCAGGTAATAACCTTTCAATATCGTCAAGG
ATAATGATGCTCATTGGAGATTTATATGCATCCTCAAAGACCTGGTCTCATTCACACCAAAACC
AATTGTCAGTGGATAGAACAGAATAACAAGAAGTAGAATGTTTCCAGAGGACAGACCTTGACAA
TGTGAGCACATTTTGTGCTCTCAGAAAGACCAATCATAGTTTCCGCAGAAACCTACAAAATAAG
AAATCAATATCACACAAAGAGTAAAAGATGGTACGGACTAAATATACTGTACAAAGAAAGATAG
ACACTTACTATCTTAACATATGGGAAGTCACTATCGATACCAATTGTTGCTGCTAAAGCAGTTT
TCCCACTGTCCAGACAAAAAAGTTAAAACAATCAGCAACAGGTTATAAAACAGTAAGCCAAAAT
AATGTGGCTATAACTACGGAAGATACCTTCCACTGGGCCCCTCCAGAAGGCAAGTGACTAGAGG
ACTTCTAGTACTAACTTTAACTTGCTCGACTAGAAGCATAGCTCTTTTGTAAATGTGATTATGC
CGATGACCACAATCTACCATCCCATTGAGT
						
					

			
		

Sequences
Splice junction sequence	TAGAGGACTTCTAGTACTAACTTTAACTTGCTCGACTAGAAGCATAGCTCTTTTGTAAATGTGA TTATGCCGATGACCACAATCTACCATCCCATTGAGTcttctttgcgtcctctttttgcagtgtc ggaacagagtgagtgacagagaagcaatcagagataccaacagactctaagaaggttacttcac ttgttgtc
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: 523 Transcript exons: 2490232-2490354,2490468-2490555,2490662-2490720,2490800- 2490859,2490944-2491004,2491090-2491221 CTTCTTTGCGTCCTCTTTTTGCAGTGTCGGAACAGAGTGAGTGACAGAGAAGCAATCAGAGATA CCAACAGACTCTAAGAAGGTTACTTCACTTGTTGTCCCAAAGACGAGAAGTTTCTTCCCCTTAG GAGGAAGTCGTTTGAGAAGGACCATCAGCGTCTGTGAAATTATGTTTGAAAAGCGAGGACCGAT TGCTATGAATTCCAACAATCTTTCAATATCGTCAAGGATAATGATGCTCATTGGAGATTTATAT GCATCCTCAAAGACCTTGACAATGTGAGCACATTTTGTGCTCTCAGAAAGACCAATCATAGTTT CCGCAGAAACTATCTTAACATATGGGAAGTCACTATCGATACCAATTGTTGCTGCTAAAGCAGT TTTCCCACTTCCACTGGGCCCCTCCAGAAGGCAAGTGACTAGAGGACTTCTAGTACTAACTTTA ACTTGCTCGACTAGAAGCATAGCTCTTTTGTAAATGTGATTATGCCGATGACCACAATCTACCA TCCCATTGAGT
Genomic sequence	CTTCTTTGCGTCCTCTTTTTGCAGTGTCGGAACAGAGTGAGTGACAGAGAAGCAATCAGAGATA CCAACAGACTCTAAGAAGGTTACTTCACTTGTTGTCCCAAAGACGAGAAGTTTCTTCCCCTGTG AACAAAGATTTTACCAATTTAAAGATGTTCAACTGTAAGAAATTAACTTATGATGATCAAGCAT ATATAAATATGGATAAGAAAATAACAAAACGGTAATGGAAGCACCTTAGGAGGAAGTCGTTTGA GAAGGACCATCAGCGTCTGTGAAATTATGTTTGAAAAGCGAGGACCGATTGCTATGAATTCCAA CAATCTGTAAATATCAGAAATTTAAGTACTTTCCAGAAGAAACTACAAACGTATGCTATAAGAT ATTGAGCCAAGGTCTGAAACGTAGAATAAAAATAGCAGGTAATAACCTTTCAATATCGTCAAGG ATAATGATGCTCATTGGAGATTTATATGCATCCTCAAAGACCTGGTCTCATTCACACCAAAACC AATTGTCAGTGGATAGAACAGAATAACAAGAAGTAGAATGTTTCCAGAGGACAGACCTTGACAA TGTGAGCACATTTTGTGCTCTCAGAAAGACCAATCATAGTTTCCGCAGAAACCTACAAAATAAG AAATCAATATCACACAAAGAGTAAAAGATGGTACGGACTAAATATACTGTACAAAGAAAGATAG ACACTTACTATCTTAACATATGGGAAGTCACTATCGATACCAATTGTTGCTGCTAAAGCAGTTT TCCCACTGTCCAGACAAAAAAGTTAAAACAATCAGCAACAGGTTATAAAACAGTAAGCCAAAAT AATGTGGCTATAACTACGGAAGATACCTTCCACTGGGCCCCTCCAGAAGGCAAGTGACTAGAGG ACTTCTAGTACTAACTTTAACTTGCTCGACTAGAAGCATAGCTCTTTTGTAAATGTGATTATGC CGATGACCACAATCTACCATCCCATTGAGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.3506126

Conservation Information
Conserved circRNAs	NA
PMCS	0.3506126

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT4G04910_circ_g.3

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